#--------------------------------------------------------------------------# # LICENSE INFO: # #--------------------------------------------------------------------------# # This file is part of CAMPARI. # # # # Version 5.0 # # # # Copyright (C) 2024, The CAMPARI development team (current and former # # contributors) # # Andreas Vitalis, Adam Steffen, Rohit Pappu, Hoang # # Tran, Albert Mao, Xiaoling Wang, Jose Pulido, # # Nicholas Lyle, Nicolas Bloechliger, Marco Bacci, # # Davide Garolini, Jiri Vymetal, Cassiano Langini, # # Alessia Del Panta, Francesco Cocina, Julian # # Widmer # # # # Website: http://sourceforge.net/projects/campari/ # # # # CAMPARI is free software: you can redistribute it and/or modify # # it under the terms of the GNU General Public License as published by # # the Free Software Foundation, either version 3 of the License, or # # (at your option) any later version. # # # # CAMPARI is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # GNU General Public License for more details. # # # # You should have received a copy of the GNU General Public License # # along with CAMPARI. If not, see . # #--------------------------------------------------------------------------# # AUTHORSHIP INFO: # #--------------------------------------------------------------------------# # # # MAIN AUTHOR: Andreas Vitalis # # CONTRIBUTIONS: Marco Bacci # # # #--------------------------------------------------------------------------# ############################# ## ## ## Literature References ## ## ## ############################# ##################################################################### # # # Combination of CHARMM36 (charges, essential bonded parameters) # # and ABSINTH LJ paradigm using parameters with 15kcal/mol adjusted # # rFOS values for polymer charged groups, modified ion parameters # # (Truhlar/Kelly), 2020 adjustments of LJ parameters, # # and additional atom types for use with unsupported entities # # # ##################################################################### ############################################################################################### # # # See: # #---------------------------------------------------------------------------------------------# # MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III: # # "Extending the treatment of backbone energetics in protein force fields: limitations # # of gas-phase quantum mechanics in reproducing protein conformational distributions # # in molecular dynamics simulations" # # Journal of Computational Chemistry, 25: 1400-1415, 2004. # # # # MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; # # Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; # # Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, # # C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, # # W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; # # Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.: # # "All-atom empirical potential for molecular modeling and dynamics Studies of # # proteins." # # Journal of Physical Chemistry B, 1998, 102, 3586-3616. # # # # Foloppe, N. and MacKerell, Jr., A.D.: # # "All-Atom Empirical Force Field for Nucleic Acids: 2) Parameter Optimization # # Based on Small Molecule and Condensed Phase Macromolecular Target Data." # # Journal of Computational Chemistry, 21: 86-104, 2000 # # # # MacKerell Jr., A.D.: # # "Empirical Force Fields for Biological Macromolecules: Overview and Issues" # # Journal of Computational Chemistry, 25 (13): 1584-1604, 2004 # # # # MacKerell Jr., A.D. and Banavali, N.: # # "All-Atom Empirical Force Field for Nucleic Acids: 2) Application to # # Molecular Dynamics Simulations of DNA and RNA in Solution." # # Journal of Computational Chemistry, 21: 105-120, 2000 # # # # Andreas Vitalis, Rohit V. Pappu: # # "ABSINTH: a new continuum solvation model for simulations of polypeptides # # in aqueous solutions." # # Journal of Computational Chemistry, 30, p673-699 (2009) # # # # Best, R. B.; Zhu, X.; Shim J.; Lopes P.E.M.; Mittal J.; Feig M.; MacKerell Jr., A.D.: # # "Optimization of the additive CHARMM all-atom protein force field targeting # # improved sampling of the backbone φ, ψ and sidechain χ1 and χ2 dihedral angles." # # Journal of Chemical Theory and Computation, 8: 3257-3273, 2012 # # # # Macias, A.T. and MacKerell, Jr., A.D.: # # "CH/π interactions involving aromatic amino acids: Refinement of the CHARMM # # tryptophan force field." # # Journal of Computational Chemistry, 26 (14): 1452-1463, 2005 # # # # Denning, E.J.; Priyakumar, U.D.; Nilsson, L.; MacKerell Jr., A.D.: # # "Impact of 2′-hydroxyl sampling on the conformational properties of RNA: # # Update of the CHARMM all-atom additive force field for RNA" # # Journal of Computational Chemistry, 32 (9): 1929-1943, 2011 # # # # Hart, K.; Foloppe, N.; Baker, C.M.; Denning, E.J.; Nilsson, L.; MacKerell Jr., A.D.: # # "Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment # # of the BI/BII Conformational Equilibrium." # # Journal of Chemical Theory and Computation, 8: 348-362, 2012 # # # # J.-R. Marchand, T. Knehans, A. Caflisch, and A. Vitalis: # # "An ABSINTH-based protocol for predicting binding affinities between proteins # # and small molecules." # # Journal of Chemical Information and Modeling (2020) # # https://doi.org/10.1021/acs.jcim.0c00558 # # # ############################################################################################### ############################# ## ## ## Atom Type Definitions ## ## ## ############################# atom 1 N "SP2 Nitrogen" 7 14.007 3 atom 2 C "SP3 Carbon" 6 12.011 4 atom 3 C "SP2 Carbon" 6 12.011 3 atom 4 H "Hydrogen Atom" 1 1.008 1 atom 5 O "SP Oxygen" 8 15.999 1 atom 6 O "SP2 Oxygen" 8 15.999 2 atom 7 S "Sulfur Atom" 16 32.066 2 atom 8 N "SP3 Nitrogen" 7 14.007 4 atom 9 H "Hydrogen Atom" 1 1.008 1 atom 10 N "Imidazole Nitrogen" 7 14.007 2 atom 11 N "Proline SP2 Nitrogen" 7 14.007 3 atom 12 NA "Sodium Ion" 11 22.990 0 atom 13 CL "Chloride Ion" 17 35.453 0 atom 14 OW "SPC Water Oxygen" 8 15.999 2 atom 15 HW "SPC Water Hydrogen" 1 1.008 1 atom 16 OW "TIP3P Water Oxygen" 8 15.999 2 atom 17 HW "TIP3P Water Hydrogen" 1 1.008 1 atom 18 OW "TIP4P Water Oxygen" 8 15.999 3 atom 19 MW "TIP4P Water Charge" 0 0.00 1 atom 20 K "Potassium Ion" 19 39.098 0 atom 21 BR "Bromide Ion" 35 79.904 0 atom 22 CS "Caesium Ion" 55 132.905 0 atom 23 I "Iodide Ion" 53 126.905 0 atom 24 P "P in Phosphate" 15 30.974 4 atom 25 OW "TIP4P-Ew Water Oxygen" 8 15.999 3 atom 26 OW "TIP5P Water Oxygen" 8 15.999 4 atom 27 C "Proline Methylene C" 6 12.011 4 atom 28 H "Proline Methylene H" 1 1.008 1 atom 29 O "SP2 Oxygen(-)" 8 15.999 1 atom 30 S "Sulfur(-) Atom" 16 32.066 1 atom 31 C "Aromatic Carbon" 6 12.011 3 atom 32 S "Sulfon* Sulfur Atom" 16 32.066 4 atom 33 S "Sulfin* Sulfur Atom" 16 32.066 3 atom 34 P "P in Phosphin*" 15 30.974 3 atom 35 F "Fluorine Ion" 9 18.999 1 atom 36 CL "Chlorine Atom" 17 35.453 1 atom 37 BR "Bromine Atom" 35 79.904 1 atom 38 I "Iodine Atom" 53 126.905 1 ####################################### ## ## ## sigma parameters in Angstroms ## ## ## ####################################### contact 1 1 3.05 # 2.70 contact 1 4 2.05 contact 2 2 3.40 contact 2 4 2.65 contact 3 3 3.15 # 3.00 contact 3 4 2.60 # small extra penalty contact 3 5 2.85 # small extra gain contact 4 4 2.35 # extra penalty contact 4 5 1.85 contact 4 6 1.95 contact 4 7 2.30 contact 4 8 2.05 contact 4 9 2.10 # small extra penalty contact 4 10 2.05 contact 4 11 2.05 contact 4 12 2.33 contact 4 13 2.92 contact 4 14 2.0828241419 contact 4 15 2.00 contact 4 16 2.075305 contact 4 17 2.00 contact 4 18 2.076825 contact 4 19 2.00 contact 4 20 2.60 contact 4 21 3.09 contact 4 22 2.88 contact 4 23 3.37 contact 4 24 2.80 contact 4 25 2.082175 contact 4 26 2.06 contact 4 27 2.65 contact 4 28 2.10 contact 4 29 2.05 contact 4 30 2.35 contact 4 31 2.575 contact 4 32 2.80 contact 4 33 2.80 contact 4 34 2.80 contact 4 35 2.00 # reduced gain contact 4 36 2.75 contact 4 37 2.85 contact 4 38 3.00 contact 5 5 2.70 contact 6 6 2.90 contact 7 7 3.60 contact 8 8 3.05 # 2.70 contact 9 9 2.00 contact 10 10 3.05 # 3.20 contact 11 11 3.05 # 2.70 contact 12 12 2.66 contact 13 13 3.84 contact 14 14 3.1656482837 contact 15 15 2.00 contact 16 16 3.15061 contact 17 17 2.00 contact 18 18 3.15365 contact 19 19 2.00 contact 20 20 3.20 contact 21 21 4.18 contact 22 22 3.76 contact 23 23 4.74 contact 24 24 3.60 contact 25 25 3.16435 contact 26 26 3.12 contact 27 27 3.40 contact 28 28 2.00 contact 29 29 3.10 contact 30 30 3.70 contact 31 31 3.25 contact 32 32 3.60 contact 33 33 3.60 contact 34 34 3.60 contact 35 35 2.90 contact 36 36 3.50 contact 37 37 3.70 contact 38 38 4.00 contact_14 1 1 2.90 contact_14 1 4 1.95 contact_14 2 2 3.30 contact_14 2 4 2.65 contact_14 3 3 3.00 contact_14 3 4 2.50 contact_14 4 4 2.20 # extra penalty contact_14 4 5 1.85 contact_14 4 6 1.85 contact_14 4 7 2.20 contact_14 4 8 1.95 contact_14 4 9 2.00 contact_14 4 10 1.95 contact_14 4 11 1.95 contact_14 4 12 2.33 contact_14 4 13 2.92 contact_14 4 14 2.0828241419 contact_14 4 15 2.00 contact_14 4 16 2.075305 contact_14 4 17 2.00 contact_14 4 18 2.076825 contact_14 4 19 2.00 contact_14 4 20 2.60 contact_14 4 21 3.09 contact_14 4 22 2.88 contact_14 4 23 3.37 contact_14 4 24 2.80 contact_14 4 25 2.082175 contact_14 4 26 2.06 contact_14 4 27 2.65 contact_14 4 28 2.00 contact_14 4 29 2.00 contact_14 4 30 2.30 contact_14 4 31 2.60 contact_14 4 32 2.80 contact_14 4 33 2.80 contact_14 4 34 2.80 contact_14 4 35 2.00 # reduced gain contact_14 4 36 2.75 contact_14 4 37 2.90 contact_14 4 38 3.05 contact_14 5 5 2.70 contact_14 6 6 2.70 contact_14 7 7 3.40 contact_14 8 8 2.90 # 2.70 contact_14 9 9 2.00 contact_14 10 10 2.90 # 3.00 contact_14 11 11 2.90 # 2.70 contact_14 12 12 2.66 contact_14 13 13 3.84 contact_14 14 14 3.1656482837 contact_14 15 15 2.00 contact_14 16 16 3.15061 contact_14 17 17 2.00 contact_14 18 18 3.15365 contact_14 19 19 2.00 contact_14 20 20 3.2 contact_14 21 21 4.18 contact_14 22 22 3.76 contact_14 23 23 4.74 contact_14 24 24 3.6 contact_14 25 25 3.16435 contact_14 26 26 3.12 contact_14 27 27 3.3 contact_14 28 28 2.0 contact_14 29 29 3.00 contact_14 30 30 3.40 contact_14 31 31 3.0 contact_14 32 32 3.4 contact_14 33 33 3.4 contact_14 34 34 3.4 contact_14 35 35 2.7 contact_14 36 36 3.3 contact_14 37 37 3.5 contact_14 38 38 3.8 #################################### ## ## ## epsilon params in kcal/mol ## ## ## #################################### interact 1 1 0.15 interact 2 2 0.1 interact 3 3 0.1 interact 4 4 0.025 interact 5 5 0.2 interact 6 6 0.15 interact 7 7 0.3 interact 8 8 0.15 interact 9 9 0.025 interact 10 10 0.15 interact 11 11 0.15 interact 12 12 0.1 interact 13 13 0.15 interact 14 14 0.1553937103 interact 15 15 0.0 interact 16 16 0.1521 interact 17 17 0.0 interact 18 18 0.1550 interact 19 19 0.0 interact 20 20 0.1 interact 21 21 0.2 interact 22 22 0.1 interact 23 23 0.3 interact 24 24 0.3 interact 25 25 0.162750 interact 26 26 0.16 interact 27 27 0.1 interact 28 28 0.025 interact 29 29 0.2 interact 30 30 0.3 interact 31 31 0.1 interact 32 32 0.3 interact 33 33 0.4 interact 34 34 0.4 interact 35 35 0.05 interact 36 36 0.3 interact 37 37 0.5 interact 38 38 0.6 interact_14 1 1 0.15 interact_14 1 4 0.061237243570 interact_14 2 2 0.1 interact_14 2 4 0.05 interact_14 3 3 0.1 interact_14 3 4 0.05 interact_14 4 4 0.025 interact_14 4 5 0.0707106781 interact_14 4 6 0.0612372436 interact_14 4 7 0.0866025404 interact_14 4 8 0.0612372436 interact_14 4 9 0.0250000000 interact_14 4 10 0.0612372436 interact_14 4 11 0.0612372436 interact_14 4 12 0.05 interact_14 4 13 0.0612372436 interact_14 4 14 0.0623285068 interact_14 4 15 0.00 interact_14 4 16 0.0616644144 interact_14 4 17 0.00 interact_14 4 18 0.0622494980 interact_14 4 19 0.00 interact_14 4 20 0.05 interact_14 4 21 0.0707106781 interact_14 4 22 0.05 interact_14 4 23 0.0866025404 interact_14 4 24 0.0866025404 interact_14 4 25 0.0637867541 interact_14 4 26 0.0632455532 interact_14 4 27 0.0158113883 interact_14 4 28 0.0079056942 interact_14 4 29 0.0707106781 interact_14 4 30 0.0866025404 interact_14 4 31 0.05 interact_14 4 32 0.0866025404 interact_14 4 33 0.10 interact_14 4 34 0.10 interact_14 4 35 0.0353553391 interact_14 4 36 0.0866025404 interact_14 4 37 0.1118033989 interact_14 4 38 0.1224744871 interact_14 5 5 0.2 interact_14 6 6 0.15 interact_14 7 7 0.3 interact_14 8 8 0.15 interact_14 9 9 0.025 interact_14 10 10 0.15 interact_14 11 11 0.15 interact_14 12 12 0.1 interact_14 13 13 0.15 interact_14 14 14 0.1553937103 interact_14 15 15 0.0 interact_14 16 16 0.1521 interact_14 17 17 0.0 interact_14 18 18 0.1550 interact_14 19 19 0.0 interact_14 20 20 0.1 interact_14 21 21 0.2 interact_14 22 22 0.1 interact_14 23 23 0.3 interact_14 24 24 0.3 interact_14 25 25 0.162750 interact_14 26 26 0.16 interact_14 27 27 0.1 interact_14 28 28 0.025 interact_14 29 29 0.2 interact_14 30 30 0.3 interact_14 31 31 0.1 interact_14 32 32 0.3 interact_14 33 33 0.4 interact_14 34 34 0.4 interact_14 35 35 0.05 interact_14 36 36 0.3 interact_14 37 37 0.5 interact_14 38 38 0.6 ######################################## ## ## ## non-LJ atomic radii in Angstroms ## ## ## ######################################## radius 4 1.0 # added radius 9 1.0 # added radius 12 1.33 radius 13 1.6 radius 20 1.5 radius 21 1.75 radius 22 1.75 radius 23 1.9 #################################### ## ## ## atomic charges in units of e ## ## ## #################################### charge 1 "Gly CA" -0.0200 charge 2 "peptide-NH" -0.4700 charge 3 "peptide-NH PRO" -0.2900 charge 4 "peptide-H" 0.3100 charge 5 "peptide-CA" 0.0700 charge 6 "peptide-CA PRO" 0.0200 charge 7 "peptide-HA" 0.0900 charge 8 "peptide C" 0.5100 charge 9 "peptide O" -0.5100 charge 10 "nonpolar H" 0.0900 charge 11 "ALA CB" -0.2700 charge 12 "VAL CB" -0.0900 charge 13 "VAL CG" -0.2700 charge 14 "ARG CB" -0.1800 charge 15 "ARG CG" -0.1800 charge 16 "ARG CD" 0.2000 charge 17 "ARG NE" -0.7000 charge 18 "ARG HE" 0.4400 charge 19 "ARG CZ" 0.6400 charge 20 "ARG NH" -0.8000 charge 21 "ARG HH" 0.4600 charge 22 "monovalent cation" 1.0 charge 23 "monovalent anion" -1.0 charge 24 "ASP CB" -0.2800 charge 25 "ASP CG" 0.6200 charge 26 "ASP OG" -0.7600 charge 27 "ASN CB" -0.1800 charge 28 "ASN CG" 0.5500 charge 29 "ASN OD1" -0.5500 charge 30 "ASN ND2" -0.6200 charge 31 "ASN HD21" 0.3100 charge 32 "ASN HD22" 0.3100 charge 33 "GLU CB" -0.1800 charge 34 "GLU CG" -0.2800 charge 35 "GLU CD" 0.6200 charge 36 "GLU OD" -0.7600 charge 37 "GLN CB" -0.1800 charge 38 "GLN CG" -0.1800 charge 39 "GLN CD" 0.5500 charge 40 "GLN OE1" -0.5500 charge 41 "SER CB" 0.0500 charge 42 "SER OG" -0.6600 charge 43 "SER HG" 0.4300 charge 44 "THR CB" 0.1400 charge 45 "THR OG1" -0.6600 charge 46 "THR HG1" 0.4300 charge 47 "THR CG2" -0.2700 charge 48 "CYS CB" -0.1100 charge 49 "CYS SG" -0.2300 charge 50 "CYS HG" 0.1600 charge 51 "PRO CB" -0.1800 charge 52 "PRO CG" -0.1800 charge 53 "PRO CD" 0.0000 charge 54 "TYR CB" -0.1800 charge 55 "TYR CG" 0.0000 charge 56 "TYR CD/E" -0.1150 charge 57 "TYR HD/E" 0.1150 charge 58 "TYR CZ" 0.1100 charge 59 "TYR OH" -0.5400 charge 60 "TYR HH" 0.4300 charge 61 "TRP CB" -0.1800 charge 62 "TRP CG" -0.0300 charge 63 "TRP CD1" -0.1500 # 0.0350 charge 64 "TRP HD1" 0.2200 # 0.1150 charge 65 "TRP CD2" 0.1100 #-0.0200 charge 66 "TRP NE1" -0.5100 charge 67 "TRP HE1" 0.3700 # 0.3800 charge 68 "TRP CE2" 0.2400 # 0.1300 charge 69 "NAP CX" -0.1150 charge 70 "NAP HX" 0.1150 charge 71 "HIE CB" -0.0800 charge 72 "HIE CG" 0.2200 charge 73 "HIE ND1" -0.7000 charge 74 "HIE CD2" -0.0500 charge 75 "HIE CE1" 0.2500 charge 76 "HIE HE1" 0.1300 charge 77 "HIE NE2" -0.3600 charge 78 "HIE HE2" 0.3200 charge 79 "HID CB" -0.0900 charge 80 "HID CG" -0.0500 charge 81 "HID ND1" -0.3600 charge 82 "HID HD1" 0.3200 charge 83 "HID CD2" 0.2200 charge 84 "HID HD2" 0.1000 charge 85 "HID CE1" 0.2500 charge 86 "HID HE1" 0.1300 charge 87 "HID NE2" -0.7000 charge 88 "HIP CB" -0.0500 charge 89 "HIP CG" 0.1900 charge 90 "HIP ND1" -0.5100 charge 91 "HIP HD1" 0.4400 charge 92 "HIP CD2" 0.1900 charge 93 "HIP HD2" 0.1300 charge 94 "HIP CE1" 0.3200 charge 95 "HIP HE1" 0.1800 charge 96 "HIP NE2" -0.5100 charge 97 "HIP HE2" 0.4400 charge 98 "LYS CB" -0.1800 charge 99 "LYS CG" -0.1800 charge 100 "LYS CD" -0.1800 charge 101 "LYS CE" 0.2100 charge 102 "LYS HE" 0.0500 charge 103 "LYS NZ" -0.3000 charge 104 "LYS HZ" 0.3300 charge 105 "ORN CB" 0.0 charge 106 "ORN CG" 0.0 charge 107 "AIB CA" 0.1600 charge 108 "AIB CB" -0.2700 charge 109 "AIB HB" 0.0900 charge 110 "MET CB" -0.1800 charge 111 "MET CG" -0.1400 charge 112 "MET SD" -0.0900 charge 113 "MET CE" -0.2200 charge 114 "PHE CB" -0.1800 charge 115 "PHE CG" 0.0000 charge 116 "PHE CX" -0.1150 charge 117 "PHE HX" 0.1150 charge 118 "LEU CB" -0.1800 charge 119 "LEU CG" -0.0900 charge 120 "LEU CD" -0.2700 charge 121 "ILE CB" -0.0900 charge 122 "ILE CG1" -0.1800 charge 123 "ILE CG2" -0.2700 charge 124 "ILE CD1" -0.2700 charge 125 "DX P" 1.5000 charge 126 "DX OP'" -0.7800 charge 127 "DX O5'" -0.5700 charge 128 "DX C5'" -0.0800 charge 129 "DX C4'" 0.1600 charge 130 "DX O4'" -0.5000 charge 131 "DX C1'" 0.1600 charge 132 "DX C2'" -0.1800 charge 133 "DX C3'" 0.0100 charge 134 "DX O3'" -0.5700 charge 135 "RX P" 1.5000 charge 136 "RX OP'" -0.7800 charge 137 "RX O5'" -0.5700 charge 138 "RX C5'" -0.0800 charge 139 "RX C4'" 0.1600 charge 140 "RX O4'" -0.5000 charge 141 "RX C1'" 0.1600 charge 142 "RX C2'" 0.1400 charge 143 "RX H2'" 0.4300 charge 144 "RX O2'" -0.6600 charge 145 "RX C3'" 0.0100 charge 146 "RX O3'" -0.5700 charge 147 "CYS CB -SS-" -0.1000 charge 148 "CYS SG -SS-" -0.0800 charge 149 "GLN NE2" -0.6200 charge 150 "GLN HE2" 0.3100 charge 151 "Gly CA" -0.0200 charge 152 "Cyt N1" -0.1300 charge 153 "Cyt C6" 0.0500 charge 154 "Cyt H6" 0.1700 charge 155 "Cyt C2" 0.5200 charge 156 "Cyt O2" -0.4900 charge 157 "Cyt N3" -0.6600 charge 158 "Cyt C4" 0.6500 charge 159 "Cyt N4" -0.7500 charge 160 "Cyt H4" 0.3500 charge 161 "Cyt C5" -0.1300 charge 162 "Cyt H5" 0.0700 charge 163 "Ura N1" -0.3400 charge 164 "Ura C6" 0.2000 charge 165 "Ura H6" 0.1400 charge 166 "Ura C2" 0.5500 charge 167 "Ura O2" -0.4500 charge 168 "Ura N3" -0.4600 charge 169 "Ura H3" 0.3600 charge 170 "Ura C4" 0.5300 charge 171 "Ura O4" -0.4800 charge 172 "Ura C5" -0.1500 charge 173 "Ura H5" 0.1000 charge 174 "Thy N1" -0.3400 charge 175 "Thy C6" 0.1700 charge 176 "Thy H6" 0.1700 charge 177 "Thy C2" 0.5100 charge 178 "Thy O2" -0.4100 charge 179 "Thy N3" -0.4600 charge 180 "Thy H3" 0.3600 