#AtSym ElemNo mmType HType formalCharge*12 val Desc Smiles #BH 5/17/2016 -- for OpenSMARTS convention requiring $(...) in [...] Li 3 92 0 12 0 LITHIUM CATION [LiD0] C 6 22 5 0 4 C IN CYCLOPROPLY [CD4r3] C 6 20 5 0 4 C IN CYCLOBUTYL [CD4r4] C 6 1 5 0 4 ALKYL CARBON [CD4] C 6 30 5 0 4 C=C IN 4-RING [$([CD3r4]=C)] C 6 2 5 0 4 VINYLIC [$([CD3]=C)] C 6 41 5 0 4 C IN CO2- ANION [$([CD3]([OD1])[OD1]), $([CD3]([SD1])[SD1])] C 6 57 5 0 4 GUANIDINIUM CARBON [$([CD3]([#7D3v3])([#7D3v3])=[#7D3v4&!r600&!$([#7][OD1])])] C 6 57 5 0 4 C IN +N=C-N RESONANCE [$([CD3]([#7D3v3])=[#7D3v4&!r600&!$([#7][OD1])])] C 6 3 5 0 4 GUANIDINE CARBON [$([CD3](=[#7D3v3])([#7D3v3])[#7D2v3])] C 6 3 5 0 4 GENERAL CARBONYL C [$([CD3]=[O,N,P,S])] C 6 80 5 0 4 C IN N-C-N, IM+ ION [$([cD3r500]([#7D3v3])=[#7D3v4&!r600&!$([#7][OD1])])] C 6 78 5 0 4 general 5-ring C both alp [$([cD3r500]1[oD2r500,sD2r500,nD3v3r500]aaa1),$([cD3r500]1a[oD2r500,sD2r500,nD3v3r500]aa1)] C 6 63 5 0 4 ALPHA AROM 5-RING C (fur [$([cD3r500]:[oD2r500,sD2r500])] C 6 64 5 0 4 BETA AROM 5-RING C (fura [$([cD3r500]:a:[oD2r500,sD2r500])] C 6 78 5 0 4 general 5-ring C (imidzol [$([cD3r500]1[nv4r500&!$(n[OD1])]aaa1),$([cr500]1a[nv4r500&!$(n[OD1])]aa1)] C 6 78 5 0 4 general 5-ring C (1,2-dia [$([cD3r500]1[cr500][cr500][nD2r500][nD2r500]1),$([cD3r500]1[cr500][nD2r500][nD2r500][cr500]1)] C 6 63 5 0 4 ALPHA AROM 5-RING C [$([cD3r500]:[nD3v3r500])] C 6 64 5 0 4 BETA AROM 5-RING C [$([cD3r500]1a[nD3v3r500]aa1)] C 6 37 5 0 4 CARBON AS IN BENZENE, PYR [cD3]1ccccc1 C 6 78 5 0 4 GENERAL AROM 5-RING C [cD3r500] C 6 37 5 0 4 AROMATIC C [cD3] C 6 4 5 0 4 ACETYLENIC C [$([#6D2]#*)] C 6 4 5 0 4 ALLENIC C (also isocyanat [$([#6D2](=*)=*)] C 6 60 0 0 3 ISONITRILE CARBON [$([CD1]#N)] N 7 42 0 0 3 N TRIPLE BONDED [$([ND1]#*)] N 7 47 0 0 2 TERMINAL N, AZIDE [$([ND1][ND2])] N 7 53 0 0 4 N TWICE DOUBLE BONDED [$([ND2](=*)=*)] N 7 9 27 0 3 N=C, IMINES [$([ND2]=[#6,#7])] N 7 43 28 0 3 N, SULFONAMIDES (S(O)2-N= [$([ND2v3]S([OD1])[OD1])] N 7 46 0 0 3 NITROSO GROUP N [$([ND2](=O)[#6,#7])] N 7 48 28 0 2 DIVALENT NITROGEN REPLACI [$([ND2][SD4]([OD1])([#6])[#6])] N 7 62 23 -12 2 SULFONAMIDE N- [$([ND2v2][SD4]),$([ND2v2][CD3])] N 7 61 0 0 4 ISONITRILE N [$([ND2]#[#6])] N 7 61 0 12 4 diazo N (+1) [$([ND2]#[#7])] N 7 38 0 0 3 AROMATIC N, PYRIDINE [nD2r600] N 7 65 0 0 3 ALPHA AROM 5-RING N (thio [$([nD2r500]:[sD2])] N 7 66 0 0 3 (BETA) AROM 5-RING N (thi [$([nD2r500]:a:[sD2])] N 7 65 0 0 3 ALPHA AROM 5-RING N (fura [$([nD2r500]:[oD2])] N 7 66 0 0 3 (BETA) AROM 5-RING N (fur [$([nD2r500]:a:[oD2])] N 7 65 0 0 3 ALPHA AROM 5-RING N [$([nD2r500]:[nD3v3])&!$([$(n:[$([nv4])&!$([#7][OD1])]),$(n:a=[$([nv4])&!$([#7][OD1])]),$(n=a:[$([nv4])&!$([#7][OD1])])])] N 7 66 0 0 3 (BETA) AROM 5-RING N [$([nD2r500]:a:[nD3v3])&!$([$(n:[$([nv4])&!$([#7][OD1])]),$(n:a=[$([nv4])&!$([#7][OD1])]),$(n=a:[$([nv4])&!$([#7][OD1])])])] N 7 76 0 -3 2 NEG N IN TETRAZOLE AN [$([nD2r500][nD2r500][nD2r500][nD2r500])] N 7 76 0 -4 2 (NEG N IN TRIAZOLE) [$([nD2r500]:[nD2r500]:[nD2r500]:c)] N 7 76 0 -6 2 NEG N IN DIAZOLE [$([nD2r500]:[nD2r500]:c:c:c)] N 7 79 0 0 3 GENERAL AROM 5-RING N [nD2r500] N 7 45 0 0 4 NITRO GROUP N [$([ND3](=O)O)] N 7 67 23 0 4 NITROGEN IN N-OXIDE [$([ND3]([OD1])([#6])[#6]),$([ND3]([OD1])=[#6,#7])] N 7 56 36 4 34 GUANIDINIUM N; Q=1/3 [$([ND3v3][#6D3]([#7D3v3&!r600&!$([#7][OD1])])=[#7D3v4&!r600&!$([#7][OD1])]),$([ND3v4]=[#6D3]([#7D3v3&!r600&!$([#7][OD1])])[#7D3v3&!r600&!$([#7][OD1])])] N 7 55 36 6 34 N IN +N=C-N: ; Q=1/2 [$([ND3v4]=[#6D3][#7D3v3]),$([ND3v3][#6D3]=[#7D3v4&!r600&!$([#7][OD1])])] N 7 54 36 12 4 IMINIUM NITROGEN [$([ND3v4]=[#6,#7])] N 7 54 36 12 4 AZONIUM NITROGEN [$([ND3v4]([H])([#6])=[#7])] N 7 43 28 0 3 N, SULFONAMIDES (and phos [$([ND3]S([OD1])[OD1]),$([ND3]P([OD1])[OD1])] N 7 10 28 0 3 N-C=O, AMIDES [$([ND3v3][#6]=O)] N 7 43 28 0 3 N, sulfinamide # not implemented: [$([ND3]S[OD1])&!$([ND3]S([OD1])[OD1])] N 7 39 23 0 3 AROMATIC N, PYRROLE (tetr [$([nD3v3r500][nD2]=[nD2][nD2])] N 7 10 28 0 3 N-C=S (DELOC LP) [$([ND3][#6]=[#16])] N 7 10 28 0 3 N-N=C (DELOC LP) # not implemented??