Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.5/data/OpenBabel/phmodel.txt @ 15:ac342506cd4e draft
CADDSuite version 1.5
| author | Marcel Schumann <schumann.marcel@gmail.com> |
|---|---|
| date | Tue, 24 Jul 2012 11:08:49 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 14:55c32b55c2c2 | 15:ac342506cd4e |
|---|---|
| 1 ############################################################################## | |
| 2 # # | |
| 3 # Open Babel file: phmodel.txt # | |
| 4 # # | |
| 5 # Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # | |
| 6 # Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison # | |
| 7 # Part of the Open Babel package, under the GNU General Public License (GPL)# | |
| 8 # # | |
| 9 # pH model data (used by phmodel.cpp:OBPhModel) # | |
| 10 # # | |
| 11 # TRANSFORM: chemical transforms can be used to modify formal charges, bond # | |
| 12 # orders, and to delete atoms (i.e hydrogens). Changes are applied# | |
| 13 # to vector bound atoms (use the [:#] SMARTS notation) and bonds # | |
| 14 # between vector bound atoms. # | |
| 15 # SEEDCHARGE: used to seed partial charges. Seed partial charges # | |
| 16 # are used as initial values in Gasteiger charge calculation # | |
| 17 # # | |
| 18 ############################################################################## | |
| 19 | |
| 20 #carboxylic acid # pKa | |
| 21 #TRANSFORM O=CO[#1:1] >> O=CO 4.0 # pKa from acid (AH) | |
| 22 TRANSFORM O=C[OD1-0:1] >> O=C[O-:1] 4.0 # pKa from acid (AH) | |
| 23 | |
| 24 #uncomment for vinylogous carboxylic acids (e.g. ascorbic acid) | |
| 25 TRANSFORM [O:1]=[C:2][C:3]=[C:4][O:5] >> [O-:1][C:2]=[C:3][C:4]=[O:5] 4.0 # pKa from acid (AH) | |
| 26 | |
| 27 #charged amine | |
| 28 TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] 10.0 # pKa from conjugated acid (BH+) | |
| 29 | |
| 30 #imidazole: note pKa=7.0 | |
| 31 #if you uncomment this, also uncomment the seedcharge statement below | |
| 32 TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 7.0 | |
| 33 | |
| 34 #imine | |
| 35 TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6] 4.0 # pKa from conjugated acid (BH+) | |
| 36 | |
| 37 #tetrazole | |
| 38 TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 4.89 #pKa from acid (AH) | |
| 39 TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1 4.89 #pKa from acid (AH) | |
| 40 TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 4.89 #pKa from acid (AH) | |
| 41 | |
| 42 #azide | |
| 43 TRANSFORM [ND1:1]=[ND2:2]=A >> [N-:1]=[N+:2]=A 1E+10 # always apply transformation | |
| 44 TRANSFORM [ND2:1]=[ND2:2]=A >> N=[N+:2]=A 1E+10 # always apply this transformation | |
| 45 | |
| 46 #hydroxamic acid | |
| 47 #TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1] 8.0 | |
| 48 TRANSFORM O=CN[OD1-0:1] >> O=CN[O-:1] 8.0 | |
| 49 | |
| 50 #sulfinic acid | |
| 51 TRANSFORM [SD3](=O)[OD1:1] >> [SD3](=O)[O-:1] 2.0 | |
| 52 TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1] 2.0 | |
| 53 | |
| 54 #sulfonic acid | |
| 55 TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] -2.6 | |
| 56 TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] -2.6 | |
| 57 #sulfuric acid (same as sulfonic acid...) | |
| 58 #TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] | |
| 59 #TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] | |
| 60 | |
| 61 #guanidine or amidine | |
| 62 TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* 12.5 | |
| 63 | |
| 64 #phosphate ester | |
| 65 TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1] 2.0 | |
| 66 #TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1] 2.0 | |
| 67 | |
| 68 #phosphoric acid | |
| 69 #TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3] 2.12 | |
| 70 TRANSFORM O=P([!D1])([O:1][#1:2])[OD1] >> O=P([!D1])([O:1])O 2.12 | |
