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superatom.txt
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superatom.txt
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# Translations of superatom labels to SMILES.
# First atom of SMILES string should be the one connected to the rest of
# the molecule.
# Empty lines and lines starting with # are ignored.
# Originally from http://cactus.nci.nih.gov/osra/
# The left-aligned form is the one recognized in MDL alias lines;
# the right-aligned form may be used in 2D depiction.
# The whole list is used to look up alias names;
# only the part up to a line starting with ## is used to generate aliases.
# and here the largest fragments should be first;
#left right SMILES color
CO2Et EtO2C C(=O)OCC
COOEt EtOOC C(=O)OCC
OiBu iBuO OCC(C)C
tBu tBu C(C)(C)C
nBu nBu CCCC
iPr iPr C(C)C
nPr nPr CCC
Et Et CC
NCF3 F3CN NC(F)(F)F
CF3 F3C C(F)(F)F
CCl3 Cl3C C(Cl)(Cl)Cl
CN NC C#N
NC CN [N+]#[C-]
N(OH)CH3 CH3(OH)N N(O)C
NO2 O2N N(=O)=O
NO ON N=O
SO3H HO3S S(=O)(=O)O
COOH HOOC C(=O)O blue
OEt EtO OCC
OAc AcO OC(=O)C
NHAc AcNH NC(=O)C
Ac Ac C(=O)C
CHO OHC C=O
NMe MeN NC
SMe MeS SC
OMe MeO OC
COO- -OOC C(=O)[O-]
## Only entries above this line are used to *generate* aliases.
Ph Ph c1ccccc1
OR RO O*
OBz BzO OCc1ccccc1
THPO THPO O[C@@H]1OCCCC1
NOH HON NO
CO2Me MeO2C C(=O)OC
COOMe MeOOC C(=O)OC
SO2Me MeO2S S(=O)(=O)C
NMe2 Me2N N(C)C
CO2R RO2C C(=O)O*
COOR ROOC C(=O)O*
NHZ ZNH NC(=O)OCC1=CC=CC=C1
CH2OH HOCH2 CO
CH2NH2 H2NCH2 CN
Me Me C
OBn BnO OCC1=CC=CC=C1
NHAm AmNH NCCCCC
OAm AmO OCCCCC
CO2Am AmO2C C(=O)OCCCCC
COOAm AmOOC C(=O)OCCCCC
SAm AmS SCCCCC
NHBn BnNH NCC1=CC=CC=C1
CO2Bn BnO2C C(=O)OCC1=CC=CC=C1
SnBu3 Bu3Sn [Sn](CCCC)(CCCC)CCCC
NHBu BuNH NCCCC
OBu BuO OCCCC
CO2Bu BuO2C C(=O)OCCCC
COOBu BuOOC C(=O)OCCCC
SBu BuS SCCCC
CBr3 Br3C C(Br)(Br)Br
NHCbz CbzNH NC(=O)OCC1=CC=CC=C1
SO2Cl ClSO2 S(Cl)(=O)=O
COBr BrCO C(=O)Br
COBu BuCO C(=O)CCCC
COCF3 F3CCO C(=O)C(F)(F)F
COCl ClCO C(=O)Cl
COCO COCO C(=O)C=O
COEt EtCO C(=O)CC
COF FCO C(=O)F
COMe MeCO C(=O)C
CONEt2 Et2NCO C(=O)(CC)NCC
CONH2 H2NCO C(=O)N
CONHEt EtHNCO C(=O)NCC
CONHMe MeHNCO C(=O)NC
CONMe2 Me2NCO C(=O)(C)NC
COSH HSOC C(=O)S
NEt2 Et2N N(CC)CC
NEt3 Et3N N(CC)(CC)CC
NHEt EtNH NCC
SO2NH2 H2NSO2 S(=O)(N)=O
NHOH HONH ON
NMe2 Me2N N(C)C
OMs MsO CS(O)(=O)=O
OCN NCO N=C=O
SCN NCS N=C=S
NHAm AmHN NCCCCC
NHBn BnHN NCC1=CC=CC=C1
NHBu BuHN NCCCC
NHOH HOHN NO
NHPr PrHN NCCC
NO ON N=O
POEt2 EtO2P P(OCC)OCC
POEt3 EtO3P P(OCC)(OCC)OCC
POOEt2 Et2OOP P(=O)(OCC)OCC
PrNH HNPr CCCN
SEt CCS SCC
#Aliases from samples provided with InChI
CH HC [CH]
CH- HC- [CH-]
D D [2H]
ND2 D2N [N]([2H])[2H]
DS SD [S][2H]
CH3 H3C C
C2H5 C2H5 CC