$([ND3][#7]=[#6,#7]) N 7 40 28 0 3 N-C=C (DELOC LP) [$([ND3][#6]=[#6]),$([ND3]c)] N 7 10 28 0 3 N-N=N (DELOC LP) [$([ND3v3][#7D2v3]=[#7D2v3])] N 7 40 28 0 3 N-C=N (DELOC LP) [$([ND3][#6]=[#7,#15])] N 7 43 28 0 3 NITROGEN ATTACHED TO CYAN [$([ND3][CD2][ND1])] N 7 8 23 0 3 AMINE N [$([ND3](-A)(-A)-A),$([ND3](-A)(-A)-n)] N 7 82 0 0 4 N-OXIDE NITROGEN IN GENER [$([nD3r500][OD1])] N 7 69 0 0 4 NITROGEN IN N-OXIDE [$([nD3][OD1])] N 7 81 36 4 4 GUANIDINIUM N; Q=1/3 [$([nD3v3][#6D3]([#7D3v3&!r600])=[#7D3v4&!r600&!$([#7][OD1])])] N 7 81 36 4 4 GUANIDINIUM N; Q=1/3 [$([nD3v4]=[#6D3]([#7D3v3&!r600])[#7D3v3&!r600&!$([#7][OD1])])] N 7 81 36 6 4 N IN N-C-N, IM+ ION [$([nD3r500v4]=[cD3][#7D3v3]),$([nD3r500v3][#6D3]=[#7D3v4&!r600&!$([#7][OD1])])] N 7 81 36 12 4 POSITIVE N5B NITROGEN - F [$([nD3r500v4]:a:[oD2,sD2])] N 7 58 36 12 4 N PYRIDINIUM ION [nD3r600v4] N 7 39 23 0 3 AROMATIC N, PYRROLE [nD3r500v3] N 7 68 23 0 4 NITROGEN IN N-OXIDE [$([ND4][OD1])] N 7 34 36 12 4 N+, QUATERNARY N [ND4] O 8 49 50 12 3 OXONIUM (TRICOORD) O [OD3] O 8 70 31 0 2 OXYGEN IN WATER [$([OD2](H)H)] O 8 59 0 0 2 AROMATIC O, FURAN [oD2r500] O 8 6 24 0 2 RCO2H [$([OD2](H)[#6]=O)] O 8 6 21 0 2 RCO2R [$([OD2]C=O)] O 8 6 29 0 2 ENOL OR PHENOLIC O [$([OD2][#6D3][#6D3])] O 8 6 29 0 2 OXYGEN IN -O-C=N MOIETY [$([OD2]-[#6D3]=[#7])] O 8 6 33 0 2 DIVALENT O IN SULFATE [$([OD2][#16])] O 8 6 24 0 2 DIVALENT O IN PHOSPHATE [$([OD2][#15])] O 8 6 31 0 2 OXYGEN IN H2O [$([OD2]([H])[H])] O 8 6 21 0 2 O-CSP3 [$([#8D2](-*)-*)] O 8 51 52 12 3 OXENIUM OXYGEN+ [$([OD2]=*)] O 8 7 0 0 2 O=S=C [$([OD1]=[#16D2]=*)] O 8 32 0 -6 12 O, CARBOXYLATE ANION [$([OD1][CD3][OD1])] O 8 32 0 0 12 NITRO-GROUP OXYGEN [$([OD1][ND3]([#6])[OD1])] O 8 32 0 0 12 NITRO-GROUP IN NITRATE [$([OD1][ND3]([OD1])[OD2])] O 8 32 0 -4 12 NITRATE ANION OXYGEN [$([OD1][ND3]([OD1])[OD1])] O 8 32 0 0 12 OXIDE ON NITROHGEN [$([OD1][#7D3]=,:*),$([OD1][#7D4])] O 8 32 0 -6 12 SO4(2-) [$([OD1][SD4]([OD1])([OD1])[OD1])] O 8 32 0 -4 12 SULFONATES, TERM OX ROSO3 [$([OD1][SD4]([OD1])[OD1])] O 8 32 0 0 12 SULFONES, SULFONAMIDES [$([OD1][SD4][OD1,ND2]),$([OD1][SD3]([OD1,ND2])=C)] O 8 32 0 -6 12 THIOSULFINATE O (-1/2) [$([OD1][SD3][OD1,SD1])] O 8 32 0 0 12 SINGLE TERM O ON TET S #[$([OD1][#16])] O 8 32 0 -6 12 TERMINAL O, O2P GROUP (RO [$([OD1][PD4]([OD1,SD1])([!