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1 <?xml version="1.0" encoding="ISO-8859-1"?>
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2 <table>
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3 <!-- This file supplies penalty scores for different
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4 atom types in bond type perception accoring to
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5
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6 Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and
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7 bond type perception in molecular mechanical calculations". Journal of
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8 Molecular Graphics and Modelling , 25, 2006, 247260
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9
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10 A penalty score of 0 means that the corresponding valence is optimal.
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11 Note that the first matching entry is taken as the final atom type.
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12
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13 Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O).
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14 The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the
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15 right rule!
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16
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17 Rev 14.12.2007 Conversion was done by Anna Dehof
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18 -->
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19 <entry id="1">
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20 <elementstring>H</elementstring>
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21 <smartstring>SMARTS([#1])</smartstring>
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22 <penalty valence="0">64</penalty>
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23 <penalty valence="1">0</penalty>
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24 <penalty valence="2">64</penalty>
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25 </entry>
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26 <entry id="2">
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27 <elementstring>F</elementstring>
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28 <smartstring>SMARTS(F)</smartstring>
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29 <penalty valence="0">64</penalty>
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30 <penalty valence="1">0</penalty>
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31 <penalty valence="2">64</penalty>
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32 </entry>
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33 <entry id="3">
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34 <elementstring>Cl</elementstring>
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35 <smartstring>SMARTS(Cl)</smartstring>
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36 <penalty valence="0">64</penalty>
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37 <penalty valence="1">0</penalty>
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38 <penalty valence="2">64</penalty>
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39 </entry>
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40 <entry id="4">
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41 <elementstring>Br</elementstring>
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42 <smartstring>SMARTS(Br)</smartstring>
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43 <penalty valence="0">64</penalty>
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44 <penalty valence="1">0</penalty>
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45 <penalty valence="2">64</penalty>
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46 </entry>
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47 <entry id="5">
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48 <elementstring>I</elementstring>
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49 <smartstring>SMARTS(I)</smartstring>
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50 <penalty valence="0">64</penalty>
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51 <penalty valence="1">0</penalty>
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52 <penalty valence="2">64</penalty>
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53 </entry>
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54 <entry id="6">
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55 <elementstring>C</elementstring>
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56 <smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>
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57 <!--SMARTS([CD1]~[ND2]) AND element(C)</smartstring> -->
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58 <penalty valence="3">0</penalty>
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59 <penalty valence="4">1</penalty>
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60 <penalty valence="5">32</penalty>
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61 </entry>
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62 <entry id="7">
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63 <elementstring>C</elementstring>
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64 <smartstring>SMARTS([#6D1])</smartstring>
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65 <penalty valence="3">1</penalty>
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66 <penalty valence="4">0</penalty>
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67 <penalty valence="5">32</penalty>
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68 </entry>
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69 <entry id="8">
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70 <elementstring>C</elementstring>
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71 <smartstring>SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
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72 <penalty valence="4">32</penalty>
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73 <penalty valence="5">0</penalty>
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74 <penalty valence="6">32</penalty>
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75 </entry>
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76 <entry id="9">
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77 <elementstring>C</elementstring>
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78 <smartstring>SMARTS([#6])</smartstring>
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79 <penalty valence="2">64</penalty>
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80 <penalty valence="3">32</penalty>
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81 <penalty valence="4">0</penalty>
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82 <penalty valence="5">32</penalty>
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83 <penalty valence="6">64</penalty>
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84 </entry>
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85 <entry id="10">
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86 <elementstring>Si</elementstring>
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87 <smartstring>SMARTS([#14])</smartstring>
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88 <penalty valence="4">0</penalty>
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89 </entry>
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90 <entry id="11">
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91 <elementstring>N</elementstring>
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92 <smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring>
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93 <penalty valence="2">0</penalty>
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94 <penalty valence="3">0</penalty>
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95 </entry>
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96 <entry id="12">
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97 <elementstring>N</elementstring>
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98 <smartstring>SMARTS([#7D1])</smartstring>
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99 <penalty valence="2">3</penalty>
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100 <penalty valence="3">0</penalty>
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101 <penalty valence="4">32</penalty>
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102 </entry>
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103 <entry id="13">
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104 <elementstring>N</elementstring>
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105 <smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring>
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106 <penalty valence="3">1</penalty>
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107 <penalty valence="4">0</penalty>
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108 </entry>
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109 <entry id="14">
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110 <elementstring>N</elementstring>
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111 <smartstring>SMARTS([#7D2])</smartstring>
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112 <penalty valence="2">4</penalty>
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113 <penalty valence="3">0</penalty>
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114 <penalty valence="4">2</penalty>
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115 </entry>
