533567797
Page 1 of 25
SMARTS Examples
Table of Contents
1. Introduction
2. Functional Groups by Element
2. Gross Structual Features
4. Meta-SMARTS
5. Electron & Proton Features
6. Breakdown of Complex SMARTS
7. Interesting Example SMARTS
1. Introduction
When using SMARTS to do searches, it is often helpful to have example queries from which to start. This
document contains many potentially useful example SMARTS which may be used to perform searches.
templates, examples and ideas.
These SMARTS have been tested, but they may still contain errors. Please send corrections, improvements,
additions, and questions to support@daylight.com.
2. Functional Groups by Element
C
C&O
C
alkane
Alkyl Carbon
[CX4]
alkene (-ene)
Allenic Carbon
[$([CX2](=C)=C)]
Vinylic Carbon
[$([CX3]=[CX3])]
Ethenyl carbon
alkyne (-yne)
H
N
O
P
S
X
533567797
Page 2 of 25
Acetylenic Carbon
[$([CX2]#C)]
arene (Ar , aryl-, aromatic hydrocarbons)
Arene
c
C&O
carbonyl
Carbonyl group. Low specificity
[CX3]=[OX1]
Hits carboxylic acid, ester, ketone, aldehyde, carbonic acid/ester,anhydride, carbamic acid/ester, acyl
halide, amide.
Carbonyl group
[$([CX3]=[OX1]),$([CX3+]-[OX1-])]
Hits either resonance structure
Carbonyl with Carbon
[CX3](=[OX1])C
Hits aldehyde, ketone, carboxylic acid (except formic), anhydride (except formic), acyl halides (acid
halides). Won't hit carbamic acid/ester, carbonic acid/ester.
Carbonyl with Nitrogen.
[OX1]=CN
Hits amide, carbamic acid/ester, poly peptide
Carbonyl with Oxygen.
[CX3](=[OX1])O
Hits ester, carboxylic acid, carbonic acid or ester, carbamic acid or ester, anhydride Won't hit aldehyde
or ketone.
Acyl Halide
[CX3](=[OX1])[F,Cl,Br,I]
acid halide, -oyl halide
Aldehyde
[CX3H1](=O)[#6]
-al
Anhydride
[CX3](=[OX1])[OX2][CX3](=[OX1])
Amide
[NX3][CX3](=[OX1])[#6]
-amide
Amidinium
[NX3][CX3]=[NX3+]
Carbamate.
[NX3,NX4+][CX3](=[OX1])[OX2,OX1-]
Hits carbamic esters, acids, and zwitterions
533567797
Carbamic ester
[NX3][CX3](=[OX1])[OX2H0]
Carbamic acid.
[NX3,NX4+][CX3](=[OX1])[OX2H,OX1-]
Hits carbamic acids and zwitterions.
Carboxylate Ion.
[CX3](=O)[O-]
Hits conjugate bases of carboxylic, carbamic, and carbonic acids.
Carbonic Acid or Carbonic Ester
[CX3](=[OX1])(O)O
Carbonic Acid, Carbonic Ester, or combination
Carbonic Acid or Carbonic Acid-Ester
[CX3](=[OX1])([OX2])[OX2H,OX1H0-1]
Hits acid and conjugate base. Won't hit carbonic acid diester
Carbonic Ester (carbonic acid diester)
C[OX2][CX3](=[OX1])[OX2]C
Won't hit carbonic acid or combination carbonic acid/ester
Carboxylic acid
[CX3](=O)[OX2H1]
-oic acid, COOH
Carboxylic acid or conjugate base.
[CX3](=O)[OX1H0-,OX2H1]
Cyanamide
[NX3][CX2]#[NX1]
Ester Also hits anhydrides
[#6][CX3](=O)[OX2H0][#6]
won't hit formic anhydride.
Ketone
[#6][CX3](=O)[#6]
-one
ether
Ether
[OD2]([#6])[#6]
H
hydrogen atoms
Hydrogen Atom
[H]
Hits SMILES that are hydrogen atoms: [H+] [2H] [H][H]
Not a Hydrogen Atom
[!#1]
Hits SMILES that are not hydrogen atoms.
Page 3 of 25
533567797
Page 4 of 25
Proton
[H+]
Hits positively charged hydrogen atoms: [H+]
hydrogen count
Mono-Hydrogenated Cation
[+H]
Hits atoms that have a positive charge and exactly one attached hydrogen: F[C+](F)[H]
Not Mono-Hydrogenated
[!H] or [!H1]
Hits atoms that don't have exactly one attached hydrogen.
N
amide see carbonyl
mine (-amino)
Primary or secondary amine, not amide.
[NX3;H2,H1;!$(NC=O)]
Not ammonium ion (N must be 3-connected), not ammonia (H count can't be 3). Primary or secondary is
specified by N's H-count (H2 &am p; H1 respectively). Also note that "&" (and) is the dafault opperator
and is higher precedence that "," (or), which is higher preceden ce than ";" (and). Will hit cyanamides
and thioamides
Enamine
[NX3][CX3]=[CX3]
Primary amine, not amide.
[NX3;H2;!$(NC=[!#6]);!$(NC#[!#6])][#6] Not amide (C not double bonded to a hetero-atom), not
ammonium ion (N must be 3-connected), n ot ammonia (N's H-count can't be 3), not cyanamide (C not
triple bonded to a hetero-atom)
Two primary or secondary amines
[NX3;H2,H1;!$(NC=O)].[NX3;H2,H1;!$(NC=O)]
Here we use the disconnection symbol (".") to match two separate unbonded identical patterns.
Enamine or Aniline Nitrogen
[NX3][$(C=C),$(cc)]
amino acids
Generic amino acid: low specificity.
[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]
For use w/ non-standard a.a. search. hits pro but not gly. Hits acids and conjugate bases. Hits single a.a.s
and specific residues w/in polypeptides (internal, or terminal).
Dipeptide group. generic amino acid: low specificity.
[NX3H2,NH3X4+][CX4H]([*])[CX3](=[OX1])[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[OX2H,OX1]
533567797
Page 5 of 25
Won't hit pro or gly. Hits acids and conjugate bases.
