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annotate CADDSuite-1.5/data/OpenBabel/mmffdef.par @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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1 *
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2 * Copyright (c) Merck and Co., Inc., 1994
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3 * All Rights Reserved
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4 *
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5 * PRIMARY
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6 * MMFF MMFF
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7 *SYMBOL TYPE DEFAULT TYPES DEFINITION
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8 *
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9 CR 1 1 1 1 0 ALKYL CARBON
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10 C=C 2 2 2 1 0 VINYLIC
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11 * CSP2 2 2 2 1 0 GENERIC CSP2
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12 * CGD 2 2 2 1 0 GUANIDINE CARBON
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13 C=O 3 3 3 1 0 GENERAL CARBONYL C
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14 * C=N 3 3 3 1 0 C=N
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15 * C=OR 3 3 3 1 0 KETONE OR ALDEHYDE CO
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16 * C=ON 3 3 3 1 0 AMIDE CARBONYL
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17 * COO 3 3 3 1 0 CARBOXYLIC ACID OF EST
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18 * COON 3 3 3 1 0 CARBAMATE CARBONYL
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19 * COOO 3 3 3 1 0 CARBONIC ACID OR ESTER
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20 * C=OS 3 3 3 1 0 THIOESTER, C=O
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21 * C=S 3 3 3 1 0 THIOESTER, C=S
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22 * C=SN 3 3 3 1 0 THIOAMIDE
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23 * CSO2 3 3 3 1 0 CARBON IN >C=SO2
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24 CSP 4 4 4 1 0 ACETYLENIC C
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25 * =C= 4 4 4 1 0 ALLENIC C
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26 HC 5 5 5 5 0 H-C
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27 * HSI 5 5 5 5 0 H-SI
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28 * HP 5 5 5 5 0 H-P
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29 OR 6 6 6 6 0 O-CSP3
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30 * OH2 6 6 6 6 0 OXYGEN IN H2O
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31 * OC=O 6 6 6 6 0 ESTER OR ACID -O-
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32 * OC=C 6 6 6 6 0 ENOL OR PHEMOLIC O
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33 * OC=N 6 6 6 6 0 OXYGEN IN -O-C=N MOIETY
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34 * OSO3 6 6 6 6 0 DIVALENT O IN SULFATE
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35 * OSO2 6 6 6 6 0 DIVALENT O IN SULFITE
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36 * OSO 6 6 6 6 0 PAIR OF DIVALENT O ON S
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37 * -OS 6 6 6 6 0 OTHER DIVALENT O ON S
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38 * OPO3 6 6 6 6 0 DIVALENT O IN PHOSPHATE
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39 * OPO2 6 6 6 6 0 DIVALENT O IN PHOSPHITE
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40 * OPO 6 6 6 6 0 PAIR OF DIVALENT O ON P
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41 * -OP 6 6 6 6 0 OTHER DIVALENT O ON P
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42 * -O- 6 6 6 6 0 GENERAL DIVALENT OX
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43 O=C 7 7 7 6 0 O=C, GENERIC
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44 * O=CN 7 7 7 6 0 O=C IN AMIDES
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45 * O=CR 7 7 7 6 0 O=C IN KET, ALD
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46 * O=CO 7 7 7 6 0 O=C IN ACIDS, ESTERS
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47 * O=S 7 7 7 6 0 TERMINAL O SULFOXIDES
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48 * O=N 7 7 7 6 0 NITROSO-GROUP OXYGEN
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49 NR 8 8 8 8 0 AMINE N
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50 N=C 9 9 9 8 0 N=C, IMINES
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51 * N=N 9 9 9 8 0 N=N, AZO COMPOUNDS
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52 NC=O 10 10 10 8 0 N-C=O, AMIDES
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53 * NC=S 10 10 10 8 0 N-C=S (DELOC LP)
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54 * NN=C 10 10 10 8 0 N-N=C (DELOC LP)
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55 * NN=N 10 10 10 8 0 N-N=N (DELOC LP)
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56 F 11 11 11 11 0 FLUORINE
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57 CL 12 12 12 12 0 CHLORINE
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58 BR 13 13 13 13 0 BROMINE
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59 I 14 14 14 14 0 IODINE
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60 S 15 15 15 15 0 THIOL, SULFIDE
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61 S=C 16 16 16 15 0 S DOUBLY BONDED TO C
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62 S=O 17 17 17 15 0 SULFOXIDE S
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63 SO2 18 18 18 15 0 SULFONE S
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64 * SO2N 18 18 18 15 0 SULFONAMIDE S
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65 * SO3 18 18 18 15 0 SULFONATE S
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66 * =SO2 18 18 18 15 0 OXYGENATED SULFONE S
