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1 //
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2 // Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl>
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3 //
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4 // This is a SMARTS template-file for GAFF-atom types
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5 //
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6 // It is attempted to obey the typing given in the "ATOMTYPE_GFF.DEF"
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7 // file included with the antechamber package of amber10.
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8 // There is no 1-to-1 correspondence between the ATD format and SMARTS.
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9 // Therefore the current definitions need to be tested and possibly changed
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10 //
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11 //
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12 //
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13 // GAFF atomtypes defined using SMARTS
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14 // [SMARTS] [atomtype id number] [description]
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15 // must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!
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16 //
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17 // Be careful lines do not exceed the maximum length of 80!
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18
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19 atom [*] X
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20 atom [#1X1] ha "other hydrogen e.g. on aromatic C"
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21 atom [#1X1][CX4] hc "hydrogen on aliphatic C"
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22 // "hydrogen on aliphatic C with 1 ewd"
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23 atom [#1X1][CX4][#7,#8,#16,#17,#35,#53] h1
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24 // "hydrogen on aliphatic C with 2 ewd"
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25 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h2
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26 // "hydrogen on aliphatic C with 3 ewd"
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27 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#7,#8] h3
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28 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#16,#17] h3
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29 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#35,#53] h3
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30 // "hydrogen on sp2 C with 1 ewd"
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31 atom [#1X1][#6X3][#7,#8,#16,#17,#35,#53] h4
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32 // "hydrogen on sp2 C with 2 ewd"
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33 atom [#1X1][#6X3]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h5
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34 atom [#1X1][#6](N)(N)(N)N hx ""
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35 atom [#1X1]O ho "hydrogen on oxygen"
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36 atom [#1X1][Oh1] hw "hydrogen on water"
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37 atom [#1X1]N hn "nitrogen"
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38 atom [#1X1]S hs "sulphur"
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39 atom [#1X1]P hp "phosphor"
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40 atom [#6X4] c3 "other sp3 C"
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41 atom [#6X4r3] cx "3-membered ring atom"
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42 atom [#6X4r4] cy "4-membered ring atom"
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43 atom [#6X3] c2 "other sp2 C"
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44 atom [#6X3](N)(N)N cz "guanidine carbon"
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45 atom [#6X3;R](=*)-*=* cc "inner sp2 C of conjugated ring systems"
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46 atom [#6X3;R](=*)-*#* cc "inner sp2 C of conjugated ring systems"
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47 atom [#6X3;R](#*)-*#* cc "inner sp2 C of conjugated ring systems"
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48 atom [#6X3;!R](=*)-*=* ce "inner sp2 C of conjugated chain systems"
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49 atom [#6X3;!R](#*)-*=* ce "inner sp2 C of conjugated chain systems"
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50 atom [#6X3;!R](#*)-*#* ce "inner sp2 C of conjugated chain systems"
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51 atom [cr6](c)(c)c cp "bridge aromatic c in byphenyl system"
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52 atom [#6X3r3] cu "sp2 carbon in a 3-membered ring"
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53 atom [#6X3r4] cv "sp2 carbon in a 4-membered ring"
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54 atom [#6X3]=[O,S] c "C=O or C=S"
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55 atom [c] ca "pure aromatic atom"
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56 atom [#6X2] c1 "other sp C"
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57 atom [#6X2](=*)-*=* cg "sp C of conjugated system"
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58 atom [#6X2](#*)-*=* cg "sp C of conjugated system"
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59 atom [#6X2](#*)-*#* cg "sp C of conjugated system"
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60 atom [#6X1] c1 "other sp C"
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61
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62 atom [F]* f (-*) "general fluorine"
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63 atom [Cl]* cl (-*) "general chlorine"
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64 atom [Br]* br (-*) "general bromine"
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65 atom [I]* i (-*) "general iodine"
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66
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67 atom [#15X1] p2 "other sp2 P"
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68 atom [#15X2] p2 "other sp2 P"
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69 atom [#15X2;R](=*)-*=* pc "inner sp2 P of conjugated ring systems"
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70 atom [#15X2;R](=*)-*#* pc "inner sp2 P of conjugated ring systems"
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71 atom [#15X2;R](#*)-*#* pc "inner sp2 P of conjugated ring systems"
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72 atom [#15X2;!R](=*)-*=* pe "inner sp2 P of conjugated chain system"
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73 atom [#15X2;!R](=*)-*#* pe "inner sp2 P of conjugated chain system"
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74 atom [#15X2;!R](#*)-*#* pe "inner sp2 P of conjugated chain system"
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75 atom [#15;a] pb "aromatic P"
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76 atom [#15X3] p3 "other sp3 P"
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77 atom [#15X3](=*)-*=* px "sp2 P of conjugated system"
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78 atom [#15X3](=*)-*#* px "sp2 P of conjugated system"
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79 atom [#15X3]=[O,S] p4 "hypervalent P"
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80 atom [#15X4] p5 "hypervalent P"
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81 atom [#15X4](=*)-*=* py "P of conjugated system"
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82 atom [#15X4](=*)-*#* py "P of conjugated system"
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83 atom [#15X5] p5 "hypervalent P"
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84 atom [#15X6] p5 "hypervalent P"
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85
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86 atom [#7X1] n1 "sp1 N"
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87
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88 atom [#7X2] n2 "sp2 N"
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89 atom [#7X2](=*)=* n1 "sp1 N"
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90 atom [#7X2](-*)#* n1 "sp1 N"
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91 atom [#7X2;R](=*)-*=* nc "inner sp2 N of conjugated ring systems"
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92 atom [#7X2;R](=*)-*#* nc "inner sp2 N of conjugated ring systems"
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93 atom [#7X2;R](#*)-*#* nc "inner sp2 N of conjugated ring systems"
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94 atom [#7X2;!R](=*)-*=* ne "inner sp2 N of conjugated chain system"
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95 atom [#7X2;!R](=*)-*#* ne "inner sp2 N of conjugated chain system"
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96 atom [#7X2;!R](#*)-*#* ne "inner sp2 N of conjugated chain system"
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97 atom [nX2] nb "aromatic N"