Amino Acid
[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]
Replace * w/ a specific a.a. side chain from the 18_standard_side_chains list to hit a specific standard
a.a. Won't work with Prolin e or Glycine, they have their own SMARTS (see side chain list). Hits acids
and conjugate bases. Hits single a.a.s and specific residues w/i n polypeptides (internal, or terminal).
{e.g. usage: Alanine side chain is [CH3X4] . Search is
[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([ CH3X4])[CX3](=[OX1])[OX2H,OX1-,N]}
amino acid side chains
Alanine side chain
[CH3X4]
Arginine side chain.
[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]
Hits acid and conjugate base.
Aspargine side chain.
[CH2X4][CX3](=[OX1])[NX3H2]
Also hits Gln side chain when used alone.
Aspartate (or Aspartic acid) side chain.
[CH2X4][CX3](=[OX1])[OH0-,OH]
Hits acid and conjugate base. Also hits Glu side chain when used alone.
Cysteine side chain.
[CH2X4][SX2H,SX1H0-]
Hits acid and conjugate base
Glutamate (or Glutamic acid) side chain.
[CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]
Hits acid and conjugate base.
Glycine
[$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])]
Histidine side chain.
[CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:
[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1
Hits acid & conjugate base for either Nitrogen. Note that the Ns can be either ([(Cationic 3-connected
with one H) or (Neutral 2-connected without any Hs)] where there is a second-neighbor who is [3connected with one H]) or (3-connected with one H).
Isoleucine side chain
[CHX4]([CH3X4])[CH2X4][CH3X4]
Leucine side chain
[CH2X4][CHX4]([CH3X4])[CH3X4]
Lysine side chain.
[CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]
Acid and conjugate base
Methionine side chain
[CH2X4][CH2X4][SX2][CH3X4]
Phenylalanine side chain
[CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1
Proline
533567797
Page 6 of 25
[$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1,N]
Serine side chain
[CH2X4][OX2H]
Thioamide
[NX3][CX3]=[SX1]
Threonine side chain
[CHX4]([CH3X4])[OX2H]
Tryptophan side chain
[CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12
Tyrosine side chain.
[CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1
Acid and conjugate base
Valine side chain
[CHX4]([CH3X4])[CH3X4]
Alanine side chain
[CH3X4]
Arginine side chain.
[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]
Hits acid and conjugate base.
Aspargine side chain.
[CH2X4][CX3](=[OX1])[NX3H2]
Also hits Gln side chain when used alone.
Aspartate (or Aspartic acid) side chain.
[CH2X4][CX3](=[OX1])[OH0-,OH]
Hits acid and conjugate base. Also hits Glu side chain when used alone.
Cysteine side chain.
[CH2X4][SX2H,SX1H0-]
Hits acid and conjugate base
Glutamate (or Glutamic acid) side chain.
[CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]
Hits acid and conjugate base.
Glycine
N[CX4H2][CX3](=[OX1])[O,N]
Histidine side chain.
[CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:
[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1
Hits acid & conjugate base for either Nitrogen. Note that the Ns can be either ([(Cationic 3-connected
with one H) or (Neutral 2-connected without any Hs)] where there is a second-neighbor who is [3connected
Isoleucine side chain
[CHX4]([CH3X4])[CH2X4][CH3X4]
Leucine side chain
[CH2X4][CHX4]([CH3X4])[CH3X4]
Lysine side chain.
[CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]
Acid and conjugate base
Methionine side chain
[CH2X4][CH2X4][SX2][CH3X4]
533567797
Page 7 of 25
Phenylalanine side chain
[CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1
Proline
N1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[O,N]
Serine side chain
[CH2X4][OX2H]
Threonine side chain
[CHX4]([CH3X4])[OX2H]
Tryptophan side chain
[CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12
Tyrosine side chain.
[CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1
Acid and conjugate base
Valine side chain
[CHX4]([CH3X4])[CH3X4]
azide (-azido)
Azide group.
[$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])]
Hits any atom with an attached azide.
Azide ion.
[$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])]
Hits N in azide ion
azo
Nitrogen.
[#7]
Nitrogen in N-containing compound. aromatic or aliphatic. Most general interpretation of "azo"
Azo Nitrogen. Low specificity.
[NX2]=N
Hits diazene, azoxy and some diazo structures
Azo Nitrogen.diazene
[NX2]=[NX2]
(diaza alkene)
Azoxy Nitrogen.
[$([NX2]=[NX3+]([O-])[#6]),$([NX2]=[NX3+0](=[O])[#6])]
Diazo Nitrogen
[$([#6]=[N+]=[N-]),$([#6-]-[N+]#[N])]
Azole.
[$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])]
5 member aromatic heterocycle w/ 2double bonds. contains N & another non C (N,O,S) subclasses are
furo-, thio-, pyrro- (replac e CH o' furfuran, thiophene, pyrrol w/ N)
hydrazine
533567797
Hydrazine H2NNH2
[NX3][NX3]
hydrazone
Hydrazone C=NNH2
[NX3][NX2]=[*]
imine
Substituted imine
[CX3;$([C]([#6])[#6]),$([CH][#6])]=[NX2][#6]
Schiff base
Substituted or un-substituted imine
[$([CX3]([#6])[#6]),$([CX3H][#6])]=[$([NX2][#6]),$([NX2H])]
Iminium
[NX3+]=[CX3]
imide
Unsubstituted dicarboximide
[CX3](=[OX1])[NX3H][CX3](=[OX1])
Substituted dicarboximide
[CX3](=[OX1])[NX3H0]([#6])[CX3](=[OX1])
Dicarboxdiimide
[CX3](=[OX1])[NX3H0]([NX3H0]([CX3](=[OX1]))[CX3](=[OX1]))[CX3](=[OX1])
nitrate
Nitrate group
[$([NX3](=[OX1])(=[OX1])O),$([NX3+]([OX1-])(=[OX1])O)]
Also hits nitrate anion
Nitrate Anion
[$([OX1]=[NX3](=[OX1])[OX1-]),$([OX1]=[NX3+]([OX1-])[OX1-])]
nitrile
Nitrile
[NX1]#[CX2]
Isonitrile
[CX1-]#[NX2+]
Page 8 of 25
533567797
Page 9 of 25
nitro
Nitro group.