charge 181 "Thy C4" 0.5000 charge 182 "Thy O4" -0.4500 charge 183 "Thy C5" -0.1500 charge 184 "Thy C7" -0.1100 charge 185 "Thy H7" 0.0700 charge 186 "Ade C5" 0.2800 charge 187 "Ade N7" -0.7100 charge 188 "Ade C8" 0.3400 charge 189 "Ade H8" 0.1200 charge 190 "Ade N9" -0.0500 charge 191 "Ade N1" -0.7400 charge 192 "Ade C2" 0.5000 charge 193 "Ade H2" 0.1300 charge 194 "Ade N3" -0.7500 charge 195 "Ade C4" 0.4300 charge 196 "Ade C6" 0.4600 charge 197 "Ade N6" -0.7700 charge 198 "Ade H6" 0.3800 charge 199 "Gua N9" -0.0200 charge 200 "Gua C4" 0.2600 charge 201 "Gua N3" -0.7400 charge 202 "Gua C2" 0.7500 charge 203 "Gua N1" -0.3400 charge 204 "Gua H1" 0.2600 charge 205 "Gua N2" -0.6800 charge 206 "Gua H2" 0.3350 charge 207 "Gua C6" 0.5400 charge 208 "Gua O6" -0.5100 charge 209 "Gua C5" 0.0000 charge 210 "Gua N7" -0.6000 charge 211 "Gua C8" 0.2500 charge 212 "Gua H8" 0.1600 charge 213 "Pro NTER N" -0.0700 charge 214 "Pro NTER HN" 0.2400 charge 215 "CTER O" -0.6700 charge 216 "TIP3P O" -0.8340 charge 217 "TIP3P H" 0.4170 charge 218 "SPC O" -0.8200 charge 219 "SPC H" 0.4100 charge 220 "AC- CT" -0.3700 charge 221 "NH4+ N guess" -0.3200 charge 222 "Methanol C" -0.0400 charge 223 "Methanethiol C" -0.2000 charge 224 "IME CT" -0.1700 charge 225 "IMD CT" -0.1800 charge 226 "FOA N" -0.6900 charge 227 "FOA HN" 0.3500 charge 228 "FOA C" 0.4200 charge 229 "FOA O" -0.5100 charge 230 "FOA HC" 0.0800 charge 231 "Dummy" 0.0000 charge 232 "Free GLY CA" 0.1300 charge 233 "Free PRO CA" 0.1600 charge 234 "5-D/RPX-O5P" -0.6800 charge 235 "5-D/RPX-HO5P madeup" 0.2100 charge 236 "R5P C1* madeup" 0.2400 charge 237 "R5P C2* madeup" 0.2000 charge 238 "R5P C3* madeup" 0.1000 charge 239 "R5P O3(3-t.) madeup" -0.5600 charge 240 "R5P HO3 madeup" 0.4200 charge 241 "D5P O3(3-t.) madeup" -0.5600 charge 242 "D5P HO3 madeup" 0.4400 charge 243 "D5P C1* madeup" 0.2800 charge 244 "D5P C3* madeup" 0.1200 charge 245 "TIP4P H" 0.5200 charge 246 "TIP4P M" -1.0400 charge 247 "TIP5P Water-LP" -0.2410 charge 248 "TIP5P Water-H" 0.2410 charge 249 "TIP4P-Ew Water-O(M)" -1.04844 charge 250 "TIP4P-Ew Water-H" 0.52422 charge 251 "CHHR in RCH2-COOH" -0.2100 charge 252 "C in (CH2)CS(-)" -0.3800 charge 253 "S in (CH2)CS(-)" -0.8000 charge 254 "OP in ROPO3H(-)" -0.8200 charge 255 "H(O) in ROPO3H(-)" 0.3400 charge 256 "O(*) in Ar-OPO3H(-)" -0.7600 charge 257 "P in Ar-OPO3H(-)" 1.4000 charge 258 "ArC in Ar-HPO4(-)" -0.1600 charge 259 "H(OP) in Ar-HPO4(-)" 0.4000 charge 260 "(RCH2)-N(HH)" -0.9600 charge 261 "TRP CE3" -0.2500 charge 262 "TRP CZ2" -0.2700 charge 263 "TRP CZ3" -0.2000 charge 264 "TRP CH2" -0.1400 charge 265 "TRP HE3" 0.1700 charge 266 "TRP HZ2" 0.1600 charge 267 "TRP HZ3" 0.1400 charge 268 "TRP HH2" 0.1400 charge 269 "(H)O-(C=O)" -0.6100 charge 270 "(H2)C-NH2" 0.0750 charge 271 "(H2)N-RR" -0.2800 # adopted; this conflicts strongly with charges derived elsewhere (~ 0.0) charge 272 "CH3(NH2R)" 0.1600 # adopted; this conflicts strongly with charges derived elsewhere (~ -0.2) charge 273 "N in NR4(+)" -0.6000 # 273-276 from NR4(+) group in CgenFF/lipid (choline) charge 274 "CH3 in C(H3)NR3(+)" -0.3500 charge 275 "CC(H2) in CNR3(+)" -0.1000 charge 276 "H in C(H)NR3(+)" 0.2500 charge 277 "HNR3(+)/H2NR2(+)" 0.3200 # minimally different from native lysine charge 278 "N in HNR3(+)" -0.5620 charge 279 "CH3 in C(H3)NR2H(+)" 0.1440 charge 280 "CE in KM2" 0.2340 charge 281 "N in (CH3)2NH2(+)" -0.5080 charge 282 "CM in (CH3)2NH2(+)" 0.1540 charge 283 "CH3 in (CH3)NH3(+)" 0.0400 charge 284 "C in CR3(NH3+)" 0.3100 charge 285 "N in CR3(NH3+)" -0.3000 charge 286 "H in CR3(NH3+)" 0.3300 charge 287 "C in Urea (CgenFF)" 0.6000 charge 288 "O in Urea (CgenFF)" -0.5800 charge 288 "N in Urea (CgenFF)" -0.6900 charge 290 "H in Urea (CgenFF)" 0.3400 #################################### ## ## ## group-based free energies of ## ## solvation ## ## ## #################################### fos NA+ -103.2 fos K+ -86.0 fos CS+ -75.1 fos CL- -74.5 fos BR- -68.3 fos I- -59.9 fos NH4 -85.2 fos AC- -77.6 fos GDN -70.0 # speculation; some sources cite values for methylguanidinium in the -65 range fos 1MN -76.4 fos 2MN -68.6 fos LCP -49.0 # from Marcus 1994, some perchlorates do have low solubility fos NO3 -71.7 # from Marcus 1991; Cramer/Truhlar 1992 has -65 fos SPC -6.325 fos T3P -6.325 fos T4P -6.325 fos T5P -6.325 fos T4E -6.325 fos NMA -10.1 fos NMF -10.0 fos ACA -9.7 fos PPA -9.4 fos DMA -8.5 fos FOA -10.5 # speculation fos URE -10.8 # computational estimate for KB urea in TIP3P fos O2 2.0 fos CH4 1.9 fos MOH -5.1 fos PCR -6.1 fos PRP 2.0 fos IBU 2.3 fos NBU 2.2 fos MSH -1.2 fos EOH -5.0 fos EMT -1.4 fos TOL -0.8 fos IMD -10.3 fos IME -10.3 fos BEN -0.9 fos NAP -2.4 fos MIN -5.9 fos PUR -6.5 # guess fos ALA 1.9 fos ABA 1.8 fos VAL 2.0 fos NVA 2.0 fos LEU 2.3 fos ILE 2.2 fos NLE 2.2 fos AIB 3.8 # 2xCH4 might not be the best model here fos PRO 2.0 fos MET -1.4 fos SER -5.1 fos THR -5.0 fos CYS -1.2 fos ASN -9.7 fos GLN -9.4 fos HYP -4.8 fos ASH -6.7 fos GLH -6.5 fos LYD -4.3 fos KAC -8.1 # based on NMA and propane fos PHE -0.8 fos TYR -6.1 fos HIE -10.3 # straight from Wolfenden fos HID -10.3 fos TRP -5.9 fos ASP -92.6 fos GLU -91.2 fos LYS -86.5 # same as ORN (weak dependence on longer substituents) fos ORN -86.5 fos DAB -88.0 # from Pliego / Riveros 2000 fos ARG -80.0 # speculation; see above fos HIP -80.0 # guess (pyrrole has -61.4, piperazine -66.0 -> Truhlar/Kelly) fos CYX -88.8 # straight from Truhlar/Kelly fos TYO -87.0 # straight from Truhlar/Kelly fos PTR -91.1 # see below NUC_HPO4, here combined with TYR/SER/THR diff fos SEP -90.1 # ditto fos TPO -90.0 # ditto fos KM1 -81.6 # based on dimethylammonium (hovers around -68) fos KM2 -74.7 # based on trimethylammonium (hovers around -62) fos KM3 -53.2 # from Marcus: there TMA(+) does indeed have only -38.2 fos LINK_CC -0.87 # inference from Et-S-S-Et and Met-S-Met fos PEP_BB -10.1 fos PEP_PRO_BB -8.5 fos PEP_BB_NH2 -9.7 fos PEP_BB_FOR -10.0 fos PEP_PRO_BB_FOR -8.5 # speculation fos PEP_CCT -92.6 fos PEP_UCT -6.7 fos PEP_CNT -91.4 fos PEP_PRO_CNT -83.6 fos PEP_UNT -4.5 fos PEP_PRO_UNT -3.9 fos CYT -20.1 # calc. fos URA -14.2 # calc. fos THY -12.8 # calc. fos ADE -15.0 # calc. fos GUA -23.7 # calc. fos XXC -17.1 # calc. + 3.0 fos XXU -11.2 # calc. + 3.0 fos XXT -9.8 # calc. + 3.0 fos XXA -12.0 # calc. + 3.0 fos XXG -20.7 # calc. + 3.0 fos NUC_PO4 -85.0 # speculation fos NUC_HPO4 -90.0 # speculation fos NUC_SUG_0 -3.5 # THF has -3.65 fos NUC_SUG_1 -6.5 # speculation fos NUC_SUG_2 -9.5 # speculation, 1,2-ethanediol has -10, but glycerol only -9 fos NUC_SUG_3 -12.5 # speculation, D-xylose and D-glucose (4/5 free hydroxyls) have -25 ####################### ## ## ## bond parameters ## ## 1) harmonic ## ## 2) morse ## ## 3) quartic ## ## ## ####################### bond 1 1 222.5 1.5000 bond 2 1 222.5 1.5380 bond 3 1 222.5 1.5300 bond 4 1 222.5 1.5280 bond 5 1 309.0 1.1110 bond 6 1 330.0 1.0800 bond 7 1 322.0 1.1110 bond 8 1 305.0 1.3750 bond 9 1 350.0 1.3650 bond 10 1 350.0 1.4300 bond 11 1 375.0 1.4920 bond 12 1 300.0 1.3600 bond 13 1 230.0 1.4900 bond 14 1 340.0 1.0800 bond 15 1 350.0 1.0800 bond 16 1 340.0 1.0830 bond 17 1 360.0 1.3850 bond 18 1 334.3 1.4110 bond 19 1 230.0 1.4000 bond 20 1 428.0 1.4200 bond 21 1 545.0 0.9600 bond 22 1 150.0 1.3340 bond 23 1 340.0 1.4300 bond 24 1 320.0 1.4300 bond 25 1 240.0 1.4550 bond 26 1 200.0 1.4800 bond 27 1 390.0 1.4900 bond 28 1 240.0 1.4550 bond 29 1 250.0 1.4900 bond 30 1 200.0 1.5220 bond 31 1 229.63 1.5000 bond 32 1 190.0 1.5310 bond 33 1 383.0 1.5040 bond 34 1 365.0 1.5020 bond 35 1 450.0 1.3300 bond 36 1 198.0 1.8180 bond 37 1 214.0 1.8160 bond 38 1 240.0 1.8160 bond 39 1 600.0 1.3350 bond 40 1 440.0 1.3400 bond 41 1 500.0 1.3420 bond 42 1 510.0 1.3300 bond 43 1 200.0 1.4900 bond 44 1 222.5 1.5270 bond 45 1 222.5 1.5370 bond 46 1 410.0 1.3600 bond 47 1 200.0 1.4800 bond 48 1 937.96 1.1600 bond 49 1 330.0 1.1100 bond 50 1 403.0 1.0400 bond 51 1 317.13 1.1000 bond 52 1 260.0 1.4200 bond 53 1 300.0 1.1110 bond 54 1 360.5 1.1000 bond 55 1 365.0 1.1000 bond 56 1 222.5 1.5280 bond 57 1 374.0 1.0900 bond 58 1 375.0 1.0830 bond 59 1 340.0 1.0900 bond 60 1 333.0 1.0700 bond 61 1 365.0 1.0830 bond 62 1 0.0 1.5139 bond 63 1 260.0 1.3000 bond 64 1 320.0 1.4340 bond 65 1 320.0 1.4550 bond 66 1 450.0 1.3650 bond 67 1 455.0 1.0000 bond 68 1 370.0 1.3450 bond 69 1 440.0 0.9970 bond 70 1 405.0 0.9800 bond 71 1 430.0 1.3600 bond 72 1 480.0 1.0000 bond 73 1 460.0 1.0000 bond 74 1 403.0 1.0400 bond 75 1 320.0 1.4850 bond 76 1 320.0 1.5020 bond 77 1 460.0 1.0060 bond 78 1 400.0 1.3800 bond 79 1 400.0 1.3600 bond 80 1 466.0 1.0000 bond 81 1 400.0 1.3200 bond 82 1 380.0 1.3700 bond 83 1 380.0 1.3200 bond 84 1 453.0 1.0000 bond 85 1 270.0 1.3700 bond 86 1 270.0 1.3700 bond 87 1 537.5 0.9760 bond 88 1 620.0 1.2300 bond 89 1 650.0 1.2300 bond 90 1 750.0 1.2200 bond 91 1 525.0 1.2600 bond 92 1 450.0 0.9572 bond 93 1 275.0 1.3250 bond 94 1 173.0 2.0290 bond 95 1 205.0 1.8360 bond 96 1 350.0 1.0900 bond 97 1 302.0 1.4090 bond 98 1 302.0 1.4030 bond 99 1 302.0 1.4800 bond 100 1 302.0 1.3600 bond 101 1 560.0 1.3600 bond 102 1 380.0 1.3670 bond 103 1 302.0 1.3480 bond 104 1 340.0 1.3960 bond 105 1 340.0 1.3890 bond 106 1 340.0 1.3830 bond 107 1 350.0 1.3350 bond 108 1 660.0 1.2340 bond 109 1 860.0 1.2300 bond 110 1 620.0 1.2450 bond 111 1 320.0 1.4060 bond 112 1 260.0 1.4050 bond 113 1 360.0 1.3580 bond 114 1 360.0 1.3660 bond 115 1 400.0 1.3920 bond 116 1 450.0 1.3430 bond 117 1 400.0 1.3420 bond 118 1 320.0 1.3260 bond 119 1 500.0 1.3260 bond 120 1 560.0 1.3200 bond 121 1 450.0 1.3600 bond 122 1 420.0 1.3500 bond 123 1 420.0 1.3200 bond 124 1 560.0 1.3350 bond 125 1 222.5 1.4900 bond 126 1 230.0 1.4800 bond 127 1 230.0 1.4780 bond 128 1 302.0 1.3430 bond 129 1 320.0 1.3430 bond 130 1 420.0 1.3150 bond 131 1 420.0 1.3550 bond 132 1 380.0 1.0900 bond 133 1 320.0 1.3740 bond 134 1 300.0 1.3780 bond 135 1 350.0 1.3650 bond 136 1 420.0 1.3220 bond 137 1 450.0 1.2950 bond 138 1 400.0 1.3050 bond 139 1 310.0 1.3610 bond 140 1 320.0 1.3500 bond 141 1 300.0 1.3750 bond 142 1 302.0 1.3750 bond 143 1 350.0 1.3120 bond 144 1 350.0 1.3150 bond 145 1 350.0 1.3320 bond 146 1 310.0 1.3550 bond 147 1 310.0 1.3650 bond 148 1 400.0 1.4600 bond 149 1 428.0 1.4200 bond 150 1 322.0 1.1110 bond 151 1 340.0 1.4300 bond 152 1 488.0 1.0000 bond 153 1 474.0 1.0100 bond 154 1 471.0 1.0100 bond 155 1 545.0 0.9600 bond 156 1 270.0 1.6000 bond 157 1 580.0 1.4800 bond 158 1 237.0 1.5800 bond 159 1 300.0 1.6800 bond 160 1 480.0 1.5300 bond 161 1 460.0 1.0100 bond 162 1 200.0 1.5180 bond 163 1 240.0 1.4460 bond 164 1 222.5 1.5290 bond 165 1 222.5 1.5160 bond 166 1 309.0 1.1110 bond 167 1 240.0 1.4800 bond 168 1 200.0 1.4500 bond 169 1 222.5 1.4600 bond 170 1 222.5 1.5120 bond 171 1 320.0 1.4400 bond 172 1 310.0 1.4330 bond 173 1 400.0 1.4560 bond 174 1 400.0 1.4580 bond 175 1 220.0 1.4560 bond 176 1 220.0 1.4580 bond 177 1 428.0 1.4000 bond 178 1 340.0 1.4400 bond 179 1 220.0 1.4620 bond 180 1 270.0 1.6100 bond 181 1 340.0 1.3800 bond 182 1 215.0 1.5100 bond 183 1 200.0 1.4900 bond 184 1 428.0 1.4300 ####################### ## ## ## angle parameters ## ## 1) harmonic ## ## 2) urey-bradley ## ## (dbl harmon.) ## ## 3) GROMOS ## ## (cos-harmon.) ## ## ## ####################### angle 1 1 50.000 111.00 angle 2 1 67.700 110.00 angle 3 1 55.000 110.50 angle 4 1 52.000 108.00 angle 5 2 38.000 109.50 50.00 2.1400 angle 6 1 50.000 107.00 angle 7 1 3000.000 180.00 angle 8 2 40.000 120.00 35.00 2.41620 angle 9 1 48.000 123.50 angle 10 1 32.000 112.20 angle 11 1 48.000 126.00 angle 12 1 47.000 125.20 angle 13 1 60.000 117.00 angle 14 1 52.000 112.30 angle 15 1 50.000 112.30 angle 16 1 70.000 108.50 angle 17 1 100.000 114.20 angle 18 1 100.000 111.00 angle 19 1 130.000 107.50 angle 20 1 130.000 104.00 angle 21 1 145.000 108.00 angle 22 1 60.000 118.00 angle 23 1 60.000 122.00 angle 24 2 85.000 106.40 25.00 2.26100 angle 25 1 110.000 108.00 angle 26 2 53.350 111.00 8.00 2.56100 angle 27 1 51.800 107.50 angle 28 1 58.350 113.00 angle 29 2 58.350 113.50 11.16 2.56100 angle 30 2 58.350 113.60 11.16 2.56100 angle 31 1 50.000 120.00 angle 32 1 45.800 122.30 angle 33 1 45.800 130.00 angle 34 1 30.000 127.00 angle 35 1 45.800 124.00 angle 36 1 45.800 120.00 angle 37 1 45.800 122.00 angle 38 1 62.300 120.00 angle 39 2 40.000 109.60 30.00 2.26510 angle 40 2 53.350 108.50 8.00 2.56100 angle 41 2 53.350 114.00 8.00 2.56100 angle 42 2 58.000 115.00 8.00 2.56100 angle 43 1 34.000 95.00 angle 44 1 130.000 133.50 angle 45 1 85.000 108.00 angle 46 1 58.350 114.00 angle 47 1 34.000 123.00 angle 48 1 35.000 117.00 angle 49 1 23.000 120.00 angle 50 2 30.000 125.50 20.00 2.15000 angle 51 2 30.000 127.00 20.00 2.14000 angle 52 2 25.000 126.00 15.00 2.13000 angle 53 2 25.000 126.00 15.00 2.09000 angle 54 1 28.000 126.00 angle 55 1 65.000 108.00 angle 56 1 55.000 115.00 angle 57 1 57.500 106.00 angle 58 2 29.000 120.00 25.00 2.15250 angle 59 1 41.000 122.00 angle 60 2 32.000 125.00 25.00 2.17300 angle 61 2 33.430 110.10 22.53 2.17900 angle 62 2 26.500 110.10 22.53 2.17900 angle 63 2 35.500 109.00 5.40 1.80200 angle 64 2 34.600 110.10 22.53 2.17900 angle 65 2 35.500 108.40 14.00 1.77500 angle 66 2 33.000 109.50 30.00 2.16300 angle 67 2 34.500 110.10 22.53 2.17900 angle 68 1 49.300 107.50 angle 69 1 45.000 111.50 angle 70 1 33.430 109.50 angle 71 1 42.000 111.50 angle 72 2 37.500 110.10 22.53 2.17900 angle 73 2 35.500 108.40 5.40 1.80200 angle 74 2 20.000 126.40 25.00 2.18600 angle 75 2 32.000 126.40 25.00 2.25500 angle 76 1 52.000 119.50 angle 77 1 42.000 118.00 angle 78 1 40.000 116.00 angle 79 1 22.000 117.00 angle 80 1 45.000 120.50 angle 81 1 55.500 120.50 angle 82 1 19.000 119.00 angle 83 1 50.000 112.00 angle 84 1 35.000 118.00 angle 85 1 50.000 109.50 angle 86 1 35.000 111.00 angle 87 1 36.000 115.00 angle 88 1 49.000 120.00 angle 89 1 40.400 120.00 angle 90 1 25.000 120.00 angle 91 1 39.000 106.50 angle 92 2 30.000 109.50 20.00 2.07400 angle 93 1 44.000 109.50 angle 94 2 33.000 109.50 4.00 2.05600 angle 95 1 51.000 107.50 angle 96 2 30.000 120.00 22.00 2.15250 angle 97 2 30.000 122.00 22.00 2.14600 angle 98 2 32.000 126.40 25.00 2.18600 angle 99 2 22.000 130.00 15.00 2.21500 angle 100 2 25.000 130.00 20.00 2.20000 angle 101 1 38.800 95.00 angle 102 1 43.000 95.00 angle 103 1 55.000 104.52 angle 104 1 20.000 112.50 angle 105 1 50.000 108.20 angle 106 1 70.000 110.80 angle 107 1 48.000 112.00 angle 108 1 70.000 110.50 angle 109 1 48.000 108.00 angle 110 2 40.000 120.00 70.00 2.31000 angle 111 1 67.700 107.50 angle 112 1 51.500 107.50 angle 113 1 80.000 116.50 angle 114 1 70.000 113.50 angle 115 1 51.500 109.50 angle 116 1 80.000 112.50 angle 117 2 50.000 116.50 50.00 2.45000 angle 118 2 44.000 111.00 50.00 1.98000 angle 119 1 43.700 110.00 angle 120 2 45.000 107.50 35.00 2.10100 angle 121 1 50.000 106.00 angle 122 1 51.500 109.15 angle 123 1 130.000 106.00 angle 124 2 25.000 124.00 20.00 2.14000 angle 125 2 25.000 122.50 20.00 2.14000 angle 126 1 130.000 110.00 angle 127 2 25.000 120.00 20.00 2.14000 angle 128 2 25.000 125.00 20.00 2.12000 angle 129 1 130.000 112.50 angle 130 2 22.000 122.00 15.00 2.18000 angle 131 2 32.000 126.00 25.00 2.14000 angle 132 2 85.000 110.50 25.00 2.24000 angle 133 2 32.000 125.00 25.00 2.17700 angle 134 1 95.000 107.40 angle 135 1 80.000 118.00 angle 136 1 80.000 121.00 angle 137 1 50.000 121.70 angle 138 1 80.000 122.50 angle 139 2 15.000 121.00 50.00 2.44000 angle 140 1 44.000 122.00 angle 141 2 75.000 122.50 50.00 2.37000 angle 142 2 70.000 125.00 20.00 2.44200 angle 143 1 40.000 120.00 angle 144 2 40.000 118.00 50.00 2.38800 angle 145 2 100.000 124.00 70.00 2.22500 angle 146 1 65.000 122.00 angle 147 1 65.000 118.30 angle 148 1 45.200 120.00 angle 149 2 50.000 123.00 210.00 2.26200 angle 150 1 75.700 110.10 angle 151 1 45.900 108.89 angle 152 2 55.000 109.00 20.00 2.32600 angle 153 2 90.000 125.90 160.00 2.25760 angle 154 1 60.000 109.50 angle 155 1 58.000 112.50 angle 156 1 58.000 114.50 angle 157 1 46.100 111.30 angle 158 1 38.000 111.00 angle 159 1 72.500 103.30 angle 160 1 55.000 118.00 angle 161 1 40.000 112.30 angle 162 1 115.000 109.70 angle 163 1 110.000 109.00 angle 164 1 90.000 106.00 angle 165 1 80.000 106.00 angle 166 1 45.200 107.24 angle 167 1 42.000 119.00 angle 168 1 30.000 116.00 angle 169 1 90.000 117.80 angle 170 1 60.000 133.00 angle 171 1 90.000 110.10 angle 172 1 60.000 127.40 angle 173 1 60.000 121.00 angle 174 1 60.000 110.70 angle 175 1 100.000 105.70 angle 176 1 100.000 110.00 angle 177 1 120.000 104.60 angle 178 1 100.000 113.40 angle 179 1 100.000 106.30 angle 180 1 100.000 126.90 angle 181 1 100.000 129.00 angle 182 1 38.000 113.50 angle 183 1 50.000 130.70 angle 184 1 50.000 118.60 angle 185 1 40.000 121.50 angle 186 1 31.000 117.00 angle 187 1 39.000 124.80 angle 188 1 39.000 121.80 angle 189 1 30.000 129.40 angle 190 1 30.000 125.00 angle 191 1 70.000 131.10 angle 192 1 70.000 122.20 angle 193 1 90.000 109.40 angle 194 1 70.000 129.90 angle 195 1 70.000 119.60 angle 196 1 70.000 107.80 angle 197 1 100.000 104.60 angle 198 1 100.000 111.40 angle 199 1 120.000 103.80 angle 200 1 100.000 113.00 angle 201 1 100.000 107.20 angle 202 1 140.000 125.50 angle 203 1 125.000 129.00 angle 204 1 45.000 113.30 angle 205 1 45.000 115.60 angle 206 1 95.000 115.40 angle 207 1 95.000 122.40 angle 208 1 50.000 127.50 angle 209 1 50.000 124.70 angle 210 1 40.000 122.20 angle 211 1 30.000 124.60 angle 212 1 30.000 129.30 angle 213 1 50.000 124.10 angle 214 1 50.000 116.80 angle 215 1 85.000 119.10 angle 216 1 85.000 119.30 angle 217 1 85.000 117.80 angle 218 1 85.000 122.90 angle 219 1 37.000 121.20 angle 220 1 37.000 114.70 angle 221 1 130.000 119.40 angle 222 1 130.000 123.80 angle 223 1 81.000 122.30 angle 224 1 81.000 118.40 angle 225 1 38.000 120.10 angle 226 1 38.000 122.10 angle 227 1 38.000 118.70 angle 228 1 38.000 124.60 angle 229 1 44.000 115.00 angle 230 1 70.000 122.00 angle 231 1 70.000 112.60 angle 232 1 50.000 114.00 angle 233 1 50.000 130.20 angle 234 1 100.000 117.60 angle 235 1 100.000 123.60 angle 236 1 40.500 122.00 angle 237 1 40.500 114.40 angle 238 1 40.500 115.40 angle 239 1 40.500 117.00 angle 240 1 32.000 116.00 angle 241 1 100.000 121.60 angle 242 1 100.000 124.40 angle 243 1 100.000 121.90 angle 244 1 100.000 125.50 angle 245 1 100.000 124.60 angle 246 1 100.000 127.00 angle 247 1 100.000 117.80 angle 248 1 100.000 124.20 angle 249 1 100.000 104.00 angle 250 1 100.000 110.00 angle 251 1 30.000 120.30 angle 