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STaGE_opls_tomoltemplate_opls.txt
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STaGE_opls_tomoltemplate_opls.txt
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* This file attempts to match the opls atom types defined
* for GROMACS in the STaGE program (opls.par) to those
* defined in oplsaa.lt for use with moltemplate. The latter
* are described as being taken from Tinker.
*
* including the AA atom types.
*
* ELE | SYMBOL | GROMACS | RULE | moltemplate | charge | description
C | CT | opls_135 | [$([CH3D4][C])] | @atom:80 | -0.18 | "Alkane CH3-"
C | CT | opls_136 | [$([CH2D4]([C])[C])] | @atom:81 | -0.12 | "Alkane -CH2-"
C | CT | opls_137 | [$([CH1D4]([C])([C])[C])] | @atom:82 | -0.06 | "Alkane >CH-"
C | CT | opls_138 | [CH4D4] | @atom:83 | -0.24 | "Methane CH4"
C | CT | opls_139 | [$([CH0D4]([C])([C])([C])[C])] | @atom:84 | 0.0 | "Alkane >C<"
H | HC | opls_140 | [$([#1][CH4])] | @atom:85 | 0.06 | "Alkane H-C"
H | HC | opls_140 | [$([#1][CD4;!$([C][CD2,O,N][#6]);!$([C][F,Cl,Br,I])])] | @atom:85 | 0.06 | "Alkane H-C"
C | CM | opls_141 | [$([CH0D3]([#6])([#6])=[#6])] | @atom:86 | 0.0 | "Alkene R2-C="
C | CM | opls_142 | [$([CH1D3]([#6])=[#6])] | @atom:87 | -0.115 | "Alkene RH-C="
C | CM | opls_143 | [$([CH2D3]=[#6])] | @atom:88 | -0.23 | "Alkene H2-C="
H | HC | opls_144 | [$([#1][CD3])] | @atom:89 | 0.115 | "Alkene H-C="
C | CA | opls_145 | [$([c]([c])[c])] | @atom:90 | -0.115 | "Aromatic C"
C | C! | opls_145B | [$([c](c)(c)-[c](c)c)] | @atom:460 | 0.0 | "Biphenyl C1"
H | HA | opls_146 | [$([#1][c]([c])[c])] | @atom:91 | 0.115 | "Aromatic H-C"
C | CA | opls_147 | [$([c](c)(c)(c))] | @atom:92 | 0.0 | "Naphthalene Fusion C"
C | CT | opls_148 | [$([CH3][c])] | @atom:93 | -0.065 | "Ethyl Benzene CH3-"
C | CT | opls_149 | [$([CH2D4][c])] | @atom:94 | -0.005 | "Ethyl Benzene -CH2-"
C | C= | opls_150 | [$([CH1](=C)-[CH1]=C)] | @atom:95 | -0.115 | "Diene =CH-CH="
* In opls.par, all halides are treated with same atom types, not so in oplsaa
*Cl | Cl | opls_151 | [$([Cl][CD4])] | @atom:800 | -0.2 | "Alkyl Chloride C-Cl"
*C | CT | opls_152 | [$([#6D4][F,Cl,Br,I])] | @atom:801 | -0.006 | "Alkyl Chloride RCH2-Cl"
*C | CT | opls_152 | [$([CD4]([#6,H])([#6,H])([F,Cl,Br,I])[F,Cl,Br,I])] | @atom:801 | -0.006 | "Alkyl Chloride RCH2-Cl"
*H | HC | opls_153 | [$([#1][#6D4][F,Cl,Br,I])] | @atom:802 | 0.103 | "Alkyl Chloride H-C-Cl"
*H | HC | opls_153 | [$([#1][CD4]([#6,H])([#6,H])([F,Cl,Br,I])[F,Cl,Br,I])] | @atom:802 | 0.103 | "Alkyl Chloride H-C-Cl"
* modified versions
Cl | Cl | opls_151 | [$([Cl][CD4])] | @atom:800 | -0.2 | "Alkyl Chloride C-Cl"
C | CT | opls_152 | [$([CH2D4]([!Cl])[Cl])] | @atom:801 | -0.006 | "Alkyl Chloride RCH2-Cl"
H | HC | opls_153 | [$([#1][#6D4][Cl])] | @atom:802 | 0.103 | "Alkyl Chloride H-C-Cl"
C | CT | opls_xxx | [$([CH1D4]([!Cl])([!Cl])[Cl])] | @atom:803 | 0.097 | "Alkyl Chloride R2CH-Cl"
C | CT | opls_xxx | [$([CH0D4]([!Cl])([!Cl])([!Cl])[Cl])] | @atom:804 | 0.200 | "Alkyl Chloride R3C-Cl"
Br | Br | opls_xxx | [$([Br][CD4])] | @atom:805 | -0.2 | "Alkyl Bromide C-Cl"
C | CT | opls_xxx | [$([CH2D4]([!Br])[Br])] | @atom:806 | -0.006 | "Alkyl Bromide RCH2-Br"
H | HC | opls_xxx | [$([#1][#6D4][Br])] | @atom:807 | 0.103 | "Alkyl Bromide H-C-Br"
C | CT | opls_xxx | [$([CH1D4]([!Br])([!Br])[Br])] | @atom:808 | 0.097 | "Alkyl Bromide R2CH-Br"
C | CT | opls_xxx | [$([CH0D4]([!Br])([!Br])([!Br])[Br])] | @atom:809 | 0.200 | "Alkyl Bromide R3C-Br"
I | I | opls_xxx | [$([I][CD4])] | @atom:838 | -0.13 | "Alkyl Iodide C-I"
C | CT | opls_xxx | [$([CH2D4]([!I])[I])] | @atom:835 | -0.07 | "Alkyl Iodide RCH2-I"
H | HC | opls_xxx | [$([#1][#6D4][I])] | @atom:839 | 0.1 | "Alkyl Iodide H-C-I"
C | CT | opls_xxx | [$([CH1D4]([!I])([!I])[I])] | @atom:836 | 0.03 | "Alkyl Iodide R2CH-I"
C | CT | opls_xxx | [$([CH0D4]([!I])([!I])([!I])[I])] | @atom:837 | 0.13 | "Alkyl Bromide R3C-I"
* end modified versions
O | OH | opls_154 | [$([OH][#6])] | @atom:96 | -0.683 | "Alcohol -OH"
H | HO | opls_155 | [$([#1][O][#6])] | @atom:97 | 0.418 | "Alcohol -OH"
H | HC | opls_156 | [$([#1][CH3][OH])] | @atom:98 | 0.04 | "Methanol CH3-"
C | CT | opls_157 | [$([C;H2,H3][OH])] | @atom:99 | 0.145 | "Alcohol CH3OH & RCH2OH"
C | CT | opls_158 | [$([CH1][OH])] | @atom:100 | 0.205 | "Alcohol R2CHOH"
C | CT | opls_159 | [$([CH0][OH])] | @atom:101 | 0.265 | "Alcohol R3COH"
C | CT | opls_160 | [$([CH2]([OH])[C](F)(F)(F))] | @atom:102 | 0.1263 | "Trifluoroethanol -CH2-"
C | CT | opls_161 | [$([C](F)(F)(F)[CH2]([OH]))] | @atom:103 | 0.5323 | "Trifluoroethanol CF3-"
O | OH | opls_162 | [$([OH][CH2][C](F)(F)(F))] | @atom:104 | -0.6351 | "Trifluoroethanol -OH"
H | HO | opls_163 | [$([#1][O][CH2][C](F)(F)(F))] | @atom:105 | 0.4286 | "Trifluoroethanol -OH"
F | F | opls_164 | [$([F][C](F)(F)[CH2][OH])] | @atom:106 | -0.2057 | "Trifluoroethanol F"
H | HC | opls_165 | [$([#1][CH2]([OH])[C](F)(F)(F))] | @atom:107 | 0.0825 | "Trifluoroethanol -CH2-"
C | CA | opls_166 | [$([c]([OH]))] | @atom:108 | 0.15 | "Phenol C-OH"
O | OH | opls_167 | [$([OH][c])] | @atom:109 | -0.585 | "Phenol -OH"
H | HO | opls_168 | [$([#1][O][c])] | @atom:110 | 0.435 | "Phenol -OH"
O | OH | opls_169 | [$([OH][C][C][OH])] | @atom:111 | -0.7 | "Diol -OH"
H | HO | opls_170 | [$([#1][O][C][C][OH])] | @atom:112 | 0.435 | "Diol -OH"
O | OH | opls_171 | [$([OH][#6][#6]([OH])[#6][OH])] | @atom:113 | -0.73 | "Triol -OH"
O | OH | opls_171 | [$([OH][#6]([#6][OH])[#6][OH])] | @atom:113 | -0.73 | "Triol -OH"
H | HO | opls_172 | [$([#1][O][#6][#6]([OH])[#6][OH])] | @atom:114 | 0.465 | "Triol -OH"
H | HO | opls_172 | [$([#1][O][#6]([#6][OH])[#6][OH])] | @atom:114 | 0.465 | "Triol -OH"
C | CT | opls_173 | [$([CH2D4]([OH])[#6]([OH])[#6][OH])] | @atom:115 | 0.145 | "Diol & Triol -CH2OH"
C | CT | opls_173 | [$([CH2D4]([OH])[#6][OH])] | @atom:115 | 0.145 | "Diol & Triol -CH2OH" [--AHS]
C | CT | opls_174 | [$([CH1D4]([OH])[#6]([OH])[#6][OH])] | @atom:116 | 0.205 | "Diol & Triol -CHROH"
C | CT | opls_174 | [$([CH1D4]([OH])([#6][OH])[#6][OH])] | @atom:116 | 0.205 | "Diol & Triol -CHROH"
C | CT | opls_174 | [$([CH1D4]([OH])[#6][OH])] | @atom:116 | 0.205 | "Diol & Triol -CHROH" [--AHS]
C | CT | opls_175 | [$([CH0D4]([OH])[#6]([OH])[#6][OH])] | @atom:117 | 0.265 | "Diol & Triol -CR2OH"
C | CT | opls_175 | [$([CH0D4]([OH])([#6][OH])[#6][OH])] | @atom:117 | 0.265 | "Diol & Triol -CR2OH"
C | CT | opls_175 | [$([CH0D4]([OH])[#6][OH])] | @atom:117 | 0.265 | "Diol & Triol -CR2OH" [--AHS]
C | CT | opls_176 | [$([#1][CD4]([OH])[#6]([OH])[#6][OH])] | @atom:118 | 0.06 | "Diol & Triol H-COH"
C | CT | opls_176 | [$([#1][CD4]([OH])([#6][OH])[#6][OH])] | @atom:118 | 0.06 | "Diol & Triol H-COH"
C | CT | opls_176 | [$([#1][CD4]([OH])[#6][OH])] | @atom:118 | 0.06 | "Diol & Triol H-COH" [--AHS]
* no opls_177 in opls.par
O | O | opls_xxx | [$([O]([c;r6])[c;r6])] | @atom:119 | -0.17 | "Diphenyl Ether" [--AHS]
C | C= | opls_178 | [$([CH0](=C)-[CH0]=C)] | @atom:120 | 0.0 | "Diene =CR-CR="
O | OS | opls_179 | [$([#8](c)[CD4])] | @atom:121 | -0.285 | "Anisole -OCH3" [mod --AHS]
O | OS | opls_180 | [$([O]([C][*;!$([#7,#8])])[C][*;!$([#7,#8])])] | @atom:122 | -0.4 | "Dialkyl Ether -O-" [mod -AHS]
C | CT | opls_181 | [$([CH3D4][O][#6][*;!$([#7,#8])])] | @atom:123 | 0.11 | "Methyl Ether CH3OR"
C | CT | opls_182 | [$([CH2D4]([*;!$([#7,#8])])[O][#6][*;!$([#7,#8])])] | @atom:124 | 0.14 | "Ethyl Ether -CH2OR"
C | CT | opls_183 | [$([CH1D4]([*;!$([#7,#8])])[O][#6][*;!$([#7,#8])])] | @atom:125 | 0.17 | "Isopropyl Ether >CHOR"
C | CT | opls_184 | [$([CH0D4]([*;!$([#7,#8])])[O][#6][*;!$([#7,#8])])] | @atom:126 | 0.2 | "t-Butyl Ether COR"
H | HC | opls_185 | [$([#1][#6]([*;!$([#7,#8])])[O][#6][*;!$([#7,#8])])] | @atom:127 | 0.03 | "Alkyl Ether H-COR"
O | OS | opls_186 | [$([O](C)[#6][O][#6])] | @atom:128 | -0.4 | "Acetal RO-CR2OX"
O | OH | opls_187 | [$([OH][C][O][#6])] | @atom:129 | -0.7 | "Hemiacetal -OH"
H | HO | opls_188 | [$([#1][O][C][O][#6])] | @atom:130 | 0.435 | "Hemiacetal -OH"
C | CO | opls_189 | [$([CH2D4]([O][#6])[O][#6])] | @atom:131 | 0.2 | "Acetal RO-CH2-OR"
H | HC | opls_190 | [$([#1][CH2D4]([O][#6])[O][#6])] | @atom:132 | 0.1 | "Acetal RO-CH2-OR"
C | CO | opls_191 | [$([CH2D4]([OH])[O][#6])] | @atom:133 | 0.265 | "Hemiacetal RO-CH2-OH"