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116 <entry id="15">
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117 <elementstring>N</elementstring>
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118 <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring>
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119 <penalty valence="3">64</penalty>
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120 <penalty valence="4">32</penalty>
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121 <penalty valence="5">0</penalty>
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122 <penalty valence="6">32</penalty>
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123 </entry>
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124 <entry id="16">
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125 <elementstring>N</elementstring>
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126 <!-- <smartstring>SMARTS([$(*OD1)&$(*aR)&n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->
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127 <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring>
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128 <penalty valence="3">1</penalty>
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129 <penalty valence="4">0</penalty>
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130 </entry>
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131 <entry id="17">
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132 <elementstring>N</elementstring>
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133 <smartstring>SMARTS([#7D3])</smartstring>
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134 <penalty valence="2">32</penalty>
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135 <penalty valence="3">0</penalty>
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136 <penalty valence="4">1</penalty>
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137 <penalty valence="5">2</penalty>
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138 </entry>
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139 <entry id="18">
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140 <elementstring>N</elementstring>
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141 <smartstring>SMARTS([#7D4])</smartstring>
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142 <penalty valence="2">64</penalty>
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143 <penalty valence="3">0</penalty>
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144 <penalty valence="4">64</penalty>
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145 </entry>
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146 <entry id="19">
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147 <elementstring>O</elementstring>
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148 <smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(O)</smartstring>
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149 <penalty valence="1">0</penalty>
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150 <penalty valence="2">1</penalty>
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151 </entry>
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152 <entry id="20">
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153 <elementstring>O</elementstring>
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154 <smartstring>SMARTS([#8D1])</smartstring>
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155 <penalty valence="1">1</penalty>
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156 <penalty valence="2">0</penalty>
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157 <penalty valence="3">64</penalty>
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158 </entry>
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159 <entry id="21">
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160 <elementstring>O</elementstring>
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161 <smartstring>SMARTS([#8D2])</smartstring>
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162 <penalty valence="1">32</penalty>
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163 <penalty valence="2">0</penalty>
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164 <penalty valence="3">64</penalty>
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165 </entry>
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166 <entry id="22">
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167 <elementstring>P</elementstring>
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168 <smartstring>SMARTS(#15D1)</smartstring>
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169 <penalty valence="2">2</penalty>
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170 <penalty valence="3">0</penalty>
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171 <penalty valence="4">32</penalty>
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172 </entry>
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173 <entry id="23">
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174 <elementstring>P</elementstring>
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175 <smartstring>SMARTS(#15D2)</smartstring>
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176 <penalty valence="2">4</penalty>
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177 <penalty valence="3">0</penalty>
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178 <penalty valence="4">2</penalty>
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179 </entry>
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180 <entry id="24">
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181 <elementstring>P</elementstring>
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182 <smartstring>SMARTS(#15D3)</smartstring>
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183 <penalty valence="2">32</penalty>
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184 <penalty valence="3">0</penalty>
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185 <penalty valence="4">1</penalty>
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186 <penalty valence="5">2</penalty>
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187 </entry>
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188 <entry id="25">
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189 <elementstring>P</elementstring>
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190 <!-- Note: this is _SLOW_ -->
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191 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
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192 <penalty valence="5">32</penalty>
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193 <penalty valence="6">0</penalty>
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194 <penalty valence="7">32</penalty>
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195 </entry>
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196 <entry id="26">
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197 <elementstring>P</elementstring>
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198 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring>
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199 <penalty valence="6">32</penalty>
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200 <penalty valence="7">0</penalty>
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201 </entry>
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202 <entry id="27">
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203 <elementstring>P</elementstring>
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204 <!-- This rule should be the last PD4 rule because it should only match when the other rules fail! -->
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205 <smartstring>SMARTS(#15D4)</smartstring>
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206 <penalty valence="3">64</penalty>
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207 <penalty valence="4">1</penalty>
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208 <penalty valence="5">0</penalty>
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209 <penalty valence="6">32</penalty>
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210 </entry>
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211 <entry id="28">
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212 <elementstring>S</elementstring>
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213 <smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(S)</smartstring>
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214 <penalty valence="1">0</penalty>
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215 <penalty valence="2">1</penalty>
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216 </entry>
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217 <entry id="29">
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218 <elementstring>S</elementstring>
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219 <smartstring>SMARTS([#16D1])</smartstring>
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220 <penalty valence="1">2</penalty>
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221 <penalty valence="2">0</penalty>
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222 <penalty valence="3">64</penalty>
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223 </entry>
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224 <entry id="30">
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225 <elementstring>S</elementstring>
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226 <smartstring>SMARTS([#16D2])</smartstring>
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227 <!-- These are the penalties given in the GAFF - paper; unfortunately, the values implemented in antechamber are different!