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67 * SNO 18 18 18 15 0 NITROGEN ANALOG OF SO2
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68 SI 19 19 19 19 0 SILICON
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69 CR4R 20 20 1 1 0 C IN CYCLOBUTYL
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70 HOR 21 21 21 5 0 H-O, ALCOHOLS
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71 * HO 21 21 21 5 0 GENERAL H ON O
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72 CR3R 22 22 22 1 0 C IN CYCLOPROPLY
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73 HNR 23 23 23 5 0 H-N, AMINES
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74 * H3N 23 23 23 5 0 H, AMMONIA
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75 * HPYL 23 23 23 5 0 H-N IN PYRROLE
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76 * HN 23 23 23 5 0 GENERAL H-N
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77 HOCO 24 24 24 5 0 H-O, ACIDS
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78 * HOP 24 21 21 5 0 H-O-P, PHOS ACIDS
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79 PO4 25 25 25 25 0 PHOSPHODIESTER
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80 * PO3 25 25 25 25 0 TETRACRD P, 3 OXYGENS
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81 * PO2 25 25 25 25 0 TETRACRD P, 2 OXYGENS
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82 * PO 25 25 25 25 0 TETRACRD P, 2 OXYGENS
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83 * PTET 25 25 25 25 0 GENERAL TETRACRD P
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84 P 26 26 26 25 0 TRICOORDINATE P
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85 HN=C 27 27 28 5 0 IMINE N-H
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86 * HN=N 27 27 28 5 0 AZO N-H
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87 HNCO 28 28 28 5 0 H-N, AMIDES
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88 * HNCC 28 28 28 5 0 H-N, ENAMINES
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89 * HNCS 28 28 28 5 0 H-N, THIOAMIDES
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90 * HNCN 28 28 28 5 0 H-N, HN-C=N
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91 * HNNC 28 28 28 5 0 H-N, HN-N=C
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92 * HNNN 28 28 28 5 0 H-N, HN-N=N
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93 * HSP2 28 28 28 5 0 GENERAL H ON SP2 N
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94 HOCC 29 29 29 5 0 H-O, ENOLS, PHENOLS
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95 * HOCN 29 29 29 5 0 H-O IN HO-C=N
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96 CE4R 30 30 2 1 0 C=C IN 4-RING
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97 HOH 31 31 31 31 0 H-OH
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98 O2CM 32 32 7 6 0 O, CARBOXYLATE ANION
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99 * OXN 32 32 7 6 0 OXIDE ON NITROHGEN
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100 * O2N 32 32 7 6 0 NITRO-GROUP OXYGEN
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101 * O2NO 32 32 7 6 0 NITRO-GROUP IN NITRATE
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102 * O3N 32 32 7 6 0 NITRATE ANION OXYGEN
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103 * O-S 32 32 7 6 0 SINGLE TERM O ON TET S
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104 * O2S 32 32 7 6 0 SULFONES, SULFONAMIDES
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105 * O3S 32 32 7 6 0 SULFONATES, TERM OX
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106 * O4S 32 32 7 6 0 SO4(3-)
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107 * OSMS 32 32 7 6 0 THIOSULFINATE O (-1/2)
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108 * OP 32 32 7 6 0 TERMINAL O, O-P
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109 * O2P 32 32 7 6 0 TERMINAL O, O2P GROUP
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110 * O3P 32 32 7 6 0 TERMINAL O, O3P GROUP
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111 * O4P 32 32 7 6 0 TERMINAL O, PO4(-3)
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112 * O4CL 32 32 7 6 0 TERMINAL O IN CLO4(-)
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113 HOS 33 33 21 5 0 H-O-S, SULF ACIDS
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114 NR+ 34 34 8 8 0 N+, QUATERNARY N
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115 OM 35 35 6 6 0 OXIDE OXYGEN ON SP3 C
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116 * OM2 35 35 6 6 0 OXIDE OXYGEN ON SP2 C
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117 HNR+ 36 36 36 5 0 H-N+
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118 * HNN+ 36 36 36 5 0 H ON IMIDAZOLIUM N
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119 * HNC+ 36 36 36 5 0 H ON PROTONATED N+=C-N
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120 * HGD+ 36 36 36 5 0 H ON GUANIDINIUM N
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121 CB 37 37 2 1 0 AROMATIC C
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122 NPYD 38 38 9 8 0 AROMATIC N, PYRIDINE
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123 NPYL 39 39 10 8 0 AROMATIC N, PYRROLE
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124 NC=C 40 40 10 8 0 N-C=C (DELOC LP)
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125 * NC=N 40 40 10 8 0 N-C=N (DELOC LP)
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126 CO2M 41 41 3 1 0 C IN CO2- ANION
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127 * CS2M 41 41 3 1 0 THIOCARBOXYLATE C
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128 NSP 42 42 42 8 0 N TRIPLE BONDED
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129 NSO2 43 43 10 8 0 N, SULFONAMIDES
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130 STHI 44 44 16 15 0 S IN THIOPHENE