H | HC | opls_192 | [$([#1][CH2D4]([OH])[O][#6])] | @atom:134 | 0.1 | "Hemiacetal RO-CH2-OH"
C | CO | opls_193 | [$([CH1D4]([O][#6])[O][#6])] | @atom:135 | 0.3 | "Acetal RO-CHR-OR"
H | HC | opls_194 | [$([#1][CH1D4]([O][#6])[O][#6])] | @atom:136 | 0.1 | "Acetal RO-CHR-OR"
C | CO | opls_195 | [$([CH1D4]([OH])[O][#6])] | @atom:137 | 0.365 | "Hemiacetal RO-CHR-OH"
H | HC | opls_196 | [$([#1][CH1D4]([OH])[O][#6])] | @atom:138 | 0.1 | "Hemiacetal RO-CHR-OH"
C | CO | opls_197 | [$([CH0D4]([O][#6])[O][#6])] | @atom:139 | 0.4 | "Acetal RO-CR2-OR"
C | CO | opls_198 | [$([CH0D4]([OH])[O][#6])] | @atom:140 | 0.465 | "Hemiacetal RO-CR2-OH"
C | CA | opls_199 | [$([c][O][#6])] | @atom:141 | 0.085 | "Anisole C-OCH3" [mod AHS]
S | SH | opls_200 | [#16D2H1] | @atom:142 | -0.335 | "Thiol -SH"
S | SH | opls_201 | [#16D2H2] | @atom:143 | -0.47 | "Hydrogen Sulfide H2S"
S | S | opls_202 | [$([#16H0]~[#6])] | @atom:144 | -0.435 | "Sulfide -S-"
S | S | opls_203 | [$([#16D2H0][#16D2H0])] | @atom:145 | -0.2175 | "Disulfide -S-S-"
H | HS | opls_204 | [$([#1][SD2H1])] | @atom:146 | 0.155 | "Thiol -SH"
H | HS | opls_205 | [$([#1][SD2H2])] | @atom:147 | 0.235 | "Hydrogen Sulfide H2S"
C | CT | opls_206 | [$([CH2][#16H1])] | @atom:148 | 0.06 | "Thiol -CH2-SH"
C | CT | opls_207 | [$([CH1][#16H1])] | @atom:149 | 0.12 | "Thiol >CH-SH"
C | CT | opls_208 | [$([CH0][#16H1])] | @atom:150 | 0.18 | "Thiol C-SH"
C | CT | opls_209 | [$([CH3][#16D2H0])] | @atom:151 | 0.0375 | "Methyl Sulfide CH3-SR"
C | CT | opls_210 | [$([CH2][#16D2H0])] | @atom:152 | 0.0975 | "Sulfide RCH2-SR"
C | CT | opls_211 | [$([CH1][#16D2H0])] | @atom:153 | 0.1575 | "Sulfide R2CH-SR"
C | CT | opls_212 | [$([CH0][#16D2H0])] | @atom:154 | 0.2175 | "Sulfide R3C-SR"
C | CT | opls_213 | [$([CH3][#16D2H0][#16D2H0])] | @atom:155 | 0.0375 | "Disulfide CH3-S-SR"
C | CT | opls_214 | [$([CH2][#16D2H0][#16D2H0])] | @atom:156 | 0.0975 | "Disulfide RCH2-S-SR"
C | CT | opls_215 | [$([CH1][#16D2H0][#16D2H0])] | @atom:157 | 0.1575 | "Disulfide R2CH-S-SR"
C | CT | opls_216 | [$([CH0][#16D2H0][#16D2H0])] | @atom:158 | 0.2175 | "Disulfide R3C-S-SR"
C | CT | opls_217 | [$([CH3][SH1])] | @atom:159 | 0.0 | "Methanethiol CH3-SH"
C | CT | opls_218 | [$([CH2](c)[OH])] | @atom:160 | 0.2 | "Benzyl Alcohol -CH2OH"
C | CT | opls_219 | [$([CH1](c)[OH])] | @atom:161 | 0.26 | "Benzyl Alcohol -CHROH"
C | CT | opls_220 | [$([CH0](c)[OH])] | @atom:162 | 0.32 | "Benzyl Alcohol -CR2OH"
C | CA | opls_221 | [$([c][CH2][OH])] | @atom:163 | -0.055 | "Benzyl Alcohol/Nitrile"
S | S | opls_222 | [$([SD2]([c])[CH3])] | @atom:164 | -0.32 | "Thioanisole -SCH3"
C | CT | opls_223 | [$([CH2D4][NH2])] | @atom:165 | 0.08 | "RCH2-NH2 & GLY CA"
C | CT | opls_224 | [$([CH1D4][NH2])] | @atom:166 | 0.14 | "RCHR-NH2 & ALA CA"
C | CT | opls_225 | [$([CH0D4][NH2])] | @atom:167 | 0.2 | "R3C-NH2 & AIB CA"
Cl | Cl | opls_226 | [$([Cl][CD3])] | @atom:168 | -0.12 | "Chloroalkene Cl-CH="
C | CM | opls_227 | [$([CD3][F,Cl,Br,I])] | @atom:169 | 0.005 | "Chloroalkene Cl-CH="
C | CA | opls_228 | [$([c][SD2][CH3])] | @atom:170 | 0.1025 | "Thioanisole C-SCH3"
C | CT | opls_229 | [$([CH1D4]([N][C]=[O]))] | @atom:171 | 0.14 | "Amide -NH-CHR2"
C | CT | opls_230 | [$([CH0D4]([N][C]=[O]))] | @atom:172 | 0.2 | "Amide -NH-CR3"
C | C | opls_231 | [$([C]([c])([c])=[O])] | @atom:173 | 0.7 | "Benzophenone C=O"
C | C_2 | opls_232 | [$([CH1]([c])=[O])] | @atom:174 | 0.565 | "Benzaldehyde C=O"
C | C_2 | opls_233 | [$([C]([c])([CH3])=[O])] | @atom:175 | 0.585 | "Acetophenone C=O"
C | C | opls_234 | [$([C]([c])([NH2D3])=[O])] | @atom:176 | 0.615 | "Benzamide C=O"
C | C | opls_235 | [$([CD3](=O)[ND3])] | @atom:177 | 0.5 | "Amide C=O"
O | O | opls_236 | [$([O]=[CD3][ND3])] | @atom:178 | -0.5 | "Amide C=O"
N | N | opls_237 | [$([ND3H2][CD3]=[O])] | @atom:179 | -0.76 | "Amide -CO-NH2"
N | N | opls_238 | [$([ND3H1][CD3]=[O])] | @atom:180 | -0.5 | "Amide -CO-NHR"
N | N | opls_239 | [$([ND3H0][CD3]=[O])] | @atom:181 | -0.14 | "Amide -CO-NR2"
H | H | opls_240 | [$([#1][ND3H2][CD3]=[O])] | @atom:182 | 0.38 | "Amide -CO-NH2"
H | H | opls_241 | [$([#1][ND3H1][CD3]=[O])] | @atom:183 | 0.3 | "Amide -CO-NHR"
C | CT | opls_242 | [$([CH3D4][NH1D3][CD3]=[O])] | @atom:184 | 0.02 | "Amide -NH-CH3"
C | CT | opls_243 | [$([CH3D4][NH0D3][CD3]=[O])] | @atom:185 | -0.11 | "Amide -NR-CH3"
C | CT | opls_244 | [$([CH2D4][NH1D3][CD3]=[O])] | @atom:186 | 0.08 | "Amide -NH-CH2R"
C | CT_3 | opls_245 | [$([CH2D4][NH0D3][CD3]=[O])] | @atom:187 | -0.05 | "Amide -NR-CH2R & PRO CD"
C | CT_2 | opls_246 | [$([CH1D4][NH0D3][CD3]=[O])] | @atom:188 | 0.01 | "Amide -NR-CHR2 & PRO CA"
C | C | opls_247 | [$([CD3](=O)([NH2D3])[NH2D3])] | @atom:189 | 0.142 | "Urea C=O"
O | O | opls_248 | [$([O]=[CD3]([NH2D3])[NH2D3])] | @atom:190 | -0.39 | "Urea C=O"
N | N | opls_249 | [$([NH2D3][CD3]([NH2D3])=[O])] | @atom:191 | -0.542 | "Urea -NH2"
H | H | opls_250 | [$([#1][NH2D3][CD3]([NH2D3])=[O])] | @atom:192 | 0.333 | "Urea -NH2"
N | N | opls_251 | [$([ND3]([CD3]=[O])[CD3]=[O])] | @atom:193 | -0.49 | "Imide -NH-"
C | C | opls_252 | [$([CD3](=[O])[ND3][CD3]=[O])] | @atom:194 | 0.42 | "Imide C=O"
O | O | opls_253 | [$([O]=[CD3][ND3][CD3]=[O])] | @atom:195 | -0.42 | "Imide C=O"
H | H | opls_254 | [$([#1][ND3]([CD3]=[O])[CD3]=[O])] | @atom:196 | 0.37 | "Imide -NH-"
H | HC | opls_255 | [$([#1][CD3](=[O])[ND3][CD3]=[O])] | @atom:197 | 0.06 | "Formimide H-C=O"
C | CT | opls_256 | [$([CH3D4][CD3](=[O])[ND3][CD3]=[O])] | @atom:198 | -0.12 | "Imide CH3-CONHCO-"
C | CT | opls_257 | [$([CH2D4][CD3](=[O])[ND3][CD3]=[O])] | @atom:199 | -0.06 | "Imide -CH2-CONHCO-"
C | CT | opls_258 | [$([CH1D4][CD3](=[O])[ND3][CD3]=[O])] | @atom:200 | 0.0 | "Imide >CH-CONHCO-"
C | CT | opls_259 | [$([CH0D4][CD3](=[O])[ND3][CD3]=[O])] | @atom:201 | 0.06 | "Imide C-CONHCO-"
C | CA | opls_260 | [$([c][CD2]#[ND1])] | @atom:202 | 0.035 | "Benzonitrile C-CN"
C | CZ | opls_261 | [$([CD2](c)#[ND1])] | @atom:203 | 0.395 | "Benzonitrile -CN"
N | NZ | opls_262 | [$([ND1]#[CD2][c])] | @atom:204 | -0.43 | "Benzonitrile -CN"
C | CA | opls_263 | [$([c][Cl])] | @atom:205 | 0.18 | "Chlorobenzene C-Cl"
Cl | Cl | opls_264 | [$([Cl][c])] | @atom:206 | -0.18 | "Chlorobenzene C-Cl"
N | N | opls_265 | [$([NH1D3](c)[CD3]=[O])] | @atom:207 | -0.385 | "N-Phenylacetamide N"
C | CA | opls_266 | [$([c][NH1D3][CD3]=[O])] | @atom:208 | 0.085 | "N-Phenylacetamide N-CA"
C | C | opls_267 | [$([CD3](=O)[OH])] | @atom:209 | 0.52 | "Carboxylic Acid -COOH"
O | OH | opls_268 | [$([OH][CD3]=[O])] | @atom:211 | -0.53 | "Carboxylic Acid -OH"
O | O_3 | opls_269 | [$([O]=[CD3][OH])] | @atom:210 | -0.44 | "Carboxylic Acid C=O"
H | HO | opls_270 | [$([#1][O][CD3]=[O])] | @atom:212 | 0.45 | "Carboxylic Acid -COOH"
C | C_3 | opls_271 | [$([#6](~[#8D1])~[#8D1])] | @atom:213 | 0.7 | "Carboxylate COO-"
O | O2 | opls_272 | [$([#8D1]~[#6]~[#8D1])] | @atom:214 | -0.8 | "Carboxylate COO-"
C | CT | opls_273 | [$([CH3D4][#6D3](~[#8D1])~[#8D1])] | @atom:215 | -0.28 | "Carboxylate CH3-COO-"
C | CT | opls_274 | [$([CH2D4][#6D3](~[#8D1])~[#8D1])] | @atom:216 | -0.22 | "Carboxylate RCH2-COO-"
C | CT | opls_275 | [$([CH1D4][#6D3](~[#8D1])~[#8D1])] | @atom:217 | -0.16 | "Carboxylate R2CH-COO-"
C | CT | opls_276 | [$([CH0D4][#6D3](~[#8D1])~[#8D1])] | @atom:218 | -0.1 | "Carboxylate R3C-COO-"
C | C_2 | opls_277 | [$([CH1]([#6])=[O])] | @atom:219 | 0.45 | "Aldehyde/Acyl Halide C=O"
O | O_2 | opls_278 | [$([O]=[CH1][#6])] | @atom:220 | -0.45 | "Aldehyde/Acyl Halide C=O"
H | HC | opls_279 | [$([#1][CH1]([#6])=[O])] | @atom:221 | 0.0 | "Aldehyde/Formamide H-C=O"
H | HC | opls_279 | [$([#1][CH1]([#7])=[O])] | @atom:221 | 0.0 | "Aldehyde/Formamide H-C=O"
C | C_2 | opls_280 | [$([CH0D3]([#6])([#6])=[O])] | @atom:222 | 0.47 | "Ketone C=O"
O | O_2 | opls_281 | [$([O]=[CH0D3]([#6])[#6])] | @atom:223 | -0.47 | "Ketone C=O"
H | HC | opls_282 | [$([#1][CD4][CH0D3](=[O])[#6])] | @atom:224 | 0.06 | "Acyl H-C-COX"
H | HC | opls_282 | [$([#1][CD4][CH1D3](=[O]))] | @atom:224 | 0.06 | "Acyl H-C-COX"
*C | CT_2 | opls_283 | [$([CH1D4]([CD4])([NH1D3])[#6D3](~[#8D1])~[#8D1])] | @atom:225 | 0.04 | "C-Terminal ALA CA" ?
*C | CT_2 | opls_284 | [$([CH2D4]([CD4])([NH1D3])[#6D3](~[#8D1])~[#8D1])] | @atom:226 | -0.02 | "C-Terminal GLY CA" ?
*C | CT_2 | opls_285 | [$([CH1D4r5](@[CH3D4r5])(@[NH1D3r5])[#6D3](~[#8D1])~[#8D1])] | @atom:227 | 0.1 | "C-Terminal AIB CA" ?
