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