[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] Hits both forms.
Two Nitro groups
[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8].[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]
nitroso
Nitroso-group
[NX2]=[OX1]
n-oxide
N-Oxide
[$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]
Hits both forms. Won't hit azoxy, nitro, nitroso,or nitrate.
O
hydroxyl (includes alcohol, phenol)
Hydroxyl
[OX2H]
Hydroxyl in Alcohol
[#6][OX2H]
Hydroxyl in Carboxylic Acid
[OX2H][CX3]=[OX1]
Hydroxyl in H-O-P[OX2H]P
Enol
[OX2H][#6X3]=[#6]
Phenol
[OX2H][cX3]:[c]
Enol or Phenol
[OX2H][$(C=C),$(cc)]
Hydroxyl_acidic
[$([OH]-*=[!#6])]
An acidic hydroxyl is a hydroxyl bonded to an atom which is multiply bonded to a hetero atom, this
includes carboxylic, sulphur, pho sphorous, halogen and nitrogen oxyacids.
peroxide
Peroxide groups.
533567797
Page 10 of 25
[OX2,OX1-][OX2,OX1-]
Also hits anions.
P
phosphoric compounds
Phosphoric_acid groups.
[$(P(=[OX1])([$([OX2H]),$([OX1-]),$([OX2]P)])([$([OX2H]),$([OX1]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)]),$([P+]([OX1-])([$([OX 2H]),$([OX1]),$([OX2]P)])([$([OX2H]),$([OX1-]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)])]
Hits both depiction forms. Hits orthophosphoric acid and polyphosphoric acid anhydrides. Doesn't hit
monophosphoric acid anhydride esters (including acidic mono- & di- esters) but will hit some
polyphosphoric acid anhydride esters (mono- esters on pyrophosphoric acid and longer, di- esters on
linear triphosphoric acid and longer).
Phosphoric_ester groups.
[$(P(=[OX1])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1]),$([OX2][#6]),$([OX2]P)]),$([P+]([OX1-])([OX2][#6])([ $([OX2H]),$([OX1]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)])]
Hits both depiction forms. Doesn't hit non-ester phosphoric_acid groups.
S
thio groups ( thio-, thi-, sulpho-, mercapto- )
Carbo-Thiocarboxylate
[S-][CX3](=S)[#6]
Carbo-Thioester
S([#6])[CX3](=O)[#6]
Thio analog of carbonyl
[#6X3](=[SX1])([!N])[!N]
Where S replaces O. Not a thioamide.
Thiol, Sulfide or Disulfide Sulfur
[SX2]
Thiol
[#16X2H]
Sulfur with at-least one hydrogen.
[#16!H0]
Thioamide
[NX3][CX3]=[SX1]
sulfide
Sulfide
[#16X2H0]
533567797
Page 11 of 25
-alkylthio Won't hit thiols. Hits disulfides.
Mono-sulfide
[#16X2H0][!#16]
alkylthio- or alkoxy- Won't hit thiols. Won't hit disulfides.
Di-sulfide
[#16X2H0][#16X2H0]
Won't hit thiols. Won't hit mono-sulfides.
Two Sulfides
[#16X2H0][!#16].[#16X2H0][!#16]
Won't hit thiols. Won't hit mono-sulfides. Won't hit disulfides.
sulfinate
Sulfinate
[$([#16X3](=[OX1])[OX2H0]),$([#16X3+]([OX1-])[OX2H0])]
Won't hit Sulfinic Acid. Hits Both Depiction Forms.
Sulfinic Acid
[$([#16X3](=[OX1])[OX2H,OX1H0-]),$([#16X3+]([OX1-])[OX2H,OX1H0-])]
Won't hit substituted Sulfinates. Hits Both Depiction Forms. Hits acid and conjugate base (sulfinate).
sulfone
Sulfone. Low specificity.
[$([#16X4](=[OX1])=[OX1]),$([#16X4+2]([OX1-])[OX1-])]
Hits all sulfones, including heteroatom-substituted sulfones: sulfonic acid, sulfonate, sulfuric acid mono& di- esters, sulfam ic acid, sulfamate, sulfonamide... Hits Both Depiction Forms.
Sulfone. High specificity.
[$([#16X4](=[OX1])(=[OX1])([#6])[#6]),$([#16X4+2]([OX1-])([OX1-])([#6])[#6])]
Only hits carbo- sulfones (Won't hit herteroatom-substituted molecules). Hits Both Depiction Forms.
Sulfonic acid. High specificity.
[$([#16X4](=[OX1])(=[OX1])([#6])[OX2H,OX1H0-]),$([#16X4+2]([OX1-])([OX1])([#6])[OX2H,OX1H0-])]
Only hits carbo- sulfonic acids (Won't hit herteroatom-substituted molecules). Hits acid and conjugate
base. Hits Both Depiction Forms. Hits Arene sulfonic acids.
Sulfonate
[$([#16X4](=[OX1])(=[OX1])([#6])[OX2H0]),$([#16X4+2]([OX1-])([OX1-])([#6])[OX2H0])]
(sulfonic ester) Only hits carbon-substituted sulfur (Oxygen may be herteroatom-substituted). Hits Both
Depiction Forms.
Sulfonamide.
[$([#16X4]([NX3])(=[OX1])(=[OX1])[#6]),$([#16X4+2]([NX3])([OX1-])([OX1-])[#6])]
Only hits carbo- sulfonamide. Hits Both Depiction Forms.
Carbo-azosulfone
[SX4](C)(C)(=O)=N
Partial N-Analog of Sulfone
Sulfonamide
[$([SX4](=[OX1])(=[OX1])([!O])[NX3]),$([SX4+2]([OX1-])([OX1-])([!O])[NX3])]
(sulf drugs) Won't hit sulfamic acid or sulfamate. Hits Both Depiction Forms.