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131 NO2 45 45 10 8 0 NITRO GROUP N
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Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
132 * NO3 45 45 10 8 0 NITRATE GROUP N
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
133 N=O 46 46 9 8 0 NITROSO GROUP N
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
134 NAZT 47 47 42 8 0 TERMINAL N, AZIDE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
135 NSO 48 48 9 8 0 DIVAL. N IN S(N)(O) GP
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
136 O+ 49 49 6 6 0 OXONIUM (TRICOORD) O
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
137 HO+ 50 50 21 5 0 H ON OXONIUM OXYGEN
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
138 O=+ 51 51 7 6 0 OXENIUM OXYGEN+
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
139 HO=+ 52 52 21 5 0 H ON OXENIUM O+
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
140 =N= 53 53 42 8 0 N TWICE DOUBLE BONDED
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
141 N+=C 54 54 9 8 0 IMINIUM NITROGEN
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
142 * N+=N 54 54 9 8 0 AZONIUM NITROGEN
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
143 NCN+ 55 55 10 8 0 N IN +N=C-N: ; Q=1/2
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
144 NGD+ 56 56 10 8 0 GUANIDINIUM N; Q=1/3
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
145 CGD+ 57 57 2 1 0 GUANIDINIUM CARBON
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
146 * CNN+ 57 57 2 1 0 C IN +N=C-N RESONANCE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
147 NPD+ 58 58 10 8 0 N PYRIDINIUM ION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
148 OFUR 59 59 6 6 0 AROMATIC O, FURAN
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
149 C% 60 60 4 1 0 ISONITRILE CARBON
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
150 NR% 61 61 42 8 0 ISONITRILE N
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
151 NM 62 62 10 8 0 SULFONAMIDE N-
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
152 C5A 63 63 2 1 0 ALPHA AROM 5-RING C
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
153 C5B 64 64 2 1 0 BETA AROM 5-RING C
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
154 N5A 65 65 9 8 0 ALPHA AROM 5-RING N
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
155 N5B 66 66 9 8 0 ALPHA AROM 5-RING N
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
156 N2OX 67 67 9 8 0 NITROGEN IN N-OXIDE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
157 N3OX 68 68 8 8 0 NITROGEN IN N-OXIDE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
158 NPOX 69 69 9 8 0 NITROGEN IN N-OXIDE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
159 OH2 70 70 70 70 70 OXYGEN IN WATER
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
160 HS 71 71 5 5 0 H-S
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
161 S2CM 72 72 16 15 0 THIOCARBOXYLATE S
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
162 * S-P 72 72 16 15 0 TERMINAL SULFUR ON P
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
163 * SM 72 72 16 15 0 TERMINAL SULFUR ON C
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
164 * SSMO 72 72 16 15 0 TERM S, THIOSULFINATE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
165 SO2M 73 73 18 15 0 SULFUR IN SULFINATE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
166 * SSOM 73 73 18 15 0 SULFUR, THIOSULFINATE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
167 =S=O 74 74 17 15 0 SULFINYL SULFUR, C=S=O
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
168 -P=C 75 75 26 25 0 P DOUBLY BONDED TO C
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
169 N5M 76 76 9 8 0 NEG N IN TETRAZOLE AN
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
170 CLO4 77 77 12 12 0 CHLORINE IN CLO4(-)
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
171 C5 78 78 2 1 0 GENERAL AROM 5-RING C
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
172 N5 79 79 9 8 0 GENERAL AROM 5-RING N
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
173 CIM+ 80 80 2 1 0 C IN N-C-N, IM+ ION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
174 NIM+ 81 81 10 8 0 N IN N-C-N, IM+ ION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
175 N5AX 82 82 9 8 0 5R NITROGEN IN N-OXIDE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
176 * N5BX 82 82 9 8 0 5R NITROGEN IN N-OXIDE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
177 * N5OX 82 82 9 8 0 5R NITROGEN IN N-OXIDE
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
178 FE+2 87 87 87 87 87 IRON +2 CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
179 FE+3 88 88 88 88 88 IRON +3 CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
180 F- 89 89 89 89 89 FLUORIDE ANION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
181 CL- 90 90 90 90 90 CHLORIDE ANION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
182 BR- 91 91 91 91 91 BROMIDE ANION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
183 LI+ 92 92 92 92 92 LITHIUM CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
184 NA+ 93 93 93 93 93 SODIUM CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
185 K+ 94 94 94 94 94 POTASSIUM CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
186 ZN+2 95 95 95 95 95 DIPOSITIVE ZINC CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
187 * ZINC 95 95 95 95 95 DIPOSITIVE ZINC CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
188 CA+2 96 96 96 96 96 DIPOSITIVE CALCIUM CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
189 CU+1 97 97 97 97 97 MONOPOSITIVE COPPER CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
190 CU+2 98 98 98 98 98 DIPOSITIVE COPPER CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
191 MG+2 99 99 99 99 99 DIPOSITIVE MAGNESIUM CATION
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
192 $