N | N3 | opls_286 | [$([#7H4D4])] | @atom:229 | -0.4 | "Ammonium NH4+"
N | N3 | opls_287 | [$([#7H3D4])] | @atom:230 | -0.3 | "Ammonium RNH3+"
N | N3 | opls_288 | [$([#7H0D4])] | @atom:231 | 0.0 | "Ammonium R4N+"
H | H3 | opls_289 | [$([#1][#7H4D4])] | @atom:232 | 0.35 | "Ammonium NH4+"
H | H3 | opls_290 | [$([#1][#7H3D4])] | @atom:233 | 0.33 | "Ammonium RNH3+"
C | CT | opls_291 | [$([CH3D4][#7H3D4])] | @atom:234 | 0.13 | "Ammonium CH3-NH3+"
C | CT | opls_292 | [$([CH2D4][#7H3D4])] | @atom:235 | 0.19 | "CH2NH3+/N-Term GLY CA" ?
C | CT_2 | opls_292B | [$([CH2D4]([CD3]=[O])[#7H3D4])] | @atom:235 | 0.19 | "CH2NH3+/N-Term GLY CA" ?
*C | CT | opls_293 | [$([CH1D4][#7H3D4])]| @atom:236 | 0.25 | "RCHNH3+/N-Term ALA CA" ?
*C | CT_2 | opls_293B | [$([CH1D4]([CD3]=[O])[#7H3D4])] | @atom:236 | 0.25 | "RCHNH3+/N-Term ALA CA" ?
*C | CT | opls_294 | [$([CH0D4][#7H3D4])] | @atom:237 | 0.31 | "R3C-NH3+/N-Term AIB CA" ?
*C | CT_2 | opls_295 | [$([CH0D4]([CD3]=[O])[#7H3D4])] | @atom:237 | 0.31 | "R3C-NH3+/N-Term AIB CA" ?
*C | CT_3 | opls_296 | [$([CH2D4r5](@[CH2D4r5])@[NH1D3r5]@[CH1D4r5][CD3]=[O])] | @atom:239 | 0.17 | "N-Terminal PRO CD" ?
C | CT | opls_297 | [$([CH3D4][#7H2D4])] | @atom:240 | 0.11 | "Ammonium CH3-NH2R+"
C | CT_2 | opls_298 | [$([CH2D4]([#7D4])[#6D3]([#8D1])[#8D1])] | @atom:241 | 0.09 | "GLY Zwitterion CA"
C | CT_2 | opls_299 | [$([CH1D4]([CH3D4])([#7D4])[#6D3]([#8D1])[#8D1])] | @atom:242 | 0.15 | "ALA Zwitterion CA"
N | N2 | opls_300 | [$([#7H2D3]~[#6H0D3](~[#7D3])~[#7D3])] | @atom:243 | -0.8 | "Guanidinium -NH2"
H | H3 | opls_301 | [$([#1][#7H2D3]~[#6H0D3](~[#7D3])~[#7D3])] | @atom:244 | 0.46 | "Guanidinium -NH2"
C | CA | opls_302 | [$([#6H0D3](~[#7D3])(~[#7D3])~[#7D3])] | @atom:245 | 0.64 | "Guanidinium C+"
N | N2 | opls_303 | [$([#7H1D3]~[#6H0D3](~[#7D3])~[#7D3])] | @atom:246 | -0.7 | "Guanidinium -NHR"
H | H3 | opls_304 | [$([#1][#7H1D3]~[#6H0D3](~[#7D3])~[#7D3])] | @atom:247 | 0.44 | "Guanidinium -NHR"
C | CT | opls_305 | [$([CH3D4][#7H1D3]~[#6H0D3](~[#7D3])~[#7D3])] | @atom:248 | 0.2 | "Me Guanidinium CH3-"
C | CT | opls_306 | [$([CH3D4][CH2D4][#7H1D3]~[#6H0D3](~[#7D3])~[#7D3])] | @atom:249 | -0.11 | "Et Guanidinium CH3-"
C | CT | opls_307 | [$([CH2D4][#7H1D3]~[#6H0D3](~[#7D3])~[#7D3])] | @atom:250 | 0.19 | "Et Guan -CH2- & ARG CD"
C | CT | opls_308 | [$([CH2D4]([CH2D4][CH1D4])[CH2D4][#7H1D3]~[#6H0D3](~[#7D3])~[#7D3])] | @atom:251 | -0.05 | "Pr Guan-CH2-ARGCG"
N | N3 | opls_309 | [$([#7H2D4])] | @atom:252 | -0.2 | "Ammonium R2NH2+"
H | H3 | opls_310 | [$([#1][#7H2D4])] | @atom:253 | 0.31 | "Ammonium R2NH2+"
N | NC | opls_311 | [$([n]([c]([NH2D3])[c])[c]([NH2D3])[c])] | @atom:254 | -0.46 | "Diaminopyridine N1"
N | NC | opls_311 | [$([#7]=[#6])] | @atom:254 | -0.46 | "Diaminopyridine N1" ?
N | NC | opls_311 | [$([n][n])] | @atom:254 | -0.46 | "Diaminopyridine N1" ?
C | CA | opls_312 | [$([c]([n][c]([NH2D3])[c])([NH2D3])[c])] | @atom:255 | 0.36 | "Diaminopyridine C2"
N | N2 | opls_313 | [$([NH2D3][c][n][c][NH2D3])] | @atom:256 | -0.85 | "Diaminopyridine -NH2"
H | H | opls_314 | [$([#1][NH2D3][c][n][c][NH2D3])] | @atom:257 | 0.37 | "Diaminopyridine -NH2"
C | CA | opls_315 | [$([c](c)[c]([NH2D3])[n][c][NH2D3])] | @atom:258 | -0.15 | "Diaminopyridine C3"
H | HA | opls_316 | [$([#1][c](c)[c]([NH2D3])[n][c][NH2D3])] | @atom:259 | 0.1 | "Diaminopyridine H3"
C | CA | opls_317 | [$([c]([c][c]([NH2D3]))[c][c]([NH2D3])[n])] | @atom:260 | -0.04 | "Diaminopyridine C4"
H | HA | opls_318 | [$([#1][c]([c][c]([NH2D3]))[c][c]([NH2D3])[n])] | @atom:261 | 0.1 | "Diaminopyridine H4"
N | NA | opls_319 | [$([#7H1D3]([#6D3])[#6D3](=O)[#7D3][#6D3]=[O])] | @atom:262 | -0.6 | "Uracil & Thymine N1"
N | N* | opls_319B | [$([#7H0D3]([#6D3])[#6D3](=O)[#7D3][#6D3]=[O])] | @atom:262 | -0.6 | "Uracil & Thymine N1" ?
C | C | opls_320 | [$([#6D3](=O)([#7D3][#6D3]=[O])[#7D3])] | @atom:263 | 0.5 | "Uracil & Thymine C2"
N | NA | opls_321 | [$([#7H1D3]([#6D3]=[O])[#6D3](=O)[#7D3][#6D3])] | @atom:264 | -0.51 | "Uracil & Thymine N3"
C | C | opls_322 | [$([#6D3](=O)([#6D3][#6D3])[#7D3][#6D3](=O)[#7D3])] | @atom:265 | 0.45 | "Uracil & Thymine C4"
C | CM | opls_323 | [$([#6D3]([#6H1D3])[#6D3](=O)[#7D3][#6D3](=O)[#7D3])] | @atom:266 | -0.07 | "Uracil & Thymine C5"
C | CM | opls_324 | [$([#6H1D3]([#6D3][#6D3]=[O])[#7D3][#6D3](=O)[#7D3])] | @atom:267 | 0.08 | "Uracil & Thymine C6"
H | H | opls_325 | [$([#1][#7H1D3]([#6D3])[#6D3](=O)[#7D3][#6D3]=[O])] | @atom:268 | 0.41 | "Uracil & Thymine HN1"
O | O | opls_326 | [$([O]=[#6D3]([#7D3][#6D3])[#7D3][#6D3]=[O])] | @atom:269 | -0.4 | "Uracil & Thymine O2"
H | H | opls_327 | [$([#1][#7H1D3]([#6D3]=[O])[#6D3](=O)[#7D3][#6D3])] | @atom:270 | 0.36 | "Uracil & Thymine HN3"
O | O | opls_328 | [$([O]=[#6D3]([#6D3])[#7D3][#6D3](=O)[#7D3])] | @atom:271 | -0.42 | "Uracil & Thymine O4"
H | HC | opls_329 | [$([#1][#6H1D3]([#6D3])[#6D3](=O)[#7D3][#6D3](=O)[#7D3])] | @atom:272 | 0.1 | "Uracil & Thymine HC5"
H | HC | opls_330 | [$([#1][#6H1D3]([#6D3][#6D3]=[O])[#7D3][#6D3](=O)[#7D3])] | @atom:273 | 0.1 | "Uracil & Thymine HC6"
C | CT | opls_331 | [$([#6D4][#6D3]([#6D3])[#6D3](=O)[#7D3][#6D3](=O)[#7D3])] | @atom:274 | -0.14 | "Thymine CH3-"
H | HC | opls_332 | [$([#1][#6D4][#6D3]([#6D3])[#6D3](=O)[#7D3][#6D3](=O)[#7D3])] | @atom:275 | 0.08 | "Thymine CH3-"
N | NA | opls_333 | [$([#7H1D3]1[#6D3](=O)[#7D2][#6D3]([NH2D3])[#6D3][#6D3]1)] | @atom:276 | -0.56 | "Cytosine N1"
N | N* | opls_333B | [$([#7H0D3]1[#6D3](=O)[#7D2][#6D3]([NH2D3])[#6D3][#6D3]1)] | @atom:276 | -0.56 | "Cytosine N1" ?
C | C | opls_334 | [$([#6D3]1(=O)[#7D2][#6D3]([NH2D3])[#6D3][#6D3][#7D3]1)] | @atom:277 | 0.55 | "Cytosine C2"
N | NC | opls_335 | [$([#7D2]1[#6D3](=O)[#7D3][#6D3][#6D3][#6D3]1[NH2D3])] | @atom:278 | -0.54 | "Cytosine N3"
C | CA | opls_336 | [$([#6D3]1([NH2D3])[#6D3][#6D3][#7D3][#6D3](=O)[#7D2]1)] | @atom:279 | 0.46 | "Cytosine C4"
C | CM | opls_337 | [$([#6D3]1[#6D3]([NH2D3])[#7D2][#6D3](=O)[#7D3][#6D3]1)] | @atom:280 | -0.06 | "Cytosine C5"
C | CM | opls_338 | [$([#6D3]1[#6D3][#6D3]([NH2D3])[#7D2][#6D3](=O)[#7D3]1)] | @atom:281 | 0.1 | "Cytosine C6"
H | H | opls_339 | [$([#1][#7H1D3]1[#6D3](=O)[#7D2][#6D3]([NH2D3])[#6D3][#6D3]1)] | @atom:282 | 0.38 | "Cytosine HN1"
O | O | opls_340 | [$([O]=[#6D3]1[#7D2][#6D3]([NH2D3])[#6D3][#6D3][#7D3]1)] | @atom:283 | -0.48 | "Cytosine O2"
N | N2 | opls_341 | [$([NH2D3][#6D3]1[#6D3][#6D3][#7D3][#6D3](=O)[#7D2]1)] | @atom:284 | -0.79 | "Cytosine NH2-"
H | H | opls_342 | [$([#1][NH2D3][#6D3]1[#6D3][#6D3][#7D3][#6D3](=O)[#7D2]1)] | @atom:285 | 0.385 | "Cytosine NH2- (N3)"
H | H | opls_343 | [$([#1][NH2D3][#6D3]1[#6D3][#6D3][#7D3][#6D3](=O)[#7D2]1)] | @atom:286 | 0.355 | "Cytosine NH2- (C5)"
H | HC | opls_344 | [$([#1][#6D3]1[#6D3]([NH2D3])[#7D2][#6D3](=O)[#7D3][#6D3]1)] | @atom:287 | 0.1 | "Cytosine HC5"
H | H4 | opls_345 | [$([#1][#6D3]1[#6D3][#6D3]([NH2D3])[#7D2][#6D3](=O)[#7D3]1)] | @atom:288 | 0.1 | "Cytosine HC6"
N | NC | opls_346 | [$([#7]1[#6][#7][#6]2[#6]([#7][#6][#7]2)[#6]1([NH2D3]))] | @atom:289 | -0.53 | "Adenine N1"
C | CQ | opls_347 | [$([#6]1[#7][#6]2[#6]([#7][#6][#7]2)[#6]([NH2D3])[#7]1)] | @atom:290 | 0.22 | "Adenine C2"
N | NC | opls_348 | [$([#7]1[#6]2[#6]([#7][#6][#7]2)[#6]([NH2D3])[#7][#6]1)] | @atom:291 | -0.55 | "Adenine N3"
C | CB | opls_349 | [$([#6]1([#7][#6][#7]2)[#6]2[#6]([NH2D3])[#7][#6][#7]1)] | @atom:292 | 0.38 | "Adenine C4"
C | CB | opls_350 | [$([#6]1([#7][#6][#7]2)[#6]2[#7][#6][#7][#6]1([NH2D3]))] | @atom:293 | 0.15 | "Adenine C5"
C | CA | opls_351 | [$([#6]1([NH2D3])[#7][#6][#7][#6]2[#6]1([#7][#6][#7]2))] | @atom:294 | 0.44 | "Adenine C6"
N | NB | opls_352 | [$([#7]1[#6][#7][#6]2[#6]1[#6][#7][#6][#7]2)] | @atom:295 | -0.49 | "Adenine & Guanine N7"
C | CK | opls_353 | [$([#6]1[#7][#6]2[#7][#6][#7][#6][#6]2[#7]1)] | @atom:296 | 0.2 | "Adenine & Guanine C8"
N | NA | opls_354 | [$([#7D3]1[#6]2[#7][#6][#7][#6][#6]2[#7][#6]1)] | @atom:297 | -0.5 | "Adenine & Guanine N9"
N | N* | opls_354B | [$([#7D2D3]1[#6]2[#7][#6][#7][#6][#6]2[#7][#6]1)] | @atom:297 | -0.5 | "Adenine & Guanine N9" ?