533567797
Page 12 of 25
sulfoxide
Sulfoxide Low specificity.
[$([#16X3]=[OX1]),$([#16X3+][OX1-])]
( sulfinyl, thionyl ) Analog of carbonyl where S replaces C. Hits all sulfoxides, including heteroatomsubstituted sulfoxides, dialkylsulfoxides carbo-sulfoxides, sulfinate, sulfinic acids... Hits Both Depiction
Forms. Won't hit sulfones.
Sulfoxide High specificity
[$([#16X3](=[OX1])([#6])[#6]),$([#16X3+]([OX1-])([#6])[#6])]
(sulfinyl , thionyl) Analog of carbonyl where S replaces C. Only hits carbo-sulfoxides (Won't hit
herteroatom-substituted molecules). Hits Both Depiction Forms. Won't hit sulfones.
sulfate
Sulfate
[$([#16X4](=[OX1])(=[OX1])([OX2H,OX1H0-])[OX2][#6]),$([#16X4+2]([OX1-])([OX1])([OX2H,OX1H0-])[OX2][#6])]
(sulfuric acid monoester) Only hits when oxygen is carbon-substituted. Hits acid and conjugate base.
Hits Both Depiction Forms.
Sulfuric acid ester (sulfate ester) Low specificity.
[$([SX4](=O)(=O)(O)O),$([SX4+2]([O-])([O-])(O)O)]
Hits sulfuric acid, sulfuric acid monoesters (sulfuric acids) and diesters (sulfates). Hits acid and
conjugate base. Hits Both Depiction Forms. i
Sulfuric Acid Diester.
[$([#16X4](=[OX1])(=[OX1])([OX2][#6])[OX2][#6]),$([#16X4](=[OX1])(=[OX1])([OX2][#6])[OX2][
#6])]
Only hits when oxygen is carbon-substituted. Hits Both Depiction Forms.
sulfamate
Sulfamate.
[$([#16X4]([NX3])(=[OX1])(=[OX1])[OX2][#6]),$([#16X4+2]([NX3])([OX1-])([OX1-])[OX2][#6])]
Only hits when oxygen is carbon-substituted. Hits Both Depiction Forms.
Sulfamic Acid.
[$([#16X4]([NX3])(=[OX1])(=[OX1])[OX2H,OX1H0-]),$([#16X4+2]([NX3])([OX1-])([OX1])[OX2H,OX1H0-])]
Hits acid and conjugate base. Hits Both Depiction Forms.
sulfene
Sulfenic acid.
[#16X2][OX2H,OX1H0-]
Hits acid and conjugate base.
533567797
Page 13 of 25
Sulfenate.
[#16X2][OX2H0]
X
halide (-halo -fluoro -chloro -bromo -iodo)
Any carbon attached to any halogen
[#6][F,Cl,Br,I]
Halogen
[F,Cl,Br,I]
Three_halides groups
[F,Cl,Br,I].[F,Cl,Br,I].[F,Cl,Br,I]
Hits SMILES that have three halides.
acyl halide
Acyl Halide
[CX3](=[OX1])[F,Cl,Br,I]
(acid halide, -oyl halide)
3. Gross Structual Features
Chirality
Orbital Configuration
Connectivity
Chains & Branching
Rotation
Cyclic Features
Chirality
Specified chiral carbon.
[$([#6X4@](*)(*)(*)*),$([#6X4@H](*)(*)*)]
Matches carbons whose chirality is specified (clockwise or anticlockwise) Will not match molecules
whose chirality is unspecified b ut that could otherwise be considered chiral. Also,therefore won't match
molecules that would be chiral due to an implicit connection (i.e.i mplicit H).
"No-conflict" chiral match
C[C@?](F)(Cl)Br
Will match molecules with chiralities as specified or unspecified.
"No-conflict" chiral match where an H is present
C[C@?H](Cl)Br
Will match molecules with chiralities as specified or unspecified.
533567797
Page 14 of 25
Orbital Configuration
sp2 cationic carbon
[$([cX2+](:*):*)]
Aromatic cationic sp2 carbon with a free electron in a non-bonding sp2 hybrid orbital
Aromatic sp2 carbon.
[$([cX3](:*):*),$([cX2+](:*):*)]
The first recursive SMARTS matches carbons that are three-connected, the second case matches twoconnected carbons (i.e cations with a free electron in a non-bonding sp2 hybrid orbital)
Any sp2 carbon.
[$([cX3](:*):*),$([cX2+](:*):*),$([CX3]=*),$([CX2+]=*)]
The first recursive SMARTS matches carbons that are three-connected and aromatic. The second case
matches two-connected aromatic ca rbons (i.e cations with a free electron in a non-bonding sp2 hybrid
orbital). The third case matches three-connected non-aromatic carbons ( alkenes). The fourth case
matches non-aromatic cationic alkene carbons.
Any sp2 nitrogen.
[$([nX3](:*):*),$([nX2](:*):*),$([#7X2]=*),$([NX3](=*)=*),$([#7X3+](-*)=*),$([#7X3+H]=*)]
Can be aromatic 3-connected with 2 aromatic bonds (eg pyrrole,Pyridine-N-oxide), aromatic 2connected with 2 aromatic bonds (and a f ree pair of electrons in a nonbonding orbital, e.g.Pyridine),
either aromatic or non-aromatic 2-connected with a double bond (and a free pai r of electrons in a
nonbonding orbital, e.g. C=N ), non aromatic 3-connected with 2 double bonds (e.g. a nitro group; this
form does not exi st in reality, SMILES can represent the charge-separated resonance structures as a
single uncharged structure), either aromatic or non-aroma tic 3-connected cation w/ 1 single bond and 1
double bond (e.g. a nitro group, here the individual charge-separated resonance structures are specified),
either aromatic or non-aromatic 3-connected hydrogenated cation with a double bond (as the previous
case but R is hydrogen), r espectively.