252 1 30.000 114.30 angle 253 1 30.000 122.10 angle 254 1 30.000 121.30 angle 255 1 30.000 122.00 angle 256 1 30.000 119.00 angle 257 1 30.000 120.00 angle 258 2 30.000 115.00 40.00 2.35 angle 259 2 30.000 120.00 40.00 2.35 angle 260 1 30.000 106.30 angle 261 1 120.000 116.70 angle 262 1 120.000 123.60 angle 263 1 120.000 122.00 angle 264 1 120.000 120.00 angle 265 1 120.000 106.25 angle 266 1 35.000 116.75 angle 267 1 35.000 115.75 angle 268 1 35.000 120.00 angle 269 1 80.000 127.50 angle 270 1 80.000 120.50 angle 271 1 80.000 117.50 angle 272 1 80.000 104.30 angle 273 1 80.000 100.00 angle 274 1 80.000 108.40 angle 275 1 140.000 128.40 angle 276 1 140.000 108.00 angle 277 1 140.000 113.70 angle 278 1 125.000 129.70 angle 279 1 125.000 124.20 angle 280 1 125.000 108.00 angle 281 1 90.000 108.40 angle 282 1 90.000 102.00 angle 283 1 90.000 108.20 angle 284 1 90.000 110.00 angle 285 1 90.000 108.00 angle 286 1 70.000 116.00 angle 287 1 70.000 115.40 angle 288 1 70.000 120.50 angle 289 1 70.000 125.90 angle 290 1 70.000 127.80 angle 291 1 70.000 126.90 angle 292 1 70.000 113.70 angle 293 1 70.000 121.70 angle 294 1 70.000 108.40 angle 295 1 45.000 118.40 angle 296 1 45.000 119.60 angle 297 1 45.000 120.00 angle 298 1 45.000 115.90 angle 299 1 45.000 126.10 angle 300 1 45.000 127.60 angle 301 1 45.000 126.50 angle 302 1 45.000 126.30 angle 303 2 45.000 140.0 40.0 3.15 angle 304 1 45.000 110.00 angle 305 1 110.000 112.00 angle 306 1 110.000 113.70 angle 307 1 110.000 111.00 angle 308 1 110.000 116.40 angle 309 1 110.000 115.00 angle 310 1 110.000 96.00 angle 311 1 43.000 111.00 angle 312 2 85.000 113.0 80.0 2.46 angle 313 2 85.000 118.5 20.0 2.43 angle 314 2 85.000 128.5 20.0 2.17 angle 315 1 5.000 107.80 angle 316 1 40.000 118.00 angle 317 1 40.000 110.20 angle 318 1 40.000 124.20 angle 319 1 40.000 108.00 angle 320 1 10.000 131.80 angle 321 1 50.000 118.00 angle 322 1 53.500 108.50 angle 323 1 43.500 128.00 angle 324 1 42.000 116.00 angle 325 1 60.000 122.00 angle 326 2 60.000 102.0 8.00 2.561 angle 327 2 60.000 100.0 8.00 2.561 angle 328 1 55.000 110.10 angle 329 1 33.430 110.10 angle 330 2 33.400 110.10 22.53 2.179 angle 331 1 20.000 114.00 angle 332 2 20.000 120.00 35.00 2.33 angle 333 1 32.000 117.40 angle 334 1 39.000 123.00 angle 335 1 39.000 106.00 angle 336 2 15.000 140.00 40.00 2.80 # this term appears with negative sign on UB force constant in CHARMM (unused for CAMPARI-supported residues) angle 337 1 48.100 108.00 angle 338 1 48.100 100.00 angle 339 1 98.900 108.23 angle 340 1 98.900 104.00 angle 341 1 98.900 111.60 angle 342 1 88.900 111.60 angle 343 1 88.900 105.00 angle 344 1 104.000 120.00 angle 345 2 34.530 110.10 22.53 2.179 angle 346 1 75.700 110.00 angle 347 1 57.500 109.00 angle 348 1 130.000 127.00 angle 349 1 130.000 126.00 angle 350 2 90.000 120.00 20.00 2.300 angle 351 1 98.900 103.00 angle 352 1 75.000 120.00 angle 353 1 130.000 129.50 angle 354 1 85.000 112.00 angle 355 1 30.000 126.70 angle 356 1 55.000 109.50 angle 357 1 50.000 113.20 angle 358 1 50.000 110.00 angle 359 1 56.500 107.50 angle 360 2 60.000 109.50 26.00 2.466 angle 361 1 67.700 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0.00000 # N torsion 270 3 2.46000 -3.86000 -0.18000 3.16000 0.00000 0.00000 # HID CA-CB-CG-ND1 torsion 271 3 1.76000 -3.10000 0.18000 2.68000 0.00000 0.00000 # HIE CA-CB-CG-ND1 torsion 272 3 2.51000 -4.05000 0.30000 3.08000 0.00000 0.00000 # HID/E CA-CB-CG-CD2 torsion 273 3 2.33000 -2.43000 -1.28000 3.48000 0.00000 0.00000 # HID/E C-CA-CB-CG torsion 274 3 0.90000 2.70000 0.00000 -3.60000 0.00000 0.00000 # N torsion 275 3 1.67000 -0.37000 -0.84000 1.20000 0.00000 0.00000 # HIP CA-CB-CG-ND1 torsion 276 3 2.17000 -2.43000 0.88000 0.52000 0.00000 0.00000 # HIP CA-CB-CG-CD2 torsion 277 3 3.61000 -3.83000 0.26000 7.44000 0.00000 0.00000 # HIP C-CA-CB-CG torsion 278 3 3.85000 8.05000 -0.44000 -9.28000 0.00000 0.00000 # N torsion 279 3 1.35000 -1.77000 -0.76000 2.36000 0.00000 0.00000 # GLU CA-CB-CG-CD torsion 280 3 3.67000 -4.91000 -1.96000 6.40000 0.00000 0.00000 # GLU C-CA-CB-CG torsion 281 3 2.06000 4.98000 0.70000 -7.04000 0.00000 0.00000 # N torsion 282 3 4.26000 3.54000 -1.96000 -5.84000 0.00000 0.00000 # ASP CA-CB-CG-ODX torsion 283 3 4.78000 -0.16000 -2.58000 2.36000 0.00000 0.00000 # ASP C-CA-CB-CG torsion 284 3 1.26000 1.82000 -0.20000 -1.52000 0.00000 0.00000 # N torsion 285 3 0.42000 0.46000 1.30000 -0.88000 0.00000 0.00000 # CYS CA-CB-SG-HG torsion 286 3 3.09000 -3.81000 -1.50000 5.40000 0.00000 0.00000 # CYS C-CA-CB-SG torsion 287 3 2.77000 3.95000 -1.00000 -5.72000 0.00000 0.00000 # N torsion 288 3 1.60000 -4.80000 0.00000 6.40000 0.00000 0.00000 # C-terminal GLU (possibly erroneous in ref.) torsion 289 3 2.00000 2.00000 0.00000 0.00000 0.00000 0.00000 torsion 290 3 1.90000 0.30000 -0.80000 0.80000 0.00000 0.00000 torsion 291 3 1.90000 1.90000 0.00000 0.00000 0.00000 0.00000 torsion 292 3 2.90000 1.50000 -13.40000 -6.00000 22.40000 4.80000 -9.60000 torsion 293 3 1.20000 0.40000 0.80000 -1.60000 0.00000 0.00000 torsion 294 3 2.20000 -1.40000 0.00000 -0.80000 0.00000 0.00000 torsion 295 3 1.80000 1.80000 -10.80000 -2.40000 28.80000 -0.00000 -19.20000 torsion 296 3 0.26000 0.78000 0.00000 -1.04000 0.00000 0.00000 torsion 297 3 4.40000 9.18000 5.12000 -9.56000 0.00000 0.00000 0.00000 torsion 298 3 0.98000 -0.90000 -0.30000 0.44000 0.00000 0.00000 0.00000 torsion 299 3 2.73000 1.53000 -0.86000 -3.40000 0.00000 0.00000 0.00000 torsion 300 3 2.98000 -1.16000 -1.94000 0.24000 0.00000 0.00000 0.00000 ######################################## ## ## ## Biopolymer Atom Type Conversions ## ## ## ######################################## biotype 1 N "Glycine" 1 2 35 biotype 2 CA "Glycine" 2 151 16 biotype 3 C "Glycine" 3 8 13 biotype 4 HN "Glycine" 4 4 1 biotype 5 O "Glycine" 5 9 42 biotype 6 HA "Glycine" 9 10 6 biotype 7 N "Alanine" 1 2 35 biotype 8 CA "Alanine" 2 5 15 biotype 9 C "Alanine" 3 8 13 biotype 10 HN "Alanine" 4 4 1 biotype 11 O "Alanine" 5 9 42 biotype 12 HA "Alanine" 9 10 6 biotype 13 CB "Alanine" 2 11 17 biotype 14 HB "Alanine" 9 10 3 biotype 15 N "Valine" 1 2 35 biotype 16 CA "Valine" 2 5 15 biotype 17 C "Valine" 3 8 13 biotype 18 HN "Valine" 4 4 1 biotype 19 O "Valine" 5 9 42 biotype 20 HA "Valine" 9 10 6 biotype 21 CB "Valine" 2 12 15 biotype 22 HB "Valine" 9 10 3 biotype 23 CG "Valine" 2 13 17 biotype 24 HG "Valine" 9 10 3 biotype 25 N "Leucine" 1 2 35 biotype 26 CA "Leucine" 2 5 15 biotype 27 C "Leucine" 3 8 13 biotype 28 HN "Leucine" 4 4 1 biotype 29 O "Leucine" 5 9 42 biotype 30 HA "Leucine" 9 10 6 biotype 31 CB "Leucine" 2 118 16 biotype 32 HB "Leucine" 9 10 3 biotype 33 CG "Leucine" 2 119 15 biotype 34 HG "Leucine" 9 10 3 biotype 35 CD "Leucine" 2 120 17 biotype 36 HD "Leucine" 9 10 3 biotype 37 N "Isoleucine" 1 2 35 biotype 38 CA "Isoleucine" 2 5 15 biotype 39 C "Isoleucine" 3 8 13 biotype 40 HN "Isoleucine" 4 4 1 biotype 41 O "Isoleucine" 5 9 42 biotype 42 HA "Isoleucine" 9 10 6 biotype 43 CB "Isoleucine" 2 121 15 biotype 44 HB "Isoleucine" 9 10 3 biotype 45 CG1 "Isoleucine" 2 122 16 biotype 46 HG1 "Isoleucine" 9 10 3 biotype 47 CG2 "Isoleucine" 2 123 17 biotype 48 HG2 "Isoleucine" 9 10 3 biotype 49 CD1 "Isoleucine" 2 124 17 biotype 50 HD1 "Isoleucine" 9 10 3 biotype 51 N "Serine" 1 2 35 biotype 52 CA "Serine" 2 5 15 biotype 53 C "Serine" 3 8 13 biotype 54 HN "Serine" 4 4 1 biotype 55 O "Serine" 5 9 42 biotype 56 HA "Serine" 9 10 6 biotype 57 CB "Serine" 2 41 16 biotype 58 HB "Serine" 9 10 3 biotype 59 OG "Serine" 6 42 45 biotype 60 HG "Serine" 4 43 1 biotype 61 N "Threonine" 1 2 35 biotype 62 CA "Threonine" 2 5 15 biotype 63 C "Threonine" 3 8 13 biotype 64 HN "Threonine" 4 4 1 biotype 65 O "Threonine" 5 9 42 biotype 66 HA "Threonine" 9 10 6 biotype 67 CB "Threonine" 2 44 15 biotype 68 HB "Threonine" 9 10 3 biotype 69 OG1 "Threonine" 6 45 45 biotype 70 HG1 "Threonine" 4 46 1 biotype 71 CG2 "Threonine" 2 47 17 biotype 72 HG2 "Threonine" 9 10 3 biotype 73 N "Cysteine (-SH)" 1 2 35 biotype 74 CA "Cysteine (-SH)" 2 5 15 biotype 75 C "Cysteine (-SH)" 3 8 13 biotype 76 HN "Cysteine (-SH)" 4 4 1 biotype 77 O "Cysteine (-SH)" 5 9 42 biotype 78 HA "Cysteine (-SH)" 9 10 6 biotype 79 CB "Cysteine (-SH)" 2 48 16 biotype 80 HB "Cysteine (-SH)" 9 10 3 biotype 81 SG "Cysteine (-SH)" 7 49 50 biotype 82 HG "Cysteine (-SH)" 4 50 10 biotype 83 N "Cystine (-SS-)" 1 2 35 biotype 84 CA "Cystine (-SS-)" 2 5 15 biotype 85 C "Cystine (-SS-)" 3 8 13 biotype 86 HN "Cystine (-SS-)" 4 4 1 biotype 87 O "Cystine (-SS-)" 5 9 42 biotype 88 HA "Cystine (-SS-)" 9 10 6 biotype 89 CB "Cystine (-SS-)" 2 147 16 biotype 90 HB "Cystine (-SS-)" 9 10 3 biotype 91 SG "Cystine (-SS-)" 7 148 51 biotype 92 N "Proline" 11 3 31 biotype 93 CA "Proline" 2 6 22 biotype 94 C "Proline" 3 8 13 biotype 95 O "Proline" 5 9 42 biotype 96 HA "Proline" 9 7 6 biotype 97 CB "Proline" 2 51 23 biotype 98 HB "Proline" 9 10 3 biotype 99 CG "Proline" 2 52 23 biotype 100 HG "Proline" 9 10 3 biotype 101 CD "Proline" 2 53 24 biotype 102 HD "Proline" 9 10 3 biotype 103 N "Phenylalanine" 1 2 35 biotype 104 CA "Phenylalanine" 2 5 15 biotype 105 C "Phenylalanine" 3 8 13 biotype 106 HN "Phenylalanine" 4 4 1 biotype 107 O "Phenylalanine" 5 9 42 biotype 108 HA "Phenylalanine" 9 10 6 biotype 109 CB "Phenylalanine" 2 114 16 biotype 110 HB "Phenylalanine" 9 10 3 biotype 111 CG "Phenylalanine" 31 115 14 biotype 112 CD "Phenylalanine" 31 116 14 biotype 113 HD "Phenylalanine" 9 117 5 biotype 114 CE "Phenylalanine" 31 116 14 biotype 115 HE "Phenylalanine" 9 117 5 biotype 116 CZ "Phenylalanine" 31 116 14 biotype 117 HZ "Phenylalanine" 9 117 5 biotype 118 N "Tyrosine" 1 2 35 biotype 119 CA "Tyrosine" 2 5 15 biotype 120 C "Tyrosine" 3 8 13 biotype 121 HN "Tyrosine" 4 4 1 biotype 122 O "Tyrosine" 5 9 42 biotype 123 HA "Tyrosine" 9 10 6 biotype 124 CB "Tyrosine" 2 54 16 biotype 125 HB "Tyrosine" 9 10 3 biotype 126 CG "Tyrosine" 31 55 14 biotype 127 CD "Tyrosine" 31 56 14 biotype 128 HD "Tyrosine" 9 57 5 biotype 129 CE "Tyrosine" 31 56 14 biotype 130 HE "Tyrosine" 9 57 5 biotype 131 CZ "Tyrosine" 31 58 14 biotype 132 OH "Tyrosine" 6 59 45 biotype 133 HH "Tyrosine" 4 60 1 biotype 134 N "Tryptophan" 1 2 35 biotype 135 CA "Tryptophan" 2 5 15 biotype 136 C "Tryptophan" 3 8 13 biotype 137 HN "Tryptophan" 4 4 1 biotype 138 O "Tryptophan" 5 9 42 biotype 139 HA "Tryptophan" 9 10 6 biotype 140 CB "Tryptophan" 2 61 16 biotype 141 HB "Tryptophan" 9 10 3 biotype 142 CG "Tryptophan" 31 62 21 biotype 143 CD1 "Tryptophan" 31 63 14 biotype 144 HD1 "Tryptophan" 9 64 5 biotype 145 CD2 "Tryptophan" 31 65 20 biotype 146 NE1 "Tryptophan" 1 66 39 biotype 147 HE1 "Tryptophan" 4 67 1 biotype 148 CE2 "Tryptophan" 31 68 20 biotype 149 CE3 "Tryptophan" 31 261 109 biotype 150 HE3 "Tryptophan" 9 265 5 biotype 151 CZ2 "Tryptophan" 31 262 109 biotype 152 HZ2 "Tryptophan" 9 266 5 biotype 153 CZ3 "Tryptophan" 31 263 14 biotype 154 HZ3 "Tryptophan" 9 267 5 biotype 155 CH2 "Tryptophan" 31 264 14 biotype 156 HH2 "Tryptophan" 9 268 5 biotype 157 N "Histidine (+)" 1 2 35 biotype 158 CA "Histidine (+)" 2 5 15 biotype 159 C "Histidine (+)" 3 8 13 biotype 160 HN "Histidine (+)" 4 4 1 biotype 161 O "Histidine (+)" 5 9 42 biotype 162 HA "Histidine (+)" 9 10 6 biotype 163 CB "Histidine (+)" 2 88 110 biotype 164 HB "Histidine (+)" 9 10 3 biotype 165 CG "Histidine (+)" 31 89 18 biotype 166 ND1 "Histidine (+)" 1 90 34 biotype 167 HD1 "Histidine (+)" 4 91 1 biotype 168 CD2 "Histidine (+)" 31 92 18 biotype 169 HD2 "Histidine (+)" 9 93 7 biotype 170 CE1 "Histidine (+)" 31 94 19 biotype 171 HE1 "Histidine (+)" 9 95 8 biotype 172 NE2 "Histidine (+)" 1 96 34 biotype 173 HE2 "Histidine (+)" 4 97 1 biotype 174 N "Histidine (HD)" 1 2 35 biotype 175 CA "Histidine (HD)" 2 5 15 biotype 176 C "Histidine (HD)" 3 8 13 biotype 177 HN "Histidine (HD)" 4 4 1 biotype 178 O "Histidine (HD)" 5 9 42 biotype 179 HA "Histidine (HD)" 9 10 6 biotype 180 CB "Histidine (HD)" 2 79 16 biotype 181 HB "Histidine (HD)" 9 10 3 biotype 182 CG "Histidine (HD)" 31 80 18 biotype 183 ND1 "Histidine (HD)" 1 81 32 biotype 184 HD1 "Histidine (HD)" 4 82 1 biotype 185 CD2 "Histidine (HD)" 31 83 18 biotype 186 HD2 "Histidine (HD)" 9 84 9 biotype 187 CE1 "Histidine (HD)" 31 85 19 biotype 188 HE1 "Histidine (HD)" 9 86 7 biotype 189 NE2 "Histidine (HD)" 10 87 33 biotype 190 N "Histidine (HE)" 1 2 35 biotype 191 CA "Histidine (HE)" 2 5 15 biotype 192 C "Histidine (HE)" 3 8 13 biotype 193 HN "Histidine (HE)" 4 4 1 biotype 194 O "Histidine (HE)" 5 9 42 biotype 195 HA "Histidine (HE)" 9 10 6 biotype 196 CB "Histidine (HE)" 2 71 16 biotype 197 HB "Histidine (HE)" 9 10 3 biotype 198 CG "Histidine (HE)" 31 72 18 biotype 199 ND1 "Histidine (HE)" 10 73 33 biotype 200 CD2 "Histidine (HE)" 31 74 18 biotype 201 HD2 "Histidine (HE)" 9 10 9 biotype 202 CE1 "Histidine (HE)" 31 75 19 biotype 203 HE1 "Histidine (HE)" 9 76 7 biotype 204 NE2 "Histidine (HE)" 1 77 32 biotype 205 HE2 "Histidine (HE)" 4 78 1 biotype 206 N "Aspartic Acid(-)" 1 2 35 biotype 207 CA "Aspartic Acid(-)" 2 5 15 biotype 208 C "Aspartic Acid(-)" 3 8 13 biotype 209 HN "Aspartic Acid(-)" 4 4 1 biotype 210 O "Aspartic Acid(-)" 5 9 42 biotype 211 HA "Aspartic Acid(-)" 9 10 6 biotype 212 CB "Aspartic Acid(-)" 2 24 110 biotype 213 HB "Aspartic Acid(-)" 9 10 3 biotype 214 CG "Aspartic Acid(-)" 3 25 25 biotype 215 OD "Aspartic Acid(-)" 29 26 44 biotype 216 N "Asparagine" 1 2 35 biotype 217 CA "Asparagine" 2 5 15 biotype 218 C "Asparagine" 3 8 13 biotype 219 HN "Asparagine" 4 4 1 biotype 220 O "Asparagine" 5 9 42 biotype 221 HA "Asparagine" 9 10 6 biotype 222 CB "Asparagine" 2 27 16 biotype 223 HB "Asparagine" 9 10 3 biotype 224 CG "Asparagine" 3 28 25 biotype 225 OD1 "Asparagine" 5 29 42 biotype 226 ND2 "Asparagine" 1 30 36 biotype 227 HD2 "Asparagine" 4 31 1 biotype 228 N "Glutamic Acid(-)" 1 2 35 biotype 229 CA "Glutamic Acid(-)" 2 5 15 biotype 230 C "Glutamic Acid(-)" 3 8 13 biotype 231 HN "Glutamic Acid(-)" 4 4 1 biotype 232 O "Glutamic Acid(-)" 5 9 42 biotype 233 HA "Glutamic Acid(-)" 9 10 6 biotype 234 CB "Glutamic Acid(-)" 2 33 110 biotype 235 HB "Glutamic Acid(-)" 9 10 3 biotype 236 CG "Glutamic Acid(-)" 2 34 16 biotype 237 HG "Glutamic Acid(-)" 9 10 3 biotype 238 CD "Glutamic Acid(-)" 3 35 25 biotype 239 OE "Glutamic Acid(-)" 29 36 44 biotype 240 N "Glutamine" 1 2 35 biotype 241 CA "Glutamine" 2 5 15 biotype 242 C "Glutamine" 3 8 13 biotype 243 HN "Glutamine" 4 4 1 biotype 244 O "Glutamine" 5 9 42 biotype 245 HA "Glutamine" 9 10 6 biotype 246 CB "Glutamine" 2 37 16 biotype 247 HB "Glutamine" 9 10 3 biotype 248 CG "Glutamine" 2 38 16 biotype 249 HG "Glutamine" 9 10 3 biotype 250 CD "Glutamine" 3 39 25 biotype 251 OE1 "Glutamine" 5 40 42 biotype 252 NE2 "Glutamine" 1 149 36 biotype 253 HE2 "Glutamine" 4 150 1 biotype 254 N "Methionine" 1 2 35 biotype 255 CA "Methionine" 2 5 15 biotype 256 C "Methionine" 3 8 13 biotype 257 HN "Methionine" 4 4 1 biotype 258 O "Methionine" 5 9 42 biotype 259 HA "Methionine" 9 10 6 biotype 260 CB "Methionine" 2 110 16 biotype 261 HB "Methionine" 9 10 3 biotype 262 CG "Methionine" 2 111 16 biotype 263 HG "Methionine" 9 10 3 biotype 264 SD "Methionine" 7 112 50 biotype 265 CE "Methionine" 2 113 17 biotype 266 HE "Methionine" 9 10 3 biotype 267 N "Lysine(+)" 1 2 35 biotype 268 CA "Lysine(+)" 2 5 15 biotype 269 C "Lysine(+)" 3 8 13 biotype 270 HN "Lysine(+)" 4 4 1 biotype 271 O "Lysine(+)" 5 9 42 biotype 272 HA "Lysine(+)" 9 10 6 biotype 273 CB "Lysine(+)" 2 98 16 biotype 274 HB "Lysine(+)" 9 10 3 biotype 275 CG "Lysine(+)" 2 99 16 biotype 276 HG "Lysine(+)" 9 10 3 biotype 277 CD "Lysine(+)" 2 100 16 biotype 278 HD "Lysine(+)" 9 10 3 biotype 279 CE "Lysine(+)" 2 101 16 biotype 280 HE "Lysine(+)" 9 102 3 biotype 281 NZ "Lysine(+)" 8 103 37 biotype 282 HZ "Lysine(+)" 4 104 2 biotype 283 N "Arginine(+)" 1 2 35 biotype 284 CA "Arginine(+)" 2 5 15 biotype 285 C "Arginine(+)" 3 8 13 biotype 286 HN "Arginine(+)" 4 4 1 biotype 287 O "Arginine(+)" 5 9 42 biotype 288 HA "Arginine(+)" 9 10 6 biotype 289 CB "Arginine(+)" 2 14 16 biotype 290 HB "Arginine(+)" 9 10 3 biotype 291 CG "Arginine(+)" 2 15 16 biotype 292 HG "Arginine(+)" 9 10 3 biotype 293 CD "Arginine(+)" 2 16 16 biotype 294 HD "Arginine(+)" 9 10 3 biotype 295 NE "Arginine(+)" 1 17 38 biotype 296 HE "Arginine(+)" 4 18 2 biotype 297 CZ "Arginine(+)" 3 19 13 biotype 298 NH "Arginine(+)" 1 20 38 biotype 299 HH "Arginine(+)" 4 21 2 biotype 300 N "Ornithine(+)" 1 2 35 biotype 301 CA "Ornithine(+)" 2 5 15 biotype 302 C "Ornithine(+)" 3 8 13 biotype 303 HN "Ornithine(+)" 4 4 1 biotype 304 O "Ornithine(+)" 5 9 42 biotype 305 HA "Ornithine(+)" 9 10 6 biotype 306 CB "Ornithine(+)" 2 100 16 biotype 307 HB "Ornithine(+)" 9 10 3 biotype 308 CG "Ornithine(+)" 2 100 16 biotype 309 HG "Ornithine(+)" 9 10 3 biotype 310 CD "Ornithine(+)" 2 101 16 biotype 311 HD "Ornithine(+)" 9 102 3 biotype 312 NE "Ornithine(+)" 8 103 37 biotype 313 HE "Ornithine(+)" 4 104 2 biotype 314 N "MethylAlanine (AIB)" 1 2 35 biotype 315 CA "MethylAlanine (AIB)" 2 107 0 biotype 316 C "MethylAlanine (AIB)" 3 8 13 biotype 317 HN "MethylAlanine (AIB)" 4 4 2 biotype 318 O "MethylAlanine (AIB)" 5 9 42 biotype 319 CB "MethylAlanine (AIB)" 2 108 17 biotype 320 HB "MethylAlanine (AIB)" 9 109 3 biotype 321 N "Pyroglutamic Acid" 0 0 0 biotype 322 CA "Pyroglutamic Acid" 0 0 0 biotype 323 C "Pyroglutamic Acid" 0 0 0 biotype 324 HN "Pyroglutamic Acid" 0 0 0 biotype 325 O "Pyroglutamic Acid" 0 0 0 biotype 326 HA "Pyroglutamic Acid" 0 0 0 biotype 327 CB "Pyroglutamic Acid" 0 0 0 biotype 328 HB "Pyroglutamic Acid" 0 0 0 biotype 329 CG "Pyroglutamic Acid" 0 0 0 biotype 330 HG "Pyroglutamic Acid" 0 0 0 biotype 331 CD "Pyroglutamic Acid" 0 0 0 biotype 332 OE "Pyroglutamic Acid" 0 0 0 biotype 333 N "N-Terminal Residue(+)" 8 103 37 biotype 334 CA "N-Terminal Residue(+)" 2 101 15 biotype 335 C "N-Terminal Residue(+)" 3 8 13 biotype 336 HN "N-Terminal Residue(+)" 4 104 2 biotype 337 O "N-Terminal Residue(+)" 5 9 42 biotype 338 HA "N-Terminal Residue(+)" 9 84 6 biotype 339 N "N-Terminal Glycine(+)" 8 103 37 biotype 340 CA "N-Terminal Glycine(+)" 2 76 16 biotype 341 C "N-Terminal Glycine(+)" 3 8 13 biotype 342 HN "N-Terminal Glycine(+)" 4 104 2 biotype 343 O "N-Terminal Glycine(+)" 5 9 42 biotype 344 HA "N-Terminal Glycine(+)" 9 10 6 biotype 345 N "N-Terminal Proline(+)" 8 213 40 biotype 346 CA "N-Terminal Proline(+)" 2 50 22 biotype 347 C "N-Terminal Proline(+)" 3 8 13 biotype 348 HN "N-Terminal Proline(+)" 4 214 2 biotype 349 O "N-Terminal Proline(+)" 5 9 42 biotype 350 HA "N-Terminal