| 71 TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2] 2.12 | |
| 72 #phosphate | |
| 73 | |
| 74 # | |
| 75 # Amino acids | |
| 76 # pKa sidechain | |
| 77 # aspartic acid | |
| 78 #TRANSFORM O=CC(N)CC(=O)O[#1:1] >> O=CC(N)CC(=O)O 3.8 | |
| 79 TRANSFORM O=C(O)C(N)CC(=O)[OD1:1] >> O=C(O)C(N)CC(=O)[O-:1] 3.8 | |
| 80 TRANSFORM O=C(NCC=O)C(N)CC(=O)[OD1:1] >> O=C(NCC=O)C(N)CC(=O)[O-:1] 3.8 | |
| 81 | |
| 82 # glutamic acid | |
| 83 #TRANSFORM O=CC(N)CCC(=O)O[#1:1] >> O=CC(N)CCC(=O)O 4.3 | |
| 84 TRANSFORM O=C(O)C(N)CCC(=O)[OD1:1] >> O=C(O)C(N)CCC(=O)[O-:1] 5.0 | |
| 85 TRANSFORM O=C(NCC=O)C(N)CCC(=O)[OD1:1] >> O=C(NCC=O)C(N)CCC(=O)[O-:1] 5.0 | |
| 86 | |
| 87 # arginine | |
| 88 TRANSFORM O=C(O)C(N)CCCNC(N)=[N:1] >> O=C(O)C(N)CCCNC(N)=[N+:1] 12.0 | |
| 89 TRANSFORM O=C(NCC=O)C(N)CCCNC(N)=[N:1] >> O=C(NCC=O)C(N)CCCNC(N)=[N+:1] 12.0 | |
| 90 | |
| 91 # lysine | |
| 92 TRANSFORM O=C(O)C(N)CCCC[N:1] >> O=C(O)C(N)CCCC[N+:1] 10.5 | |
| 93 TRANSFORM O=C(NCC=O)C(N)CCCC[N:1] >> O=C(NCC=O)C(N)CCCC[N+:1] 10.5 | |
| 94 | |
| 95 # histidine | |
| 96 TRANSFORM O=C(O)C(N)Cc1nc[n:1]c1 >> O=C(O)C(N)Cc1nc[n+:1]c1 6.08 | |
| 97 TRANSFORM O=C(NCC=O)C(N)Cc1nc[n:1]c1 >> O=C(NCC=O)C(N)Cc1nc[n+:1]c1 6.08 | |
| 98 | |
| 99 # cysteine | |
| 100 TRANSFORM O=C(O)C(N)C[S:1] >> O=C(O)C(N)C[S-:1] 8.28 | |
| 101 TRANSFORM O=C(NCC=O)C(N)C[S:1] >> O=C(NCC=O)C(N)C[S-:1] 8.28 | |
| 102 | |
| 103 # tyrosine | |
| 104 TRANSFORM O=C(O)C(N)Cc1ccc([O:1])cc1 >> O=C(O)C(N)Cc1ccc([O-:1])cc1 10.1 | |
| 105 TRANSFORM O=C(NCC=O)C(N)Cc1ccc([O:1])cc1 >> O=C(NCC=O)C(N)Cc1ccc([O-:1])cc1 10.1 | |
| 106 | |
| 107 # old: | |
| 108 # histidine | |
| 109 #TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1 | |
| 110 # uncomment for tryptophan | |
| 111 # TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1 | |
| 112 #, histidine pKa=6.0 | |
| 113 | |
| 114 | |
| 115 # | |
| 116 # Seeding partial charges for gasteiger calculation | |
| 117 # | |
| 118 #default charges | |
| 119 SEEDCHARGE [#6+] 1.0 | |
| 120 SEEDCHARGE [#6-] -1.0 | |
| 121 SEEDCHARGE [#7+] 1.0 | |
| 122 SEEDCHARGE [#7-] -1.0 | |
| 123 SEEDCHARGE [#8+] 1.0 | |
| 124 SEEDCHARGE [#8-] -1.0 | |
| 125 SEEDCHARGE [#15+] 1.0 | |
| 126 SEEDCHARGE [#15-] -1.0 | |
| 127 SEEDCHARGE [#16+] 1.0 | |
| 128 SEEDCHARGE [#16-] -1.0 | |
| 129 | |
| 130 #charges spread over multiple atoms | |
| 131 #carboxylic acid | |
| 132 SEEDCHARGE C(=O)[O-] 0.0 -0.5 -0.5 | |
| 133 | |
| 134 #amines | |
| 135 SEEDCHARGE [N+] 1.0 | |
| 136 #tetrazole | |
| 137 SEEDCHARGE [nD2]1[nD2][nD2][nD2]c1 -0.2 -0.2 -0.2 -0.2 -0.2 | |
| 138 | |
| 139 #sulfinic | |
| 140 SEEDCHARGE [SD3](=O)[O-] 0.0 -0.5 -0.5 | |
| 141 #sulfuric acid | |
| 142 SEEDCHARGE [SD4](=O)(=O)([O-])[OH1] 0.0 -0.33 -0.33 -0.33 0.0 | |
| 143 #sulfonic acid | |
| 144 SEEDCHARGE [SD4]([D2])(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33 | |
| 145 | |
| 146 #guanidine | |
| 147 SEEDCHARGE [#7^2]~[C^2](~[N^2])~[N^2] 0.33 0.0 0.33 0.33 | |
| 148 | |
| 149 #amidine | |
| 150 SEEDCHARGE [#6]~[C^2](~[N^2])~[N^2] 0.0 0.0 0.5 0.5 | |
| 151 | |
| 152 #phosphoate ester | |
| 153 SEEDCHARGE [PD4](=O)([OD2])([OD2])[OD1] 0.0 -0.5 0.0 0.0 -0.5 | |
| 154 #phosphoric acid | |
| 155 SEEDCHARGE O=P([!D1])([O-])[O-] -0.66 0.0 0.0 -0.66 -0.66 | |
| 156 | |
| 157 | |
| 158 #phosphuric acid | |
| 159 SEEDCHARGE P(=O)(=O)([O-])[O-] 0.0 0.0 0.0 -0.5 -0.5 | |
| 160 #phosphonic acid | |
| 161 SEEDCHARGE [#6]P(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33 | |
| 162 | |
| 163 #hydroxamic acid | |
| 164 SEEDCHARGE O=C[N;!$(N(C=O)C=O)][OD1] -0.5 0.0 0.0 -0.5 | |
| 165 SEEDCHARGE O=CN([OD1])NC=O -0.33 0.0 0.0 -0.33 0.0 0.0 -0.33 | |
| 166 | |
| 167 #imidazole: note pKa=7.0, histidine pKa=6.0 | |
| 168 #if you uncomment this, also uncomment the transform statement above | |
| 169 SEEDCHARGE [n+H]1c[nH]cc1 0.5 0.0 0.5 0.0 0.0 |