Explicit Hydrogen on sp2-Nitrogen
[$([#1X1][$([nX3](:*):*),$([nX2](:*):*),$([#7X2]=*),$([NX3](=*)=*),$([#7X3+](*)=*),$([#7X3+H]=*)])]
(H must be an isotope or ion)
sp3 nitrogen
[$([NX4+]),$([NX3]);!$(*=*)&!$(*:*)]
One atom that is (a 4-connected N cation or a 3-connected N) and is not double bonded and is not
aromatically bonded.
Explicit Hydrogen on an sp3 N.
[$([#1X1][$([NX4+]),$([NX3]);!$(*=*)&!$(*:*)])]
One atom that is a 1-connected H that is bonded to an sp3 N. (H must be an isotope or ion)
sp2 N in N-Oxide
[$([$([NX3]=O),$([NX3+][O-])])]
sp3 N in N-Oxide Exclusive:
[$([$([NX4]=O),$([NX4+][O-])])]
Only hits if O is explicitly present. Won't hit if * is in SMILES in place of O.
sp3 N in N-Oxide Inclusive:
[$([$([NX4]=O),$([NX4+][O-,#0])])]
Hits if O could be present. Hits if * if used in place of O in smiles.
Connectivity
533567797
Page 15 of 25
Quaternary Nitrogen
[$([NX4+]),$([NX4]=*)]
Hits non-aromatic Ns.
Tricoordinate S double bonded to N.
[$([SX3]=N)]
S double-bonded to Carbon
[$([SX1]=[#6])]
Hits terminal (1-connected S)
Triply bonded N
[$([NX1]#*)]
Divalent Oxygen
[$([OX2])]
Chains & Branching
Unbranched_alkane groups.
[R0;D2][R0;D2][R0;D2][R0;D2]
Only hits alkanes (single-bond chains). Only hits chains of at-least 4 members. All non-(implicithydrogen) atoms count as branches (e.g. halide substituted chains count as branched).
Unbranched_chain groups.
[R0;D2]~[R0;D2]~[R0;D2]~[R0;D2]
Hits any bond (single, double, triple). Only hits chains of at-least 4 members. All non-(implicithydrogen) atoms count as branches (e.g. halide substituted chains count as branched).
Long_chain groups.
[AR0]~[AR0]~[AR0]~[AR0]~[AR0]~[AR0]~[AR0]~[AR0]
Aliphatic chains at-least 8 members long.
Atom_fragment
[!$([#6+0]);!$(C(F)(F)F);!$(c(:[!c]):[!c])!$([#6]=,#[!#6])]
(CLOGP definition) A fragment atom is a not an isolating carbon
Carbon_isolating
[$([#6+0]);!$(C(F)(F)F);!$(c(:[!c]):[!c])!$([#6]=,#[!#6])]
This definition is based on that in CLOGP, so it is a charge-neutral carbon, which is not a CF3 or an
aromatic C between two aromati c hetero atoms eg in tetrazole, it is not multiply bonded to a hetero
atom.
Terminal S bonded to P
[$([SX1]~P)]
Nitrogen on -N-C=N[$([NX3]C=N)]
Nitrogen on -N-N=C[$([NX3]N=C)]
Nitrogen on -N-N=N[$([NX3]N=N)]
Oxygen in -O-C=N[$([OX2]C=N)]
Rotation
533567797
Page 16 of 25
Rotatable bond
[!$(*#*)&!D1]-!@[!$(*#*)&!D1]
An atom which is not triply bonded and not one-connected i.e.terminal connected by a single non-ring
bond to and equivalent atom. No te that logical operators can be applied to bonds ("-&!@"). Here, the
overall SMARTS consists of two atoms and one bond. The bond is "si ngle and not ring". *#* any atom
triple bonded to any atom. By enclosing this SMARTS in parentheses and preceding with $, this enables
us t o use $(*#*) to write a recursive SMARTS using that string as an atom primitive. The purpose is to
avoid bonds such as c1ccccc1-C#C which wo uld be considered rotatable without this specification.
Cyclic Features
Bicyclic
[$([*R2]([*R])([*R])([*R]))].[$([*R2]([*R])([*R])([*R]))]
Bicyclic compounds have 2 bridgehead atoms with 3 arms connecting the bridgehead atoms.
Ortho
*-!:aa-!:*
Ortho-substituted ring
Meta
*-!:aaa-!:*
Meta-substituted ring
Para
*-!:aaaa-!:*
Para-substituted ring
Acylic-bonds
*!@*
Single bond and not in a ring
*-!@*
Non-ring atom
[R0] or [!R]
Macrocycle groups.
[r;!r3;!r4;!r5;!r6;!r7]
S in aromatic 5-ring with lone pair
[sX2r5]
Aromatic 5-Ring O with Lone Pair
[oX2r5]
N in 5-sided aromatic ring
[nX2r5]
Spiro-ring center
[X4;R2;r4,r5,r6](@[r4,r5,r6])(@[r4,r5,r6])(@[r4,r5,r6])@[r4,r5,r6]rings size 4-6
N in 5-ring arom
[$([nX2r5]:[a-]),$([nX2r5]:[a]:[a-])] anion
CIS or TRANS double bond in a ring
*/,\[R]=;@[R]/,\*
An isomeric SMARTS consisting of four atoms and three bonds.
CIS or TRANS double or aromatic bond in a ring
*/,\[R]=,:;@[R]/,\*
Unfused benzene ring
[cR1]1[cR1][cR1][cR1][cR1][cR1]1
533567797
Page 17 of 25
To find a benzene ring which is not fused, we write a SMARTS of 6 aromatic carbons in a ring where
each atom is only in one ring:
Multiple non-fused benzene rings
[cR1]1[cR1][cR1][cR1][cR1][cR1]1.[cR1]1[cR1][cR1][cR1][cR1][cR1]1
Fused benzene rings
c12ccccc1cccc2
4. Meta-SMARTS
Amino Acids
Recursive or Multiple
Tools &Tricks
Amino Acids
Generic amino acid: low specificity.
[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]
For use w/ non-standard a.a. search. hits pro but not gly. Hits acids and conjugate bases. Hits single a.a.s
and specific residues w/in polypeptides (internal, or terminal).