H | H5 | opls_355 | [$([#1][#6]1[#7][#6]2[#6]([#7][#6][#7]2)[#6]([NH2D3])[#7]1)] | @atom:298 | 0.2 | "Adenine HC2"
N | N2 | opls_356 | [$([NH2D3][#6]1[#7][#6][#7][#6]2[#6]1([#7][#6][#7]2))] | @atom:299 | -0.81 | "Adenine NH2-"
H | H | opls_357 | [$([#1][NH2D3][#6]1[#7][#6][#7][#6]2[#6]1([#7][#6][#7]2))] | @atom:300 | 0.385 | "Adenine NH2- (N1)"
H | H | opls_358 | [$([#1][NH2D3][#6]1[#7][#6][#7][#6]2[#6]1([#7][#6][#7]2))] | @atom:301 | 0.355 | "Adenine NH2- (C5)"
H | H5 | opls_359 | [$([#1][#6]1[#7][#6]2[#7][#6][#7][#6][#6]2[#7]1)] | @atom:302 | 0.2 | "Adenine & Guanine HC8"
H | H | opls_360 | [$([#1][#7D3]1[#6]2[#7][#6][#7][#6][#6]2[#7][#6]1)] | @atom:303 | 0.35 | "Adenine & Guanine HN9"
N | NA | opls_361 | [$([#7H1]1[#6](=[#8])[#6]([#7H0][#6][#7H1]2)[#6]2[#7H0][#6]1[NH2D3])] | @atom:304 | -0.56 | "Guanine N1"
C | CA | opls_362 | [$([#6]1([NH2D3])[#7H1][#6](=[#8])[#6]([#7H0][#6][#7H1]2)[#6]2[#7H0]1)] | @atom:305 | 0.46 | "Guanine C2"
N | NC | opls_363 | [$([#7H0]1[#6]([#7H1][#6][#7H0]2)[#6]2[#6](=[#8])[#7H1][#6]1[NH2D3])] | @atom:306 | -0.51 | "Guanine N3"
C | CB | opls_364 | [$([#6]1([#7H1][#6][#7H0]2)[#6]2[#6](=[#8])[#7H1][#6]([NH2D3])[#7H0]1)] | @atom:307 | 0.34 | "Guanine C4"
C | CB | opls_365 | [$([#6]1([#7H0][#6][#7H1]2)[#6]2[#7H0][#6]([NH2D3])[#7H1][#6]1(=[#8]))] | @atom:308 | 0.12 | "Guanine C5"
C | C | opls_366 | [$([#6]1(=[#8])[#6]([#7H0][#6][#7H1]2)[#6]2[#7H0][#6]([NH2D3])[#7H1]1)] | @atom:309 | 0.52 | "Guanine C6"
H | H | opls_367 | [$([#1][#7H1]1[#6](=[#8])[#6]([#7H0][#6][#7H1]2)[#6]2[#7H0][#6]1[NH2D3])] | @atom:310 | 0.38 | "Guanine HN1"
N | N2 | opls_368 | [$([NH2D3][#6]1[#7H1][#6](=[#8])[#6]([#7H0][#6][#7H1]2)[#6]2[#7H0]1)] | @atom:311 | -0.8 | "Guanine NH2-"
H | H | opls_369 | [$([#1][NH2D3][#6]1[#7H1][#6](=[#8])[#6]([#7H0][#6][#7H1]2)[#6]2[#7H0]1)] | @atom:312 | 0.4 | "Guanine NH2-"
O | O | opls_370 | [$([#8]=[#6]1[#6]([#7H0][#6][#7H1]2)[#6]2[#7H0][#6]([NH2D3])[#7H1]1)] | @atom:313 | -0.51 | "Guanine O6"
C | CT | opls_371 | [$([CD4][nD3]1c2ncncc2nc1)] | @atom:314 | -0.01 | "9-Me A & 9-Me-G CH3-"
H | HC | opls_372 | [$([#1][CD4][nD3]1c2ncncc2nc1)] | @atom:315 | 0.12 | "9-Me-A & 9-Me-G CH3-"
C | CT | opls_373 | [$([CD4][#7D3]([#6D3])[#6D3](=O)[#7D3][#6D3]=[O])] | @atom:316 | -0.01 | "1-Me-U & 1-Me-T CH3-"
H | HC | opls_374 | [$([#1][CD4][#7D3]([#6D3])[#6D3](=O)[#7D3][#6D3]=[O])] | @atom:317 | 0.14 | "1-Me-U & 1-Me-T CH3-"
C | CT | opls_375 | [$([CD4][#7D3]([#6D3])[#6D3](=O)[#7D2][#6D3][NH2D3])] | @atom:318 | -0.01 | "1-Me-Cytosine CH3-"
H | HC | opls_376 | [$([#1][CD4][#7D3]([#6D3])[#6D3](=O)[#7D2][#6D3][NH2D3])] | @atom:319 | 0.13 | "1-Me-Cytosine CH3-"
N | NA | opls_377 | [$([#7H1D3]1[#6D3](=O)[#7H1D3][#6D3]([NH2D3])[#6D3][#6D3]1)] | @atom:320 | -0.64 | "CytosineH+ N1"
N | N* | opls_377B | [$([#7H0D3]1[#6D3](=O)[#7H1D3][#6D3]([NH2D3])[#6D3][#6D3]1)] | @atom:320 | -0.64 | "CytosineH+ N1"
C | C | opls_378 | [$([#6D3]1(=O)[#7D3][#6D3]([NH2D3])[#6D3][#6D3][#7D3]1)] | @atom:321 | 0.65 | "CytosineH+ C2"
N | NA | opls_379 | [$([#7D3]1[#6D3](=O)[#7D3][#6D3][#6D3][#6D3]1[NH2D3])] | @atom:322 | -0.74 | "CytosineH+ N3"
C | CA | opls_380 | [$([#6D3]1([NH2D3])[#6D3][#6D3][#7D3][#6D3](=O)[#7D3]1)] | @atom:323 | 0.66 | "CytosineH+ C4"
C | CM | opls_381 | [$([#6D3]1[#6D3]([NH2D3])[#7D3][#6D3](=O)[#7D3][#6D3]1)] | @atom:324 | -0.06 | "CytosineH+ C5"
C | CM | opls_382 | [$([#6D3]1[#6D3][#6D3]([NH2D3])[#7D3][#6D3](=O)[#7D3]1)] | @atom:325 | 0.1 | "CytosineH+ C6"
H | H | opls_383 | [$([#1][#7H1D3]1[#6D3](=O)[#7H1D3][#6D3]([NH2D3])[#6D3][#6D3]1)] | @atom:326 | 0.49 | "CytosineH+ HN1"
O | O | opls_384 | [$([O]=[#6D3]1[#7D3][#6D3]([NH2D3])[#6D3][#6D3][#7D3]1)] | @atom:327 | -0.3 | "CytosineH+ O2"
H | H | opls_385 | [$([#1][#7D3]1[#6D3](=O)[#7D3][#6D3][#6D3][#6D3]1[NH2D3])] | @atom:328 | 0.48 | "CytosineH+ HN3"
N | N2 | opls_386 | [$([NH2D3][#6D3]1[#6D3][#6D3][#7D3][#6D3](=O)[#7D3]1)] | @atom:329 | -0.81 | "CytosineH+ NH2-"
H | H | opls_387 | [$([#1][NH2D3][#6D3]1[#6D3][#6D3][#7D3][#6D3](=O)[#7D3]1)] | @atom:330 | 0.46 | "CytosineH+ NH2- (N3)"
H | H | opls_388 | [$([#1][NH2D3][#6D3]1[#6D3][#6D3][#7D3][#6D3](=O)[#7D3]1)] | @atom:331 | 0.43 | "CytosineH+ NH2- (C5)"
H | HA | opls_389 | [$([#1][#6D3]1[#6D3]([NH2D3])[#7D3][#6D3](=O)[#7D3][#6D3]1)] | @atom:332 | 0.14 | "CytosineH+ HC5"
H | H4 | opls_390 | [$([#1][#6D3]1[#6D3][#6D3]([NH2D3])[#7D3][#6D3](=O)[#7D3]1)] | @atom:333 | 0.14 | "CytosineH+ HC6"
C | CT | opls_391 | [$([CD4][#7H0D3]1[#6D3](=O)[#7H1D3][#6D3]([NH2D3])[#6D3][#6D3]1)] | @atom:334 | 0.01 | "1-Me-CytosineH+ CH3-"
H | HC | opls_392 | [$([#1][CD4][#7H0D3]1[#6D3](=O)[#7H1D3][#6D3]([NH2D3])[#6D3][#6D3]1)] | @atom:335 | 0.16 | "1-Me-CytosineH+ CH3-"
* no 393-399 in opls.par
F | F- | opls_400 | [F-] | @atom:343 | -1.0 | "Fluoride Ion F-"
Cl | Cl- | opls_401 | [Cl-] | @atom:344 | -1.0 | "Chloride Ion Cl-"
Br | Br- | opls_402 | [Br-] | @atom:345 | -1.0 | "Bromide Ion Br-"
I | I- | opls_403 | [I-] | @atom:346 | -1.0 | "Iodide Ion I-"
Li | Li+ | opls_404 | [Li+] | @atom:348 | 1.0 | "Lithium Ion Li+"
Na | Na+ | opls_405 | [Na+] | @atom:349 | 1.0 | "Sodium Ion Na+"
* Li | Li+ | opls_406 | [Li+] |
* Na | Na+ | opls_407 | [Na+] |
K | K+ | opls_408 | [K+] | @atom:350 | 1.0 | "Potassium Ion K+"
Rb | Rb+ | opls_409 | [Rb+] | @atom:351 | 1.0 | "Rubidium Ion Rb+"
Cs | Cs+ | opls_410 | [Cs+] | @atom:352 | 1.0 | "Cesium Ion Cs+"
Mg | Mg2+ | opls_411 | [Mg+2] | @atom:353 | 2.0 | "Magnesium Ion Mg+2"
Ca | Ca2+ | opls_412 | [Ca+2] | @atom:354 | 2.0 | "Calcium Ion Ca+2"
Sr | Sr2+ | opls_413 | [Sr+2] | @atom:355 | 2.0 | "Strontium Ion Sr+2"
Ba | Ba2+ | opls_414 | [Ba+2] | @atom:356 | 2.0 | "Barium Ion Ba+2"
C | C3 | opls_415 | [$([CH3D4][S-])] | @atom:357 | -0.4 | "Methyl Thiolate CH3S-"
H | HC | opls_416 | [$([#1][CH3D4][S-])] | @atom:358 | 0.1 | "Methyl Thiolate CH3S-"
S | SH | opls_417 | [$([S-][CH3D4])] | @atom:359 | -0.9 | "Methyl Thiolate CH3S-"
C | C3 | opls_418 | [$([CH3D4][O-])] | @atom:360 | -0.2 | "Methoxide CH3O-"
H | HC | opls_419 | [$([#1][CH3D4][O-])] | @atom:361 | 0.06 | "Methoxide CH3O-"
O | OH | opls_420 | [$([O-][CH3D4])] | @atom:362 | -0.98 | "Methoxide CH3O-" *** mod AHS
C | CT | opls_421 | [$([CH2D3][CH0D2][ND1])] | @atom:363 | -1.07 | "Nitrile Anion CNCH2-"
H | HC | opls_422 | [$([#1][CH2D3][CH0D2][ND1])] | @atom:364 | 0.19 | "Nitrile Anion CNCH2-"
C | CZ | opls_423 | [$([CH0D2]([CH2D3])[ND1])] | @atom:365 | 0.51 | "Nitrile Anion CNCH2-"
N | NZ | opls_424 | [$([ND1][CH0D2][CH2D3])] | @atom:366 | -0.82 | "Nitrile Anion CNCH2-"
C | C3 | opls_425 | [$([CH3D3][NH1D2])] | @atom:367 | -0.3 | "Me Amine Anion CH3NH-"
H | HC | opls_426 | [$([#1][CH3D3][NH1D2])] | @atom:368 | 0.07 | "Me Amine Anion CH3NH-"
N | N3 | opls_427 | [$([NH1D2][CH3D3])] | @atom:369 | -1.31 | "Me Amine Anion CH3NH-"
H | H | opls_428 | [$([#1][NH1D2][CH3D3])] | @atom:370 | 0.4 | "Methyl Amine Anion"
C | C3 | opls_429 | [$([CH2D3-])] | @atom:371 | -0.4 | "Ethyl Anion CH3-CH2-"
* Need extra site for lone pair @atom:375 -0.98 # "Ethyl Anion CH3-CH2-"
H | HC | opls_430 | [$([#1][CH2D3-])] | @atom:372 | 0.08 | "Ethyl Anion CH3-CH2-"
C | CT | opls_431 | [$([CH3D4][CH2D3-])] | @atom:373 | 0.0 | "Ethyl Anion CH3-CH2-"
H | HC | opls_432 | [$([#1][CH3D4][CH2D3-])] | @atom:374 | 0.07 | "Ethyl Anion CH3-CH2-"
O | OH | opls_434 | [$([OH1D1-])] | @atom:376 | -1.3 | "Hydroxide Ion OH-"
H | HO | opls_435 | [$([#1][OH1D1-])] | @atom:377 | 0.3 | "Hydroxide Ion OH-"
* no 436-439 in opls.par
P | P | opls_440 | [$([PD4]([OD2])([OD2])(=[O,S])-[O,S])] | @atom:381 | 1.62 | "DiMe Phosphate P"
O | O2 | opls_441 | [$([O]=[PD4]([OD2])([OD2])-[O,S])] | @atom:382 | -0.92 | "DiMe Phosphate O=P-O"
O | OS | opls_442 | [$([O]([#6])[PD4]([OD2])(=[O,S])-[O,S])] | @atom:383 | -0.6 | "DiMe Phosphate CH3-O"
C | CT | opls_443 | [$([#6][O][PD4]([OD2])(=[O,S])-[O,S])] | @atom:384 | 0.3 | "DiMe Phosphate CH3-O"
H | HC | opls_444 | [$([#1][#6][O][PD4]([OD2])(=[O,S])-[O,S])] | @atom:385 | -0.03 | "DiMe Phosphate CH3-O"
P | P | opls_445 | [$([PD4]([OD2])(=[O,S])(-[O,S])-[O,S])] | @atom:386 | 1.92 | "Me Phosphate P"