Proline(+)" 9 10 6 biotype 351 CD "N-Terminal Proline(+)" 2 50 24 biotype 352 HD "N-Terminal Proline(+)" 9 10 3 biotype 353 N "C-Terminal Residue(-)" 1 2 35 biotype 354 CA "C-Terminal Residue(-)" 2 5 15 biotype 355 C "C-Terminal Residue(-)" 3 188 25 biotype 356 HN "C-Terminal Residue(-)" 4 4 1 biotype 357 OXT "C-Terminal Residue(-)" 29 215 44 #5inplaceof29 biotype 358 HA "C-Terminal Residue(-)" 9 10 6 biotype 359 N "C-Terminal Glycine(-)" 1 2 35 biotype 360 CA "C-Terminal Glycine(-)" 2 151 16 biotype 361 C "C-Terminal Glycine(-)" 3 188 25 biotype 362 HN "C-Terminal Glycine(-)" 4 4 1 biotype 363 OXT "C-Terminal Glycine(-)" 29 215 44 biotype 364 HA "C-Terminal Glycine(-)" 9 10 6 biotype 365 N "C-Terminal Proline(-)" 11 3 31 biotype 366 CA "C-Terminal Proline(-)" 2 6 22 biotype 367 C "C-Terminal Proline(-)" 3 188 25 biotype 368 OXT "C-Terminal Proline(-)" 29 215 44 biotype 369 HA "C-Terminal Proline(-)" 9 10 6 biotype 370 CD "C-Terminal Proline(-)" 2 53 24 biotype 371 HD "C-Terminal Proline(-)" 9 10 3 biotype 372 CH3 "Acetyl N-Terminus" 2 13 17 biotype 373 H "Acetyl N-Terminus" 9 7 3 biotype 374 C "Acetyl N-Terminus" 3 8 13 biotype 375 O "Acetyl N-Terminus" 5 9 42 biotype 376 C "Formyl N-Terminus" 3 8 13 biotype 377 H "Formyl N-Terminus" 9 231 3 biotype 378 O "Formyl N-Terminus" 5 9 42 biotype 379 N "N-MeAmide C-Terminus" 1 2 35 biotype 380 HN "N-MeAmide C-Terminus" 4 4 1 biotype 381 CH3 "N-MeAmide C-Terminus" 2 48 17 biotype 382 H "N-MeAmide C-Terminus" 9 7 3 biotype 383 N "Amide C-Terminus" 1 30 36 biotype 384 HN "Amide C-Terminus" 4 31 1 biotype 385 N "Gamma Residue" 0 0 0 biotype 386 CA "Gamma Residue" 0 0 0 biotype 387 C "Gamma Residue" 0 0 0 biotype 388 HN "Gamma Residue" 0 0 0 biotype 389 O "Gamma Residue" 0 0 0 biotype 390 HA "Gamma Residue" 0 0 0 biotype 391 CB "Gamma Residue" 0 0 0 biotype 392 HB "Gamma Residue" 0 0 0 biotype 393 CG "Gamma Residue" 0 0 0 biotype 394 HG "Gamma Residue" 0 0 0 biotype 395 N "Hydroxyproline" 11 3 31 biotype 396 CA "Hydroxyproline" 2 6 22 biotype 397 C "Hydroxyproline" 3 8 13 biotype 398 O "Hydroxyproline" 5 9 42 biotype 399 HA "Hydroxyproline" 9 7 6 biotype 400 CB "Hydroxyproline" 2 51 23 biotype 401 HB "Hydroxyproline" 9 10 3 biotype 402 CG "Hydroxyproline" 2 44 23 biotype 403 HG "Hydroxyproline" 9 10 3 biotype 404 CD "Hydroxyproline" 2 53 24 biotype 405 HD "Hydroxyproline" 9 10 3 biotype 406 OE "Hydroxyproline" 6 45 45 biotype 407 HE "Hydroxyproline" 4 46 1 biotype 408 N "Alpha amino N-butyric" 1 2 35 biotype 409 CA "Alpha amino N-butyric" 2 5 15 biotype 410 C "Alpha amino N-butyric" 3 8 13 biotype 411 HN "Alpha amino N-butyric" 4 4 1 biotype 412 O "Alpha amino N-butyric" 5 9 42 biotype 413 HA "Alpha amino N-butyric" 9 10 6 biotype 414 CB "Alpha amino N-butyric" 2 122 16 biotype 415 HB "Alpha amino N-butyric" 9 10 3 biotype 416 CG "Alpha amino N-butyric" 2 123 17 biotype 417 HG "Alpha amino N-butyric" 9 10 3 biotype 418 N "Norvaline" 1 2 35 biotype 419 CA "Norvaline" 2 5 15 biotype 420 C "Norvaline" 3 8 13 biotype 421 HN "Norvaline" 4 4 1 biotype 422 O "Norvaline" 5 9 42 biotype 423 HA "Norvaline" 9 10 6 biotype 424 CB "Norvaline" 2 122 16 biotype 425 HB "Norvaline" 9 10 3 biotype 426 CG "Norvaline" 2 122 16 biotype 427 HG "Norvaline" 9 10 3 biotype 428 CD "Norvaline" 2 123 17 biotype 429 HD "Norvaline" 9 10 3 biotype 430 N "Norleucine" 1 2 35 biotype 431 CA "Norleucine" 2 5 15 biotype 432 C "Norleucine" 3 8 13 biotype 433 HN "Norleucine" 4 4 1 biotype 434 O "Norleucine" 5 9 42 biotype 435 HA "Norleucine" 9 10 6 biotype 436 CB "Norleucine" 2 122 16 biotype 437 HB "Norleucine" 9 10 3 biotype 438 CG "Norleucine" 2 122 16 biotype 439 HG "Norleucine" 9 10 3 biotype 440 CD "Norleucine" 2 122 16 biotype 441 HD "Norleucine" 9 10 3 biotype 442 CE "Norleucine" 2 123 17 biotype 443 HE "Norleucine" 9 10 3 biotype 444 NA "Sodium Ion" 12 22 0 biotype 445 CL "Chloride Ion" 13 23 0 biotype 446 C "Urea" 3 287 25 biotype 447 O "Urea" 5 288 42 biotype 448 N "Urea" 1 289 36 biotype 449 HN "Urea" 4 290 1 biotype 450 OW "SPC Water" 14 218 0 biotype 451 HW "SPC Water" 15 219 0 biotype 452 OW "TIP3P Water" 16 216 47 biotype 453 HW "TIP3P Water" 17 217 4 biotype 454 C "N-Methyl Formamide" 3 8 13 biotype 455 O "N-Methyl Formamide" 5 9 42 biotype 456 N "N-Methyl Formamide" 1 2 35 biotype 457 HN "N-Methyl Formamide" 4 4 1 biotype 458 CNT "N-Methyl Formamide" 2 48 17 biotype 459 HNT "N-Methyl Formamide" 9 10 3 biotype 460 HC "N-Methyl Formamide" 9 231 3 biotype 461 C "N-Methyl Acetamide" 3 8 13 biotype 462 O "N-Methyl Acetamide" 5 9 42 biotype 463 N "N-Methyl Acetamide" 1 2 35 biotype 464 HN "N-Methyl Acetamide" 4 4 1 biotype 465 CCT "N-Methyl Acetamide" 2 123 17 biotype 466 HCT "N-Methyl Acetamide" 9 10 3 biotype 467 CNT "N-Methyl Acetamide" 2 48 17 biotype 468 HNT "N-Methyl Acetamide" 9 10 3 biotype 469 C "Acetamide" 3 28 25 biotype 470 O "Acetamide" 5 29 42 biotype 471 N "Acetamide" 1 30 36 biotype 472 HN "Acetamide" 4 31 1 biotype 473 CCT "Acetamide" 2 123 17 biotype 474 HCT "Acetamide" 9 10 3 biotype 475 C "Propionamide" 3 39 25 biotype 476 O "Propionamide" 5 40 42 biotype 477 N "Propionamide" 1 149 36 biotype 478 HN "Propionamide" 4 150 1 biotype 479 CCT "Propionamide" 2 122 16 biotype 480 HCT "Propionamide" 9 10 3 biotype 481 CBT "Propionamide" 2 123 17 biotype 482 HBT "Propionamide" 9 10 3 biotype 483 OW "TIP4P Water" 18 231 0 biotype 484 HW "TIP4P Water" 17 245 0 biotype 485 MW "TIP4P Water" 19 246 0 biotype 486 OW "TIP5P Water" 26 231 0 biotype 487 HW "TIP5P Water" 17 248 0 biotype 488 MW "TIP5P Water" 19 247 0 biotype 489 CT "Methane" 2 0 0 biotype 490 HT "Methane" 9 0 0 biotype 491 C "Formamide" 3 228 25 biotype 492 O "Formamide" 5 229 42 biotype 493 N "Formamide" 1 226 36 biotype 494 HN "Formamide" 4 227 1 biotype 495 HC "Formamide" 9 230 3 biotype 496 C "N,N'-Dimethyl Acetamide" 3 0 0 biotype 497 O "N,N'-Dimethyl Acetamide" 5 0 0 biotype 498 N "N,N'-Dimethyl Acetamide" 1 0 0 biotype 499 CCT "N,N'-Dimethyl Acetamide" 2 0 0 biotype 500 HCT "N,N'-Dimethyl Acetamide" 9 0 0 biotype 501 C1 "N,N'-Dimethyl Acetamide" 2 0 0 biotype 502 H1 "N,N'-Dimethyl Acetamide" 9 0 0 biotype 503 C2 "N,N'-Dimethyl Acetamide" 2 0 0 biotype 504 H2 "N,N'-Dimethyl Acetamide" 9 0 0 biotype 505 CT "Methanol" 2 222 17 biotype 506 O "Methanol" 6 42 45 biotype 507 HT "Methanol" 9 10 3 biotype 508 HO "Methanol" 4 43 1 biotype 509 CT "p-Cresol" 2 123 17 biotype 510 HCT "p-Cresol" 9 10 3 biotype 511 C1 "p-Cresol" 31 55 14 biotype 512 C2 "p-Cresol" 31 56 14 biotype 513 H2 "p-Cresol" 9 57 5 biotype 514 C3 "p-Cresol" 31 56 14 biotype 515 H3 "p-Cresol" 9 57 5 biotype 516 C4 "p-Cresol" 31 58 14 biotype 517 O "p-Cresol" 6 59 45 biotype 518 HO "p-Cresol" 4 60 1 biotype 519 N "a,g-Diaminobut. Acid(+)" 1 2 35 biotype 520 CA "a,g-Diaminobut. Acid(+)" 2 5 15 biotype 521 C "a,g-Diaminobut. Acid(+)" 3 8 13 biotype 522 HN "a,g-Diaminobut. Acid(+)" 4 4 1 biotype 523 O "a,g-Diaminobut. Acid(+)" 5 9 42 biotype 524 HA "a,g-Diaminobut. Acid(+)" 9 10 6 biotype 525 CB "a,g-Diaminobut. Acid(+)" 2 100 16 biotype 526 HB "a,g-Diaminobut. Acid(+)" 9 10 3 biotype 527 CG "a,g-Diaminobut. Acid(+)" 2 101 16 biotype 528 HG "a,g-Diaminobut. Acid(+)" 9 102 3 biotype 529 ND "a,g-Diaminobut. Acid(+)" 8 103 37 biotype 530 HD "a,g-Diaminobut. Acid(+)" 4 104 2 biotype 531 K "Potassium Ion" 20 22 0 biotype 532 BR "Bromide Ion" 21 23 0 biotype 533 CS "Caesium Ion" 22 22 0 biotype 534 I "Iodide Ion" 23 23 0 biotype 535 N "Ammonium Ion" 8 221 37 biotype 536 HN "Ammonium Ion" 4 104 2 biotype 537 C "Acetate Ion" 3 25 25 biotype 538 OXT "Acetate Ion" 29 26 44 biotype 539 CH3 "Acetate Ion" 2 220 17 biotype 540 H "Acetate Ion" 9 10 3 biotype 541 C "Guanidinium Ion" 3 19 13 biotype 542 N "Guanidinium Ion" 1 20 38 biotype 543 HN "Guanidinium Ion" 4 21 2 biotype 544 N "N-Terminal AIB(+)" 8 285 0 biotype 545 CA "N-Terminal AIB(+)" 2 284 0 biotype 546 C "N-Terminal AIB(+)" 3 8 0 biotype 547 HN "N-Terminal AIB(+)" 4 286 0 biotype 548 O "N-Terminal AIB(+)" 5 9 0 biotype 549 N "C-Terminal AIB(-)" 1 2 0 biotype 550 CA "C-Terminal AIB(-)" 2 107 0 biotype 551 C "C-Terminal AIB(-)" 3 188 0 biotype 552 HN "C-Terminal AIB(-)" 4 4 0 biotype 553 OXT "C-Terminal AIB(-)" 29 215 0 biotype 554 CA "Free Amino Acid(+/-)" 2 101 15 biotype 555 CA "Free GLY(+/-)" 2 232 16 biotype 556 CA "Free PRO(+/-)" 2 233 22 biotype 557 CA "Free AIB(+/-)" 2 0 0 biotype 558 N1 "Cytosine" 1 0 83 biotype 559 H1 "Cytosine" 4 0 54 biotype 560 C2 "Cytosine" 3 0 63 biotype 561 O2 "Cytosine" 5 0 95 biotype 562 N3 "Cytosine" 10 0 87 biotype 563 C4 "Cytosine" 31 0 66 biotype 564 N4 "Cytosine" 1 0 82 biotype 565 H4 "Cytosine" 4 0 53 biotype 566 C5 "Cytosine" 31 0 67 biotype 567 H5 "Cytosine" 9 0 55 biotype 568 C6 "Cytosine" 31 0 67 biotype 569 H6 "Cytosine" 9 0 55 biotype 570 N1 "Uracil" 1 0 84 biotype 571 H1 "Uracil" 4 0 54 biotype 572 C2 "Uracil" 3 0 65 biotype 573 O2 "Uracil" 5 0 94 biotype 574 N3 "Uracil" 1 0 85 biotype 575 H3 "Uracil" 4 0 54 biotype 576 C4 "Uracil" 3 0 63 biotype 577 O4 "Uracil" 5 0 94 biotype 578 C5 "Uracil" 31 0 67 biotype 579 H5 "Uracil" 9 0 55 biotype 580 C6 "Uracil" 31 0 67 biotype 581 H6 "Uracil" 9 0 55 biotype 582 N1 "Thymine" 1 0 84 biotype 583 H1 "Thymine" 4 0 54 biotype 584 C2 "Thymine" 3 0 65 biotype 585 O2 "Thymine" 5 0 94 biotype 586 N3 "Thymine" 1 0 85 biotype 587 H3 "Thymine" 4 0 54 biotype 588 C4 "Thymine" 3 0 63 biotype 589 O4 "Thymine" 5 0 94 biotype 590 C5 "Thymine" 31 0 72 biotype 591 C5M "Thymine" 2 0 81 biotype 592 H5M "Thymine" 9 0 62 biotype 593 C6 "Thymine" 31 0 67 biotype 594 H6 "Thymine" 9 0 55 biotype 595 N1 "Adenine" 10 0 88 biotype 596 C2 "Adenine" 31 0 73 biotype 597 H2 "Adenine" 9 0 55 biotype 598 N3 "Adenine" 10 0 88 biotype 599 C4 "Adenine" 31 0 74 biotype 600 C5 "Adenine" 31 0 74 biotype 601 C6 "Adenine" 31 0 66 biotype 602 N6 "Adenine" 1 0 82 biotype 603 H6 "Adenine" 4 0 53 biotype 604 N7 "Adenine" 10 0 91 biotype 605 C8 "Adenine" 31 0 73 biotype 606 H8 "Adenine" 9 0 55 biotype 607 N9 "Adenine" 1 0 83 biotype 608 H9 "Adenine" 4 0 54 biotype 609 N1 "Guanine" 1 0 86 biotype 610 H1 "Guanine" 4 0 54 biotype 611 C2 "Guanine" 31 0 66 biotype 612 N2 "Guanine" 1 0 82 biotype 613 H2 "Guanine" 4 0 103 biotype 614 N3 "Guanine" 10 0 86 biotype 615 C4 "Guanine" 31 0 74 biotype 616 C5 "Guanine" 31 0 75 biotype 617 C6 "Guanine" 3 0 63 biotype 618 O6 "Guanine" 5 0 94 biotype 619 N7 "Guanine" 10 0 91 biotype 620 C8 "Guanine" 31 0 73 biotype 621 H8 "Guanine" 9 0 55 biotype 622 N9 "Guanine" 1 0 84 biotype 623 H9 "Guanine" 4 0 54 biotype 624 P "Ribose-5'-Phosphate" 24 135 102 biotype 625 O5P "Ribose-5'-Phosphate" 6 137 96 biotype 626 O3P "Ribose-5'-Phosphate" 6 146 96 biotype 627 OP "Ribose-5'-Phosphate" 29 136 97 biotype 628 C5* "Ribose-5'-Phosphate" 2 138 80 biotype 629 H5* "Ribose-5'-Phosphate" 9 10 61 biotype 630 C4* "Ribose-5'-Phosphate" 2 139 76 biotype 631 O4* "Ribose-5'-Phosphate" 6 140 101 biotype 632 H4* "Ribose-5'-Phosphate" 9 10 60 biotype 633 C3* "Ribose-5'-Phosphate" 2 238 76 biotype 634 O3* "Ribose-5'-Phosphate" 6 239 99 biotype 635 H3* "Ribose-5'-Phosphate" 9 10 60 biotype 636 HO3 "Ribose-5'-Phosphate" 4 240 58 biotype 637 C2* "Ribose-5'-Phosphate" 2 237 77 biotype 638 O2* "Ribose-5'-Phosphate" 6 144 99 biotype 639 H2* "Ribose-5'-Phosphate" 9 10 60 biotype 640 HO2 "Ribose-5'-Phosphate" 4 43 58 biotype 641 C1* "Ribose-5'-Phosphate" 2 236 77 biotype 642 O1* "Ribose-5'-Phosphate" 6 144 99 biotype 643 H1* "Ribose-5'-Phosphate" 9 10 60 biotype 644 HO1 "Ribose-5'-Phosphate" 4 43 58 biotype 645 P "dCM-5-P" 24 125 111 biotype 646 O5P "dCM-5-P" 6 127 96 biotype 647 O3P "dCM-5-P" 6 134 96 biotype 648 OP "dCM-5-P" 29 126 97 biotype 649 C5* "dCM-5-P" 2 128 80 biotype 650 H5* "dCM-5-P" 9 10 61 biotype 651 C4* "dCM-5-P" 2 129 76 biotype 652 O4* "dCM-5-P" 6 130 100 biotype 653 H4* "dCM-5-P" 9 10 60 biotype 654 C3* "dCM-5-P" 2 133 76 biotype 655 H3* "dCM-5-P" 9 10 60 biotype 656 C2* "dCM-5-P" 2 14 79 biotype 657 H2* "dCM-5-P" 9 10 61 biotype 658 C1* "dCM-5-P" 2 131 77 biotype 659 H1* "dCM-5-P" 9 10 60 biotype 660 N1 "dCM-5-P" 1 152 83 biotype 661 C2 "dCM-5-P" 3 155 63 biotype 662 O2 "dCM-5-P" 5 156 95 biotype 663 N3 "dCM-5-P" 10 157 87 biotype 664 C4 "dCM-5-P" 31 158 66 biotype 665 N4 "dCM-5-P" 1 159 82 biotype 666 H4 "dCM-5-P" 4 160 53 biotype 667 C5 "dCM-5-P" 31 161 67 biotype 668 H5 "dCM-5-P" 9 162 55 biotype 669 C6 "dCM-5-P" 31 153 67 biotype 670 H6 "dCM-5-P" 9 154 55 biotype 671 P "CM-5-P" 24 135 102 biotype 672 O5P "CM-5-P" 6 137 96 biotype 673 O3P "CM-5-P" 6 146 96 biotype 674 OP "CM-5-P" 29 136 97 biotype 675 C5* "CM-5-P" 2 138 80 biotype 676 H5* "CM-5-P" 9 10 61 biotype 677 C4* "CM-5-P" 2 139 76 biotype 678 O4* "CM-5-P" 6 140 101 biotype 679 H4* "CM-5-P" 9 10 60 biotype 680 C3* "CM-5-P" 2 145 76 biotype 681 H3* "CM-5-P" 9 10 60 biotype 682 C2* "CM-5-P" 2 142 77 biotype 683 O2* "CM-5-P" 6 144 99 biotype 684 H2* "CM-5-P" 9 10 60 biotype 685 C1* "CM-5-P" 2 141 77 biotype 686 H1* "CM-5-P" 9 10 60 biotype 687 N1 "CM-5-P" 1 152 83 biotype 688 C2 "CM-5-P" 3 155 63 biotype 689 O2 "CM-5-P" 5 156 95 biotype 690 N3 "CM-5-P" 10 157 87 biotype 691 C4 "CM-5-P" 31 158 66 biotype 692 N4 "CM-5-P" 1 159 82 biotype 693 H4 "CM-5-P" 4 160 53 biotype 694 C5 "CM-5-P" 31 161 67 biotype 695 H5 "CM-5-P" 9 162 55 biotype 696 C6 "CM-5-P" 31 153 67 biotype 697 H6 "CM-5-P" 9 154 55 biotype 698 P "dUM-5-P" 24 125 111 biotype 699 O5P "dUM-5-P" 6 127 96 biotype 700 O3P "dUM-5-P" 6 134 96 biotype 701 OP "dUM-5-P" 29 126 97 biotype 702 C5* "dUM-5-P" 2 128 80 biotype 703 H5* "dUM-5-P" 9 10 61 biotype 704 C4* "dUM-5-P" 2 129 76 biotype 705 O4* "dUM-5-P" 6 130 100 biotype 706 H4* "dUM-5-P" 9 10 60 biotype 707 C3* "dUM-5-P" 2 133 76 biotype 708 H3* "dUM-5-P" 9 10 60 biotype 709 C2* "dUM-5-P" 2 14 79 biotype 710 H2* "dUM-5-P" 9 10 61 biotype 711 C1* "dUM-5-P" 2 131 77 biotype 712 H1* "dUM-5-P" 9 10 60 biotype 713 N1 "dUM-5-P" 1 163 84 biotype 714 C2 "dUM-5-P" 3 166 65 biotype 715 O2 "dUM-5-P" 5 167 94 biotype 716 N3 "dUM-5-P" 1 168 85 biotype 717 H3 "dUM-5-P" 4 169 54 biotype 718 C4 "dUM-5-P" 3 170 63 biotype 719 O4 "dUM-5-P" 5 171 94 biotype 720 C5 "dUM-5-P" 31 172 67 biotype 721 H5 "dUM-5-P" 9 173 55 biotype 722 C6 "dUM-5-P" 31 164 67 biotype 723 H6 "dUM-5-P" 9 165 55 biotype 724 P "UM-5-P" 24 135 102 biotype 725 O5P "UM-5-P" 6 137 96 biotype 726 O3P "UM-5-P" 6 146 96 biotype 727 OP "UM-5-P" 29 136 97 biotype 728 C5* "UM-5-P" 2 138 80 biotype 729 H5* "UM-5-P" 9 10 61 biotype 730 C4* "UM-5-P" 2 139 76 biotype 731 O4* "UM-5-P" 6 140 101 biotype 732 H4* "UM-5-P" 9 10 60 biotype 733 C3* "UM-5-P" 2 145 76 biotype 734 H3* "UM-5-P" 9 10 60 biotype 735 C2* "UM-5-P" 2 142 77 biotype 736 O2* "UM-5-P" 6 144 99 biotype 737 H2* "UM-5-P" 9 10 60 biotype 738 C1* "UM-5-P" 2 141 77 biotype 739 H1* "UM-5-P" 9 10 60 biotype 740 N1 "UM-5-P" 1 163 84 biotype 741 C2 "UM-5-P" 3 166 65 biotype 742 O2 "UM-5-P" 5 167 94 biotype 743 N3 "UM-5-P" 1 168 85 biotype 744 H3 "UM-5-P" 4 169 54 biotype 745 C4 "UM-5-P" 3 170 63 biotype 746 O4 "UM-5-P" 5 171 94 biotype 747 C5 "UM-5-P" 31 172 67 biotype 748 H5 "UM-5-P" 9 173 55 biotype 749 C6 "UM-5-P" 31 164 67 biotype 750 H6 "UM-5-P" 9 165 55 biotype 751 P "dTM-5-P" 24 125 111 biotype 752 O5P "dTM-5-P" 6 127 96 biotype 753 O3P "dTM-5-P" 6 134 96 biotype 754 OP "dTM-5-P" 29 126 97 biotype 755 C5* "dTM-5-P" 2 128 80 biotype 756 H5* "dTM-5-P" 9 10 61 biotype 757 C4* "dTM-5-P" 2 129 76 biotype 758 O4* "dTM-5-P" 6 130 100 biotype 759 H4* "dTM-5-P" 9 10 60 biotype 760 C3* "dTM-5-P" 2 133 76 biotype 761 H3* "dTM-5-P" 9 10 60 biotype 762 C2* "dTM-5-P" 2 14 79 biotype 763 H2* "dTM-5-P" 9 10 61 biotype 764 C1* "dTM-5-P" 2 131 77 biotype 765 H1* "dTM-5-P" 9 10 60 biotype 766 N1 "dTM-5-P" 1 174 84 biotype 767 C2 "dTM-5-P" 3 177 65 biotype 768 O2 "dTM-5-P" 5 178 94 biotype 769 N3 "dTM-5-P" 1 179 85 biotype 770 H3 "dTM-5-P" 4 180 54 biotype 771 C4 "dTM-5-P" 3 181 63 biotype 772 O4 "dTM-5-P" 5 182 94 biotype 773 C5 "dTM-5-P" 31 183 72 biotype 774 C5M "dTM-5-P" 2 184 81 biotype 775 H5M "dTM-5-P" 9 185 62 biotype 776 C6 "dTM-5-P" 31 175 67 biotype 777 H6 "dTM-5-P" 9 176 55 biotype 778 P "TM-5-P" 24 135 102 biotype 779 O5P "TM-5-P" 6 137 96 biotype 780 O3P "TM-5-P" 6 146 96 biotype 781 OP "TM-5-P" 29 136 97 biotype 782 C5* "TM-5-P" 2 138 80 biotype 783 H5* "TM-5-P" 9 10 61 biotype 784 C4* "TM-5-P" 2 139 76 biotype 785 O4* "TM-5-P" 6 140 101 biotype 786 H4* "TM-5-P" 9 10 60 biotype 787 C3* "TM-5-P" 2 145 76 biotype 788 H3* "TM-5-P" 9 10 60 biotype 789 C2* "TM-5-P" 2 142 77 biotype 790 O2* "TM-5-P" 6 144 99 biotype 791 H2* "TM-5-P" 9 10 60 biotype 792 C1* "TM-5-P" 2 141 77 biotype 793 H1* "TM-5-P" 9 10 60 biotype 794 N1 "TM-5-P" 1 174 84 biotype 795 C2 "TM-5-P" 3 177 65 biotype 796 O2 "TM-5-P" 5 178 94 biotype 797 N3 "TM-5-P" 1 179 85 biotype 798 H3 "TM-5-P" 4 180 54 biotype 799 C4 "TM-5-P" 3 181 63 biotype 800 O4 "TM-5-P" 5 182 94 biotype 801 C5 "TM-5-P" 31 183 72 biotype 802 C5M "TM-5-P" 2 184 81 biotype 803 H5M "TM-5-P" 9 185 62 biotype 804 C6 "TM-5-P" 31 175 67 biotype 805 H6 "TM-5-P" 9 176 55 biotype 806 P "dAM-5-P" 24 125 111 biotype 807 O5P "dAM-5-P" 6 127 96 biotype 808 O3P "dAM-5-P" 6 134 96 biotype 809 OP "dAM-5-P" 29 126 97 biotype 810 C5* "dAM-5-P" 2 128 80 biotype 811 H5* "dAM-5-P" 9 10 61 biotype 812 C4* "dAM-5-P" 2 129 76 biotype 813 O4* "dAM-5-P" 6 130 100 biotype 814 H4* "dAM-5-P" 9 10 60 biotype 815 C3* "dAM-5-P" 2 133 76 biotype 816 H3* "dAM-5-P" 9 10 60 biotype 817 C2* "dAM-5-P" 2 14 79 biotype 818 H2* "dAM-5-P" 9 10 61 biotype 819 C1* "dAM-5-P" 2 131 77 biotype 820 H1* "dAM-5-P" 9 10 60 biotype 821 N1 "dAM-5-P" 10 191 88 biotype 822 C2 "dAM-5-P" 31 192 73 biotype 823 H2 "dAM-5-P" 9 193 55 biotype 824 N3 "dAM-5-P" 10 194 88 biotype 825 C4 "dAM-5-P" 31 195 74 biotype 826 C5 "dAM-5-P" 31 186 74 biotype 827 C6 "dAM-5-P" 31 196 66 biotype 828 N6 "dAM-5-P" 1 197 82 biotype 829 H6 "dAM-5-P" 4 198 53 biotype 830 N7 "dAM-5-P" 10 187 91 biotype 831 C8 "dAM-5-P" 31 188 73 biotype 832 H8 "dAM-5-P" 9 189 55 biotype 833 N9 "dAM-5-P" 1 190 83 biotype 834 P "AM-5-P" 24 135 102 biotype 835 O5P "AM-5-P" 6 137 96 biotype 836 O3P "AM-5-P" 6 146 96 biotype 837 OP "AM-5-P" 29 136 97 biotype 838 C5* "AM-5-P" 2 138 80 biotype 839 H5* "AM-5-P" 9 10 61 biotype 840 C4* "AM-5-P" 2 139 76 biotype 841 O4* "AM-5-P" 6 140 101 biotype 842 H4* "AM-5-P" 9 10 60 biotype 843 C3* "AM-5-P" 2 145 76 biotype 844 H3* "AM-5-P" 9 10 60 biotype 845 C2* "AM-5-P" 2 142 77 biotype 846 O2* "AM-5-P" 6 144 99 biotype 847 H2* "AM-5-P" 9 10 60 biotype 848 C1* "AM-5-P" 2 141 77 biotype 849 H1* "AM-5-P" 9 10 60 biotype 850 N1 "AM-5-P" 