A.A. Template for 20 standard a.a.s
[$([$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,O
X1-,N]),
$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX 4H2][CX3](=[OX1])[OX2H,OX1,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N])]
Pro, Gly, Other. Replace * w/ the entire 18_standard_side_chains list to get "any standard a.a." Hits
acids and conjugate bases. Hits single a.a.s and specific residues w/in polypeptides (internal, or
terminal).
Proline
[$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1,N]
Glycine
[$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])]
Other a.a.
[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]
Replace * w/ a specific a.a. side chain from the 18_standard_side_chains list to hit a specific standard
a.a. Won't work with Prolin e or Glycine, they have their own SMARTS (see side chain list). Hits acids
and conjugate bases. Hits single a.a.s and specific residues w/i n polypeptides (internal, or terminal).
Example usage:
Alanine side chain is [CH3X4]
Alanine Search is
[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([CH3X4])[CX3](=[OX1])[OX2H,OX1-,N]
18_standard_aa_side_chains.
([$([CH3X4]),$([CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]),
$([CH2X4][CX3](=[OX1])[NX3H2]),$([CH2X4][CX3](=[OX1])[OH0-,OH]),
$([CH2X4][SX2H,SX1H0-]),$([CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]),
$([CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:
533567797
Page 18 of 25
[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1),
$([CHX4]([CH3X4])[CH2X4][CH3X4]),$([CH2X4][CHX4]([CH3X4])[CH3X4]),
$([CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]),$([CH2X4][CH2X4][SX2][CH3X4]),
$([CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1),$([CH2X4][OX2H]),
$([CHX4]([CH3X4])[OX2H]),$([CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][c
X3]12),
$([CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1])[cX3H][cX3H]1),$([CHX4]([CH3X4])[CH3X4])])
Can be any of the standard 18 (Pro & Gly are treated separately) Hits acids and conjugate bases.
N in Any_standard_amino_acid.
[$([$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3]
(=[OX1])[OX2H,OX1-,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3]
(=[OX1])[OX2H,OX1-,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([$([CH3X4]),
$([CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]),$
([CH2X4][CX3](=[OX1])[NX3H2]),$([CH2X4][CX3](=[OX1])[OH0-,OH]),
$([CH2X4][SX2H,SX1H0-]),$([CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]),
$([CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:
[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1),
$([CHX4]([CH3X4])[CH2X4][CH3X4]),$([CH2X4][CHX4]([CH3X4])[CH3X4]),
$([CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]),$([CH2X4][CH2X4][SX2][CH3X4]),
$([CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1),$([CH2X4][OX2H]),
$([CHX4]([CH3X4])[OX2H]),$([CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][c
X3]12),
$([CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1),
$([CHX4]([CH3X4])[CH3X4])])[CX3](=[OX1])[OX2H,OX1-,N])]
Format is A.A.Template for 20 standard a.a.s. where * is replaced by the entire 18_standard_side_chains
list (or'd together). A gen eric amino acid with any of the 18 side chains or, proline or glycine. Hits
"standard" amino acids that have terminally appended groups (i.e . "standard" refers to the side chains).
(Pro, Gly, or 18 normal a.a.s.) Hits single a.a.s and specific residues w/in polypeptides (intern al, or
terminal).
Non-standard amino acid.
[$([NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]);!$([$([$([NX3H,NX4H2+]),
$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]),
$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N]),
$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([$([CH3X4]),$([CH2X4][CH2X4][CH2X4][NHX
3][CH0X3]
(=[NH2X3+,NHX2+0])[NH2X3]),$([CH2X4][CX3](=[OX1])[NX3H2]),$([CH2X4][CX3](=[OX1])[O
H0-,OH]),
$([CH2X4][SX2H,SX1H0-]),$([CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]),$([CH2X4][#6X3]1:
[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:
[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),
$([#7X3H])]:[#6X3H]1),$([CHX4]([CH3X4])[CH2X4][CH3X4]),$([CH2X4][CHX4]([CH3X4])[CH3
X4]),
$([CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]),$([CH2X4][CH2X4][SX2][CH3X4]),
$([CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1),$([CH2X4][OX2H]),$([CHX4]([CH3X4])[O
X2H]),
$([CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12),
$([CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1),
$([CHX4]([CH3X4])[CH3X4])])[CX3](=[OX1])[OX2H,OX1-,N])])]
533567797
Page 19 of 25
Generic amino acid but not a "standard" amino acid ("standard" refers to the 20 normal side chains).
Won't hit amino acids that are non-standard due solely to the fact that groups are terminally-appended to
the polypeptide chain (N or C term). format is [$(generic a.a.); !$(not a standard one)] Hits single a.a.s
and specific residues w/in polypeptides (internal, or terminal).
Recursive or Multiple
Recursive SMARTS: Atoms connected to particular SMARTS
Ortho
[SMARTS_expression]-!:aa-!:[SMARTS_expression]
Meta
[SMARTS_expression]-!:aaa-!:[SMARTS_expression]
Para
[SMARTS_expression]-!:aaaa-!:[SMARTS_expression]
Hydrogen
[$([#1][SMARTS_expression])]
Hydrogen must be explicit i.e. an isotope or charged
Nitrogen
[$([#7][SMARTS_expression])]
Oxygen
[$([#8][SMARTS_expression])]
Fluorine
[$([#9][SMARTS_expression])]
Recursive SMARTS: Multiple groups
Two possible groups
[$(SMARTS_expression_A),$(SMARTS_expression_B)]
Hits atoms in either environment or group of interest, A or B.
Example usages:
Azide group is : [$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])]
Azide ion is: [$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])]
Azide or azide ion is: [$([$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])]),$([$([NX1]=[NX2+]=[NX1-]),$( [NX1]#[NX2+]-[NX1-2])])]
Recursive SMARTS
[$([atom_that_gets_hit][other_atom][other_atom])]
Hits first atom within parenthesis Example usages:
[$([CX3]=[OX1])] hits Carbonyl Carbon [$([OX1]=[CX3])] hits Carbonyl Oxygen
Single only, Double only, Single or Double
Sulfide
[#16X2H0]
(-alkylthio) Won't hit thiols. Hits disulfides too.