O | O2 | opls_446 | [$([O]=[PD4]([OD2])(-[O,S])-[O,S])] | @atom:387 | -1.12 | "Me Phosphate O=PO2"
O | OS | opls_447 | [$([O]([#6])[PD4](=[O,S])(-[O,S])-[O,S])] | @atom:388 | -0.7 | "Me Phosphate CH3-O"
C | CT | opls_448 | [$([#6][O][PD4](=[O,S])(-[O,S])-[O,S])] | @atom:389 | 0.44 | "Me Phosphate CH3-O"
H | HC | opls_449 | [$([#1][#6][O][PD4](=[O,S])(-[O,S])-[O,S])] | @atom:390 | -0.1 | "Me Phosphate CH3-O"
P | P | opls_450 | [$([PD4]([#6])(=[O,S])(-[O,S])[OD2])] | @atom:391 | 1.62 | "Me MePhosphonate P"
O | O2 | opls_451 | [$([O]=[PD4]([#6])(-[O,S])[OD2])] | @atom:392 | -0.97 | "Me MePhosphonate O=P-O"
O | OS | opls_452 | [$([O]([#6])[PD4]([#6])(=[O,S])-[O,S])] | @atom:393 | -0.63 | "Me MePhosphonate CH3-O"
C | CT | opls_453 | [$([#6][O][PD4]([#6])(=[O,S])-[O,S])] | @atom:394 | 0.28 | "Me MePhosphonate CH3-O"
H | HC | opls_454 | [$([#1][#6][O][PD4]([#6])(=[O,S])-[O,S])] | @atom:395 | -0.02 | "Me MePhosphonate CH3-O"
C | CT | opls_455 | [$([#6][PD4](=[O,S])(-[O,S])[OD2])] | @atom:396 | -0.51 | "Me MePhosphonate CH3-P"
H | HC | opls_456 | [$([#1][#6][PD4](=[O,S])(-[O,S])[OD2])] | @atom:397 | 0.08 | "Me MePhosphonate CH3-P"
C | CA | opls_457 | [$([c][#6][O][PD4](=[O,S])[OD2])] | @atom:398 | -0.14 | "Bz MePhosphonate Cipso"
C | CT | opls_458 | [$([#6](c)[O][PD4](=[O,S])[OD2])] | @atom:399 | 0.32 | "Bz MePhosphonate CH3-O"
H | HC | opls_459 | [$([#1][#6](c)[O][PD4](=[O,S])[OD2])] | @atom:400 | 0.02 | "Bz MePhosphonate CH3-O"
C | CA | opls_460 | [$([c][#6][PD4](=[O,S])(O)[OD2])] | @atom:401 | -0.04 | "Me BzPhosphonate Cipso"
C | CT | opls_461 | [$([#6](c)[PD4](=[O,S])(O)[OD2])] | @atom:402 | -0.47 | "Me BzPhosphonate CH3-P"
H | HC | opls_462 | [$([#1][#6](c)[PD4](=[O,S])(O)[OD2])] | @atom:403 | 0.12 | "Me BzPhosphonate CH3-P"
C | CA | opls_463 | [$([c][#8][PD4](=[O,S])([OD1])[OD1])] | @atom:404 | 0.14 | "Ph Phosphate Cipso"
* no 464 in opls.par
C | C_2 | opls_465 | [$([#6D3](=[O,S])[O][#6])] | @atom:406 | 0.51 | "Ester -COOR"
O | O_2 | opls_466 | [$([O]=[#6D3][O][#6])] | @atom:407 | -0.43 | "Ester C=O"
O | OS | opls_467 | [$([O]([#6])[#6D3]=[O,S])] | @atom:408 | -0.33 | "Ester CO-O-R"
C | CT | opls_468 | [$([CH3][O][CD3]=[O,S])] | @atom:409 | 0.16 | "Methyl Ester -OCH3"
H | HC | opls_469 | [$([#1][CD4][O][CD3]=[O,S])] | @atom:410 | 0.03 | "Ester -OCH<"
C | C | opls_470 | [$([CD3]([c])(=[O,S])[O])] | @atom:411 | 0.635 | "Benzoic Acid -COOH"
C | C | opls_471 | [$([CD3]([c])(=[O,S])[O][CD4])] | @atom:412 | 0.625 | "Aryl Ester -COOR"
C | CA | opls_472 | [$([c][O][CD3]=[O,S])] | @atom:413 | 0.135 | "Phenyl Ester Cipso"
O | OS | opls_473 | [$([O]([c])[CD3]=[O,S])] | @atom:414 | -0.215 | "Phenyl Ester -OPh"
S | SY | opls_474 | [$([SH0D3](=O))] | @atom:415 | 1.48 | "Sulfonamide -SO2N<"
S | SY | opls_474 | [$([SH0D4](=O)(=O)[N,O])] | @atom:415 | 1.48 | "Sulfonamide -SO2N<"
O | OY | opls_475 | [$([O]=[SH0D4](=O)[N,O])] | @atom:416 | -0.68 | "Sulfonamide -SO2N<"
C | CT | opls_476 | [$([CH3D4][SH0D4](=O)(=O)[N,O])] | @atom:417 | -0.54 | "Sulfonamide CH3-S"
H | HC | opls_477 | [$([#1][CH3D4][SH0D4](=O)(=O)[N,O])] | @atom:418 | 0.18 | "Sulfonamide CH3-S"
N | N | opls_478 | [$([NH2D3][SH0D4](=O)=[O])] | @atom:419 | -1.0 | "Sulfonamide -SO2NH2"
H | H | opls_479 | [$([#1][NH2D3][SH0D4](=O)=[O])] | @atom:420 | 0.44 | "Sulfonamide -SO2NH2"
N | N | opls_480 | [$([NH1D3][SH0D4](=O)=[O])] | @atom:421 | -0.8 | "Sulfonamide -SO2NHR"
H | H | opls_481 | [$([#1][NH1D3][SH0D4](=O)=[O])] | @atom:422 | 0.41 | "Sulfonamide -SO2NHR"
C | CT | opls_482 | [$([CH3D4][ND3][SH0D4](=O)=[O])] | @atom:423 | 0.18 | "N-Me Sulfonamide CH3-"
H | HC | opls_483 | [$([#1][CH3D4][ND3][SH0D4](=O)=[O])] | @atom:424 | 0.03 | "N-Me Sulfonamide CH3-"
C | CT | opls_484 | [$([CH2D4][ND3][SH0D4](=O)=[O])] | @atom:425 | 0.39 | "Sulfonamide N-CH2-R"
H | HC | opls_485 | [$([#1][CH2D4][ND3][SH0D4](=O)=[O])] | @atom:426 | -0.06 | "Sulfonamide N-CH2-R"
C | CT | opls_486 | [$([CH3D4][CD4][ND3][SH0D4](=O)=[O])] | @atom:427 | -0.18 | "N-Et Sulfonamide CH3-"
H | HC | opls_487 | [$([#1][CH3D4][CD4][ND3][SH0D4](=O)=[O])] | @atom:428 | 0.06 | "N-Et Sulfonamide CH3-"
C | CA | opls_488 | [$([c][SH0D4](=O)(=O)[N,O])] | @atom:429 | 0.0 | "Aryl Sulfonamide C-SO2N"
* no opls_489 in opls.par
C | CT | opls_490 | [$([CH2D4]([#6])[O][CD3]=[O])] | @atom:431 | 0.19 | "Et Ester -OCH2R"
C | CT | opls_491 | [$([CH1D4]([#6])([#6])[O][CD3]=[O])] | @atom:432 | 0.22 | "i-Pr Ester -OCHR2"
C | CT | opls_492 | [$([CH0D4]([#6])([#6])([#6])[O][CD3]=[O])] | @atom:433 | 0.25 | "t-Bu Ester -OCR3"
S | SY2 | opls_493 | [$([SD4](=O)=[O])] | @atom:434 | 1.374 | "Sulfone R-SO2-R"
O | OY | opls_494 | [$([O]=[SD4]=[O])] | @atom:435 | -0.687 | "Sulfone R-SO2-R"
*S | SZ | opls_496 | [$([SD3]=[O])] | @atom:436 | 0.245 | "Alkyl Aryl Sulfoxide" ??
* which is which @atom:437 0.13 # "Dialkyl Sulfoxide"
O | OY | opls_497 | [$([O]=[SD3])] | @atom:438 | -0.42 | "Sulfoxide R-SO-R"
C | CT | opls_498 | [$([CH3D4][SD3]=[O])] | @atom:439 | -0.035 | "Sulfoxide CH3-SO-R"
C | CT | opls_499 | [$([CH2D4][SD3]=[O])] | @atom:440 | 0.025 | "Sulfoxide -CH2-SO-R"
C | C* | opls_500 | [$([c]1([CH2D4])cnc2c1cccc2)] | @atom:441 | 0.075 | "TRP CG"
* Is 501 correct? --note from opls.par [AHS]
C | CB | opls_501 | [$([c]1nc2c(c1[CH2D4])cccc2)] | @atom:442 | -0.055 | "TRP CD"
C | CN | opls_502 | [$([c]1(ncc2([CH2D4]))c2cccc1)] | @atom:443 | 0.13 | "TRP CE"
N | NA | opls_503 | [$([nD3]1c2c(c([CH2D4])c1)cccc2)] | @atom:444 | -0.57 | "TRP NE, HID ND & HIE NE" only hits TRP--AHS
H | H | opls_504 | [$([#1][nD3]1c2c(c([CH2D4])c1)cccc2)] | @atom:445 | 0.42 | "TRP HNE & HID/HIE HN" only hits TRPH+ --AHS
C | CT | opls_505 | [$([CH2D4]([CH1D4][NH2D3])c1ncnc1)] | @atom:446 | -0.005 | "HIS CB"
C | CR | opls_506 | [$([c]1[nD3]cc[nD2]1)] | @atom:447 | 0.295 | "HID & HIE CE1"
C | CV | opls_507 | [$([c]1[nD2]c[nD3]c1)] | @atom:448 | -0.015 | "HID CD2 & HIE CG"
C | CW | opls_508 | [$([c]1[nD3]c[nD2]c1)] | @atom:449 | 0.015 | "HID CG & HIE CD2"
C | CR | opls_509 | [$([c]1[nD3]cc[nD3]1)] | @atom:450 | 0.385 | "HIP CE1"
C | CX | opls_510 | [$([c]1[nD3]c[nD3]c1)] | @atom:451 | 0.215 | "HIP CG & CD2"
N | NB | opls_511 | [$([nD2]1c[nD3]cc1)] | @atom:452 | -0.49 | "HID NE & HIE ND"
N | NA | opls_512 | [$([nD3]1c[nD3]cc1)] | @atom:453 | -0.54 | "HIP ND & NE"
H | H | opls_513 | [$([#1][nD3]1c[nD3]cc1)] | @atom:454 | 0.46 | "HIP HND & HNE"
C | CW | opls_514 | [$([c]1(cccc2)c2ncc1[CH2D4])] | @atom:455 | -0.115 | "TRP CD1"
C | CT | opls_515 | [$([CH1D4][c])] | @atom:456 | 0.055 | "i-Pr Benzene -CHMe2"
C | CT | opls_516 | [$([CH0D4][c])] | @atom:457 | 0.115 | "t-Bu Benzene -CMe3"
* Are 517 and 518 correct? --note from OPLS.par
C | CM | opls_517 | [$([CH1D3](=[CD3])[O][CD4])] | @atom:458 | -0.03 | "Vinyl Ether =CH-OR"
C | CM | opls_518 | [$([CH0D3](=[CD3])[O][CD4])] | @atom:459 | 0.085 | "Vinyl Ether =CR-OR"
* no opls_519 in opls.par,
N | NC | opls_520 | [$([nD2]1ccccc1)] | @atom:461 | -0.678 | "Pyridine N"
C | CA | opls_521 | [$([c]1cccc[nD2]1)] | @atom:462 | 0.473 | "Pyridine C1"
C | CA | opls_522 | [$([c]1ccc[nD2]c1)] | @atom:463 | -0.447 | "Pyridine C2"
C | CA | opls_523 | [$([c]1cc[nD2]cc1)] | @atom:464 | 0.227 | "Pyridine C3"
H | HA | opls_524 | [$([#1]c1cccc[nD2]1)] | @atom:465 | 0.012 | "Pyridine H1"
H | HA | opls_525 | [$([#1]c1ccc[nD2]c1)] | @atom:466 | 0.155 | "Pyridine H2"
H | HA | opls_526 | [$([#1]c1cc[nD2]cc1)] | @atom:467 | 0.065 | "Pyridine H3"
N | NC | opls_527 | [$([nD2]1cc[nD2]cc1)] | @atom:468 | -0.468 | "Pyrazine N"
C | CA | opls_528 | [$([c]1[nD2]cc[nD2]c1)] | @atom:469 | 0.192 | "Pyrazine CH"
H | HA | opls_529 | [$([#1]c1[nD2]cc[nD2]c1)] | @atom:470 | 0.042 | "Pyrazine CH"
N | NC | opls_530 | [$([nD2]1c[nD2]ccc1)] | @atom:471 | -0.839 | "Pyrimidine N"
C | CQ | opls_531 | [$([c]1[nD2]ccc[nD2]1)] | @atom:472 | 0.874 | "Pyrimidine C2"
C | CA | opls_532 | [$([c]1cc[nD2]c[nD2]1)] | @atom:473 | 0.653 | "Pyrimidine C4"
C | CA | opls_533 | [$([c]1c[nD2]c[nD2]c1)] | @atom:474 | -0.689 | "Pyrimidine C5"
H | HA | opls_534 | [$([#1]c1[nD2]ccc[nD2]1)] | @atom:475 | -0.032 | "Pyrimidine HC2"
H | HA | opls_535 | [$([#1]c1cc[nD2]c[nD2]1)] | @atom:476 | 0.011 | "Pyrimidine HC4"