#Updates 3 Dec 2012 from Chris Swain
Ace Ace C(=O)C
Acetyl Acetyl C(=O)C
Acyl Acyl C(=O)C
AcAc AcAc C(=O)CC(C)=O
Ad Ad C1(C2)CC3CC2CC(C3)C1
AOC AOC C(=O)OC=C
Alloc Alloc C(=O)OC=C
Allyl Allyl CC=C
All All CC=C
BDMS BDMS [Si](C)(C)c1ccc(c2ccccc2)cc1
Boc Boc C(=O)OC(C)(C)C
BOC BOC C(=O)OC(C)(C)C
t-Boc t-Boc C(=O)OC(C)(C)C
BOM BOM COCc1ccccc1
Bn Bn Cc1ccccc1
Benzyl Benzyl Cc1ccccc1
Bz Bz C(=O)c1ccccc1
Benzoyl Benzoyl C(=O)c1ccccc1
Bromo Bromo Br
n-Bu n-Bu CCCC
t-Bu t-Bu CC(C)(C)
cBu cBu C1CCC1
c-Bu c-Bu C1CCC1
c-But c-But C1CCC1
nButyl nButyl CCCC
n-Butyl n-Butyl CCCC
n-But n-But CCCC
t-Butyl t-Butyl CC(C)(C)
cButyl cButyl C1CCC1
c-Butyl c-Butyl C1CCC1
Bs Bs S(=O)(=O)C1=CC=C(Br)C=C1
Cbz Cbz C(=O)OCC1=CC=CC=C1
Z Z C(=O)OCC1=CC=CC=C1
CE CE CCC#N
cinnamyl cinnamyl C/C=C/C1=CC=CC=C1
Chloro Chloro Cl
Dansyl Dansyl S(=O)(=O)C(C=CC=C12)=C1C=CC=C2N(C)C
Dan Dan S(=O)(=O)C(C=CC=C12)=C1C=CC=C2N(C)C
DEM DEM CC(OC)OC
DEIPS DEIPS [Si](CC)(CC)C(C)C
Dip Dip OC1=C(C(C)C)C=CC=C1(C(C)C)
Dmb Dmb CC1=CC=C(OC)C=C1OC
DPA DPA C(C=O)(C1=CC=CC=C1)C2=CC=CC=C2
DPhAc DPhAc C(C=O)(C1=CC=CC=C1)C2=CC=CC=C2
DTBMS DTBMS [Si](C)(C(C)(C)C)C(C)(C)C
Et Et CC
Ethyl Ethyl CC
EE EE CCOCC
EOM EOM COCC
Fluoro Fluoro F
Formyl Formyl C=O
FMOC FMOC C(=O)OCC1C2=CC=CC=C2C3=CC=CC=C13
nHeptyl nHeptyl CCCCCCC
n-Heptyl n-Heptyl CCCCCCC
cHeptyl cHeptyl C1CCCCCC1
c-Heptyl c-Heptyl C1CCCCCC1
nHexyl nHexyl CCCCCC
n-Hexyl n-Hexyl CCCCCC
cHexyl cHexyl C1CCCCC1
c-Hexyl c-Hexyl C1CCCCC1
Iodo Iodo I
IPDMS IPDMS [Si](C)(C(C)C)C
Methoxy Methoxy OC
MEM MEM COCCOC
Mesityl Mesityl C1=C(C)C=C(C)C=C1(C)
MOM MOM COC
Mesyl Mesyl S(=O)(C)=O
Ms Ms S(=O)(C)=O
Nitro Nitro N(=O)[O-]
nOctyl nOctyl CCC
n-Octyl n-Octyl CCC
n-Oct n-Oct CCC
PAB PAB CC1=CC=C(N)C=C1
nPentyl nPentyl CCCCC
n-Pentyl n-Pentyl CCCCC
cPentyl cPentyl C1CCCC1
c-Pentyl c-Pentyl C1CCCC1
Phenyl Phenyl c1ccccc1
PMB PMB CC1=CC=C(OC)C=C1
Pv Pv C(=O)C(C)(C)C
Pivaloyl Pivaloyl C(=O)C(C)(C)C
Propargyl Propargyl CC#C
nPropyl nPropyl CCC
n-Propyl n-Propyl CCC
n-Pr n-Pr CCC
n-Pro n-Pro CCC
cPropyl cPropyl C1CC1
c-Propyl c-Propyl C1CC1
c-Pr c-Pr C1CC1
c-Pro c-Pro C1CC1
cPr cPr C1CC1
i-Propyl i-Propyl C(C)C
i-Pr i-Pr C(C)C
i-Pro i-Pro C(C)C
SEM SEM ClCOCC[Si](C)(C)C
THP THP C1OCCCC1
TMS TMS [Si](C)(C)C
TBDMS TBDMS [Si](C)(C)C(C)(C)C
TBDPS TBDPS [Si](c1ccccc1)(c1ccccc1)C(C)(C)C
TES TES [Si](CC)(CC)CC
Tf Tf S(=O)(C(F)(F)F)=O
TIPS TIPS [Si](C(C)C)(C(C)C)C(C)C
Tos Tos S(=O)(=O)c1ccc(C)cc1
p-Tos p-Tos S(=O)(=O)c1ccc(C)cc1
p-Tosyl p-Tosyl S(=O)(=O)c1ccc(C)cc1
4-Tosyl 4-Tosyl S(=O)(=O)c1ccc(C)cc1
Tr Tr C(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3
Troc Troc C(=O)OCC(Cl)(Cl)Cl
Vinyl Vinyl C=C
Voc Voc C(=O)OC=C