533567797
Page 20 of 25
Mono-sulfide
[#16X2H0][!#16]
(alkylthio- or alkoxy-) R-S-R Won't hit thiols. Won't hit disulfides.
Di-sulfide
[#16X2H0][#16X2H0]
Won't hit thiols. Won't hit mono-sulfides.
Two sulfides
[#16X2H0][!#16].[#16X2H0][!#16]
Won't hit thiols. Won't hit mono-sulfides. Won't hit disulfides.
Acid/conj-base
[OX2H,OX1H0-]
Hits acid and conjugate base. acid/base
Non-acid Oxygen
[OX2H0]
Acid/base
[H1,H0-]
Works for any atom if base form has no Hs & acid has only one.
Muntiple Disconnected Groups
Two disconnected SMARTS fragments
([Cl!$(Cl~c)].[c!$(c~Cl)])
A molecule that contains a chlorine and an aromatic carbon but which are not connected to each other.
Uses component-level SMARTS. B oth SMARTS fragments must be in the same SMILES target
fragment.
Two disconnected SMARTS fragments
([Cl]).([c])
Hits SMILES that contain a chlorine and an aromatic carbon but which are in different SMILES
fragments.
Two not-necessarily connected SMARTS fragments
([Cl].[c])
Uses component-level SMARTS. Both SMARTS fragments must be in the same SMILES target
fragment.
Two not-necessarily connected fragments
([SMARTS_expression]).([SMARTS_expression])
Uses component-level SMARTS. SMARTS fragments are each in different SMILES target fragments.
Two primary or secondary amines
[NX3;H2,H1;!$(NC=O)].[NX3;H2,H1;!$(NC=O)]
Here we use the "disconnection" symbol (".") to match two separate not-necessarily bonded identical
patterns.
Tools &Tricks
Alternative/Equivalent Representations
Any carbon aromatic or non-aromatic
533567797
Page 21 of 25
[#6] or [c,C]
SMILES wildcard
[#0]
This SMARTS hits the SMILES *
Factoring
[OX2,OX1-][OX2,OX1-] or [O;X2,X1-][O;X2,X1-]
Factor out common atomic expressions in the recursive SMARTS. May improve human readability.
High-precidence "and"
[N&X4&+,N&X3&+0] or [NX4+,NX3+0]
High-precidence "and" (&) is the default logical operator. "Or" (,) is higher precidence than & and lowprecidence "and" (;) is lower precidence than &.
Hydrogens
Any atom w/ at-least 1 H
[*!H0,#1]
In SMILES and SMARTS, Hydrogen is not considered an atom (unless it is specified as an isotope).
The hydrogen count is instead consi dered a property of an atom. This SMARTS provides a way to
effectively hit Hs themselves.
Hs on Carbons
[#6!H0,#1]
Atoms w/ 1 H
[H,#1]
5. Electron & Proton Features
Acids & Bases
Charge
H-bond Donors & Acceptors
Radicals
Acids & Bases
Acid
[!H0;F,Cl,Br,I,N+,$([OH]-*=[!#6]),+]
Proton donor
Carboxylic acid
[CX3](=O)[OX2H1]
(-oic acid, COOH)
Carboxylic acid or conjugate base.
[CX3](=O)[OX1H0-,OX2H1]
Hydroxyl_acidic
[$([OH]-*=[!#6])]
An acidic hydroxyl is a hydroxyl bonded to an atom which is multiply bonded to a hetero atom, this
includes carboxylic, sulphur, pho sphorous, halogen and nitrogen oxyacids
533567797
Page 22 of 25
Phosphoric_Acid
[$(P(=[OX1])([$([OX2H]),$([OX1-]),$([OX2]P)])([$([OX2H]),$([OX1]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)]),$([P+]([OX1-])([$([OX 2H]),$([OX1]),$([OX2]P)])([$([OX2H]),$([OX1-]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)])]
Hits both forms. Hits orthophosphoric acid and polyphosphoric acid anhydrides. Doesn't hit
monophosphoric acid anhydride esters (in cluding acidic mono- & di- esters) but will hit some
polyphosphoric acid anhydride esters (mono- esters on pyrophosphoric acid and longe r, di- esters on
linear triphosphoric acid and longer). Hits acid and conjugate base.
Sulfonic Acid. High specificity.
[$([#16X4](=[OX1])(=[OX1])([#6])[OX2H,OX1H0-]),$([#16X4+2]([OX1-])([OX1])([#6])[OX2H,OX1H0-])]
Only hits carbo- sulfonic acids (Won't hit herteroatom-substituted molecules). Hits acid and conjugate
base. Hits Both Depiction Fo rms. Hits Arene sulfonic acids.
Acyl Halide
[CX3](=[OX1])[F,Cl,Br,I]
(acid halide, -oyl halide)
Charge
Anionic divalent Nitrogen
[NX2-]
Oxenium Oxygen
[OX2H+]=*
Oxonium Oxygen
[OX3H2+]
Carbocation
[#6+]
sp2 cationic carbon.
[$([cX2+](:*):*)]
Aromatic cationic sp2 carbon with a free electron in a non-bonding sp2 hybrid orbital
Azide ion.
[$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])]
Hits N in azide ion
Zwitterion High Specificity
[+1]~*~*~[-1]
+1 charged atom separated by any 3 bonds from a -1 charged atom.
Zwitterion Low Specificity, Crude
[$([!-0!-1!-2!-3!-4]~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!3!-4]~*~*~*~[!+0!+1!+2!+3!+4]),$([ !-0!-1!-2!-3!-4]~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!4]~*~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~*~*~*~[!+0!+1!+2!+3!+ 4]),$([!-0!-1!2!-3!-4]~*~*~*~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!4]~*~*~*~*~*~*~*~*~[!+0!+1!+2!+3!+4]),$([!-0!-1!-2!-3!-4]~*~*~*~*~
*~*~*~*~*~[!+0!+1!+2!+3!+4])]
Variously charged moieties separated by up to ten bonds.