H | HA | opls_536 | [$([#1]c1c[nD2]c[nD2]c1)] | @atom:477 | 0.197 | "Pyrimidine HC5"
N | NC | opls_537 | [$([nD2]1[nD2]cccc1)] | @atom:478 | -0.331 | "Pyridazine N"
C | CA | opls_538 | [$([c]1[nD2][nD2]ccc1)] | @atom:479 | 0.378 | "Pyridazine C3"
C | CA | opls_539 | [$([c]1c[nD2][nD2]cc1)] | @atom:480 | -0.16 | "Pyridazine C4"
H | HA | opls_540 | [$([#1][c]1[nD2][nD2]ccc1)] | @atom:481 | -0.009 | "Pyridazine HC3"
H | HA | opls_541 | [$([#1][c]1c[nD2][nD2]cc1)] | @atom:482 | 0.122 | "Pyridazine HC4"
N | NA | opls_542 | [$([nD3]1cccc1)] | @atom:483 | -0.239 | "Pyrrole N"
C | CW | opls_543 | [$([c]1ccc[nD3]1)] | @atom:484 | -0.163 | "Pyrrole C2"
C | CS | opls_544 | [$([c]1cc[nD3]c1)] | @atom:485 | -0.149 | "Pyrrole C3"
H | H | opls_545 | [$([#1][nD3]1cccc1)] | @atom:486 | 0.317 | "Pyrrole HN"
H | HA | opls_546 | [$([#1][c]1ccc[nD3]1)] | @atom:487 | 0.155 | "Pyrrole HC2"
H | HA | opls_547 | [$([#1][c]1cc[nD3]c1)] | @atom:488 | 0.118 | "Pyrrole HC3"
N | NA | opls_548 | [$([nD3]1[nD2]ccc1)] | @atom:489 | -0.059 | "Pyrazole N1"
N | NB | opls_549 | [$([nD2]1ccc[nD3]1)] | @atom:490 | -0.491 | "Pyrazole N2"
C | CU | opls_550 | [$([c]1cc[nD3][nD2]1)] | @atom:491 | 0.246 | "Pyrazole C3"
C | CA | opls_551 | [$([c]1c[nD3][nD2]c1)] | @atom:492 | -0.32 | "Pyrazole C4"
C | CW | opls_552 | [$([c]1[nD3][nD2]cc1)] | @atom:493 | -0.034 | "Pyrazole C5"
H | H | opls_553 | [$([#1][nD3]1[nD2]ccc1)] | @atom:494 | 0.301 | "Pyrazole HN1"
H | HA | opls_554 | [$([#1][c]1cc[nD3][nD2]1)] | @atom:495 | 0.072 | "Pyrazole HC3"
H | HA | opls_555 | [$([#1][c]1c[nD3][nD2]c1)] | @atom:496 | 0.15 | "Pyrazole HC4"
H | HA | opls_556 | [$([#1][c]1[nD3][nD2]cc1)] | @atom:497 | 0.135 | "Pyrazole HC5"
N | NA | opls_557 | [$([nD3]1c[nD2]cc1)] | @atom:498 | -0.257 | "Imidazole N1"
C | CR | opls_558 | [$([c]1[nD2]cc[nD3]1)] | @atom:499 | 0.275 | "Imidazole C2"
N | NB | opls_559 | [$([nD2]1cc[nD3]c1)] | @atom:500 | -0.563 | "Imidazole N3"
C | CV | opls_560 | [$([c]1c[nD3]c[nD2]1)] | @atom:501 | 0.185 | "Imidazole C4"
C | CW | opls_561 | [$([c]1[nD3]c[nD2]c1)] | @atom:502 | -0.286 | "Imidazole C5"
H | H | opls_562 | [$([#1][nD3]1c[nD2]cc1)] | @atom:503 | 0.306 | "Imidazole HN1"
H | HA | opls_563 | [$([#1][c]1[nD2]cc[nD3]1)] | @atom:504 | 0.078 | "Imidazole HC2"
H | HA | opls_564 | [$([#1][c]1c[nD3]c[nD2]1)] | @atom:505 | 0.075 | "Imidazole HC4"
H | HA | opls_565 | [$([#1][c]1[nD3]c[nD2]c1)] | @atom:506 | 0.187 | "Imidazole HC5"
O | OS | opls_566 | [$([o]1cccc1)] | @atom:507 | -0.19 | "Furan O"
C | CW | opls_567 | [$([c]1ccc[o,s]1)] | @atom:508 | -0.019 | "Furan C2"
C | CS | opls_568 | [$([c]1cc[o,s]c1)] | @atom:509 | -0.154 | "Furan C3"
H | HA | opls_569 | [$([#1][c]1ccc[o,s]1)] | @atom:510 | 0.142 | "Furan HC2"
H | HA | opls_570 | [$([#1][c]1cc[o,s]c1)] | @atom:511 | 0.126 | "Furan HC3"
O | OS | opls_571 | [$([o,s]1cncc1)] | @atom:512 | -0.257 | "Oxazole O"
C | CR | opls_572 | [$([c]1ncc[o,s]1)] | @atom:513 | 0.511 | "Oxazole C2"
N | NB | opls_573 | [$([n]1cc[o,s]c1)] | @atom:514 | -0.59 | "Oxazole N"
C | CV | opls_574 | [$([c]1c[o,s]cn1)] | @atom:515 | 0.169 | "Oxazole C4"
C | CW | opls_575 | [$([c]1[o,s]cnc1)] | @atom:516 | -0.148 | "Oxazole C5"
H | HA | opls_576 | [$([#1]c1ncc[o,s]1)] | @atom:517 | 0.043 | "Oxazole HC2"
H | HA | opls_577 | [$([#1]c1c[o,s]cn1)] | @atom:518 | 0.091 | "Oxazole HC4"
H | HA | opls_578 | [$([#1]c1[o,s]cnc1)] | @atom:519 | 0.181 | "Oxazole HC5"
* O | OS | opls_579 | [$([#8D2H0](~[#6])~[*])]
O | OS | opls_579 | [$([o,s]1nccc1)] | @atom:520 | -0.122 | "Isoxazole O"
N | NB | opls_580 | [$([n]1ccc[o,s]1)] | @atom:521 | -0.413 | "Isoxazole N"
C | CU | opls_581 | [$([c]1cc[o,s]n1)] | @atom:522 | 0.405 | "Isoxazole C3"
C | CA | opls_582 | [$([c]1c[o,s]nc1)] | @atom:523 | -0.455 | "Isoxazole C4"
C | CW | opls_583 | [$([c]1[o,s]ncc1)] | @atom:524 | 0.25 | "Isoxazole C5"
H | HA | opls_584 | [$([#1]c1cc[o,s]n1)] | @atom:525 | 0.053 | "Isoxazole HC3"
H | HA | opls_585 | [$([#1]c1c[o,s]nc1)] | @atom:526 | 0.184 | "Isoxazole HC4"
H | HA | opls_586 | [$([#1]c1[o,s]ncc1)] | @atom:527 | 0.098 | "Isoxazole HC5"
** not sure why indole atom types are corrected --AHS
* N | NA | opls_587 | [$([n]1ccc2c1cccc2)]
N | NA | opls_587 | [$([#7]1[#6][#6][#6]2[#6]1[#6][#6][#6][#6]2)] | @atom:528 | -0.5 | "Indole N1"
* C | CW | opls_588 | [$([c]1cc2ccccc2n1)]
C | CW | opls_588 | [$([#6]1[#6][#6]2[#6][#6][#6][#6][#6]2[#7]1)] | @atom:529 | 0.001 | "Indole C2"
* C | CS | opls_589 | [$([c]1c2ccccc2nc1)]
C | CS | opls_589 | [$([#6]1[#6]2[#6][#6][#6][#6][#6]2[#7][#6]1)] | @atom:530 | -0.39 | "Indole C3"
* C | CA | opls_590 | [$([c]1cccc2c1ccn2)]
C | CA | opls_590 | [$([#6]1[#6][#6][#6][#6]2[#6]1[#6][#6][#7]2)] | @atom:531 | -0.27 | "Indole C4"
* C | CA | opls_591 | [$([c]1ccc2nccc2c1)]
C | CA | opls_591 | [$([#6]1[#6][#6][#6]2[#7][#6][#6][#6]2[#6]1)] | @atom:532 | -0.127 | "Indole C5"
* C | CA | opls_592 | [$([c]1cc2nccc2cc1)]
C | CA | opls_592 | [$([#6]1[#6][#6]2[#7][#6][#6][#6]2[#6][#6]1)] | @atom:533 | -0.108 | "Indole C6"
* C | CA | opls_593 | [$([c]1c2nccc2ccc1)]
C | CA | opls_593 | [$([#6]1[#6]2[#7][#6][#6][#6]2[#6][#6][#6]1)] | @atom:534 | -0.258 | "Indole C7"
* C | CN | opls_594 | [$([c]1(c2cccc1)ncc2)]
C | CN | opls_594 | [$([#6]1([#6]2[#6][#6][#6][#6]1)[#7][#6][#6]2)] | @atom:535 | 0.22 | "Indole C8"
* C | CB | opls_595 | [$([c]1(c2cccc1)ccn2)]
C | CB | opls_595 | [$([#6]1([#6]2[#6][#6][#6][#6]1)[#6][#6][#7]2)] | @atom:536 | 0.225 | "Indole C9"
* H | H | opls_596 | [$([#1]n1ccc2c1cccc2)]
H | H | opls_596 | [$([#1][#7]1[#6][#6][#6]2[#6]1[#6][#6][#6][#6]2)] | @atom:537 | 0.376 | "Indole HN1"
* H | HA | opls_597 | [$([#1]c1cc2ccccc2n1)]
H | HA | opls_597 | [$([#1][#6]1[#6][#6]2[#6][#6][#6][#6][#6]2[#7]1)] | @atom:538 | 0.147 | "Indole HC2"
* H | HA | opls_598 | [$([#1]c1c2ccccc2nc1)]
H | HA | opls_598 | [$([#1][#6]1[#6]2[#6][#6][#6][#6][#6]2[#7][#6]1)] | @atom:539 | 0.172 | "Indole HC3"
* H | HA | opls_599 | [$([#1]c1cccc2c1ccn2)]
H | HA | opls_599 | [$([#1][#6]1[#6][#6][#6][#6]2[#6]1[#6][#6][#7]2)] | @atom:540 | 0.155 | "Indole HC4"
* H | HA | opls_600 | [$([#1]c1ccc2nccc2c1)]
H | HA | opls_600 | [$([#1][#6]1[#6][#6][#6]2[#7][#6][#6][#6]2[#6]1)] | @atom:541 | 0.107 | "Indole HC5"
* H | HA | opls_601 | [$([#1]c1cc2nccc2cc1)]
H | HA | opls_601 | [$([#1][#6]1[#6][#6]2[#7][#6][#6][#6]2[#6][#6]1)] | @atom:542 | 0.11 | "Indole HC6"
* H | HA | opls_602 | [$([#1]c1c2nccc2ccc1)]
H | HA | opls_602 | [$([#1][#6]1[#6]2[#7][#6][#6][#6]2[#6][#6][#6]1)] | @atom:543 | 0.14 | "Indole HC7"
N | NC | opls_603 | [$([n]1cccc2c1cccc2)] | @atom:544 | -0.694 | "Quinoline N1"
C | CA | opls_604 | [$([c]1ccc2ccccc2n1)] | @atom:545 | 0.425 | "Quinoline C2"
C | CA | opls_605 | [$([c]1cc2ccccc2nc1)] | @atom:546 | -0.359 | "Quinoline C3"
C | CA | opls_606 | [$([c]1c2ccccc2ncc1)] | @atom:547 | -0.008 | "Quinoline C4"
C | CA | opls_607 | [$([c]1cccc2c1cccn2)] | @atom:548 | -0.197 | "Quinoline C5"
C | CA | opls_608 | [$([c]1ccc2ncccc2c1)] | @atom:549 | -0.112 | "Quinoline C6"
C | CA | opls_609 | [$([c]1cc2ncccc2cc1)] | @atom:550 | -0.07 | "Quinoline C7"
C | CA | opls_610 | [$([c]1c2ncccc2ccc1)] | @atom:551 | -0.307 | "Quinoline C8"
C | CA | opls_611 | [$([c]1(c2cccc1)nccc2)] | @atom:552 | 0.563 | "Quinoline C9"
C | CA | opls_612 | [$([c]1(c2cccc1)cccn2)] | @atom:553 | -0.051 | "Quinoline C10"
H | HA | opls_613 | [$([#1]c1ccc2ccccc2n1)] | @atom:554 | 0.028 | "Quinoline HC2"
H | HA | opls_614 | [$([#1]c1cc2ccccc2nc1)] | @atom:555 | 0.146 | "Quinoline HC3"
H | HA | opls_615 | [$([#1]c1c2ccccc2ncc1)] | @atom:556 | 0.119 | "Quinoline HC4"
H | HA | opls_616 | [$([#1]c1cccc2c1cccn2)] | @atom:557 | 0.133 | "Quinoline HC5"
H | HA | opls_617 | [$([#1]c1ccc2ncccc2c1)] | @atom:558 | 0.113 | "Quinoline HC6"
H | HA | opls_618 | [$([#1]c1cc2ncccc2cc1)] | @atom:559 | 0.114 | "Quinoline HC7"
H | HA | opls_619 | [$([#1]c1c2ncccc2ccc1)] | @atom:560 | 0.157 | "Quinoline HC8"
N | NC | opls_620 | [$([n]1cnc2c(c1)ncn2)] | @atom:561 | -0.76 | "Purine N1"
C | CQ | opls_621 | [$([c]1nc2c(cn1)ncn2)] | @atom:562 | 0.679 | "Purine C2"
N | NC | opls_622 | [$([n]1c2c(cnc1)ncn2)] | @atom:563 | -0.788 | "Purine N3"