$([OD1,SD1])])[!$([OD1,SD1])])] O 8 32 0 -8 12 TERMINAL O, O3P GROUP ROP [$([OD1][PD4]([OD1])([OD1])[OD2,SD2])] O 8 32 0 -9 12 TERMINAL O, PO4(-3) [$([OD1][PD4]([OD1])([OD1])[OD1])] O 8 32 0 0 12 TERMINAL O, O-P [$([OD1][#15])] O 8 32 0 -3 12 TERMINAL O IN CLO4(-) [$([OD1][ClD4]([OD1])([OD1])[OD1])] O 8 7 0 0 2 O=C, GENERIC [$([#8D1]=[#6,#7,#16])] O 8 35 21 -12 1 RO- or HO- [OD1] F 9 11 0 0 1 FLUORINE [FD1] F 9 89 0 -12 0 FLUORIDE ANION [FD0] Na 11 93 0 12 0 SODIUM CATION [NaD0] Mg 12 99 0 24 0 DIPOSITIVE MAGNESIUM CATI [MgD0] Si 14 19 5 0 4 SILICON [SiD4] P 15 25 71 0 4 GENERAL TETRACRD P [PD4] P 15 26 71 0 3 TRICOORDINATE P [PD3] P 15 75 71 0 3 P DOUBLY BONDED TO C [$([PD2]=C)] S 16 18 0 0 4 SULFONAMIDE S [$([SD4]([OD1,ND2])[OD1,ND2]),$([SD3](=C)([OD1,ND2])[OD1,ND2])] S 16 17 71 0 4 SULFOXIDE S (also S(=O)[N [$([SD3]([OD1,ND2])([#6,#7D3,#8D2])[#6,#7D3,#8D2])] S 16 73 0 0 3 SULFUR IN SULFINATE [$([SD3]([OD1,SD1])[OD1])] S 16 44 0 0 2 S IN THIOPHENE [sD2r500] S 16 15 71 0 2 THIOL, SULFIDE [$([SD2](-*)-*)] S 16 74 0 0 4 SULFINYL SULFUR, C=S=O [$([SD2]([CD3])[OD1])] S 16 72 0 -6 1 THIOCARBOXYLATE S [$([SD1][CD3][SD1])] S 16 16 0 0 2 S DOUBLY BONDED TO C [$([SD1]=[#6D3])] S 16 72 0 -6 1 TERMINAL SULFUR ON C (P,S [$([SD1][#15,#6,#16][OD1])] S 16 72 0 -12 1 TERMINAL SULFUR on alken [$([SD1][#6])] S 16 72 0 0 1 TERMINAL SULFUR ON P [$([SD1][#15,#16])] Cl 17 12 0 0 1 CHLORINE [ClD1] Cl 17 77 0 0 4 CHLORINE IN CLO4(-) [$([ClD4]([OD1])([OD1])([OD1])[OD1])] Cl 17 90 0 -12 0 CHLORIDE ANION [ClD0] K 19 94 0 12 0 POTASSIUM CATION [KD0] Ca 20 96 0 24 0 DIPOSITIVE CALCIUM CATION [CaD0] Fe 26 87 0 24 0 IRON +2 CATION [FeD0+2] Fe 26 88 0 36 0 IRON +3 CATION [FeD0+3] Cu 29 97 0 12 0 MONOPOSITIVE COPPER CATIO [CuD0+1] Cu 29 98 0 24 0 DIPOSITIVE COPPER CATION [CuD0+2] Zn 30 95 0 24 0 DIPOSITIVE ZINC CATION [ZnD0+2] Br 35 13 0 0 1 BROMINE [BrD1] Br 35 91 0 -12 0 BROMIDE ANION [BrD0] I 53 14 0 0 1 IODINE [ID1]