Zwitterion Low Specificity
([!-0!-1!-2!-3!-4].[!+0!+1!+2!+3!+4])
Variously charged moieties that are within the same molecule but not-necessarily connected. Uses
component-level grouping.
533567797
Page 23 of 25
H-bond Donors & Acceptors
Hydrogen-bond acceptor
[#6,#7;R0]=[#8]
Only hits carbonyl and nitroso. Matches a 2-atom pattern consisting of a carbon or nitrogen not in a ring,
double bonded to an oxyge n.
Hydrogen-bond acceptor
[!$([#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3,])]
A H-bond acceptor is a heteroatom with no positive charge, note that negatively charged oxygen or
sulphur are included. Excluded are halogens, including F, heteroaromatic oxygen, sulphur and pyrrole
N. Higher oxidation levels of N,P,S are excluded. Note P(III) is currentl y included. Zeneca's work
would imply that (O=S=O) shoud also be excluded.
Hydrogen-bond donor.
[!$([#6,H0,-,-2,-3])]
A H-bond donor is a non-negatively charged heteroatom with at least one H
Hydrogen-bond donor.
[!H0;#7,#8,#9]
Must have an N-H bond, an O-H bond, or a F-H bond
Possible intramolecular H-bond
[O,N;!H0]-*~*-*=[$([C,N;R0]=O)]
Note that the overall SMARTS consists of five atoms. The fifth atom is defined by a "recursive
SMARTS", where "$()" encloses a valid nested SMARTS and acts syntactically like an atom-primitive
in the overall SMARTS. Multiple nesting is allowed.
Radicals
Carbon Free-Radical
[#6;X3v3+0]
Hits a neutral carbon with three single bonds.
Nitrogen Free-Radical
[#7;X2v4+0]
Hits a neutral nitrogen with two single bonds or with a single and a triple bond.
6. Breakdown of Complex SMARTS
<!--/a>
Amino Acid
Amino Acid
Ester or Amide
533567797
Page 24 of 25
[$([$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][ CX3](=[OX1])[OX2H,OX1,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N])] i
[$(
[
$([
NX3H
,
NX4H2+])
,
$([NX3](C)(C)(C))]1
[CX4H]
([CH2][CH2][CH2]1)
[CX3]
(=[OX1])
[OX2H,OX1-,N]
),
$(
[
$([
NX3H2
,
NX4H3+])
,
$([NX3H](C)(C))
[CX4H2]
[CX3]
(=[OX1])
[OX2H,OX1-,N]
),
$(
[
$([
NX3H2
,
NX4H3+])
,
$([NX3H](C)(C))]
[CX4H]
([*])
[CX3]
(=[OX1])
[OX2H,OX1-,N]
)]
Proline
N:
terminal
neutral
or
+ charged
or
internal
C: alpha
pro side chain
C: of COOH
O: =O of COOH
O: term COOH (neutral or -) or intern
OR
Glycine
N:
terminal
neutral
or
+ charged
or
internal
C: alpha (w/ H side chain)
C: of COOH
O: =O of COOH
O: term COOH (neutral or -) or intern
OR
Other amino acid
N:
terminal
neutral
or
+ charged
or
internal
C: alpha
any side chain
C: of COOH
O: =O of COOH
O: term COOH (neutral or -) or intern
Ester or Amide
[#6][CX3](=O)[$([OX2H0]([#6])[#6]),$([#7])]
[#6]
[CX3]
(=O)
[
$(
[OX2H0]
([#6])[#6])
carbonyl C
An atom that is a carbon
Connected to an atom that is a three-connected carbon
Which is double bonded to an oxygen
Connected to an atom
That is in an environment where
An atom that is a two-connected oxygen, without hydrogens
Is connected to two carbons, one of them being the
533567797
,
$(
[#7]
)]
Page 25 of 25
Or
That is in an environment where
An atom is a nitrogen.
7. Interesting Example SMARTS
Oxygen double bonded to aliphatic carbon or nitrogen, single bonded to an aromatic ring, with a halogen in
meta position
[#8]=[C,N]-aaa[F,Cl,Br,I]
Aliphatic carbon attached to oxygen with any bond
C~O
Oxygen or nitrogen, with at least one hydrogen attached and not in a ring
[O,N;!H0;R0]
Oxygen double bonded to aliphatic carbon or nitrogen
[#8]=[C,N] or O=[C,N]
Aliphatic atom single-bonded to any carbon which isn't a trifluromethyl carbon
A[#6;!$(C(F)(F)F)]
PCB
[$(c:cCl),$(c:c:cCl),$(c:c:c:cCl)]-[$(c:cCl),$(c:c:cCl),$(c:c:c:cCl)]
Polychlorinated Biphenyls. Overall SMARTS is atom-bond-atom. Note that ":" is explicit aromatic
bond, and "-" is explicit single bo nd. On each side of the single bond, we use three nested SMARTS to
represent the ortho, meta, and para position.
Imidazolium Nitrogen
[nX3r5+]:c:n
1-methyl-2-hydroxy benzene with either a Cl or H at the 5 position.
[c;$([*Cl]),$([*H1])]1ccc(O)c(C)c1 or Cc1:c(O):c:c:[$(cCl),$([cH])]:c1
The "H" primitive in SMARTS means "total number of attached hydrogens", i.e., [C] will match C in
[CH4] methane, [CH3] methyl, [CH2] methylene, etc., [CH3] will only match methyl. This is similar to
the use of "H" in SMILES to specify hydrogen count. The default value for the SMARTS "H" primitive
is 1 (same as SMILES, e.g., [CH2]=[CH]-[OH] same as CC=O). This H-specification value includes all
attached hydrogens: implicit and explicit (e.g., isotopic [2H]).
Nonstandard atom groups.
[!#1;!#2;!#3;!#5;!#6;!#7;!#8;!#9;!#11;!#12;!#15;!#16;!#17;!#19;!#20;!#35;!#53]