10 191 88 biotype 851 C2 "AM-5-P" 31 192 73 biotype 852 H2 "AM-5-P" 9 193 55 biotype 853 N3 "AM-5-P" 10 194 88 biotype 854 C4 "AM-5-P" 31 195 74 biotype 855 C5 "AM-5-P" 31 186 74 biotype 856 C6 "AM-5-P" 31 196 66 biotype 857 N6 "AM-5-P" 1 197 82 biotype 858 H6 "AM-5-P" 4 198 53 biotype 859 N7 "AM-5-P" 10 187 91 biotype 860 C8 "AM-5-P" 31 188 73 biotype 861 H8 "AM-5-P" 9 189 55 biotype 862 N9 "AM-5-P" 1 190 83 biotype 863 P "dGM-5-P" 24 125 111 biotype 864 O5P "dGM-5-P" 6 127 96 biotype 865 O3P "dGM-5-P" 6 134 96 biotype 866 OP "dGM-5-P" 29 126 97 biotype 867 C5* "dGM-5-P" 2 128 80 biotype 868 H5* "dGM-5-P" 9 10 61 biotype 869 C4* "dGM-5-P" 2 129 76 biotype 870 O4* "dGM-5-P" 6 130 100 biotype 871 H4* "dGM-5-P" 9 10 60 biotype 872 C3* "dGM-5-P" 2 133 76 biotype 873 H3* "dGM-5-P" 9 10 60 biotype 874 C2* "dGM-5-P" 2 14 79 biotype 875 H2* "dGM-5-P" 9 10 61 biotype 876 C1* "dGM-5-P" 2 131 77 biotype 877 H1* "dGM-5-P" 9 10 60 biotype 878 N1 "dGM-5-P" 1 203 86 biotype 879 H1 "dGM-5-P" 4 204 54 biotype 880 C2 "dGM-5-P" 31 202 66 biotype 881 N2 "dGM-5-P" 1 205 82 biotype 882 H2 "dGM-5-P" 4 206 103 biotype 883 N3 "dGM-5-P" 10 201 90 biotype 884 C4 "dGM-5-P" 31 200 74 biotype 885 C5 "dGM-5-P" 31 209 75 biotype 886 C6 "dGM-5-P" 3 207 63 biotype 887 O6 "dGM-5-P" 5 208 94 biotype 888 N7 "dGM-5-P" 10 210 91 biotype 889 C8 "dGM-5-P" 31 211 73 biotype 890 H8 "dGM-5-P" 9 212 55 biotype 891 N9 "dGM-5-P" 1 199 84 biotype 892 P "GM-5-P" 24 135 102 biotype 893 O5P "GM-5-P" 6 137 96 biotype 894 O3P "GM-5-P" 6 146 96 biotype 895 OP "GM-5-P" 29 136 97 biotype 896 C5* "GM-5-P" 2 138 80 biotype 897 H5* "GM-5-P" 9 10 61 biotype 898 C4* "GM-5-P" 2 139 76 biotype 899 O4* "GM-5-P" 6 140 101 biotype 900 H4* "GM-5-P" 9 10 60 biotype 901 C3* "GM-5-P" 2 145 76 biotype 902 H3* "GM-5-P" 9 10 60 biotype 903 C2* "GM-5-P" 2 142 77 biotype 904 O2* "GM-5-P" 6 144 99 biotype 905 H2* "GM-5-P" 9 10 60 biotype 906 C1* "GM-5-P" 2 141 77 biotype 907 H1* "GM-5-P" 9 10 60 biotype 908 N1 "GM-5-P" 1 203 86 biotype 909 H1 "GM-5-P" 4 204 54 biotype 910 C2 "GM-5-P" 31 202 66 biotype 911 N2 "GM-5-P" 1 205 82 biotype 912 H2 "GM-5-P" 4 206 103 biotype 913 N3 "GM-5-P" 10 201 90 biotype 914 C4 "GM-5-P" 31 200 74 biotype 915 C5 "GM-5-P" 31 209 75 biotype 916 C6 "GM-5-P" 3 207 63 biotype 917 O6 "GM-5-P" 5 208 94 biotype 918 N7 "GM-5-P" 10 210 91 biotype 919 C8 "GM-5-P" 31 211 73 biotype 920 H8 "GM-5-P" 9 212 55 biotype 921 N9 "GM-5-P" 1 199 84 biotype 922 P "5'-terminal (d)XM-5-P" 24 135 102 biotype 923 O3P "5'-terminal (d)XM-5-P" 6 234 98 biotype 924 HOP "5'-terminal (d)XM-5-P" 4 235 57 biotype 925 C3* "3'-terminal XM-5-P" 2 44 76 biotype 926 O3* "3'-terminal XM-5-P" 6 45 99 biotype 927 HO3 "3'-terminal XM-5-P" 4 43 58 biotype 928 C3* "3'-terminal dXM-5-P" 2 44 76 biotype 929 O3* "3'-terminal dXM-5-P" 6 45 99 biotype 930 HO3 "3'-terminal dXM-5-P" 4 43 58 biotype 931 HO2 "2'-OH in CM-5-P" 4 43 58 biotype 932 HO2 "2'-OH in UM-5-P" 4 43 58 biotype 933 HO2 "2'-OH in TM-5-P" 4 43 58 biotype 934 HO2 "2'-OH in AM-5-P" 4 43 58 biotype 935 HO2 "2'-OH in GM-5-P" 4 43 58 biotype 936 P "Deoxyribose-5'-P" 24 125 111 biotype 937 O5P "Deoxyribose-5'-P" 6 127 96 biotype 938 O3P "Deoxyribose-5'-P" 6 134 96 biotype 939 OP "Deoxyribose-5'-P" 29 126 97 biotype 940 C5* "Deoxyribose-5'-P" 2 128 80 biotype 941 H5* "Deoxyribose-5'-P" 9 10 61 biotype 942 C4* "Deoxyribose-5'-P" 2 129 76 biotype 943 O4* "Deoxyribose-5'-P" 6 130 100 biotype 944 H4* "Deoxyribose-5'-P" 9 10 60 biotype 945 C3* "Deoxyribose-5'-P" 2 244 76 biotype 946 O3* "Deoxyribose-5'-P" 6 241 99 biotype 947 H3* "Deoxyribose-5'-P" 9 10 60 biotype 948 HO3 "Deoxyribose-5'-P" 4 242 58 biotype 949 C2* "Deoxyribose-5'-P" 2 14 79 biotype 950 H2* "Deoxyribose-5'-P" 9 10 61 biotype 951 C1* "Deoxyribose-5'-P" 2 243 77 biotype 952 O1* "Deoxyribose-5'-P" 6 144 99 biotype 953 H1* "Deoxyribose-5'-P" 9 10 60 biotype 954 HO1 "Deoxyribose-5'-P" 4 43 58 biotype 955 HOP "Deoxyribose-5'-P" 4 235 57 biotype 956 HOP "Ribose-5'-Phosphate" 4 235 57 biotype 957 O5* "5'-Ribonucleosides" 6 144 99 biotype 958 C5* "5'-Ribonucleosides" 2 153 80 biotype 959 HO5 "5'-Ribonucleosides" 4 143 58 biotype 960 O5* "5'-Deoxyribonucleosides" 6 144 99 biotype 961 C5* "5'-Deoxyribonucleosides" 2 153 80 biotype 962 HO5 "5'-Deoxyribonucleosides" 4 143 58 biotype 963 CT "Propane" 2 123 17 biotype 964 HT "Propane" 9 10 3 biotype 965 CB "Propane" 2 122 16 biotype 966 HB "Propane" 9 10 3 biotype 967 CT "n-Butane" 2 123 17 biotype 968 HT "n-Butane" 9 10 3 biotype 969 CB "n-Butane" 2 122 16 biotype 970 HB "n-Butane" 9 10 3 biotype 971 CT "i-Butane" 2 123 17 biotype 972 HT "i-Butane" 9 10 3 biotype 973 CB "i-Butane" 2 121 16 biotype 974 HB "i-Butane" 9 10 3 biotype 975 CT "Toluene" 2 123 17 biotype 976 HT "Toluene" 9 10 3 biotype 977 C1 "Toluene" 31 115 14 biotype 978 C2 "Toluene" 31 116 14 biotype 979 H2 "Toluene" 9 117 5 biotype 980 C3 "Toluene" 31 116 14 biotype 981 H3 "Toluene" 9 117 5 biotype 982 C4 "Toluene" 31 116 14 biotype 983 H4 "Toluene" 9 117 5 biotype 984 CT "Ethanol" 2 123 17 biotype 985 HT "Ethanol" 9 10 3 biotype 986 CB "Ethanol" 2 41 16 biotype 987 HB "Ethanol" 9 10 3 biotype 988 O "Ethanol" 6 42 45 biotype 989 HO "Ethanol" 4 43 1 biotype 990 CT "Methanethiol" 2 223 17 biotype 991 S "Methanethiol" 7 49 50 biotype 992 HT "Methanethiol" 9 10 3 biotype 993 HS "Methanethiol" 4 50 10 biotype 994 CNT "Ethylmethylthioether" 2 113 17 biotype 995 HNT "Ethylmethylthioether" 9 10 3 biotype 996 S "Ethylmethylthioether" 7 112 50 biotype 997 CB "Ethylmethylthioether" 2 111 16 biotype 998 HB "Ethylmethylthioether" 9 10 3 biotype 999 CCT "Ethylmethylthioether" 2 123 17 biotype 1000 HCT "Ethylmethylthioether" 9 10 3 biotype 1001 CT "Methylimidazole (delta-H)" 2 225 17 biotype 1002 HT "Methylimidazole (delta-H)" 9 10 3 biotype 1003 C1 "Methylimidazole (delta-H)" 31 80 18 biotype 1004 N2 "Methylimidazole (delta-H)" 1 81 32 biotype 1005 HN2 "Methylimidazole (delta-H)" 4 82 1 biotype 1006 C2 "Methylimidazole (delta-H)" 31 83 18 biotype 1007 HC2 "Methylimidazole (delta-H)" 9 84 9 biotype 1008 C3 "Methylimidazole (delta-H)" 31 85 19 biotype 1009 HC3 "Methylimidazole (delta-H)" 9 86 7 biotype 1010 N3 "Methylimidazole (delta-H)" 10 87 33 biotype 1011 CT "Methylimidazole (eps-H)" 2 224 17 biotype 1012 HT "Methylimidazole (eps-H)" 9 10 3 biotype 1013 C1 "Methylimidazole (eps-H)" 31 72 18 biotype 1014 N2 "Methylimidazole (eps-H)" 10 73 33 biotype 1015 C2 "Methylimidazole (eps-H)" 31 74 18 biotype 1016 HC2 "Methylimidazole (eps-H)" 9 10 9 biotype 1017 C3 "Methylimidazole (eps-H)" 31 75 19 biotype 1018 HC3 "Methylimidazole (eps-H)" 9 76 7 biotype 1019 N3 "Methylimidazole (eps-H)" 1 77 32 biotype 1020 HN3 "Methylimidazole (eps-H)" 4 78 1 biotype 1021 CT "Methylindole" 2 123 17 biotype 1022 HT "Methylindole" 9 10 3 biotype 1023 C3 "Methylindole" 31 62 21 biotype 1024 C2 "Methylindole" 31 63 14 biotype 1025 H2 "Methylindole" 9 64 5 biotype 1026 C3A "Methylindole" 31 65 20 biotype 1027 N1 "Methylindole" 1 66 39 biotype 1028 H1 "Methylindole" 4 67 1 biotype 1029 C7A "Methylindole" 31 68 20 biotype 1030 C4 "Methylindole" 31 261 109 biotype 1031 H4 "Methylindole" 9 265 5 biotype 1032 C7 "Methylindole" 31 262 109 biotype 1033 H7 "Methylindole" 9 266 5 biotype 1034 C5 "Methylindole" 31 263 14 biotype 1035 H5 "Methylindole" 9 267 5 biotype 1036 C6 "Methylindole" 31 264 14 biotype 1037 H6 "Methylindole" 9 268 5 biotype 1038 N "Methylammonium (+)" 8 103 37 biotype 1039 HN "Methylammonium (+)" 4 104 2 biotype 1040 CT "Methylammonium (+)" 2 283 17 biotype 1041 HT "Methylammonium (+)" 9 10 3 biotype 1042 N "Dimethylammonium (+)" 8 281 40 biotype 1043 HN "Dimethylammonium (+)" 4 104 2 biotype 1044 CT "Dimethylammonium (+)" 2 282 17 biotype 1045 HT "Dimethylammonium (+)" 9 10 3 biotype 1046 CL "Perchlorate (-)" 0 0 104 biotype 1047 O "Perchlorate (-)" 0 0 105 biotype 1048 N "Nitrate (-)" 0 0 106 biotype 1049 O "Nitrate (-)" 0 0 107 biotype 1050 OW "TIP4P-Ew Water" 25 231 0 biotype 1051 HW "TIP4P-Ew Water" 17 250 0 biotype 1052 MW "TIP4P-Ew Water" 19 249 0 biotype 1053 C "Benzene" 31 116 14 biotype 1054 HC "Benzene" 9 117 5 biotype 1055 C1 "Naphthalene" 31 115 20 biotype 1056 C2 "Naphthalene" 31 69 14 biotype 1057 C3 "Naphthalene" 31 69 14 biotype 1058 H2 "Naphthalene" 9 70 5 biotype 1059 H3 "Naphthalene" 9 70 5 biotype 1060 N1 "Purine" 10 0 88 biotype 1061 C2 "Purine" 3 0 73 biotype 1062 H2 "Purine" 9 0 55 biotype 1063 N3 "Purine" 10 0 88 biotype 1064 C4 "Purine" 3 0 74 biotype 1065 C5 "Purine" 3 0 74 biotype 1066 C6 "Purine" 3 0 66 biotype 1067 H6 "Purine" 9 0 55 biotype 1068 N7 "Purine" 10 0 91 biotype 1069 C8 "Purine" 3 0 73 biotype 1070 H8 "Purine" 9 0 55 biotype 1071 N9 "Purine" 1 0 83 biotype 1072 H9 "Purine" 4 0 54 biotype 1073 O "Oxygen" 5 115 0 biotype 1074 N "Glutamic Acid" 1 2 35 biotype 1075 CA "Glutamic Acid" 2 5 15 biotype 1076 C "Glutamic Acid" 3 8 13 biotype 1077 HN "Glutamic Acid" 4 4 1 biotype 1078 O "Glutamic Acid" 5 9 42 biotype 1079 HA "Glutamic Acid" 9 10 6 biotype 1080 CB "Glutamic Acid" 2 33 110 biotype 1081 HB "Glutamic Acid" 9 10 3 biotype 1082 CG "Glutamic Acid" 2 251 16 biotype 1083 HG "Glutamic Acid" 9 10 3 biotype 1084 CD "Glutamic Acid" 3 202 26 biotype 1085 OE1 "Glutamic Acid" 5 40 43 biotype 1086 OE2 "Glutamic Acid" 6 269 45 biotype 1087 HE2 "Glutamic Acid" 4 91 1 biotype 1088 N "Aspartic Acid" 1 2 35 biotype 1089 CA "Aspartic Acid" 2 5 15 biotype 1090 C "Aspartic Acid" 3 8 13 biotype 1091 HN "Aspartic Acid" 4 4 1 biotype 1092 O "Aspartic Acid" 5 9 42 biotype 1093 HA "Aspartic Acid" 9 10 6 biotype 1094 CB "Aspartic Acid" 2 251 110 biotype 1095 HB "Aspartic Acid" 9 10 3 biotype 1096 CG "Aspartic Acid" 3 202 26 biotype 1097 OD1 "Aspartic Acid" 5 29 43 biotype 1098 OD2 "Aspartic Acid" 6 269 45 biotype 1099 HD2 "Aspartic Acid" 4 91 1 biotype 1100 N "Deprotonated Lysine" 1 2 35 biotype 1101 CA "Deprotonated Lysine" 2 5 15 biotype 1102 C "Deprotonated Lysine" 3 8 13 biotype 1103 HN "Deprotonated Lysine" 4 4 1 biotype 1104 O "Deprotonated Lysine" 5 9 42 biotype 1105 HA "Deprotonated Lysine" 9 10 6 biotype 1106 CB "Deprotonated Lysine" 2 98 16 biotype 1107 HB "Deprotonated Lysine" 9 10 3 biotype 1108 CG "Deprotonated Lysine" 2 99 16 biotype 1109 HG "Deprotonated Lysine" 9 10 3 biotype 1110 CD "Deprotonated Lysine" 2 100 16 biotype 1111 HD "Deprotonated Lysine" 9 10 3 biotype 1112 CE "Deprotonated Lysine" 2 76 16 biotype 1113 HE "Deprotonated Lysine" 9 270 3 biotype 1114 NZ "Deprotonated Lysine" 1 260 36 biotype 1115 HZ "Deprotonated Lysine" 4 255 2 biotype 1116 N "Cystine (thiolate)" 1 2 35 biotype 1117 CA "Cystine (thiolate)" 2 5 15 biotype 1118 C "Cystine (thiolate)" 3 8 13 biotype 1119 HN "Cystine (thiolate)" 4 4 1 biotype 1120 O "Cystine (thiolate)" 5 9 42 biotype 1121 HA "Cystine (thiolate)" 9 10 6 biotype 1122 CB "Cystine (thiolate)" 2 252 27 biotype 1123 HB "Cystine (thiolate)" 9 10 3 biotype 1124 SG "Cystine (thiolate)" 30 253 52 biotype 1125 N "Tyrosine (-)" 1 2 35 biotype 1126 CA "Tyrosine (-)" 2 5 15 biotype 1127 C "Tyrosine (-)" 3 8 13 biotype 1128 HN "Tyrosine (-)" 4 4 1 biotype 1129 O "Tyrosine (-)" 5 9 42 biotype 1130 HA "Tyrosine (-)" 9 10 6 biotype 1131 CB "Tyrosine (-)" 2 54 16 biotype 1132 HB "Tyrosine (-)" 9 10 3 biotype 1133 CG "Tyrosine (-)" 31 54 14 biotype 1134 CD "Tyrosine (-)" 31 55 14 biotype 1135 HD "Tyrosine (-)" 9 56 5 biotype 1136 CE "Tyrosine (-)" 31 0 14 biotype 1137 HE "Tyrosine (-)" 9 0 5 biotype 1138 CZ "Tyrosine (-)" 31 0 0 biotype 1139 OZ "Tyrosine (-)" 29 0 0 biotype 1140 N "Phosphotyrosine (-)" 1 2 35 biotype 1141 CA "Phosphotyrosine (-)" 2 5 15 biotype 1142 C "Phosphotyrosine (-)" 3 8 13 biotype 1143 HN "Phosphotyrosine (-)" 4 4 1 biotype 1144 O "Phosphotyrosine (-)" 5 9 42 biotype 1145 HA "Phosphotyrosine (-)" 9 10 6 biotype 1146 CB "Phosphotyrosine (-)" 2 54 16 biotype 1147 HB "Phosphotyrosine (-)" 9 10 3 biotype 1148 CG "Phosphotyrosine (-)" 31 55 14 biotype 1149 CD "Phosphotyrosine (-)" 31 56 14 biotype 1150 HD "Phosphotyrosine (-)" 9 57 5 biotype 1151 CE "Phosphotyrosine (-)" 31 251 14 biotype 1152 HE "Phosphotyrosine (-)" 9 235 5 biotype 1153 CZ "Phosphotyrosine (-)" 31 258 14 biotype 1154 OZ "Phosphotyrosine (-)" 6 77 108 biotype 1155 P "Phosphotyrosine (-)" 24 257 102 biotype 1156 OP "Phosphotyrosine (-)" 29 256 97 biotype 1157 OH "Phosphotyrosine (-)" 6 256 98 biotype 1158 HOP "Phosphotyrosine (-)" 4 259 57 biotype 1159 N "Phosphoserine (-)" 1 2 35 biotype 1160 CA "Phosphoserine (-)" 2 5 15 biotype 1161 C "Phosphoserine (-)" 3 8 13 biotype 1162 HN "Phosphoserine (-)" 4 4 1 biotype 1163 O "Phosphoserine (-)" 5 9 42 biotype 1164 HA "Phosphoserine (-)" 9 10 6 biotype 1165 CB "Phosphoserine (-)" 2 138 16 biotype 1166 HB "Phosphoserine (-)" 9 10 3 biotype 1167 OG "Phosphoserine (-)" 6 30 96 biotype 1168 P "Phosphoserine (-)" 24 135 102 biotype 1169 OP "Phosphoserine (-)" 29 254 97 biotype 1170 OH "Phosphoserine (-)" 6 234 98 biotype 1171 HOP "Phosphoserine (-)" 4 255 57 biotype 1172 N "Phosphothreonine (-)" 1 2 35 biotype 1173 CA "Phosphothreonine (-)" 2 5 15 biotype 1174 C "Phosphothreonine (-)" 3 8 13 biotype 1175 HN "Phosphothreonine (-)" 4 4 1 biotype 1176 O "Phosphothreonine (-)" 5 9 42 biotype 1177 HA "Phosphothreonine (-)" 9 10 6 biotype 1178 CB "Phosphothreonine (-)" 2 145 15 biotype 1179 HB "Phosphothreonine (-)" 9 10 3 biotype 1180 OG1 "Phosphothreonine (-)" 6 30 96 biotype 1181 CG2 "Phosphothreonine (-)" 2 47 17 biotype 1182 HG2 "Phosphothreonine (-)" 9 10 3 biotype 1183 P "Phosphothreonine (-)" 24 135 102 biotype 1184 OP "Phosphothreonine (-)" 29 254 97 biotype 1185 OH "Phosphothreonine (-)" 6 234 98 biotype 1186 HOP "Phosphothreonine (-)" 4 255 57 biotype 1187 N "Acetylated Lysine" 1 2 35 biotype 1188 CA "Acetylated Lysine" 2 5 15 biotype 1189 C "Acetylated Lysine" 3 8 13 biotype 1190 HN "Acetylated Lysine" 4 4 1 biotype 1191 O "Acetylated Lysine" 5 9 42 biotype 1192 HA "Acetylated Lysine" 9 10 6 biotype 1193 CB "Acetylated Lysine" 2 98 16 biotype 1194 HB "Acetylated Lysine" 9 10 3 biotype 1195 CG "Acetylated Lysine" 2 99 16 biotype 1196 HG "Acetylated Lysine" 9 10 3 biotype 1197 CD "Acetylated Lysine" 2 100 16 biotype 1198 HD "Acetylated Lysine" 9 10 3 biotype 1199 CE "Acetylated Lysine" 2 151 16 biotype 1200 HE "Acetylated Lysine" 9 10 3 biotype 1201 NZ "Acetylated Lysine" 1 2 35 biotype 1202 HZ "Acetylated Lysine" 4 4 1 biotype 1203 CH "Acetylated Lysine" 3 8 13 biotype 1204 OH "Acetylated Lysine" 5 9 42 biotype 1205 CI "Acetylated Lysine" 2 13 17 biotype 1206 HI "Acetylated Lysine" 9 7 3 biotype 1207 N "Mono(CH3)-Lysine(+)" 1 2 35 biotype 1208 CA "Mono(CH3)-Lysine(+)" 2 5 15 biotype 1209 C "Mono(CH3)-Lysine(+)" 3 8 13 biotype 1210 HN "Mono(CH3)-Lysine(+)" 4 4 1 biotype 1211 O "Mono(CH3)-Lysine(+)" 5 9 42 biotype 1212 HA "Mono(CH3)-Lysine(+)" 9 10 6 biotype 1213 CB "Mono(CH3)-Lysine(+)" 2 98 16 biotype 1214 HB "Mono(CH3)-Lysine(+)" 9 10 3 biotype 1215 CG "Mono(CH3)-Lysine(+)" 2 99 16 biotype 1216 HG "Mono(CH3)-Lysine(+)" 9 10 3 biotype 1217 CD "Mono(CH3)-Lysine(+)" 2 100 16 biotype 1218 HD "Mono(CH3)-Lysine(+)" 9 10 3 biotype 1219 CE "Mono(CH3)-Lysine(+)" 2 101 16 biotype 1220 HE "Mono(CH3)-Lysine(+)" 9 102 3 biotype 1221 NZ "Mono(CH3)-Lysine(+)" 8 271 113 biotype 1222 HZ "Mono(CH3)-Lysine(+)" 4 104 2 biotype 1223 CH "Mono(CH3)-Lysine(+)" 2 272 17 biotype 1224 HH "Mono(CH3)-Lysine(+)" 9 102 3 biotype 1225 N "Di(CH3)-Lysine(+)" 1 2 35 biotype 1226 CA "Di(CH3)-Lysine(+)" 2 5 15 biotype 1227 C "Di(CH3)-Lysine(+)" 3 8 13 biotype 1228 HN "Di(CH3)-Lysine(+)" 4 4 1 biotype 1229 O "Di(CH3)-Lysine(+)" 5 9 42 biotype 1230 HA "Di(CH3)-Lysine(+)" 9 10 6 biotype 1231 CB "Di(CH3)-Lysine(+)" 2 98 16 biotype 1232 HB "Di(CH3)-Lysine(+)" 9 10 3 biotype 1233 CG "Di(CH3)-Lysine(+)" 2 99 16 biotype 1234 HG "Di(CH3)-Lysine(+)" 9 10 3 biotype 1235 CD "Di(CH3)-Lysine(+)" 2 100 16 biotype 1236 HD "Di(CH3)-Lysine(+)" 9 10 3 biotype 1237 CE "Di(CH3)-Lysine(+)" 2 280 16 biotype 1238 HE "Di(CH3)-Lysine(+)" 9 10 3 biotype 1239 NZ "Di(CH3)-Lysine(+)" 8 278 0 biotype 1240 HZ "Di(CH3)-Lysine(+)" 4 277 2 biotype 1241 CH "Di(CH3)-Lysine(+)" 2 279 17 biotype 1242 HH "Di(CH3)-Lysine(+)" 9 10 3 biotype 1243 N "Tri(CH3)-Lysine(+)" 1 2 35 biotype 1244 CA "Tri(CH3)-Lysine(+)" 2 5 15 biotype 1245 C "Tri(CH3)-Lysine(+)" 3 8 13 biotype 1246 HN "Tri(CH3)-Lysine(+)" 4 4 1 biotype 1247 O "Tri(CH3)-Lysine(+)" 5 9 42 biotype 1248 HA "Tri(CH3)-Lysine(+)" 9 10 6 biotype 1249 CB "Tri(CH3)-Lysine(+)" 2 98 16 biotype 1250 HB "Tri(CH3)-Lysine(+)" 9 10 3 biotype 1251 CG "Tri(CH3)-Lysine(+)" 2 99 16 biotype 1252 HG "Tri(CH3)-Lysine(+)" 9 10 3 biotype 1253 CD "Tri(CH3)-Lysine(+)" 2 100 16 biotype 1254 HD "Tri(CH3)-Lysine(+)" 9 10 3 biotype 1255 CE "Tri(CH3)-Lysine(+)" 2 275 16 biotype 1256 HE "Tri(CH3)-Lysine(+)" 9 276 3 biotype 1257 NZ "Tri(CH3)-Lysine(+)" 8 273 112 biotype 1258 CH "Tri(CH3)-Lysine(+)" 2 274 17 biotype 1259 HH "Tri(CH3)-Lysine(+)" 9 276 3 biotype 1260 DU "Dummy" 0 0 11 biotype 1261 DU "Dummy" 0 0 12 biotype 1262 DU "Dummy" 0 0 27 biotype 1263 DU "Dummy" 0 0 28 biotype 1264 DU "Dummy" 0 0 29 biotype 1265 DU "Dummy" 0 0 30 biotype 1266 DU "Dummy" 0 0 41 biotype 1267 DU "Dummy" 0 0 46 biotype 1268 DU "Dummy" 0 0 48 biotype 1269 DU "Dummy" 0 0 49 biotype 1270 DU "Dummy" 0 0 56 biotype 1271 DU "Dummy" 0 0 59 biotype 1272 DU "Dummy" 0 0 64 biotype 1273 DU "Dummy" 0 0 68 biotype 1274 DU "Dummy" 0 0 69 biotype 1275 DU "Dummy" 0 0 70 biotype 1276 DU "Dummy" 0 0 71 biotype 1277 DU "Dummy" 0 0 78 biotype 1278 DU "Dummy" 0 0 89 biotype 1279 DU "Dummy" 0 0 92 biotype 1280 DU "Dummy" 0 0 93 #################################################### # # # Bond length stretch potentials in CHARMM36 # # # #################################################### # # bondtype bonded_type_bond 36 15 28 bonded_type_bond 30 49 48 bonded_type_bond 13 13 39 bonded_type_bond 14 14 8 bonded_type_bond 14 109 8 bonded_type_bond 28 28 40 bonded_type_bond 28 29 41 bonded_type_bond 28 16 34 bonded_type_bond 28 17 33 bonded_type_bond 29 29 42 bonded_type_bond 22 13 29 bonded_type_bond 22 25 29 bonded_type_bond 22 26 43 bonded_type_bond 23 22 44 bonded_type_bond 23 23 45 bonded_type_bond 24 23 45 bonded_type_bond 18 18 46 bonded_type_bond 20 14 12 bonded_type_bond 20 109 12 bonded_type_bond 20 20 17 bonded_type_bond 15 13 29 bonded_type_bond 15 25 30 bonded_type_bond 15 26 30 bonded_type_bond 15 27 32 # compat. bonded_type_bond 15 15 1 bonded_type_bond 16 13 29 bonded_type_bond 16 14 13 bonded_type_bond 16 25 30 bonded_type_bond 16 26 30 bonded_type_bond 110 25 30 bonded_type_bond 110 26 30 