C | CB | opls_623 | [$([c]1(c2ncn1)ncnc2)] | @atom:564 | 0.736 | "Purine C4"
C | CB | opls_624 | [$([c]1(c2ncn1)cncn2)] | @atom:565 | 0.038 | "Purine C5"
C | CA | opls_625 | [$([c]1ncnc2c1ncn2)] | @atom:566 | 0.343 | "Purine C6"
N | NB | opls_626 | [$([n]1cnc2c1cncn2)] | @atom:567 | -0.642 | "Purine N7"
C | CK | opls_627 | [$([c]1nc2c(n1)cncn2)] | @atom:568 | 0.452 | "Purine C8"
N | NA | opls_628 | [$([n]1c2c(nc1)cncn2)] | @atom:569 | -0.682 | "Purine N9"
H | HA | opls_629 | [$([#1][c]1nc2c(cn1)ncn2)] | @atom:570 | 0.024 | "Purine HC2"
H | HA | opls_630 | [$([#1][c]1ncnc2c1ncn2)] | @atom:571 | 0.101 | "Purine HC6"
H | HA | opls_631 | [$([#1][c]1nc2c(n1)cncn2)] | @atom:572 | 0.086 | "Purine HC8"
H | H | opls_632 | [$([#1][n]1c2c(nc1)cncn2)] | @atom:573 | 0.413 | "Purine HN9"
S | S | opls_633 | [$([s]1cncc1)] | @atom:574 | -0.03 | "Thiazole S"
S | S | opls_633 | [$([s]1cccc1)] | @atom:574 | -0.03 | "Thiazole S"
C | CR | opls_634 | [$([c]1nccs1)] | @atom:575 | 0.242 | "Thiazole C2"
N | NB | opls_635 | [$([n]1ccsc1)] | @atom:576 | -0.515 | "Thiazole N"
C | CV | opls_636 | [$([c]1cscn1)] | @atom:577 | 0.228 | "Thiazole C4"
C | CW | opls_637 | [$([c]1scnc1)] | @atom:578 | -0.299 | "Thiazole C5"
H | HA | opls_638 | [$([#1][c]1nccs1)] | @atom:579 | 0.101 | "Thiazole HC2"
H | HA | opls_639 | [$([#1][c]1cscn1)] | @atom:580 | 0.068 | "Thiazole HC4"
H | HA | opls_640 | [$([#1][c]1scnc1)] | @atom:581 | 0.205 | "Thiazole HC5"
N | NC | opls_641 | [$([n]1cncnc1)] | @atom:582 | -0.951 | "1,3,5-Triazine N"
C | CQ | opls_642 | [$([c]1ncncn1)] | @atom:583 | 0.965 | "1,3,5-Triazine CH"
H | HA | opls_643 | [$([#1][c]1ncncn1)] | @atom:584 | -0.014 | "1,3,5-Triazine CH"
C | CA | opls_644 | [$([c]1([OH])ccc2c(c1)ccn2)] | @atom:585 | 0.13 | "Serotonin C5-OH"
C | CT | opls_645 | [$([CH2D4]c1cnc2c1cc([OH])cc2)] | @atom:586 | 0.052 | "Serotonin CH2 on C3"
N | NC | opls_646 | [$([nR1]1[cR2]2[cR2]([cR1][cR1][cR2][cR2]2)[cR1][cR1][cR1]1)] | @atom:587 | -0.599 | "1,10-Phenanthroline N"
C | CA | opls_647 | [$([cR1]1[nR1][cR2]2[cR2]([cR1][cR1][cR2][cR2]2)[cR1][cR1]1)] | @atom:588 | 0.392 | "1,10-Phenanthroline C2"
C | CA | opls_648 | [$([cR1]1[cR1][nR1][cR2]2[cR2]([cR1][cR1][cR2][cR2]2)[cR1]1)] | @atom:589 | -0.348 | "1,10-Phenanthroline C3"
C | CA | opls_649 | [$([cR1]1[cR1][cR1][nR1][cR2]2[cR2]1[cR1][cR1][cR2][cR2]2)] | @atom:590 | 0.02 | "1,10-Phenanthroline C4"
C | CA | opls_650 | [$([cR2]1([cR1][cR1][cR1][nR1]2)[cR2]2[cR2][cR2][cR1][cR1]1)] | @atom:591 | -0.042 | "1,10-Phenanthroline C12"
C | CA | opls_651 | [$([cR2]1([nR1][cR1][cR1][cR1]2)[cR2]2[cR1][cR1][cR2][cR2]1)] | @atom:592 | 0.347 | "1,10-Phenanthroline C11"
C | CA | opls_652 | [$([cR1]([cR1][cR2]1)[cR2]2[cR1][cR1][cR1][nR1][cR2]2[cR2]1)] | @atom:593 | -0.196 | "1,10-Phenanthroline C5"
H | HA | opls_653 | [$([#1][cR1]1[nR1][cR2]2[cR2]([cR1][cR1][cR2][cR2]2)[cR1][cR1]1)] | @atom:594 | 0.032 | "1,10-Phenanthroline HC2"
H | HA | opls_654 | [$([#1][cR1]1[cR1][nR1][cR2]2[cR2]([cR1][cR1][cR2][cR2]2)[cR1]1)] | @atom:595 | 0.146 | "1,10-Phenanthroline HC3"
H | HA | opls_655 | [$([#1][cR1]1[cR1][cR1][nR1][cR2]2[cR2]1[cR1][cR1][cR2][cR2]2)] | @atom:596 | 0.108 | "1,10-Phenanthroline HC4"
H | HA | opls_656 | [$([#1][cR1]([cR1][cR2]1)[cR2]2[cR1][cR1][cR1][nR1][cR2]2[cR2]1)] | @atom:597 | 0.14 | "1,10-Phenanthroline HC5"
* opls_657-669 not in opls.par
C | CT | opls_670 | [$([CH3D4][cr6]([cr6])[nr6])] | @atom:611 | -0.168 | "2-Me Pyridine CH3"
C | CT | opls_671 | [$([CH2D4][cr6]([cr6])[nr6])] | @atom:612 | -0.108 | "2-Et Pyridine CH2"
C | CT | opls_672 | [$([CH3D4][cr6]([cr6])[cr6][nr6])] | @atom:613 | -0.189 | "3-Me Pyridazine CH3"
C | CT | opls_673 | [$([CH2D4][cr6]([cr6])[cr6][nr6])] | @atom:614 | -0.129 | "3-Et Pyridazine CH2"
C | CT | opls_674 | [$([CH3D4][cr6]([cr6])[cr6][cr6][nr6])] | @atom:615 | -0.169 | "4-Me Pyrimidine CH3"
C | CT | opls_675 | [$([CH2D4][cr6]([cr6])[cr6][cr6][nr6])] | @atom:616 | -0.109 | "4-Et Pyrimidine CH2"
C | CT | opls_676 | [$([CH3D4][cr6]([cr6][nr6])[nr6])] | @atom:617 | -0.138 | "2-Me Pyrazine CH3"
C | CT | opls_677 | [$([CH2D4][cr6]([cr6][nr6])[nr6])] | @atom:618 | -0.078 | "2-Et Pyrazine CH2"
C | CT | opls_678 | [$([CH3D4][cr5]([cr5])[nr5])] | @atom:619 | -0.025 | "2-Me Pyrrole CH3"
C | CT | opls_679 | [$([CH2D4][cr5]([cr5])[nr5])] | @atom:620 | 0.035 | "2-Et Pyrrole CH2"
C | CT | opls_680 | [$([CH3D4][cr5]([cr5])[or5])] | @atom:621 | -0.038 | "2-Me Furan CH3"
C | CT | opls_681 | [$([CH2D4][cr5]([cr5])[or5])] | @atom:622 | 0.022 | "2-Et Furan CH2"
* opls 682-699 not in opls.par
C | C+ | opls_700 | [$([CH0+]([CH3D4])([CH3D4])[CH3D4])] | @atom:641 | 0.619 | "t-Butyl Cation C+"
C | CT | opls_701 | [$([CH3D4][CH0+]([CH3D4])[CH3D4])] | @atom:642 | -0.395 | "t-Butyl Cation CH3-"
H | HC | opls_702 | [$([#1][CH3D4][CH0+]([CH3D4])[CH3D4])] | @atom:643 | 0.174 | "t-Butyl Cation CH3-"
* opls 703-710 not in opls.par
C | CY | opls_711 | [$([CH2D4]1[CD4][CD4]1)] | @atom:652 | -0.12 | "Cyclopropane -CH2-"
C | CY | opls_712 | [$([CH1D4]1[CD4][CD4]1)] | @atom:653 | -0.06 | "Cyclopropane -CHR-"
C | CY | opls_713 | [$([CH0D4]1[CD4][CD4]1)] | @atom:654 | 0.0 | "Cyclopropane -CR2-"
C | CA | opls_714 | [$([c]1cccc1)] | @atom:655 | -0.23 | "Cyclopentadienyl Anion"
H | HA | opls_715 | [$([#1][c]1cccc1)] | @atom:656 | 0.03 | "Cyclopentadienyl Anion"
* opls 716-717 not in opls.par
C | CA | opls_718 | [$([c][F])] | @atom:659 | 0.22 | "Fluorobenzene CF"
F | F | opls_719 | [$([F][c])] | @atom:660 | -0.22 | "Fluorobenzene CF"
C | CA | opls_720 | [$([c](F)[c](F)[c](F)[c](F)[c](F)[c](F))] | @atom:661 | 0.13 | "Hexafluorobenzene CF"
F | F | opls_721 | [$([F][c][c](F)[c](F)[c](F)[c](F)[c](F))] | @atom:662 | -0.13 | "Hexafluorobenzene CF"
* opls 722-723 confusing in opls.par
C | CA | opls_724 | [$([c][CD4](F)(F)[F])] | @atom:665 | 0.15 | "TrifluoroMeBenzene C-CF3"
C | CT | opls_725 | [$([CD4](c)(F)(F)[F])] | @atom:666 | 0.45 | "TrifluoroMeBenzene CF3-"
F | F | opls_726 | [$([F][CD4](c)(F)[F])] | @atom:667 | -0.2 | "TrifluoroMeBenzene CF3-"
C | CA | opls_727 | [$([c](F)[c](F))] | @atom:668 | 0.2 | "Difluorobenzene CF"
C | CA | opls_727 | [$([c](F)[c][c](F))] | @atom:668 | 0.2 | "Difluorobenzene CF"
C | CA | opls_727 | [$([c](F)[c][c][c](F))] | @atom:668 | 0.2 | "Difluorobenzene CF"
F | F | opls_728 | [$([F][c][c][F])] | @atom:669 | -0.2 | "Difluorobenzene CF"
F | F | opls_728 | [$([F][c][c][c][F])] | @atom:669 | -0.2 | "Difluorobenzene CF"
F | F | opls_728 | [$([F][c][c][c][c][F])] | @atom:669 | -0.2 | "Difluorobenzene CF"
C | CA | opls_729 | [$([c][Br])] | @atom:670 | 0.2 | "Bromobenzene CBr"
Br | Br | opls_730 | [$([Br][#6])] | @atom:671 | -0.2 | "Bromobenzene CBr"
C | CA | opls_731 | [$([c][I])] | @atom:672 | 0.1 | "Iodobenzene CI"
I | I | opls_732 | [$([I][#6])] | @atom:673 | -0.1 | "Iodobenzene CI"
C | CY | opls_733 | [$([CH1D4r3](c)[CD4r3][CD4r3])] | @atom:674 | 0.055 | "cProp/cBut Benzene C-Ar"
S | SH | opls_734 | [$([SH1D2][c])] | @atom:675 | -0.22 | "Thiophenol SH"
C | CA | opls_735 | [$([c][SH1D2])] | @atom:676 | 0.065 | "Thiophenol C-SH"
C | CA | opls_736 | [$([c][c][c][c][#6D3](~[#7H2D3])~[#7H2D3])] | @atom:677 | 0.013 | "Benzamidine CG"
C | CA | opls_737 | [$([c][c][c][#6D3](~[#7H2D3])~[#7H2D3])] | @atom:678 | -0.106 | "Benzamidine CD"
C | CA | opls_738 | [$([c][c][#6D3](~[#7H2D3])~[#7H2D3])] | @atom:679 | -0.09 | "Benzamidine CE"
C | CA | opls_739 | [$([c][#6D3](~[#7H2D3])~[#7H2D3])] | @atom:680 | -0.119 | "Benzamidine CZ"
H | HA | opls_740 | [$([#1][c][c][c][#6D3](~[#7H2D3])~[#7H2D3])] | @atom:681 | 0.141 | "Benzamidine HCD"
H | HA | opls_741 | [$([#1][c][c][#6D3](~[#7H2D3])~[#7H2D3])] | @atom:682 | 0.129 | "Benzamidine HCE"
C | CA | opls_742 | [$([#6D3](~[#7H2D3])~[#7H2D3])] | @atom:683 | 0.827 | "Benzamidine C+"
N | N2 | opls_743 | [$([#7H2D3]~[#6D3](c)~[#7H2D3])] | @atom:684 | -0.885 | "Benzamidine -NH2"
H | H | opls_744 | [$([#1][#7H2D3]~[#6D3](~[#7H2D3])[c])] | @atom:685 | 0.426 | "Benzamidine H1-N"
H | H | opls_745 | [$([#1][#7H2D3]~[#6D3](~[#7H2D3])[c])] | @atom:686 | 0.465 | "Benzamidine H2-N"
