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List of Functional Groups Recognized by Checkmol

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List of functional groups recognized by checkmol Current program version: v0.5 Norbert Haider, University of Vienna, 2005–2013 http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html For background information and for appropriate citation, please refer tio this article: Haider, N., Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: an Open-Source Approach. Molecules, 15, 5079-5092 (2010). The table below lists the functional group ID number, the English name (as obtained with the –e option), the 8-letter code (as obtained with the –c option [deprecated]) and the structures of the groups recognized by checkmol. The red circles in the structure drawing indicate the “key atoms” which are assigned to each functionality (as listed with the –p option). Wherever possible, a single “key atom” is used to identify and localize a functional group, but in some cases (e.g., for disulfides, peroxides, etc.) a pair of connectred atoms serves as a key. No. functional group name code general structure remarks 001 cation 000000T2 any positive charge 002 anion 000000T1 any negative charge 003 carbonyl compound C2O10000 O ketone or aldehyde R1 = H, alkyl, aryl R2 = H, alkyl, aryl R1 R2 004 aldehyde C2O1H000 O R = H, alkyl, aryl R H 005 ketone C2O1C000 O R1 = alkyl, aryl R2 = alkyl, aryl R1 R2 006 thiocarbonyl compound C2S10000 S thioketone or thioaldehyde R1 = H, alkyl, aryl R2 = H, alkyl, aryl R1 R2 007 thioaldehyde C2S1H000 S R = H, alkyl, aryl R H 008 thioketone C2S1C000 S R1 = alkyl, aryl R2 = alkyl, aryl R1 R2 009 imine C2N10000 R3 N R1 = H, alkyl, aryl 2 1 2 R = H, alkyl, aryl R R R3 = H, alkyl, aryl 010 hydrazone C2N1N000 R3 N 1 R4 R = H, alkyl, aryl N R2 = H, alkyl, aryl R3 = H, alkyl, aryl R1 R2 R4 = H, alkyl, aryl 011 semicarbazone C2NNC4ON R4 O N R5 1 N 3 R = H, alkyl, aryl R 2 N R = H, alkyl, aryl R3 = H, alkyl, aryl 4 1 2 R = H, alkyl, aryl, R R R5 = H, alkyl, aryl 012 thiosemicarbazone C2NNC4SN R4 S N R5 1 N 3 R = H, alkyl, aryl R 2 N R = H, alkyl, aryl R3 = H, alkyl, aryl 4 1 2 R = H, alkyl, aryl, R R R5 = H, alkyl, aryl 013 oxime C2N1OH00 OH N R1 = H, alkyl, aryl R2 = H, alkyl, aryl R1 R2 014 oxime ether C2N1OC00 OR3 N R1 = H, alkyl, aryl 2 1 2 R = H, alkyl, aryl R R R3 = alkyl, aryl 015 ketene C3OC0000 O R1 = H, alkyl, aryl R2 = H, alkyl, aryl R1 R2 016 ketene acetal derivative C3OCC000 X Y R1 = H, alkyl, aryl R2 = H, alkyl, aryl X = any hetero atom 1 2 R R Y = any hetero atom 017 carbonyl hydrate C2O2H200 HO OH R1 = H, alkyl, aryl R2 = H, alkyl, aryl R1 R2 018 hemiacetal C2O2HC00 3 R O OH R1 = H, alkyl, aryl 2 1 2 R = H, alkyl, aryl R R R3 = alkyl, aryl 019 acetal C2O2CC00 R3O OR4 R1 = H, alkyl, aryl R2 = H, alkyl, aryl 3 R1 R2 R = alkyl, aryl R4 = alkyl, aryl 4 3 020 hemiaminal C2NOHC10 R R1 = H, alkyl, aryl in a true hemiaminal, R would be H 3 5 2 R O N R R = H, alkyl, aryl R3 = H, alkyl, aryl 1 2 R4 = H, alkyl, aryl R R R5 = H, alkyl, aryl 1 021 aminal C2N2CC10 R4 R5 R = H, alkyl, aryl R2 = H, alkyl, aryl 3 6 R N N R R3 = H, alkyl, aryl R4 = H, alkyl, aryl 1 2 R R R5 = H, alkyl, aryl R6 = H, alkyl, aryl 4 022 thiohemiaminal C2NSHC10 R R1 = H, alkyl, aryl 3 5 2 R S N R R = H, alkyl, aryl R3 = H, alkyl, aryl 1 2 R4 = H, alkyl, aryl R R R5 = H, alkyl, aryl 023 thioacetal C2S2CC00 R3S SR4 R1 = H, alkyl, aryl R2 = H, alkyl, aryl 3 R1 R2 R = alkyl, aryl R4 = alkyl, aryl 024 enamine C2CNH000 5 4 R4, R5 = acyl should be types as R R 1 N R = H, acyl, alkyl, aryl enamide R2 = H, acyl, alkyl, aryl 1 3 R 3 R = H, acyl, alkyl, aryl R R4 = H, acyl, alkyl, aryl R2 R5 = H, acyl, alkyl, aryl 025 enol C2COH000 OH 1 R1 = H, acyl, alkyl, aryl R R3 R2 = H, acyl, alkyl, aryl R3 = H, acyl, alkyl, aryl R2 026 enolether C2COC000 OR4 1 1 R = H, acyl, alkyl, aryl 2 R 3 R = H, acyl, alkyl, aryl R R3 = H, acyl, alkyl, aryl R2 R4 = alkyl, aryl 027 hydroxy compound O1H00000 alcohol or phenol ROH R = alkyl, aryl 028 alcohol O1H0C000 ROH R = alkyl 029 prim. alcohol O1H1C000 R OH R = alkyl, aryl 030 sec. alcohol O1H2C000 R2 R1 = alkyl, aryl 1 R OH R2 = alkyl, aryl 031 tert. alcohol O1H3C000 2 R3 R R1 = alkyl, aryl 1 R OH R2 = alkyl, aryl R3 = alkyl, aryl 032 1,2-diol O1H0CO1H HO OH R1 = H, alkyl, aryl 1 3 R2 = H, alkyl, aryl R R 3 R2 R4 R = H, alkyl, aryl R4 = H, alkyl, aryl 1 033 1,2-aminoalcohol O1H0CN1C HO NH2 R = H, alkyl, aryl 1 3 R2 = H, alkyl, aryl R R 3 R2 R4 R = H, alkyl, aryl R4 = H, alkyl, aryl 034 phenol O1H1A000 OH any aromatic or heteroaromatic ring with an OH substituent 035 1,2-diphenol O1H2A000 OH any aromatic or heteroaromatic ring with two adjacent OH substituents (except tautomeric lactams) OH 036 enediol C2COH200 HO OH R1 = H, alkyl, aryl R2 = H, alkyl, aryl R1 R2 037 ether O1C00000 1 1 O 2 R = alkyl, aryl R R R2 = alkyl, aryl 038 dialkylether O1C0CC00 1 1 O 2 R = alkyl R R 2 R = alkyl 039 alkylarylether O1C0CA00 1 1 O 2 R = alkyl R R 2 R = aryl 040 diarylether O1C0AA00 1 1 O 2 R = aryl R R 2 R = aryl 041 thioether S1C00000 1 1 S 2 R = alkyl, aryl R R R2 = alkyl, aryl 042 disulfide S1S1C000 2 1 1 S R R = alkyl, aryl R S R2 = alkyl, aryl 043 peroxide O1O1C000 2 1 1 O R R = alkyl, aryl R O R2 = alkyl, aryl 044 hydroperoxide O1O1H000 O R = alkyl, aryl R OH 045 hydrazine derivative N1N10000 2 R R1 = H, acyl, alkyl, aryl 3 R2 = H, acyl, alkyl, aryl 1 N R R N R3 = H, acyl, alkyl, aryl 4 R4 R = H, acyl, alkyl, aryl 046 hydroxylamine N1O1H000 2 R R1 = H, alkyl, aryl 3 R2 = H, alkyl, aryl 1 N R R O R3 = H, alkyl, aryl 3 047 amine N1C00000 R R1 = alkyl, aryl R2 = H, alkyl, aryl N R1 R2 R3 = H, alkyl, aryl 048 prim. amine N1C10000 RNH R = alkyl, aryl 2 049 prim. aliphat. amine N1C1C000 RNH2 R = alkyl 050 prim. aromat. amine N1C1A000 RNH2 R = aryl 051 sec. amine N1C20000 H R1 = alkyl, aryl N R1 R2 R2 = alkyl, aryl 052 sec. aliphat. amine N1C2CC00 H R1 = alkyl N 1 2 R2 = alkyl R R 053 sec. mixed amine (aryl alkyl) N1C2AC00 H R1 = alkyl N 1 2 R2 = aryl R R 054 sec. aromat. amine N1C2AA00 H R1 = aryl N 1 2 R2 = aryl R R 3 055 tert. amine N1C30000 R R1 = alkyl, aryl R2 = alkyl, aryl N R1 R2 R3 = alkyl, aryl 3 056 tert. aliphat. amine N1C3CC00 R R1 = alkyl R2 = alkyl N R1 R2 R3 = alkyl 3 057 tert. mixed amine N1C3AC00 R R1 = alkyl R2 = aryl N R1 R2 R3 = alkyl, aryl 3 058 tert. arom_amine N1C3AA00 R R1 = aryl R2 = aryl N R1 R2 R3 = aryl 059 quaternary ammonium salt N1C400T2 3 1 4 R R = alkyl, aryl R + R2 = alkyl, aryl N 3 R1 R2 R = alkyl, aryl R4 = alkyl, aryl 060 N-oxide N0O10000 the N-O bond may be formulated as O a double bond O + 1 N + R = alkyl, aryl 2 1 N 3 R = alkyl, aryl R R 3 R2 R = alkyl, aryl 061 halogen deriv. XX000000 RX X = F, Cl, Br, I R = alkyl, alkenyl, aryl 062 alkyl halide XX00C000 RX X = F, Cl, Br, I R = alkyl 063 alkyl fluoride XF00C000 RF R = alkyl 064 alkyl chloride XC00C000 RCl R = alkyl 065 alkyl bromide XB00C000 RBr R = alkyl 066 alkyl iodide XI00C000 RI R = alkyl 067 aryl halide XX00A000 RX X = F, Cl, Br, I R = aryl 068 aryl fluoride XF00A000 RF R = aryl 069 aryl chloride XC00A000 RCl R = aryl 070 aryl bromide XB00A000 RBr R = aryl 071 aryl iodide XI00A000 RI R = aryl 072 organometallic compound 000000MX R M M = any metal R = alkyl, aryl 073 organolithium compound 000000ML RLi R = alkyl, aryl 074 organomagnesium compound 000000MM RMg R = alkyl, aryl 075 carboxylic acid deriv. C3O20000 O R = H, alkyl, aryl R X X = any hetero atom 076 carboxylic acid C3O2H000 O R = H, alkyl, aryl R OH 077 carboxylic acid salt C3O200T1 O R = H, alkyl, aryl R O 078 carboxylic acid ester C3O2C000 O 2 R1 = H, alkyl, aryl 1 R 2 R O R = alkyl, aryl 079 lactone C3O2CZ00 O a cyclic ester (any ring size) O 080 carboxylic acid amide C3ONC000 O 2 R1 = H, alkyl, aryl 1 R 2 R N R = H, alkyl, aryl R3 = H, alkyl, aryl R3 081 carboxylic acid prim. amide C3ONC100 O R = H, alkyl, aryl R NH2 082 carboxylic acid sec. amide C3ONC200 O 2 R1 = H, alkyl, aryl 1 R 2 R N R = alkyl, aryl H 083 carboxylic acid tert. amide C3ONC300 O 2 R1 = H, alkyl, aryl 1 R 2 R N R = alkyl, aryl R3 = alkyl, aryl R3 084 lactam C3ONCZ00 O a cyclic amide (any ring size) R N R = H, alkyl, aryl 085 carboxylic acid hydrazide C3ONN100 4 O R R1 = H, alkyl, aryl R2 = H, alkyl, aryl 1 N 3 R N R R3 = H, alkyl, aryl 4 2 R = H, alkyl, aryl R 086 carboxylic acid azide C3ONN200 O R = H, alkyl, aryl + R N N N 087 hydroxamic acid C3ONOH00 O R = H, alkyl, aryl OH R N H 088 carboxylic acid amidine C3N2H000 R4 N R1 = H, alkyl, aryl 3 R2 = H, alkyl, aryl 1 R R N R3 = H, alkyl, aryl 4 2 R = H, alkyl, aryl R 089 carboxylic acid amidrazone C3NNN100 5 R 4 N R R1 = H, alkyl, aryl R2 = H, alkyl, aryl N R1 N R3 R3 = H, alkyl, aryl 4 2 R = H, alkyl, aryl R R5 = H, alkyl, aryl 090 nitrile C3N00000 RCN R = H, alkyl, aryl 091 acyl halide C3OXX000 O R = H, alkyl, aryl R X X = F, Cl, Br, I 092 acyl fluoride C3OXF000 O R = H, alkyl, aryl R F 093 acyl chloride C3OXC000 O R = H, alkyl, aryl R Cl 094 acyl bromide C3OXB000 O R = H, alkyl, aryl R Br 095 acyl iodide C3OXI000 O R = H, alkyl, aryl R I 096 acyl cyanide C2OC3N00 O R = H, alkyl, aryl R C N 097 imido ester C3NOC000 R3 N 2 R1 = H, alkyl, aryl 1 R 2 R O R = alkyl, aryl R3 = H, alkyl, aryl 098 imidoyl halide C3NXX000 R2 N R1 = H, alkyl, aryl 1 2 R X R = H, alkyl, aryl X = F, Cl, Br, I 099 thiocarboxylic acid deriv.
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  • Chip Incompatibility Filters

    Chip Incompatibility Filters

    ChIP Incompatibility Filters Filter Name Type Description includes carboxylic acid halides and >1 acyl halide and related SMARTS derivatives like chloroformates, carbamoyl- , imidoyl halides, etc. >1 aldehyde SMARTS R no heteroatom no isocyanate, ketene, etc. >1 alkyl bromide / iodide SMARTS no acyl halide or related or vinyl halide >1 amine aromatic primary SMARTS aromatic carbon bound to N, N not charged >1 amines (aromatic/aliphatic, primary no amide, enamine, etc., no heteroatom SMARTS or secondary) bound to N, N not charged no amide, enamine, etc, no heteroatom >1 amines nucleophilic (aliphatic SMARTS bound to N, no aromatic carbon bound to primary or secondary) N, N not charged >1 aryl bromide / iodide SMARTS any aryl bromide / iodide >1 aryl halide SMARTS any aryl halide any boronic acid derivative, aromatic or >1 boronic acid derivative SMARTS aliphatic >1 carbonyl acid SMARTS any carboxylic or carbamic acid, etc. >1 carboxylic acid anhydrides SMARTS carbon must be bound to carbonyl no heteroatom bound to carbonyl or >1 carboxylic acid ester SMARTS oxygen, no acid, no anydride, etc >1 isocyanate / isothiocyanate SMARTS no restrictions to nitrogen substituents R no heteroatom, no isocyanate, ketene, >1 ketone or aldehyde SMARTS etc. >1 NH any SMARTS R can be anything >1 thioamide and related (any) SMARTS any substitution >1 thiol and related (nucleophic) SMARTS any SH or negative S >2 NH any SMARTS R can be anything acidic compounds I combination sulfonyl acids and carboxylic acids anhydrides, bicarbonates, thio and imino acyl anhydrides and derivatives SMARTS derivatives, etc. includes carboxylic acid halides and acyl halide and related SMARTS derivatives like chloroformates, carbamoyl- , imidoyl halides, etc.