bonded_type_bond 16 18 31 bonded_type_bond 110 18 31 bonded_type_bond 16 15 2 bonded_type_bond 110 15 2 bonded_type_bond 16 16 3 bonded_type_bond 16 110 3 bonded_type_bond 17 13 29 bonded_type_bond 17 14 13 bonded_type_bond 17 25 30 bonded_type_bond 17 26 30 bonded_type_bond 17 18 31 bonded_type_bond 17 27 32 bonded_type_bond 17 15 2 bonded_type_bond 17 16 4 bonded_type_bond 17 17 3 bonded_type_bond 21 14 9 bonded_type_bond 21 20 10 bonded_type_bond 21 16 11 bonded_type_bond 21 17 11 bonded_type_bond 1 26 49 bonded_type_bond 3 13 51 bonded_type_bond 3 25 51 bonded_type_bond 3 23 5 bonded_type_bond 3 24 5 bonded_type_bond 3 27 53 bonded_type_bond 3 15 5 bonded_type_bond 3 16 5 bonded_type_bond 3 110 5 bonded_type_bond 3 17 7 bonded_type_bond 3 21 6 bonded_type_bond 11 28 54 bonded_type_bond 12 29 55 bonded_type_bond 6 22 6 bonded_type_bond 6 15 6 bonded_type_bond 6 16 6 bonded_type_bond 6 17 6 bonded_type_bond 5 14 14 bonded_type_bond 5 109 14 bonded_type_bond 5 21 15 bonded_type_bond 7 18 58 bonded_type_bond 7 19 59 bonded_type_bond 8 19 60 bonded_type_bond 9 18 61 bonded_type_bond 4 4 62 bonded_type_bond 31 13 63 bonded_type_bond 31 22 64 bonded_type_bond 31 24 65 bonded_type_bond 38 13 66 bonded_type_bond 38 16 27 bonded_type_bond 38 17 27 bonded_type_bond 38 2 67 bonded_type_bond 35 13 68 bonded_type_bond 35 15 24 bonded_type_bond 35 16 24 bonded_type_bond 35 17 24 bonded_type_bond 35 1 69 bonded_type_bond 35 2 70 bonded_type_bond 36 13 71 bonded_type_bond 36 25 71 bonded_type_bond 36 16 25 bonded_type_bond 36 17 25 bonded_type_bond 36 1 72 bonded_type_bond 36 2 73 bonded_type_bond 37 15 26 bonded_type_bond 37 16 26 bonded_type_bond 37 17 26 bonded_type_bond 37 2 74 bonded_type_bond 113 2 74 bonded_type_bond 40 22 75 bonded_type_bond 40 24 76 bonded_type_bond 40 2 77 bonded_type_bond 32 18 78 bonded_type_bond 32 19 79 bonded_type_bond 32 1 80 bonded_type_bond 33 18 78 bonded_type_bond 33 19 81 bonded_type_bond 34 18 82 bonded_type_bond 34 19 83 bonded_type_bond 34 1 84 bonded_type_bond 39 14 85 bonded_type_bond 39 20 86 bonded_type_bond 39 1 87 bonded_type_bond 42 13 88 bonded_type_bond 42 25 89 bonded_type_bond 43 25 90 bonded_type_bond 43 26 90 bonded_type_bond 44 14 91 bonded_type_bond 44 25 91 bonded_type_bond 44 16 35 bonded_type_bond 44 17 35 bonded_type_bond 45 14 18 bonded_type_bond 45 26 19 bonded_type_bond 45 15 20 bonded_type_bond 45 16 20 bonded_type_bond 45 17 20 bonded_type_bond 45 1 21 bonded_type_bond 45 23 184 bonded_type_bond 46 26 22 bonded_type_bond 46 17 23 bonded_type_bond 47 4 92 bonded_type_bond 50 16 36 bonded_type_bond 50 17 38 bonded_type_bond 50 10 93 bonded_type_bond 51 16 37 bonded_type_bond 51 17 37 bonded_type_bond 51 51 94 bonded_type_bond 52 27 95 bonded_type_bond 79 93 47 bonded_type_bond 93 53 50 bonded_type_bond 100 80 52 bonded_type_bond 79 80 56 bonded_type_bond 70 59 57 bonded_type_bond 67 59 96 bonded_type_bond 63 67 97 bonded_type_bond 63 72 98 bonded_type_bond 64 67 99 bonded_type_bond 63 75 100 bonded_type_bond 64 82 101 bonded_type_bond 63 83 102 bonded_type_bond 65 84 103 bonded_type_bond 63 86 104 bonded_type_bond 63 85 105 bonded_type_bond 65 85 106 bonded_type_bond 63 87 107 bonded_type_bond 63 94 108 bonded_type_bond 64 94 109 bonded_type_bond 65 94 109 bonded_type_bond 63 95 110 bonded_type_bond 66 67 111 bonded_type_bond 66 71 112 bonded_type_bond 66 74 113 bonded_type_bond 66 82 114 bonded_type_bond 66 86 115 bonded_type_bond 66 87 116 bonded_type_bond 66 88 117 bonded_type_bond 66 90 118 bonded_type_bond 67 67 119 bonded_type_bond 67 72 120 bonded_type_bond 68 67 121 bonded_type_bond 69 67 122 bonded_type_bond 70 67 121 bonded_type_bond 71 67 124 bonded_type_bond 67 79 125 bonded_type_bond 71 81 126 bonded_type_bond 72 81 127 bonded_type_bond 67 55 96 bonded_type_bond 72 55 96 bonded_type_bond 67 56 96 bonded_type_bond 68 56 96 bonded_type_bond 69 56 96 bonded_type_bond 70 55 57 bonded_type_bond 67 83 128 bonded_type_bond 67 84 129 bonded_type_bond 69 83 130 bonded_type_bond 70 83 131 bonded_type_bond 73 55 132 bonded_type_bond 73 83 133 bonded_type_bond 73 84 134 bonded_type_bond 73 86 135 bonded_type_bond 73 88 136 bonded_type_bond 73 89 137 bonded_type_bond 73 91 138 bonded_type_bond 74 74 139 bonded_type_bond 74 75 140 bonded_type_bond 74 83 141 bonded_type_bond 74 84 142 bonded_type_bond 74 88 143 bonded_type_bond 74 90 144 bonded_type_bond 74 89 145 bonded_type_bond 74 91 146 bonded_type_bond 75 91 147 bonded_type_bond 79 79 56 bonded_type_bond 79 81 56 bonded_type_bond 79 83 148 bonded_type_bond 79 99 149 bonded_type_bond 81 62 150 bonded_type_bond 81 96 151 bonded_type_bond 53 82 152 bonded_type_bond 103 82 152 bonded_type_bond 54 83 153 bonded_type_bond 54 84 153 bonded_type_bond 54 86 154 bonded_type_bond 54 85 153 bonded_type_bond 57 98 155 bonded_type_bond 96 102 156 bonded_type_bond 97 102 157 bonded_type_bond 98 102 158 bonded_type_bond 96 111 156 bonded_type_bond 97 111 157 bonded_type_bond 98 111 158 bonded_type_bond 92 53 161 bonded_type_bond 77 100 52 bonded_type_bond 77 79 162 bonded_type_bond 76 100 163 bonded_type_bond 76 76 164 bonded_type_bond 76 79 165 bonded_type_bond 76 81 165 bonded_type_bond 76 60 166 bonded_type_bond 79 61 166 bonded_type_bond 77 60 166 bonded_type_bond 77 101 52 bonded_type_bond 76 101 167 bonded_type_bond 77 77 168 bonded_type_bond 76 77 169 bonded_type_bond 77 78 162 bonded_type_bond 76 78 165 bonded_type_bond 78 60 166 bonded_type_bond 76 80 170 bonded_type_bond 80 96 171 bonded_type_bond 15 96 172 bonded_type_bond 16 96 171 bonded_type_bond 14 108 181 bonded_type_bond 80 99 149 bonded_type_bond 76 96 172 bonded_type_bond 77 96 172 bonded_type_bond 76 99 149 bonded_type_bond 81 83 173 bonded_type_bond 79 84 174 bonded_type_bond 81 84 174 bonded_type_bond 77 83 175 bonded_type_bond 77 84 176 bonded_type_bond 80 61 166 bonded_type_bond 99 58 21 bonded_type_bond 77 99 177 bonded_type_bond 78 99 177 bonded_type_bond 79 96 178 bonded_type_bond 77 32 179 bonded_type_bond 102 108 180 bonded_type_bond 16 112 182 bonded_type_bond 17 112 182 bonded_type_bond 16 113 183 bonded_type_bond 17 113 183 ################################################### # # # The following are bond angle parameter # # assignments in CHARMM36 # # # ################################################### bonded_type_angle 1 36 15 1 bonded_type_angle 36 15 16 2 bonded_type_angle 15 26 45 3 bonded_type_angle 17 15 26 4 bonded_type_angle 36 15 6 5 bonded_type_angle 36 15 13 6 bonded_type_angle 49 30 49 7 bonded_type_angle 14 14 14 8 bonded_type_angle 109 14 14 8 bonded_type_angle 28 28 16 9 bonded_type_angle 28 28 17 9 bonded_type_angle 28 16 17 10 bonded_type_angle 29 28 16 11 bonded_type_angle 29 28 17 12 bonded_type_angle 22 31 13 13 bonded_type_angle 23 22 13 14 bonded_type_angle 23 22 25 14 bonded_type_angle 23 22 26 15 bonded_type_angle 23 23 22 16 bonded_type_angle 24 23 23 16 bonded_type_angle 24 31 13 13 bonded_type_angle 24 31 22 17 bonded_type_angle 24 40 22 18 bonded_type_angle 19 32 18 19 bonded_type_angle 19 33 18 20 bonded_type_angle 19 34 18 21 bonded_type_angle 20 14 14 22 bonded_type_angle 20 109 14 357 bonded_type_angle 20 20 14 23 bonded_type_angle 20 20 109 358 bonded_type_angle 20 21 14 24 bonded_type_angle 20 39 14 354 bonded_type_angle 15 15 13 4 bonded_type_angle 15 15 25 4 bonded_type_angle 15 15 15 26 bonded_type_angle 15 16 14 27 bonded_type_angle 15 16 25 4 bonded_type_angle 15 16 26 4 bonded_type_angle 15 110 25 4 bonded_type_angle 15 110 26 4 bonded_type_angle 15 16 18 28 bonded_type_angle 15 110 18 28 bonded_type_angle 15 16 15 29 bonded_type_angle 15 35 13 31 bonded_type_angle 16 14 14 32 bonded_type_angle 16 18 18 33 bonded_type_angle 110 18 18 33 bonded_type_angle 16 15 13 4 bonded_type_angle 16 15 25 4 bonded_type_angle 16 15 26 4 bonded_type_angle 110 15 13 4 bonded_type_angle 110 15 25 4 bonded_type_angle 110 15 26 4 bonded_type_angle 27 15 25 4 # compat. bonded_type_angle 16 15 15 26 bonded_type_angle 16 16 13 4 bonded_type_angle 16 16 25 4 bonded_type_angle 110 16 25 4 bonded_type_angle 17 16 25 4 bonded_type_angle 16 16 26 4 bonded_type_angle 110 16 26 4 bonded_type_angle 16 16 15 29 bonded_type_angle 16 110 15 29 bonded_type_angle 16 16 16 30 bonded_type_angle 16 17 15 29 bonded_type_angle 16 21 14 34 bonded_type_angle 16 21 20 355 bonded_type_angle 17 21 14 34 bonded_type_angle 17 21 20 355 bonded_type_angle 16 38 13 38 bonded_type_angle 16 35 13 31 bonded_type_angle 16 46 26 39 bonded_type_angle 17 14 14 32 bonded_type_angle 17 18 18 33 bonded_type_angle 17 15 13 4 bonded_type_angle 17 15 25 4 bonded_type_angle 17 15 15 40 bonded_type_angle 17 15 16 41 bonded_type_angle 17 15 17 41 bonded_type_angle 17 16 14 27 bonded_type_angle 17 16 18 28 bonded_type_angle 17 16 15 29 bonded_type_angle 17 16 16 42 bonded_type_angle 17 16 17 41 bonded_type_angle 17 38 13 38 bonded_type_angle 17 35 13 31 bonded_type_angle 17 46 26 39 bonded_type_angle 17 50 16 43 bonded_type_angle 21 20 14 44 bonded_type_angle 21 20 109 44 bonded_type_angle 21 20 20 45 bonded_type_angle 21 16 15 46 bonded_type_angle 21 16 17 46 bonded_type_angle 27 15 13 4 # compat. bonded_type_angle 1 35 13 47 bonded_type_angle 1 35 15 48 bonded_type_angle 1 35 16 48 bonded_type_angle 1 35 17 48 bonded_type_angle 1 36 13 31 bonded_type_angle 1 36 25 31 bonded_type_angle 1 36 1 49 bonded_type_angle 1 32 18 50 bonded_type_angle 1 32 19 51 bonded_type_angle 1 34 18 52 bonded_type_angle 1 34 19 53 bonded_type_angle 1 39 14 54 bonded_type_angle 1 39 20 54 bonded_type_angle 1 45 14 55 bonded_type_angle 1 45 26 56 bonded_type_angle 1 45 15 57 bonded_type_angle 1 45 16 57 bonded_type_angle 1 45 17 57 bonded_type_angle 1 45 23 365 bonded_type_angle 3 14 14 58 bonded_type_angle 3 14 20 59 bonded_type_angle 3 14 21 60 bonded_type_angle 3 23 22 61 bonded_type_angle 3 23 23 62 bonded_type_angle 3 23 24 62 bonded_type_angle 3 23 3 63 bonded_type_angle 3 23 45 364 bonded_type_angle 3 24 23 62 bonded_type_angle 3 24 3 63 bonded_type_angle 3 27 17 64 bonded_type_angle 3 27 3 65 bonded_type_angle 3 15 13 66 bonded_type_angle 3 15 26 66 bonded_type_angle 3 15 15 67 bonded_type_angle 3 15 16 67 bonded_type_angle 3 15 17 67 bonded_type_angle 3 15 3 63 bonded_type_angle 3 16 13 66 bonded_type_angle 3 16 14 68 bonded_type_angle 3 16 25 66 bonded_type_angle 3 16 26 66 bonded_type_angle 3 110 25 66 bonded_type_angle 3 110 26 66 bonded_type_angle 3 16 28 69 bonded_type_angle 3 16 18 70 bonded_type_angle 3 110 18 70 bonded_type_angle 3 16 15 62 # 61 bonded_type_angle 3 110 15 62 bonded_type_angle 3 16 16 62 bonded_type_angle 3 110 16 62 bonded_type_angle 3 16 110 62 bonded_type_angle 3 16 17 64 bonded_type_angle 3 16 21 356 bonded_type_angle 3 16 3 63 bonded_type_angle 3 110 3 63 bonded_type_angle 3 17 13 66 bonded_type_angle 3 17 14 68 bonded_type_angle 3 17 21 356 bonded_type_angle 3 17 25 66 bonded_type_angle 3 17 26 66 bonded_type_angle 3 17 28 71 bonded_type_angle 3 17 18 70 bonded_type_angle 3 17 27 64 bonded_type_angle 3 17 15 61 bonded_type_angle 3 17 16 64 bonded_type_angle 3 17 17 72 bonded_type_angle 3 17 3 73 bonded_type_angle 3 21 14 74 bonded_type_angle 3 21 20 75 bonded_type_angle 3 27 15 61 # compat bonded_type_angle 11 28 28 76 bonded_type_angle 11 28 29 77 bonded_type_angle 11 28 16 78 bonded_type_angle 11 28 17 79 bonded_type_angle 12 29 28 80 bonded_type_angle 12 29 29 81 bonded_type_angle 12 29 12 82 bonded_type_angle 6 22 13 83 bonded_type_angle 6 22 25 83 bonded_type_angle 6 22 26 83 bonded_type_angle 6 22 23 84 bonded_type_angle 6 15 13 85 bonded_type_angle 6 15 25 85 bonded_type_angle 6 15 26 85 bonded_type_angle 6 15 15 86 bonded_type_angle 6 15 16 86 bonded_type_angle 6 15 110 86 bonded_type_angle 6 15 17 86 bonded_type_angle 6 15 27 86 # compat. bonded_type_angle 6 16 13 85 bonded_type_angle 6 16 25 85 bonded_type_angle 6 16 26 85 bonded_type_angle 6 16 6 87 bonded_type_angle 6 16 16 62 # compat. bonded_type_angle 6 17 13 85 bonded_type_angle 2 38 13 88 bonded_type_angle 2 38 16 89 bonded_type_angle 2 38 17 89 bonded_type_angle 2 38 2 90 bonded_type_angle 2 36 16 1 bonded_type_angle 2 36 17 1 bonded_type_angle 2 36 2 91 bonded_type_angle 2 37 15 92 bonded_type_angle 2 37 16 92 bonded_type_angle 2 37 17 92 bonded_type_angle 2 37 2 93 bonded_type_angle 2 40 22 94 bonded_type_angle 2 40 24 94 bonded_type_angle 2 40 2 95 bonded_type_angle 5 14 14 96 bonded_type_angle 5 14 109 96 bonded_type_angle 5 109 14 96 bonded_type_angle 5 14 20 97 bonded_type_angle 5 109 20 97 bonded_type_angle 5 14 21 60 bonded_type_angle 5 21 14 98 bonded_type_angle 5 21 20 75 bonded_type_angle 7 18 18 99 bonded_type_angle 9 18 18 100 bonded_type_angle 10 50 16 101 bonded_type_angle 10 50 17 102 bonded_type_angle 4 47 4 103 bonded_type_angle 31 13 22 104 bonded_type_angle 31 13 15 104 bonded_type_angle 31 13 16 104 bonded_type_angle 31 13 17 104 bonded_type_angle 31 22 13 105 bonded_type_angle 31 22 25 105 bonded_type_angle 31 22 26 105 bonded_type_angle 31 22 23 106 bonded_type_angle 31 22 6 107 bonded_type_angle 31 24 23 108 bonded_type_angle 31 24 3 109 bonded_type_angle 38 13 38 110 bonded_type_angle 38 16 16 111 bonded_type_angle 38 16 3 359 bonded_type_angle 38 17 3 359 bonded_type_angle 35 13 22 113 bonded_type_angle 35 13 15 113 bonded_type_angle 35 13 16 113 bonded_type_angle 35 13 17 113 bonded_type_angle 35 15 13 6 bonded_type_angle 35 15 25 6 bonded_type_angle 35 15 26 6 bonded_type_angle 35 15 15 114 bonded_type_angle 35 15 16 114 bonded_type_angle 35 15 110 114 bonded_type_angle 35 15 17 114 bonded_type_angle 35 15 27 114 # compat. bonded_type_angle 35 15 6 109 bonded_type_angle 35 16 13 6 bonded_type_angle 35 16 25 6 bonded_type_angle 35 16 26 6 bonded_type_angle 35 16 16 114 bonded_type_angle 35 16 3 115 bonded_type_angle 35 16 6 109 bonded_type_angle 35 17 3 115 bonded_type_angle 36 25 22 116 bonded_type_angle 36 25 15 117 bonded_type_angle 36 25 16 117 bonded_type_angle 36 25 17 117 bonded_type_angle 36 25 36 368 # urea bonded_type_angle 36 13 15 117 bonded_type_angle 36 13 16 117 bonded_type_angle 36 13 17 117 bonded_type_angle 36 13 22 116 bonded_type_angle 36 25 3 118 bonded_type_angle 35 13 3 118 bonded_type_angle 36 16 3 5 bonded_type_angle 36 16 6 5 bonded_type_angle 36 16 26 4 bonded_type_angle 36 16 16 2 bonded_type_angle 36 17 3 5 bonded_type_angle 37 15 13 119 bonded_type_angle 37 15 25 119 bonded_type_angle 37 15 15 2 bonded_type_angle 37 15 16 2 bonded_type_angle 37 15 110 2 bonded_type_angle 37 15 17 2 bonded_type_angle 37 15 27 2 # compat. bonded_type_angle 37 15 6 112 bonded_type_angle 37 16 13 119 bonded_type_angle 37 16 25 119 bonded_type_angle 37 16 26 119 bonded_type_angle 37 16 16 2 bonded_type_angle 37 16 17 2 bonded_type_angle 37 16 3 120 bonded_type_angle 37 16 6 112 bonded_type_angle 37 17 3 120 bonded_type_angle 40 22 13 121 bonded_type_angle 40 22 25 121 bonded_type_angle 40 22 26 121 bonded_type_angle 40 22 23 16 bonded_type_angle 40 22 6 112 bonded_type_angle 40 24 23 16 bonded_type_angle 40 24 3 122 bonded_type_angle 32 18 18 123 bonded_type_angle 32 18 16 35 bonded_type_angle 32 18 17 35 bonded_type_angle 32 18 9 124 bonded_type_angle 32 19 7 125 bonded_type_angle 33 18 18 126 bonded_type_angle 33 18 16 36 bonded_type_angle 33 18 17 36 bonded_type_angle 33 18 9 127 bonded_type_angle 33 19 7 128 bonded_type_angle 33 19 32 129 bonded_type_angle 34 18 18 21 bonded_type_angle 34 18 16 37 bonded_type_angle 34 18 110 37 bonded_type_angle 34 18 7 130 bonded_type_angle 34 19 8 131 bonded_type_angle 34 19 34 21 bonded_type_angle 39 14 21 132 bonded_type_angle 39 14 3 133 bonded_type_angle 39 14 5 133 bonded_type_angle 39 20 14 353 bonded_type_angle 39 20 109 353 bonded_type_angle 39 20 20 134 bonded_type_angle 42 13 22 135 bonded_type_angle 42 13 15 136 bonded_type_angle 42 13 16 136 bonded_type_angle 42 13 17 136 bonded_type_angle 42 13 1 137 bonded_type_angle 42 13 31 138 bonded_type_angle 42 13 35 138 bonded_type_angle 42 25 22 135 bonded_type_angle 42 25 15 139 bonded_type_angle 42 25 16 139 bonded_type_angle 42 25 17 139 bonded_type_angle 42 25 3 140 bonded_type_angle 42 13 3 140 bonded_type_angle 42 13 36 141 bonded_type_angle 42 25 36 141 bonded_type_angle 43 26 22 142 bonded_type_angle 43 26 15 142 bonded_type_angle 43 26 16 142 bonded_type_angle 43 26 110 142 bonded_type_angle 43 26 17 142 bonded_type_angle 44 14 14 143 bonded_type_angle 44 25 22 144 bonded_type_angle 44 25 15 144 bonded_type_angle 44 25 16 144 bonded_type_angle 44 25 110 144 bonded_type_angle 44 25 17 144 bonded_type_angle 44 25 44 145 bonded_type_angle 44 16 17 146 bonded_type_angle 44 16 3 147 bonded_type_angle 44 17 3 147 bonded_type_angle 45 14 14 148 bonded_type_angle 108 14 14 352 bonded_type_angle 45 26 16 3 bonded_type_angle 45 26 110 3 bonded_type_angle 45 26 17 3 bonded_type_angle 45 26 43 149 bonded_type_angle 45 15 15 150 bonded_type_angle 45 15 17 150 bonded_type_angle 45 15 3 151 bonded_type_angle 45 16 15 150 bonded_type_angle 45 16 16 150 bonded_type_angle 45 16 17 150 bonded_type_angle 45 16 3 151 bonded_type_angle 45 17 3 151 bonded_type_angle 45 23 23 366 bonded_type_angle 45 23 24 367 bonded_type_angle 46 26 22 152 bonded_type_angle 46 26 15 152 bonded_type_angle 46 26 16 152 bonded_type_angle 46 26 17 152 bonded_type_angle 46 26 43 153 bonded_type_angle 46 16 3 154 bonded_type_angle 46 17 3 154 bonded_type_angle 50 16 15 155 bonded_type_angle 50 16 16 156 bonded_type_angle 50 16 17 156 bonded_type_angle 50 16 3 157 bonded_type_angle 50 17 3 157 bonded_type_angle 51 16 15 155 bonded_type_angle 51 16 16 155 bonded_type_angle 51 16 17 155 bonded_type_angle 51 16 3 158 bonded_type_angle 51 17 3 158 bonded_type_angle 51 51 16 159 bonded_type_angle 51 51 17 159 bonded_type_angle 52 27 15 160 # exp. bonded_type_angle 52 27 17 160 bonded_type_angle 52 27 3 161 bonded_type_angle 76 79 79 30 bonded_type_angle 79 76 79 30 bonded_type_angle 79 79 79 30 bonded_type_angle 53 93 79 92 bonded_type_angle 93 79 61 120 bonded_type_angle 76 79 96 162 bonded_type_angle 93 79 79 2 bonded_type_angle 53 93 53 93 bonded_type_angle 96 79 79 162 bonded_type_angle 76 100 80 163 bonded_type_angle 100 80 79 164 bonded_type_angle 80 79 76 165 bonded_type_angle 100 80 61 166 bonded_type_angle 61 80 79 67 bonded_type_angle 61 79 80 67 bonded_type_angle 83 70 59 167 bonded_type_angle 59 70 67 167 bonded_type_angle 59 67 79 168 bonded_type_angle 70 67 59 167 bonded_type_angle 66 88 73 169 bonded_type_angle 88 73 88 170 bonded_type_angle 73 88 74 171 bonded_type_angle 