H | HA | opls_746 | [$([#1][c][c][c][c][#6D3](~[#7H2D3])~[#7H2D3])] | @atom:687 | 0.119 | "Benzamidine HCG"
C | CT | opls_747 | [$([CH3D4][#7D2][#6D4]([#7D3])[#7D3])] | @atom:688 | -0.02 | "Neutral MeGdn CH3-"
C | CT | opls_748 | [$([CH2D4][#7H1D3][#6D3]([#7H2D3])[#7H1D2])] | @atom:689 | 0.04 | "Neutral ARG CD"
N | NY | opls_749 | [$([#7H1D3][#6D3]([#7H2D3])[#7H1D2])] | @atom:690 | -0.62 | "Neutral ARG NE"
N | NZ | opls_750 | [$([#7H1D2][#6D3]([#7H2D3])[#7H1D3])] | @atom:691 | -0.785 | "Neutral ARG N1 (HN=C)"
N | NY | opls_751 | [$([#7H2D3][#6D3]([#7H1D2])[#7H1D3])] | @atom:692 | -0.785 | "Neutral ARG N2 (H2N-C)"
C | CA | opls_752 | [$([#6D3]([#7H1D2])([#7H2D3])[#7H1D3])] | @atom:693 | 0.55 | "Neutral ARG CZ (>C=)"
N | NZ | opls_753 | [$([ND1]#[CD2])] | @atom:694 | -0.56 | "Alkyl Nitrile -CN"
C | CZ | opls_754 | [$([CD2]#[ND1])] | @atom:695 | 0.46 | "Alkyl Nitrile -CN"
C | CT | opls_755 | [$([CH3D4][CD2]#[ND1])] | @atom:696 | -0.08 | "Acetonitrile CH3-CN"
C | CT | opls_756 | [$([CH2D4][CD2]#[ND1])] | @atom:697 | -0.02 | "Alkyl Nitrile RCH2-CN"
C | CT | opls_757 | [$([CH1D4][CD2]#[ND1])] | @atom:698 | 0.04 | "Alkyl Nitrile R2CH-CN"
C | CT | opls_758 | [$([CH0D4][CD2]#[ND1])] | @atom:699 | 0.1 | "Alkyl Nitrile R3C-CN"
H | HC | opls_759 | [$([#1][CD4][CD2]#[ND1])] | @atom:700 | 0.06 | "Alkyl Nitrile H-C-CN"
N | NO | opls_760 | [$([#7D3]([!c])(~[#8])~[#8])] | @atom:701 | 0.54 | "Nitroalkane -NO2"
O | ON | opls_761 | [$([#8D1]~[#7D3]~[#8D1])] | @atom:702 | -0.37 | "Nitroalkane -NO2"
C | CT | opls_762 | [$([CH3D4][#7D3](~[#8])~[#8])] | @atom:703 | 0.02 | "Nitromethane CH3-NO2"
H | HC | opls_763 | [$([#1][CD4][#7D3](~[#8])~[#8])] | @atom:704 | 0.06 | "Nitroalkane H-C-NO2"
C | CT | opls_764 | [$([CH2D4][#7D3](~[#8])~[#8])] | @atom:705 | 0.08 | "Nitroalkane RCH2-NO2"
C | CT | opls_765 | [$([CH1D4][#7D3](~[#8])~[#8])] | @atom:706 | 0.14 | "Nitroalkane R2CH-NO2"
C | CT | opls_766 | [$([CH0D4][#7D3](~[#8])~[#8])] | @atom:707 | 0.2 | "Nitroalkane R3C-NO2"
N | NO | opls_767 | [$([#7D3](c)(~[#8D1])~[#8D1])] | @atom:708 | 0.65 | "Nitrobenzene -NO2"
C | CA | opls_768 | [$([c][#7D3](~[#8])~[#8])] | @atom:709 | 0.09 | "Nitrobenzene C-NO2"
* 769-770 not in opls.par
O | O | opls_771 | [$([O]=[CD3]1[O][CD4][CD4][O]1)] | @atom:712 | -0.5 | "Propylene Carbonate C=O"
C | C | opls_772 | [$([CD3]1(=[O])[O][CD4][CD4][O]1)] | @atom:713 | 0.86 | "Propylene Carbonate C=O"
O | OS | opls_773 | [$([O]1[CD3](=[O])[O][CD4][CD4]1)] | @atom:714 | -0.45 | "Propylene Carbonate C-O"
C | CT | opls_774 | [$([CH2D4]1[O][CD3](=[O])[O][CD4]1)] | @atom:715 | 0.21 | "Propylene Carbonate CH2"
C | CT | opls_775 | [$([CH1D4]1[O][CD3](=[O])[O][CD4]1)] | @atom:716 | 0.16 | "Propylene Carbonate CH"
C | CT | opls_776 | [$([CH3D4][CH1D4]1[O][CD3](=[O])[O][CD4]1)] | @atom:717 | -0.1 | "Propylene Carbonate CH3"
H | HC | opls_777 | [$([#1][CH2D4]1[O][CD3](=[O])[O][CD4]1)] | @atom:718 | 0.03 | "Propylene Carbonate CH2"
H | HC | opls_778 | [$([#1][CH1D4]1[O][CD3](=[O])[O][CD4]1)] | @atom:719 | 0.03 | "Propylene Carbonate CH"
H | HC | opls_779 | [$([#1][CH3D4][CH1D4]1[O][CD3](=[O])[O][CD4]1)] | @atom:720 | 0.06 | "Propylene Carbonate CH3"
* opls 780 not in opls.par
P | P+ | opls_781 | [PD4+] | @atom:722 | 0.9684 | "Phosphonium R4P+"
C | CT | opls_782 | [$([CH3D4][PD4+])] | @atom:723 | -0.5081 | "Phosphonium CH3-PR3+"
C | CT | opls_783 | [$([CH2D4][PD4+])] | @atom:724 | -0.008 | "Phosphonium RCH2-PR3+"
H | HC | opls_784 | [$([#1][CH3D4][PD4+])] | @atom:725 | 0.172 | "Phosphonium CH3-PR3+"
P | P | opls_785 | [$([P-](F)(F)(F)(F)(F)F)] | @atom:726 | 1.34 | "Hexafluorophosphate Ion"
F | F | opls_786 | [$([F][P-](F)(F)(F)(F)F)] | @atom:727 | -0.39 | "Hexafluorophosphate Ion"
N | N | opls_787 | [$([ND3](~[#8D1])(~[#8D1])~[#8D1])] | @atom:728 | 0.794 | "Nitrate Ion NO3-"
O | O | opls_788 | [$([#8D1]~[ND3](~[#8D1])~[#8D1])] | @atom:729 | -0.598 | "Nitrate Ion NO3-"
* opls 789-899 not in opls.par
* No specific atom types for imines. Using NC type. [Note from opls.par --AHS]
N | NT | opls_900 | [$([NH2D3][!#8,!$([#6]=[#8])])] | @atom:730 | -0.9 | "Amine RNH2"
N | NT | opls_901 | [$([NH1D3]([!#8,!$([#6]=[#8])])[!#8,!$([#6]=[#8])])] | @atom:731 | -0.78 | "Amine R2NH"
N | NT | opls_902 | [$([NH0D3]([!#8,!$([#6]=[#8])])([!#8,!$([#6]=[#8])])[!#8,!$([#6]=[#8])])] | @atom:732 | -0.63 | "Amine R3N"
C | CT | opls_903 | [$([CH3D4][NH2D3])] | @atom:733 | 0.0 | "Amine CH3-NH2"
C | CT | opls_904 | [$([CH3D4][NH1D3][!#8,!$([#6]=[#8])])] | @atom:734 | 0.02 | "Amine CH3-NHR"
C | CT | opls_905 | [$([CH3D4][NH0D3]([!#8,!$([#6]=[#8])])[!#8,!$([#6]=[#8])])] | @atom:735 | 0.03 | "Amine CH3-NR2"
C | CT | opls_906 | [$([CH2D4]([!#8])[NH2D3])] | @atom:736 | 0.06 | "Amine RCH2-NH2"
C | CT_2 | opls_906B | [$([CH2D4]([NH2D3])[CD3](~[#8D1])~[#8D1])] | @atom:736 | 0.06 | "Amine RCH2-NH2"
C | CT | opls_907 | [$([CH2D4]([!#8])[NH1D3])] | @atom:737 | 0.08 | "Amine RCH2-NHR"
C | CT | opls_908 | [$([CH2D4]([!#8])[NH0D3])] | @atom:738 | 0.09 | "Amine RCH2-NR2"
H | H | opls_909 | [$([#1][NH2D3])] | @atom:739 | 0.36 | "Amine RNH2"
H | H | opls_910 | [$([#1][NH1D3])] | @atom:740 | 0.38 | "Amine R2NH"
H | HC | opls_911 | [$([#1][CD4][ND3])] | @atom:741 | 0.06 | "Amine H-C-N"
C | CT | opls_912 | [$([CH1D4]([CD4])([CD4])[NH2D3])] | @atom:742 | 0.12 | "Amine R2CH-NH2"
C | CT_2 | opls_912B | [$([CH1D4]([CD4])([NH2D3])[CD3](~[#8D1])~[#8D1])] | @atom:742 | 0.12 | "Amine R2CH-NH2"
C | CT | opls_913 | [$([CH0D4]([CD4])([CD4])([CD4])[NH2D3])] | @atom:743 | 0.18 | "Amine R3C-NH2"
C | CT | opls_914 | [$([CH1D4]([CD4])([CD4])[NH1D3])] | @atom:744 | 0.14 | "Amine R2CH-NHR"
C | CT | opls_915 | [$([CH1D4]([CD4])([CD4])[NH0D3])] | @atom:745 | 0.15 | "Amine R2CH-NR2"
C | CA | opls_916 | [$([c][NH2D3])] | @atom:746 | 0.18 | "Aniline C-NH2"
C | CA | opls_917 | [$([c][NH1D3][CD4])] | @atom:747 | 0.2 | "N-Me Aniline C-NHR"
C | CA | opls_918 | [$([c][NH0D3]([CD4])[CD4])] | @atom:748 | 0.21 | "N-DiMe Aniline C-NR2" [mod AHS]
* opls 919-924 not in opls.par
C | CZ | opls_925 | [$([CH1D2]#[CD2])] | @atom:755 | -0.21 | "Alkyne HCC-"
H | HC | opls_926 | [$([#1][CH1D2]#[CD2])] | @atom:756 | 0.2 | "Alkyne HCC-"
C | CZ | opls_927 | [$([CD2](#[CH1D2])[CD4;H2,H3])] | @atom:757 | 0.01 | "Alkyne RCCH R w/ 2/3 H"
C | CZ | opls_928 | [$([CD2](#[CH1D2])[CH1D4])] | @atom:758 | 0.01 | "Alkyne RCCH R w/ 1 H"
C | CZ | opls_929 | [$([CD2](#[CH1D2])[CH0D4,c])] | @atom:759 | 0.01 | "Alkyne RCCH R w/ O H/Ph"
H | HC | opls_930 | [$([#1][CD4][CD2]#[CH1D2])] | @atom:760 | 0.06 | "Alkyne H-C-CC-"
C | CZ | opls_931 | [$([CD2H0]#[CD2H0])] | @atom:769 | 0.0 | "Alkyne RCCR"
* opls 932-949 not in opls.par
N | N3 | opls_940 | [$([#7H1D4])] | @atom:770 | -0.1 | "Ammonium R3NH+"
H | H3 | opls_941 | [$([#1][#7H1D4])] | @atom:771 | 0.29 | "Ammonium R3NH+"
C | CT | opls_942 | [$([CH3D4][#7H1D4])] | @atom:772 | 0.09 | "Ammonium CH3-NHR2+"
C | CT | opls_943 | [$([CH2D4][#7H1D4])] | @atom:773 | 0.15 | "Ammonium RCH2-NHR2+"
C | CT | opls_944 | [$([CH1D4][#7H1D4])] | @atom:774 | 0.21 | "Ammonium R2CH-NHR2+"
C | CT | opls_945 | [$([CH0D4][#7H1D4])] | @atom:775 | 0.27 | "Ammonium R3C-NHR2+"
* opls 946-955 not in opls.par
F | F | opls_956 | [$([F][CD4]([!F])([!F])[!F])] | @atom:786 | -0.22 | "Alkyl Fluoride C-F"
C | CT | opls_957 | [$([CH2D4]([F])[!F])] | @atom:787 | 0.02 | "Alkyl Fluoride RCH2-F"
H | HC | opls_958 | [$([#1][CD4]([F])([!F])[!F])] | @atom:788 | 0.1 | "Alkyl Fluoride H-C-F"
C | CT | opls_959 | [$([CH1D4]([F])([!F])[!F])] | @atom:789 | 0.12 | "Alkyl Fluoride R2CH-F"
C | CT | opls_960 | [$([CH0D4]([F])([!F])([!F])([!F]))] | @atom:790 | 0.22 | "Alkyl Fluoride R3C-F"
* Perfluoroalkanes cannot be properly described. [note from opls.par -AHS]
*C | CT | opls_961 | [$([CH0D4](F)(F)(F)[CH0])]
*C | CT | opls_962 | [$([CH0D3](F)(F)[CH0][CH0])]
*C | CT | opls_963 | [$([CH0D2](F)[CH0][CH0][CH0][CH0])]
C | CT | opls_964 | [$([CH0D4](F)(F)(F)F)] | @atom:794 | 0.48 | "Tetrafluoromethane CF4"
F | F | opls_965 | [$([F][CH0]([F])([F])[F])] | @atom:795 | -0.12 | "Perfluoroalkane C-F"
* no matches for these in oplsaa
*Cu | Cu2+ | Cu2+ | [Cu+2]
*Fe | Fe2+ | Fe2+ | [Fe+2]
*Si | SI | SI | [Si]