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98
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99 atom [#7X3] n3 "sp3 N"
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100 atom [#7X3]a nh "amine N connected to aromatic ring"
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101 atom [#7X3]=[CX3] nh ""
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102 atom [#7X3]=[N2] nh ""
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103 atom [#7X3]=[P2] nh ""
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104 atom [#7X3]-[CX3]=[O,S] n "sp2 N in amides"
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105 atom [#7X3](O)O no "N in nitro group"
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106 atom [nX3] na "aromatic N"
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107
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108 atom [#7X4] n4 "sp3 N"
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109
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110 atom [OX1] o "sp2 O"
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111 atom [OX2] os "sp3 O in esters and ethers"
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112 atom [OX3] os "sp3 O in esters and ethers"
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113 atom [OX2H] oh "sp3 O in hydroxyl group"
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114 atom [OX3H] oh "sp3 O in hydroxyl group"
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115
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116 atom [SX1] s ""
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117 atom [SX2] ss "sp3 sulphur"
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118 atom [SX2]=* s2 "sp2 sulphur"
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119 atom [SX2]#* s2 "sp2 sulphur"
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120 atom [SX2H] sh "sp3 S in thiol"
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121 atom [SX3] s4 "hypervalent S"
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122 atom [SX3](=*)-*=* sx "conjugated S"
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123 atom [SX3](=*)-*#* sx "conjugated S"
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124 atom [SX4] s6 "hypervalent S"
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125 atom [SX4](=*)-*=* sy "conjugated S"
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126 atom [SX4](=*)-*#* sy "conjugated S"
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127 atom [SX5] s6 "hypervalent S"
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128 atom [SX6] s6 "hypervalent S"
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129
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130 atom [He] He ""
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131 atom [Li] Li ""
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132 atom [Be] Be ""
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133 atom [B] B ""
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134 atom [Ne] Ne ""
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135 atom [Na] Na ""
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136 atom [Mg] Mg ""
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137 atom [Al] Al ""
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138 atom [Si] Si ""
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139 atom [Ar] Ar ""
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140 atom [K] K ""
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141 atom [Ca] Ca ""
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142 atom [Sc] Sc ""
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143 atom [Ti] Ti ""
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144 atom [V] V ""
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145 atom [Cr] Cr ""
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146 atom [Mn] Mn ""
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147 atom [Fe] Fe ""
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148 atom [Co] Co ""
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149 atom [Ni] Ni ""
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150 atom [Cu] Cu ""
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151 atom [Zn] Zn ""
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152 atom [Ga] Ga ""
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153 atom [Ge] Ge ""
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154 atom [As] As ""
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155 atom [Se] Se ""
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156 atom [Kr] Kr ""
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157 atom [Rb] Rb ""
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158 atom [Sr] Sr ""
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159 atom [Y] Y ""
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160 atom [Zr] Zr ""
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161 atom [Nb] Nb ""
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162 atom [Mo] Mo ""
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163 atom [Tc] Tc ""
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164 atom [Ru] Ru ""
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165 atom [Rh] Rh ""
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166 atom [Pd] Pd ""
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167 atom [Ag] Ag ""
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168 atom [Cd] Cd ""
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169 atom [In] In ""
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170 atom [Sn] Sn ""
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171 atom [Sb] Sb ""
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172 atom [Te] Te ""
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173 atom [Xe] Xe ""
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174 atom [Cs] Cs ""
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175 atom [Ba] Ba ""
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176 atom [La] La ""
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177 atom [Ce] Ce ""
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178 atom [Pr] Pr ""
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179 atom [Nd] Nd ""
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180 atom [Pm] Pm ""
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181 atom [Sm] Sm ""
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182 atom [Eu] Eu ""
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183 atom [Gd] Gd ""
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184 atom [Tb] Tb ""
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185 atom [Dy] Dy ""
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186 atom [Ho] Ho ""
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187 atom [Er] Er ""
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188 atom [Tm] Tm ""
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189 atom [Yb] Yb ""
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190 atom [Lu] Lu ""
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191 atom [Hf] Hf ""
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192 atom [Ta] Ta ""
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193 atom [W] W ""
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194 atom [Re] Re ""
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195 atom [Os] Os ""
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196 atom [Ir] Ir ""
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197 atom [Pt] Pt ""
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198 atom [Au] Au ""
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199 atom [Hg] Hg ""
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200 atom [Tl] Tl ""
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201 atom [Pb] Pb ""
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202 atom [Bi] Bi ""
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203 atom [Po] Po ""
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204 atom [At] At ""
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205 atom [Rn] Rn ""
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206 atom [Fr] Fr ""
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207 atom [Ra] Ra ""
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208 atom [Ac] Ac ""
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209 atom [Th] Th ""
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210 atom [Pa] Pa ""
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211 atom [U] U ""
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212 atom [Np] Np ""
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213 atom [Pu] Pu ""
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214 atom [Am] Am ""
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215 atom [Cm] Cm ""
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216 atom [Bk] Bk ""
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217 atom [Cf] Cf ""
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218 atom [Es] Es ""
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219 atom [Fm] Fm ""
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220 atom [Md] Md ""
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221 atom [No] No ""
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222 atom [Lr] Lr ""
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