74 74 88 172 bonded_type_angle 66 74 74 173 bonded_type_angle 74 66 88 174 bonded_type_angle 74 74 83 175 bonded_type_angle 74 74 91 176 bonded_type_angle 73 91 74 177 bonded_type_angle 83 73 91 178 bonded_type_angle 73 83 74 179 bonded_type_angle 83 74 88 180 bonded_type_angle 66 74 91 181 bonded_type_angle 55 73 88 182 bonded_type_angle 88 66 82 183 bonded_type_angle 74 66 82 184 bonded_type_angle 66 82 53 185 bonded_type_angle 53 82 53 186 bonded_type_angle 66 82 103 185 bonded_type_angle 103 82 103 186 bonded_type_angle 91 73 55 187 bonded_type_angle 83 73 55 188 bonded_type_angle 74 83 54 189 bonded_type_angle 73 83 54 190 bonded_type_angle 63 86 66 191 bonded_type_angle 86 66 90 192 bonded_type_angle 66 90 74 193 bonded_type_angle 75 74 90 194 bonded_type_angle 63 75 74 195 bonded_type_angle 75 63 86 196 bonded_type_angle 75 74 84 197 bonded_type_angle 74 75 91 198 bonded_type_angle 73 91 75 199 bonded_type_angle 84 73 91 200 bonded_type_angle 73 84 74 201 bonded_type_angle 84 74 90 202 bonded_type_angle 63 75 91 203 bonded_type_angle 63 86 54 204 bonded_type_angle 66 86 54 205 bonded_type_angle 82 66 86 206 bonded_type_angle 82 66 90 207 bonded_type_angle 86 63 94 208 bonded_type_angle 75 63 94 209 bonded_type_angle 55 73 84 210 bonded_type_angle 73 84 54 211 bonded_type_angle 74 84 54 212 bonded_type_angle 63 83 67 213 bonded_type_angle 83 63 87 214 bonded_type_angle 63 87 66 215 bonded_type_angle 67 66 87 216 bonded_type_angle 66 67 67 217 bonded_type_angle 67 67 83 218 bonded_type_angle 63 83 54 219 bonded_type_angle 67 83 54 220 bonded_type_angle 83 63 95 221 bonded_type_angle 87 63 95 222 bonded_type_angle 87 66 82 223 bonded_type_angle 67 66 82 224 bonded_type_angle 66 67 55 225 bonded_type_angle 67 67 55 226 bonded_type_angle 55 67 83 229 bonded_type_angle 65 84 67 230 bonded_type_angle 84 65 85 232 bonded_type_angle 65 85 63 233 bonded_type_angle 85 63 67 231 bonded_type_angle 63 67 67 234 bonded_type_angle 67 67 84 235 bonded_type_angle 65 84 54 236 bonded_type_angle 67 84 54 240 bonded_type_angle 84 65 94 241 bonded_type_angle 85 65 94 242 bonded_type_angle 65 85 54 237 bonded_type_angle 63 85 54 238 bonded_type_angle 85 63 94 243 bonded_type_angle 67 63 94 244 bonded_type_angle 63 67 55 251 bonded_type_angle 55 67 84 252 bonded_type_angle 72 63 85 114 bonded_type_angle 63 72 67 261 bonded_type_angle 72 67 84 262 bonded_type_angle 72 63 94 245 bonded_type_angle 63 72 81 227 bonded_type_angle 67 72 81 228 bonded_type_angle 72 67 55 253 bonded_type_angle 55 73 89 266 bonded_type_angle 55 73 86 267 bonded_type_angle 89 73 86 269 bonded_type_angle 75 74 89 246 bonded_type_angle 84 74 89 275 bonded_type_angle 63 86 73 278 bonded_type_angle 73 86 54 239 bonded_type_angle 73 89 74 281 bonded_type_angle 65 84 81 286 bonded_type_angle 67 84 81 230 bonded_type_angle 63 83 81 287 bonded_type_angle 67 83 81 288 bonded_type_angle 74 83 81 289 bonded_type_angle 73 83 81 290 bonded_type_angle 74 84 81 289 bonded_type_angle 73 84 81 291 bonded_type_angle 74 84 79 289 bonded_type_angle 73 84 79 291 bonded_type_angle 84 79 81 292 bonded_type_angle 65 84 77 295 bonded_type_angle 67 84 77 296 bonded_type_angle 63 83 77 297 bonded_type_angle 67 83 77 298 bonded_type_angle 74 83 77 299 bonded_type_angle 73 83 77 300 bonded_type_angle 74 84 77 301 bonded_type_angle 73 84 77 302 bonded_type_angle 100 77 83 25 bonded_type_angle 101 77 83 305 bonded_type_angle 79 77 83 306 bonded_type_angle 76 77 83 307 bonded_type_angle 77 77 83 307 bonded_type_angle 78 77 83 307 bonded_type_angle 100 77 84 25 bonded_type_angle 101 77 84 305 bonded_type_angle 79 77 84 306 bonded_type_angle 76 77 84 307 bonded_type_angle 77 77 84 307 bonded_type_angle 78 77 84 307 bonded_type_angle 60 77 83 311 bonded_type_angle 60 77 84 311 bonded_type_angle 100 77 99 25 bonded_type_angle 101 77 99 305 bonded_type_angle 67 64 82 312 bonded_type_angle 67 64 94 313 bonded_type_angle 82 64 94 314 bonded_type_angle 71 66 82 308 bonded_type_angle 71 66 87 254 bonded_type_angle 64 67 70 315 bonded_type_angle 64 67 79 279 bonded_type_angle 66 71 67 247 bonded_type_angle 66 71 81 316 bonded_type_angle 68 67 64 317 bonded_type_angle 69 67 64 320 bonded_type_angle 67 68 67 321 bonded_type_angle 68 67 69 316 bonded_type_angle 67 67 79 322 bonded_type_angle 69 67 79 322 bonded_type_angle 70 67 79 323 bonded_type_angle 67 71 81 318 bonded_type_angle 71 67 55 255 bonded_type_angle 69 67 56 255 bonded_type_angle 68 67 56 256 bonded_type_angle 67 70 55 167 bonded_type_angle 70 67 55 324 bonded_type_angle 67 68 56 136 bonded_type_angle 67 69 56 270 bonded_type_angle 67 69 83 263 bonded_type_angle 67 70 83 325 bonded_type_angle 71 67 83 248 bonded_type_angle 79 67 55 168 bonded_type_angle 56 69 83 271 bonded_type_angle 55 70 83 167 bonded_type_angle 67 79 67 280 bonded_type_angle 67 79 61 328 bonded_type_angle 81 79 61 64 bonded_type_angle 81 76 60 64 bonded_type_angle 61 79 83 329 bonded_type_angle 61 79 99 151 bonded_type_angle 67 81 62 61 bonded_type_angle 72 81 62 61 bonded_type_angle 71 81 62 61 bonded_type_angle 79 81 62 64 bonded_type_angle 62 81 76 61 bonded_type_angle 62 81 83 329 bonded_type_angle 62 81 84 329 bonded_type_angle 61 79 84 329 bonded_type_angle 62 81 96 154 bonded_type_angle 64 82 53 268 bonded_type_angle 64 82 103 268 bonded_type_angle 69 83 69 257 bonded_type_angle 70 83 70 331 bonded_type_angle 69 83 77 293 bonded_type_angle 70 83 77 293 bonded_type_angle 69 83 54 333 bonded_type_angle 70 83 54 334 bonded_type_angle 53 92 53 335 bonded_type_angle 81 96 102 332 bonded_type_angle 102 96 102 336 bonded_type_angle 57 98 102 258 bonded_type_angle 57 98 111 258 bonded_type_angle 58 99 79 57 bonded_type_angle 58 99 81 57 bonded_type_angle 96 102 96 272 bonded_type_angle 96 111 96 272 bonded_type_angle 96 102 98 337 bonded_type_angle 96 111 98 337 bonded_type_angle 108 102 98 337 bonded_type_angle 97 102 98 339 bonded_type_angle 97 111 98 339 bonded_type_angle 98 102 98 340 bonded_type_angle 98 111 98 340 bonded_type_angle 76 79 99 150 bonded_type_angle 62 81 62 73 bonded_type_angle 76 100 77 25 bonded_type_angle 100 77 79 282 bonded_type_angle 77 79 76 273 bonded_type_angle 79 76 76 326 bonded_type_angle 81 76 76 326 bonded_type_angle 76 76 100 249 bonded_type_angle 79 76 100 249 bonded_type_angle 60 76 100 166 bonded_type_angle 60 77 100 166 bonded_type_angle 60 76 76 319 bonded_type_angle 77 79 61 330 bonded_type_angle 79 77 60 330 bonded_type_angle 60 76 79 67 bonded_type_angle 61 79 76 345 bonded_type_angle 61 79 79 345 bonded_type_angle 61 79 61 63 bonded_type_angle 60 76 60 63 bonded_type_angle 76 101 77 309 bonded_type_angle 76 76 101 250 bonded_type_angle 79 76 101 250 bonded_type_angle 101 77 77 164 bonded_type_angle 77 77 76 310 bonded_type_angle 77 77 79 310 bonded_type_angle 77 76 76 327 bonded_type_angle 60 76 101 166 bonded_type_angle 60 77 101 166 bonded_type_angle 77 77 60 330 bonded_type_angle 60 77 60 63 bonded_type_angle 100 77 78 282 bonded_type_angle 77 78 76 273 bonded_type_angle 78 76 76 326 bonded_type_angle 77 78 60 330 bonded_type_angle 78 77 60 330 bonded_type_angle 60 76 78 67 bonded_type_angle 60 78 76 345 bonded_type_angle 60 78 60 63 bonded_type_angle 100 76 80 283 bonded_type_angle 100 76 81 283 bonded_type_angle 76 76 80 304 bonded_type_angle 79 76 80 30 bonded_type_angle 76 80 96 294 bonded_type_angle 76 76 96 162 bonded_type_angle 76 77 96 162 bonded_type_angle 77 77 96 162 bonded_type_angle 79 77 96 162 bonded_type_angle 79 76 96 162 bonded_type_angle 3 16 96 154 bonded_type_angle 3 15 96 154 bonded_type_angle 15 16 96 294 bonded_type_angle 16 96 102 332 bonded_type_angle 15 15 96 162 bonded_type_angle 17 15 96 162 bonded_type_angle 15 96 102 332 bonded_type_angle 14 108 102 350 bonded_type_angle 80 96 102 332 bonded_type_angle 76 96 102 332 bonded_type_angle 77 96 102 332 bonded_type_angle 80 96 111 332 bonded_type_angle 76 96 111 332 bonded_type_angle 77 96 111 332 bonded_type_angle 60 76 80 67 bonded_type_angle 61 80 96 154 bonded_type_angle 58 99 80 57 bonded_type_angle 61 80 61 63 bonded_type_angle 61 80 76 345 bonded_type_angle 60 76 96 154 bonded_type_angle 60 77 96 154 bonded_type_angle 76 80 99 150 bonded_type_angle 80 76 99 283 bonded_type_angle 61 80 99 151 bonded_type_angle 99 76 79 346 bonded_type_angle 99 76 76 150 bonded_type_angle 60 76 99 154 bonded_type_angle 58 99 76 347 bonded_type_angle 101 76 80 283 bonded_type_angle 101 76 81 283 bonded_type_angle 96 76 77 284 bonded_type_angle 99 76 77 284 bonded_type_angle 99 77 77 274 bonded_type_angle 99 77 76 285 bonded_type_angle 99 77 79 285 bonded_type_angle 60 77 99 154 bonded_type_angle 58 99 77 347 bonded_type_angle 60 77 76 345 bonded_type_angle 60 76 77 345 bonded_type_angle 78 76 96 162 bonded_type_angle 99 76 78 346 bonded_type_angle 99 78 77 274 bonded_type_angle 99 78 76 285 bonded_type_angle 60 78 99 154 bonded_type_angle 58 99 78 347 bonded_type_angle 79 96 102 332 bonded_type_angle 96 102 97 341 bonded_type_angle 96 111 97 341 bonded_type_angle 97 102 97 264 bonded_type_angle 97 111 97 264 bonded_type_angle 97 102 108 351 bonded_type_angle 61 79 96 154 bonded_type_angle 99 102 97 341 bonded_type_angle 100 77 32 276 bonded_type_angle 101 77 32 276 bonded_type_angle 79 77 32 277 bonded_type_angle 77 77 32 277 bonded_type_angle 77 32 19 348 bonded_type_angle 77 32 18 349 bonded_type_angle 60 77 32 260 bonded_type_angle 100 77 76 265 bonded_type_angle 77 76 79 30 bonded_type_angle 3 16 112 120 bonded_type_angle 3 17 112 362 bonded_type_angle 16 16 112 361 bonded_type_angle 16 112 16 360 bonded_type_angle 16 112 17 360 bonded_type_angle 17 112 17 360 bonded_type_angle 3 16 113 120 bonded_type_angle 3 17 113 362 bonded_type_angle 16 16 113 363 bonded_type_angle 16 113 16 360 bonded_type_angle 16 113 17 360 bonded_type_angle 17 113 17 360 bonded_type_angle 2 113 16 92 bonded_type_angle 2 113 17 92 bonded_type_angle 2 113 2 112 #################################################### # # # Improper dihedral angle potential assignments # # in CHARMM36 # # # #################################################### # # amino acids # carbonyl groups (C) bonded_type_imptors 13 17 35 42 2 bonded_type_imptors 13 16 35 42 2 bonded_type_imptors 13 15 35 42 2 bonded_type_imptors 13 22 35 42 2 bonded_type_imptors 13 22 31 42 2 bonded_type_imptors 13 17 31 42 2 bonded_type_imptors 13 16 31 42 2 bonded_type_imptors 13 15 31 42 2 bonded_type_imptors 13 17 36 42 2 bonded_type_imptors 13 16 36 42 2 bonded_type_imptors 13 15 36 42 2 bonded_type_imptors 13 22 36 42 2 # guanidinium (C) bonded_type_imptors 13 38 38 38 211 # bonded_type_imptors 38 2 2 13 214 # QUESTION IN CHARMM PARAMETER FILE # sec amide groups (N) bonded_type_imptors 35 13 17 1 3 bonded_type_imptors 35 13 16 1 3 bonded_type_imptors 35 13 15 1 3 bonded_type_imptors 35 13 22 24 3 bonded_type_imptors 31 13 22 24 12 # primary amide groups (both) bonded_type_imptors 25 16 36 42 209 bonded_type_imptors 36 1 25 1 17 bonded_type_imptors 36 25 1 1 17 bonded_type_imptors 36 1 13 1 17 bonded_type_imptors 36 13 1 1 17 bonded_type_imptors 25 17 36 42 209 bonded_type_imptors 25 36 42 3 209 bonded_type_imptors 13 35 42 3 209 bonded_type_imptors 25 36 36 42 219 # carboxylate C-termini (C) bonded_type_imptors 25 17 44 44 29 bonded_type_imptors 25 16 44 44 29 bonded_type_imptors 25 110 44 44 29 bonded_type_imptors 25 15 44 44 29 bonded_type_imptors 25 22 44 44 29 # carboxylic acids (C) bonded_type_imptors 26 17 45 43 230 bonded_type_imptors 26 16 45 43 230 bonded_type_imptors 26 110 45 43 230 bonded_type_imptors 26 15 45 43 230 # histidine bonded_type_imptors 18 32 18 9 30 bonded_type_imptors 18 33 18 9 30 bonded_type_imptors 19 32 33 7 30 bonded_type_imptors 32 19 18 1 32 bonded_type_imptors 34 19 18 1 213 # # nucleotides # # CYT bonded_type_imptors 63 83 87 95 219 bonded_type_imptors 66 67 87 82 220 bonded_type_imptors 82 53 66 53 218 # # ADE bonded_type_imptors 66 88 74 82 224 # # GUA bonded_type_imptors 82 103 66 103 225 bonded_type_imptors 66 90 86 82 224 bonded_type_imptors 63 86 75 94 222 # # URA bonded_type_imptors 65 84 85 94 223 bonded_type_imptors 63 67 85 94 222 # # THY bonded_type_imptors 63 72 85 94 222 bonded_type_imptors 72 67 63 81 221 ################################################ # # # Proper dihedral angle potential assignments # # in CHARMM36 # # # ################################################ # amides bonded_type_torsion 22 13 31 22 15 bonded_type_torsion 24 31 13 22 15 bonded_type_torsion 15 35 13 22 24 bonded_type_torsion 16 13 31 22 15 bonded_type_torsion 16 13 31 24 15 bonded_type_torsion 16 13 35 15 24 bonded_type_torsion 16 13 35 16 24 bonded_type_torsion 16 13 35 17 24 bonded_type_torsion 3 13 35 17 24 bonded_type_torsion 3 13 35 16 24 bonded_type_torsion 3 13 35 15 24 bonded_type_torsion 15 13 31 22 15 bonded_type_torsion 15 13 31 24 15 bonded_type_torsion 15 13 35 15 24 bonded_type_torsion 17 35 13 22 24 bonded_type_torsion 17 35 13 15 24 bonded_type_torsion 1 35 13 22 25 bonded_type_torsion 1 35 13 15 25 bonded_type_torsion 1 35 13 16 25 bonded_type_torsion 1 35 13 17 25 bonded_type_torsion 1 36 25 15 40 bonded_type_torsion 1 36 25 16 40 bonded_type_torsion 1 36 25 17 40 bonded_type_torsion 1 36 25 22 25 bonded_type_torsion 1 36 25 36 121 # urea bonded_type_torsion 1 36 13 15 40 bonded_type_torsion 1 36 13 16 40 bonded_type_torsion 1 36 13 17 40 bonded_type_torsion 1 36 13 22 25 bonded_type_torsion 16 35 13 22 24 bonded_type_torsion 16 35 13 15 24 bonded_type_torsion 17 13 31 22 15 bonded_type_torsion 17 13 31 24 15 bonded_type_torsion 17 13 35 15 24 bonded_type_torsion 17 13 35 16 24 bonded_type_torsion 17 13 35 17 24 bonded_type_torsion 42 13 31 22 15 bonded_type_torsion 42 13 31 24 15 bonded_type_torsion 42 13 35 15 25 bonded_type_torsion 42 13 35 16 25 bonded_type_torsion 42 13 35 17 25 bonded_type_torsion 42 13 35 1 25 bonded_type_torsion 42 25 36 1 40 bonded_type_torsion 42 13 36 1 40 bonded_type_torsion 3 25 36 1 40 bonded_type_torsion 3 13 35 1 40 # alkenes bonded_type_torsion 11 28 28 11 41 bonded_type_torsion 17 28 28 11 41 bonded_type_torsion 11 28 29 12 36 bonded_type_torsion 12 29 28 16 36 bonded_type_torsion 17 28 29 12 36 # 6-ring aromatics, TRP, TYR, PHE, PTR, ... bonded_type_torsion 14 14 14 14 6 bonded_type_torsion 109 14 14 109 6 bonded_type_torsion 14 20 20 14 8 # 6 bonded_type_torsion 109 20 20 109 8 # 6 bonded_type_torsion 14 21 20 14 8 bonded_type_torsion 14 21 20 109 8 bonded_type_torsion 14 39 20 14 8 bonded_type_torsion 14 39 20 109 8 bonded_type_torsion 16 14 14 14 6 bonded_type_torsion 17 14 14 14 6 bonded_type_torsion 20 14 14 14 8 # 6 bonded_type_torsion 20 109 14 14 8 bonded_type_torsion 20 20 14 14 8 # 6 bonded_type_torsion 20 20 109 14 8 bonded_type_torsion 20 20 21 14 23 # 22 bonded_type_torsion 20 20 39 14 260 # 23 bonded_type_torsion 5 14 14 14 55 bonded_type_torsion 5 14 14 109 55 bonded_type_torsion 5 109 14 14 55 bonded_type_torsion 5 14 14 20 8 bonded_type_torsion 5 14 109 20 8 bonded_type_torsion 5 14 14 16 55 bonded_type_torsion 5 14 14 17 55 bonded_type_torsion 5 14 14 5 56 bonded_type_torsion 5 14 109 5 56 bonded_type_torsion 5 14 20 20 8 bonded_type_torsion 5 109 20 20 8 bonded_type_torsion 5 14 20 21 22 # 8 bonded_type_torsion 5 109 20 21 22 # 8 bonded_type_torsion 5 14 21 20 59 # 57 bonded_type_torsion 5 14 21 16 51 bonded_type_torsion 5 14 21 17 51 bonded_type_torsion 5 14 39 20 257 # 57 bonded_type_torsion 5 14 39 1 58 bonded_type_torsion 5 21 14 5 41 bonded_type_torsion 5 21 20 14 59 bonded_type_torsion 5 21 20 20 257 # 59 bonded_type_torsion 39 14 21 20 154 # 22 bonded_type_torsion 39 14 21 16 25 # 50 bonded_type_torsion 39 14 21 17 25 # 50 bonded_type_torsion 39 14 21 3 50 bonded_type_torsion 39 14 21 5 5 bonded_type_torsion 39 20 14 14 8 # 71 bonded_type_torsion 39 20 109 14 8 # 71 bonded_type_torsion 39 20 14 3 22 bonded_type_torsion 39 20 14 5 8 bonded_type_torsion 39 20 109 5 8 bonded_type_torsion 39 20 20 14 22 # 39 bonded_type_torsion 39 20 20 109 22 # 39 bonded_type_torsion 39 20 20 21 260 # 23 bonded_type_torsion 1 39 14 21 259 # 42 bonded_type_torsion 1 39 20 14 148 # 42 bonded_type_torsion 1 39 20 109 148 bonded_type_torsion 1 39 20 20 258 # 42 bonded_type_torsion 1 45 14 14 43 bonded_type_torsion 44 14 14 14 6 bonded_type_torsion 44 14 14 5 55 bonded_type_torsion 45 14 14 14 6 bonded_type_torsion 45 14 14 5 55 bonded_type_torsion 3 14 14 14 50 bonded_type_torsion 3 14 14 20 50 bonded_type_torsion 3 14 14 3 25 bonded_type_torsion 3 14 20 20 8 bonded_type_torsion 3 14 20 21 22 bonded_type_torsion 3 14 21 20 51 bonded_type_torsion 3 14 21 16 51 bonded_type_torsion 3 14 21 17 51 bonded_type_torsion 3 14 39 20 8 bonded_type_torsion 3 14 39 1 41 bonded_type_torsion 3 21 14 20 51 bonded_type_torsion 3 21 14 3 51 bonded_type_torsion 3 21 20 14 8 bonded_type_torsion 3 21 20 20 8 bonded_type_torsion 21 14 39 20 122 # 23 bonded_type_torsion 21 20 14 14 22 # 8 bonded_type_torsion 21 20 20 14 22 # 39 bonded_type_torsion 21 20 109 14 22 bonded_type_torsion 21 20 20 109 22 bonded_type_torsion 16 21 20 14 25 # 8 bonded_type_torsion 16 21 20 109 25 bonded_type_torsion 16 21 20 20 8 bonded_type_torsion 17 21 20 14 25 # 8 bonded_type_torsion 17 21 20 109 25 bonded_type_torsion 17 21 20 20 8 bonded_type_torsion 102 108 14 14 233 bonded_type_torsion 108 14 14 14 6 bonded_type_torsion 108 14 14 5 55 # histidines, other 5-ring heteroaromatics bonded_type_torsion 17 18 32 19 8 bonded_type_torsion 19 32 18 18 20 bonded_type_torsion 19 33 18 18 20 bonded_type_torsion 19 34 18 18 21 bonded_type_torsion 16 18 32 19 8 bonded_type_torsion 16 18 33 19 8 bonded_type_torsion 17 18 33 19 8 bonded_type_torsion 16 18 34 19 25 bonded_type_torsion 110 18 34 19 25 bonded_type_torsion 7 18 18 16 41 bonded_type_torsion 7 18 18 110 41 bonded_type_torsion 7 18 18 17 41 bonded_type_torsion 7 18 18 7 41 bonded_type_torsion 7 18 34 19 25 bonded_type_torsion 7 18 34 1 8 bonded_type_torsion 7 19 32 18 8 bonded_type_torsion 7 19 32 1 41 bonded_type_torsion 7 19 33 18 8 bonded_type_torsion 8 19 34 18 8 bonded_type_torsion 8 19 34 1 60 bonded_type_torsion 9 18 18 16 57 bonded_type_torsion 9 18 18 17 57 bonded_type_torsion 9 18 18 9 57 bonded_type_torsion 9 18 32 19 8 bonded_type_torsion 9 18 32 1 41 bonded_type_torsion 9 18 33 19 8 bonded_type_torsion 32 18 18 16 8 bonded_type_torsion 32 18 18 17 8 bonded_type_torsion 32 18 18 9 8 bonded_type_torsion 32 19 33 18 20 bonded_type_torsion 33 18 18 16 8 bonded_type_torsion 33 18 18 17 8 bonded_type_torsion 33 18 18 