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228 <penalty valence="1">32</penalty>
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229 <penalty valence="2">0</penalty>
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230 <penalty valence="3">32</penalty>
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231 <penalty valence="4">1</penalty> -->
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232 <penalty valence="1">2</penalty>
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233 <penalty valence="2">0</penalty>
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234 <penalty valence="3">64</penalty>
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235 </entry>
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236 <entry id="31">
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237 <elementstring>S</elementstring>
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238 <smartstring>SMARTS([#16D3])</smartstring>
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239 <penalty valence="3">1</penalty>
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240 <penalty valence="4">0</penalty>
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241 <penalty valence="5">2</penalty>
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242 <penalty valence="6">2</penalty>
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243 </entry>
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244 <entry id="32">
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245 <elementstring>S</elementstring>
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246 <smartstring> SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring>
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247 <penalty valence="6">0</penalty>
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248 <penalty valence="7">32</penalty>
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249 </entry>
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250 <entry id="33">
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251 <elementstring>S</elementstring>
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252 <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring>
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253 <penalty valence="6">32</penalty>
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254 <penalty valence="7">0</penalty>
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255 </entry>
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256 <entry id="34">
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257 <elementstring>S</elementstring>
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258 <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
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259 <penalty valence="6">32</penalty>
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260 <penalty valence="7">0</penalty>
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261 </entry>
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262 <entry id="35">
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263 <elementstring>S</elementstring>
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264 <smartstring>SMARTS([#16D4])</smartstring>
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265 <penalty valence="4">4</penalty>
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266 <penalty valence="5">2</penalty>
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267 <penalty valence="6">0</penalty>
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268 </entry>
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269 <!-- The following rules are added to cope with ions -->
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270 <entry id="40">
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271 <elementstring>Li</elementstring>
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272 <smartstring>SMARTS([#3])</smartstring>
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273 <penalty valence="0">0</penalty>
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274 </entry>
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275 <entry id="41">
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276 <elementstring>Na</elementstring>
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277 <smartstring>SMARTS([#11])</smartstring>
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278 <penalty valence="0">0</penalty>
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279 </entry>
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280 <entry id="42">
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281 <elementstring>Mg</elementstring>
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282 <smartstring>SMARTS([#12])</smartstring>
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283 <penalty valence="0">0</penalty>
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284 </entry>
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285 <entry id="43">
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286 <elementstring>K</elementstring>
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287 <smartstring>SMARTS([#19])</smartstring>
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288 <penalty valence="0">0</penalty>
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289 </entry>
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290 <entry id="44">
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291 <elementstring>Ca</elementstring>
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292 <smartstring>SMARTS([#20])</smartstring>
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293 <penalty valence="0">0</penalty>
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294 </entry>
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295 <entry id="45">
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296 <elementstring>Cu</elementstring>
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297 <smartstring>SMARTS([#29])</smartstring>
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298 <penalty valence="0">0</penalty>
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299 </entry>
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300 <entry id="46">
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301 <elementstring>Zn</elementstring>
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302 <smartstring>SMARTS([#30])</smartstring>
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303 <penalty valence="0">0</penalty>
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304 </entry>
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305
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306 </table>
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