9 8 bonded_type_torsion 33 18 18 32 20 bonded_type_torsion 33 19 32 18 20 bonded_type_torsion 33 19 32 1 41 bonded_type_torsion 34 18 18 16 25 bonded_type_torsion 34 18 18 110 25 bonded_type_torsion 34 18 18 17 25 bonded_type_torsion 34 18 18 7 25 bonded_type_torsion 34 18 18 34 21 bonded_type_torsion 34 19 34 18 21 bonded_type_torsion 34 19 34 1 40 bonded_type_torsion 1 32 18 18 41 bonded_type_torsion 1 32 18 16 41 bonded_type_torsion 1 32 18 17 41 bonded_type_torsion 1 34 18 18 40 bonded_type_torsion 1 34 18 16 8 bonded_type_torsion 1 34 18 110 8 bonded_type_torsion 1 34 18 17 8 # guanidinium bonded_type_torsion 16 38 13 38 80 bonded_type_torsion 38 13 38 2 80 # esters and carboxylic acids bonded_type_torsion 43 26 46 16 73 bonded_type_torsion 43 26 46 17 73 bonded_type_torsion 1 45 26 43 81 bonded_type_torsion 1 45 26 15 81 bonded_type_torsion 1 45 26 16 81 bonded_type_torsion 1 45 26 110 81 bonded_type_torsion 1 45 26 17 81 # proline/hydroxyproline-specific # CA-CB :) bonded_type_torsion 31 22 23 23 85 bonded_type_torsion 31 22 23 3 85 bonded_type_torsion 6 22 23 23 85 bonded_type_torsion 6 22 23 3 85 bonded_type_torsion 13 22 23 23 85 bonded_type_torsion 13 22 23 3 85 bonded_type_torsion 25 22 23 3 85 bonded_type_torsion 25 22 23 23 85 bonded_type_torsion 40 22 23 3 85 bonded_type_torsion 40 22 23 23 85 # N-CD :) bonded_type_torsion 23 24 31 22 18 bonded_type_torsion 3 24 31 22 18 bonded_type_torsion 23 24 40 22 19 bonded_type_torsion 3 24 40 22 19 bonded_type_torsion 2 40 24 23 19 bonded_type_torsion 2 40 24 3 19 # CG-CD :) bonded_type_torsion 31 24 23 23 85 bonded_type_torsion 31 24 23 45 297 bonded_type_torsion 31 24 23 3 85 bonded_type_torsion 23 23 24 3 85 bonded_type_torsion 3 23 24 3 85 bonded_type_torsion 3 24 23 45 85 bonded_type_torsion 40 24 23 3 85 bonded_type_torsion 40 24 23 23 85 # CB-CG :) bonded_type_torsion 22 23 23 24 54 bonded_type_torsion 22 23 23 3 54 bonded_type_torsion 22 23 23 45 300 bonded_type_torsion 24 23 23 3 54 bonded_type_torsion 3 23 23 3 54 bonded_type_torsion 3 23 23 45 54 # CG-OE :) bonded_type_torsion 23 23 45 1 299 bonded_type_torsion 24 23 45 1 298 bonded_type_torsion 3 23 45 1 85 # CA-N :) bonded_type_torsion 24 40 22 13 19 bonded_type_torsion 24 40 22 25 19 bonded_type_torsion 24 40 22 26 19 bonded_type_torsion 24 40 22 23 19 bonded_type_torsion 6 22 40 24 19 bonded_type_torsion 2 40 22 13 19 bonded_type_torsion 2 40 22 25 19 bonded_type_torsion 2 40 22 26 19 bonded_type_torsion 2 40 22 23 19 bonded_type_torsion 2 40 22 6 19 bonded_type_torsion 24 31 22 13 18 bonded_type_torsion 24 31 22 25 18 bonded_type_torsion 24 31 22 23 18 bonded_type_torsion 23 22 31 13 5 bonded_type_torsion 25 22 31 13 5 bonded_type_torsion 26 22 31 13 9 bonded_type_torsion 13 31 22 13 5 bonded_type_torsion 6 22 31 13 5 bonded_type_torsion 6 22 31 24 18 # sugars (mostly for ribose and d-ribose) # C4*-C3* :) bonded_type_torsion 96 76 76 100 179 bonded_type_torsion 99 76 76 100 179 bonded_type_torsion 79 76 76 100 292 # 1 bonded_type_torsion 60 76 76 60 89 bonded_type_torsion 60 76 76 80 89 bonded_type_torsion 60 76 76 96 89 bonded_type_torsion 60 76 76 99 89 bonded_type_torsion 60 76 76 77 89 bonded_type_torsion 60 76 76 100 202 bonded_type_torsion 60 76 76 101 202 bonded_type_torsion 99 76 76 101 163 bonded_type_torsion 96 76 76 101 163 bonded_type_torsion 79 76 76 80 182 bonded_type_torsion 77 76 76 80 194 bonded_type_torsion 96 76 76 80 185 bonded_type_torsion 99 76 76 80 185 bonded_type_torsion 78 76 76 80 182 bonded_type_torsion 77 76 76 76 164 # 163 bonded_type_torsion 76 76 76 100 178 # 176 bonded_type_torsion 96 76 76 76 177 # 100 bonded_type_torsion 99 76 76 76 177 # 100 bonded_type_torsion 60 76 76 76 89 bonded_type_torsion 76 76 76 80 182 # O4*-C1* :) bonded_type_torsion 76 77 100 76 104 bonded_type_torsion 79 77 100 76 104 bonded_type_torsion 78 77 100 76 104 # C2*-C1* in RNA :) bonded_type_torsion 60 77 77 76 89 bonded_type_torsion 60 77 77 79 89 bonded_type_torsion 60 77 77 101 89 bonded_type_torsion 96 77 77 101 163 # 164 bonded_type_torsion 76 77 77 101 164 bonded_type_torsion 79 77 77 101 164 bonded_type_torsion 60 77 77 96 89 # C2*-C1* in DNA :) bonded_type_torsion 60 77 79 76 89 bonded_type_torsion 61 79 77 100 89 bonded_type_torsion 60 77 79 61 89 bonded_type_torsion 76 79 77 100 178 bonded_type_torsion 61 79 77 96 89 bonded_type_torsion 96 77 79 76 100 bonded_type_torsion 61 79 77 101 89 bonded_type_torsion 61 79 77 77 89 # C3*-C2* in RNA :) bonded_type_torsion 60 76 77 77 89 bonded_type_torsion 60 76 77 99 89 bonded_type_torsion 99 76 77 60 202 bonded_type_torsion 96 76 77 60 89 bonded_type_torsion 60 77 76 76 89 bonded_type_torsion 96 76 77 77 176 bonded_type_torsion 99 76 77 77 176 bonded_type_torsion 60 76 77 60 89 bonded_type_torsion 96 77 76 76 177 # 100 bonded_type_torsion 76 76 77 100 178 # 176 bonded_type_torsion 79 76 77 100 176 bonded_type_torsion 100 77 76 99 174 bonded_type_torsion 60 76 77 100 89 bonded_type_torsion 60 76 77 96 89 bonded_type_torsion 60 76 77 83 89 bonded_type_torsion 96 76 77 100 179 bonded_type_torsion 60 77 76 79 89 # C3*-C2* in DNA :) bonded_type_torsion 61 79 76 76 89 bonded_type_torsion 60 76 79 61 89 bonded_type_torsion 60 76 79 77 89 bonded_type_torsion 96 76 79 61 89 bonded_type_torsion 77 79 76 76 164 bonded_type_torsion 99 76 79 61 202 bonded_type_torsion 96 76 79 77 177 bonded_type_torsion 99 76 79 77 177 bonded_type_torsion 80 79 76 60 89 # 96 bonded_type_torsion 80 79 76 99 100 bonded_type_torsion 80 79 76 96 100 bonded_type_torsion 76 76 79 80 109 # C4*-O4* :) bonded_type_torsion 60 76 100 77 89 bonded_type_torsion 60 76 101 77 89 bonded_type_torsion 77 100 76 80 5 bonded_type_torsion 77 101 76 80 200 bonded_type_torsion 76 76 100 77 104 bonded_type_torsion 77 101 76 79 200 bonded_type_torsion 77 101 76 81 200 bonded_type_torsion 80 76 100 80 97 bonded_type_torsion 60 76 100 80 89 # 96 bonded_type_torsion 80 100 76 76 11 # 111 # nucleotide bases and other N-heteroaromatic, multicyclic compounds bonded_type_torsion 77 83 74 88 121 bonded_type_torsion 84 65 85 63 121 bonded_type_torsion 65 85 63 67 121 bonded_type_torsion 85 63 67 67 121 bonded_type_torsion 63 67 67 84 122 bonded_type_torsion 67 67 84 65 121 bonded_type_torsion 67 84 65 85 121 bonded_type_torsion 55 67 67 55 123 bonded_type_torsion 55 67 63 94 122 bonded_type_torsion 54 84 67 55 121 bonded_type_torsion 84 65 85 54 125 bonded_type_torsion 67 63 85 54 125 bonded_type_torsion 67 67 84 54 126 bonded_type_torsion 85 65 84 54 126 bonded_type_torsion 65 84 67 72 127 bonded_type_torsion 63 72 67 84 123 bonded_type_torsion 84 63 72 81 128 bonded_type_torsion 84 67 72 81 128 bonded_type_torsion 67 72 63 85 127 bonded_type_torsion 85 63 72 81 132 bonded_type_torsion 72 63 85 54 130 bonded_type_torsion 67 83 63 87 131 bonded_type_torsion 83 63 87 66 131 bonded_type_torsion 63 87 66 67 122 bonded_type_torsion 87 66 67 67 131 bonded_type_torsion 66 67 67 83 122 bonded_type_torsion 67 67 83 63 131 bonded_type_torsion 87 66 82 53 132 bonded_type_torsion 67 66 82 53 132 bonded_type_torsion 87 66 82 103 132 bonded_type_torsion 67 66 82 103 132 bonded_type_torsion 67 72 63 94 132 bonded_type_torsion 63 72 67 55 132 bonded_type_torsion 81 72 67 55 132 bonded_type_torsion 81 72 63 94 132 bonded_type_torsion 82 66 87 63 133 bonded_type_torsion 82 66 67 67 133 bonded_type_torsion 82 66 67 55 133 bonded_type_torsion 95 63 83 54 123 bonded_type_torsion 95 63 87 66 126 bonded_type_torsion 95 63 83 67 126 bonded_type_torsion 87 66 67 55 134 bonded_type_torsion 83 67 67 55 134 bonded_type_torsion 66 67 67 55 135 bonded_type_torsion 63 83 67 55 135 bonded_type_torsion 83 67 71 66 123 bonded_type_torsion 67 71 66 87 132 bonded_type_torsion 71 66 87 63 136 bonded_type_torsion 71 67 83 63 132 bonded_type_torsion 71 66 82 53 133 bonded_type_torsion 71 66 82 103 133 bonded_type_torsion 83 67 71 81 137 bonded_type_torsion 66 71 67 55 137 bonded_type_torsion 81 71 67 55 137 bonded_type_torsion 66 88 73 88 127 bonded_type_torsion 88 73 88 74 133 bonded_type_torsion 73 88 74 74 127 bonded_type_torsion 88 74 74 66 133 bonded_type_torsion 74 74 66 88 127 bonded_type_torsion 74 66 88 73 136 bonded_type_torsion 74 74 91 73 122 bonded_type_torsion 74 91 73 83 140 bonded_type_torsion 91 73 83 74 122 bonded_type_torsion 73 83 74 74 122 bonded_type_torsion 83 74 74 91 140 bonded_type_torsion 66 88 73 55 141 bonded_type_torsion 74 88 73 55 141 bonded_type_torsion 74 91 73 55 142 bonded_type_torsion 74 83 73 55 142 bonded_type_torsion 74 74 83 54 143 bonded_type_torsion 91 73 83 54 143 bonded_type_torsion 73 88 66 82 137 bonded_type_torsion 74 74 66 82 137 bonded_type_torsion 65 84 67 55 41 bonded_type_torsion 84 67 67 55 41 bonded_type_torsion 67 67 63 94 41 bonded_type_torsion 85 63 67 55 41 bonded_type_torsion 63 67 67 55 41 bonded_type_torsion 77 84 67 67 41 bonded_type_torsion 67 84 65 94 150 bonded_type_torsion 94 65 85 63 150 bonded_type_torsion 65 85 63 94 150 bonded_type_torsion 65 85 63 72 150 bonded_type_torsion 80 84 67 67 144 bonded_type_torsion 74 66 82 53 144 bonded_type_torsion 88 66 82 53 144 bonded_type_torsion 74 66 82 103 144 bonded_type_torsion 88 66 82 103 144 bonded_type_torsion 88 74 74 91 145 bonded_type_torsion 66 74 74 83 145 bonded_type_torsion 88 66 74 91 133 bonded_type_torsion 66 74 91 73 133 bonded_type_torsion 73 88 74 83 133 bonded_type_torsion 88 74 83 73 133 bonded_type_torsion 63 86 66 90 148 bonded_type_torsion 86 66 90 74 133 bonded_type_torsion 66 90 74 75 148 bonded_type_torsion 90 74 75 63 133 bonded_type_torsion 74 75 63 86 148 bonded_type_torsion 75 63 86 66 148 bonded_type_torsion 74 75 91 73 122 bonded_type_torsion 75 91 73 84 147 bonded_type_torsion 91 73 84 74 122 bonded_type_torsion 73 84 74 75 122 bonded_type_torsion 84 74 75 91 136 bonded_type_torsion 94 63 75 74 140 bonded_type_torsion 94 63 86 66 140 bonded_type_torsion 82 66 86 63 137 bonded_type_torsion 82 66 90 74 137 bonded_type_torsion 86 66 82 53 143 bonded_type_torsion 90 66 82 53 143 bonded_type_torsion 86 66 82 103 143 bonded_type_torsion 90 66 82 103 143 bonded_type_torsion 54 86 63 75 146 bonded_type_torsion 54 86 66 90 146 bonded_type_torsion 55 73 91 75 128 bonded_type_torsion 55 73 84 74 128 bonded_type_torsion 54 84 74 75 143 bonded_type_torsion 54 84 74 90 143 bonded_type_torsion 54 84 73 91 143 bonded_type_torsion 90 74 75 91 136 bonded_type_torsion 63 75 74 83 136 bonded_type_torsion 86 63 75 91 133 bonded_type_torsion 63 75 91 73 133 bonded_type_torsion 66 90 74 84 133 bonded_type_torsion 90 74 84 73 133 bonded_type_torsion 74 74 89 73 122 bonded_type_torsion 86 73 89 74 122 bonded_type_torsion 89 73 86 54 121 bonded_type_torsion 89 73 86 63 121 bonded_type_torsion 55 73 86 54 121 bonded_type_torsion 55 73 86 63 121 bonded_type_torsion 67 83 69 56 145 bonded_type_torsion 54 83 69 56 123 bonded_type_torsion 56 67 68 56 133 bonded_type_torsion 56 67 69 56 132 bonded_type_torsion 83 69 67 56 145 bonded_type_torsion 67 64 67 56 145 bonded_type_torsion 64 67 69 56 132 bonded_type_torsion 64 67 68 56 154 bonded_type_torsion 67 64 67 55 145 bonded_type_torsion 64 67 67 55 132 bonded_type_torsion 68 67 64 94 155 bonded_type_torsion 69 67 64 94 155 bonded_type_torsion 68 67 64 82 156 bonded_type_torsion 69 67 64 82 158 bonded_type_torsion 67 68 67 64 123 bonded_type_torsion 67 68 67 69 122 bonded_type_torsion 83 69 67 68 145 bonded_type_torsion 69 83 69 67 137 bonded_type_torsion 79 67 64 94 161 bonded_type_torsion 79 67 64 82 165 bonded_type_torsion 70 67 64 94 166 bonded_type_torsion 70 67 64 82 167 bonded_type_torsion 54 83 70 55 137 bonded_type_torsion 67 83 70 55 145 bonded_type_torsion 83 70 67 55 145 bonded_type_torsion 79 67 70 83 169 bonded_type_torsion 70 67 79 67 170 bonded_type_torsion 64 67 70 83 160 bonded_type_torsion 70 83 70 67 169 bonded_type_torsion 77 83 73 55 186 bonded_type_torsion 77 83 74 74 187 bonded_type_torsion 77 83 73 91 187 bonded_type_torsion 77 83 73 88 187 bonded_type_torsion 77 83 67 55 186 bonded_type_torsion 77 83 63 95 187 bonded_type_torsion 77 83 63 87 187 bonded_type_torsion 77 83 67 67 187 bonded_type_torsion 77 84 67 55 186 bonded_type_torsion 77 84 65 94 187 bonded_type_torsion 77 84 65 85 187 bonded_type_torsion 77 84 67 72 187 bonded_type_torsion 77 84 73 55 186 bonded_type_torsion 77 84 73 91 187 bonded_type_torsion 77 84 74 75 187 bonded_type_torsion 77 84 74 90 187 ################################################### # # # The list below encompasses the bonded types # # used here with a short description. # # Note that this list is not processed in any # # way by the software. # # # ################################################### # bonded_type 0 ! dummy # bonded_type 1 ! H polar H # bonded_type 2 ! HC N-ter H # bonded_type 3 ! HA nonpolar H # bonded_type 4 ! HT TIPS3P WATER HYDROGEN # bonded_type 5 ! HP aromatic H # bonded_type 6 ! HB backbone H # bonded_type 7 ! HR1 his he1, (+) his HG,HD2 # bonded_type 8 ! HR2 (+) his HE1 # bonded_type 9 ! HR3 neutral his HG, HD2 # bonded_type 10 ! HS thiol hydrogen # bonded_type 11 ! HE1 for alkene; RHC=CR # bonded_type 12 ! HE2 for alkene; H2C=CR # bonded_type 13 ! C carbonyl C, peptide backbone # bonded_type 14 ! CA aromatic C # bonded_type 15 ! CT1 aliphatic sp3 C for CH # bonded_type 16 ! CT2 aliphatic sp3 C for CH2 # bonded_type 17 ! CT3 aliphatic sp3 C for CH3 # bonded_type 18 ! CPH1 his CG and CD2 carbons # bonded_type 19 ! CPH2 his CE1 carbon # bonded_type 20 ! CPT trp C between rings # bonded_type 21 ! CY TRP C in pyrrole ring # bonded_type 22 ! CP1 tetrahedral C (proline CA) # bonded_type 23 ! CP2 tetrahedral C (proline CB/CG) # bonded_type 24 ! CP3 tetrahedral C (proline CD) # bonded_type 25 ! CC carbonyl C, asn,asp,gln,glu,cter,ct2 # bonded_type 26 ! CD carbonyl C, pres aspp,glup,ct1 # bonded_type 27 ! CS thiolate carbon # bonded_type 28 ! CE1 for alkene; RHC=CR # bonded_type 29 ! CE2 for alkene; H2C=CR # bonded_type 30 ! CST CO2 carbon # bonded_type 31 ! N proline N # bonded_type 32 ! NR1 neutral his protonated ring nitrogen # bonded_type 33 ! NR2 neutral his unprotonated ring nitrogen # bonded_type 34 ! NR3 charged his ring nitrogen # bonded_type 35 ! NH1 peptide nitrogen # bonded_type 36 ! NH2 amide nitrogen # bonded_type 37 ! NH3 ammonium nitrogen # bonded_type 38 ! NC2 guanidinium nitroogen # bonded_type 39 ! NY TRP N in pyrrole ring # bonded_type 40 ! NP Proline ring NH2+ (N-terminal) # bonded_type 41 ! NPH heme pyrrole N # bonded_type 42 ! O carbonyl oxygen # bonded_type 43 ! OB carbonyl oxygen in acetic acid # bonded_type 44 ! OC carboxylate oxygen # bonded_type 45 ! OH1 hydroxyl oxygen # bonded_type 46 ! OS ester oxygen # bonded_type 47 ! OT TIPS3P WATER OXYGEN # bonded_type 48 ! OM heme CO/O2 oxygen # bonded_type 49 ! OST CO2 oxygen # bonded_type 50 ! S sulphur # bonded_type 51 ! SM sulfur C-S-S-C type # bonded_type 52 ! SS thiolate sulfur # bonded_type 53 ! HN1 Nucleic acid amine proton # bonded_type 54 ! HN2 Nucleic acid ring nitrogen proton # bonded_type 55 ! HN3 Nucleic acid aromatic carbon proton # bonded_type 56 ! HN3B NAD+ aromatic hydrogen # bonded_type 57 ! HN4 Nucleic acid phosphate hydroxyl proton # bonded_type 58 ! HN5 Nucleic acid ribose hydroxyl proton # bonded_type 59 ! HN6 Nicotinamide aliphatic proton # bonded_type 60 ! HN7 Nucleic acid proton (equivalent to protein HA) # bonded_type 61 ! HN8 Bound to CN8 in nucleic acids/model compounds # bonded_type 62 ! HN9 Bound to CN9 in nucleic acids/model compounds # bonded_type 63 ! CN1 Nucleic acid carbonyl carbon # bonded_type 64 ! CN1A NAD+/NADH amide carbonyl carbon # bonded_type 65 ! CN1T Nucleic acid carbonyl carbon (T/U C2) # bonded_type 66 ! CN2 Nucleic acid aromatic carbon to amide # bonded_type 67 ! CN3 Nucleic acid aromatic carbon # bonded_type 68 ! CN3A NAD+ aromatic carbon # bonded_type 69 ! CN3B NAD+ aromatic carbon # bonded_type 70 ! CN3C NADH aromatic carbon # bonded_type 71 ! CN3D Nucleic acid aromatic carbon for 5MC # bonded_type 72 ! CN3T Nucleic acid aromatic carbon, Thy C5 # bonded_type 73 ! CN4 Nucleic acid purine C8 and ADE C2 # bonded_type 74 ! CN5 Nucleic acid purine C4 and C5 # bonded_type 75 ! CN5G Nucleic acid guanine C5 # bonded_type 76 ! CN7 Nucleic acid carbon (equivalent to protein CT1) # bonded_type 77 ! CN7B Nucleic acid aliphatic carbon for C1' # bonded_type 78 ! CN7C C2' in arabinose # bonded_type 79 ! CN8 Nucleic acid carbon (equivalent to protein CT2) # bonded_type 80 ! CN8B Nucleic acid carbon (equivalent to protein CT2) # bonded_type 81 ! CN9 Nucleic acid carbon (equivalent to protein CT3) # bonded_type 82 ! NN1 Nucleic acid amide nitrogen # bonded_type 83 ! NN2 Nucleic acid protonated ring nitrogen # bonded_type 84 ! NN2B From NN2, for N9 in GUA different from ADE # bonded_type 85 ! NN2U Nucleic acid protonated ring nitrogen, ura N3 # bonded_type 86 ! NN2G Nucleic acid protonated ring nitrogen, gua N1 # bonded_type 87 ! NN3 Nucleic acid unprotonated ring nitrogen # bonded_type 88 ! NN3A Nucleic acid unprotonated ring nitrogen, ade N1 and N3 # bonded_type 89 ! NN3I Nucleic acid unprotonated ring nitrogen, inosine N3 # bonded_type 90 ! NN3G Nucleic acid unprotonated ring nitrogen, gua N3 # bonded_type 91 ! NN4 Nucleic acid purine N7 # bonded_type 92 ! NN5 Nucleic acid sp2 amine nitrogen # bonded_type 93 ! NN6 Nucleic acid sp3 amine nitrogen (equiv to protein nh3) # bonded_type 94 ! ON1 Nucleic acid carbonyl oxygen # bonded_type 95 ! ON1C Nucleic acid carbonyl oxygen, cyt O2 # bonded_type 96 ! ON2 Nucleic acid phosphate ester oxygen # bonded_type 97 ! ON3 Nucleic acid =O in phosphate # bonded_type 98 ! ON4 Nucleic acid phosphate hydroxyl oxygen # bonded_type 99 ! ON5 Nucleic acid ribose hydroxyl oxygen # bonded_type 100 ! ON6 Nucleic acid deoxyribose ring oxygen # bonded_type 101 ! ON6B Nucleic acid ribose ring oxygen # bonded_type 102 ! P phosphorus # bonded_type 103 ! HN2 in GUA # bonded_type 104 ! CL in perchlorate # bonded_type 105 ! O in perchlorate # bonded_type 106 ! N in nitrate # bonded_type 107 ! O in nitrate # bonded_type 108 ! ON2B Aryl phosphate ester oxygen # bonded_type 109 ! Special bonded type CAI (indol aromatic carbon adjacent to CPT1) # bonded_type 110 ! Special bonded type CTA2 (polypeptide side chains GLU, ASP, HSP) # bonded_type 111 ! P2 Phosphorous in phosphate diester linkages in DNA only # bonded_type 112 ! quat. ammonium nitrogen (partially from CGENFF NG3P0) # bonded_type 113 ! sec. ammonium nitrogen but not N-terminal PRO (partially from CGENFF NG3P2)