# # SMARTS Patterns for Functional Group Classification # # written by Christian Laggner # Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH # # Released under the Lesser General Public License (LGPL license) # see http://www.gnu.org/copyleft/lesser.html # Modified from Version 221105 ##################################################################################################### # General Stuff: # These patters were written in an attempt to represent the classification of organic compounds # from the viewpoint of an organic chemist. # They are often very restrictive. This may be generally a good thing, but it also takes some time # for filtering/indexing large compound sets. # For filtering undesired groups (in druglike compounds) one will want to have more general patterns # (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...). # # Part I: Carbon # ============== # I.1: Carbon-Carbon Bonds # ------------------------ # I.1.1 Alkanes: Primary_carbon: [CX4H3][#6] Secondary_carbon: [CX4H2]([#6])[#6] Tertiary_carbon: [CX4H1]([#6])([#6])[#6] Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6] # I.1.2 C-C double and Triple Bonds Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] # sp2 C may be substituted only by C or H - # does not hit ketenes and allenes, nor enamines, enols and the like Alkyne: [CX2]#[CX2] # non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination Allene: [CX3]=[CX2]=[CX3] # I.2: One Carbon-Hetero Bond # --------------------------- # I.2.1 Alkyl Halogenides Alkylchloride: [ClX1][CX4] # will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats # a more restrictive version can be obtained by modifying the Alcohol string. Alkylfluoride: [FX1][CX4] Alkylbromide: [BrX1][CX4] Alkyliodide: [IX1][CX4] # I.2.2 Alcohols and Ethers Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])] # nonspecific definition, no acetals, aminals, and the like Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])] Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])] Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])] Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] # no acetals and the like; no enolethers Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] # no acetals and the like; no enolethers Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] # no acetals and the like; no enolethers Diarylether: [c][OX2][c] Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] Diarylthioether: [c][SX2][c] Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])] # can't be aromatic, thus O and not #8 # I.2.3 Amines Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])] # hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ... # the following amines include also the protonated forms Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] Primary_arom_amine: [NX3H2+0,NX4H3+]c Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])] Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])] Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])] Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])] # only C and H substituents allowed. Quaternary or protonated amines # NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present # I.2.4 Others Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])] Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])] Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])] Disulfide: [SX2D2][SX2D2] 1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])] # does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc. 1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H] # does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc. 1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H] Hydroperoxide: [OX2H][OX2] #does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides Peroxo: [OX2D2][OX2D2] Organolithium_compounds: [LiX1][#6,#14] Organomagnesium_compounds: [MgX2][#6,#14] # not restricted to Grignard compounds, also dialkyl Mg Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-] # very general, includes all metals covalently bound to carbon # I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives) # ---------------------------- # I.3.1 Double Bond to Hetero Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1] # hits aldehydes including formaldehyde Ketone: [#6][CX3](=[OX1])[#6] # does not include oxo-groups connected to a (hetero-) aromatic ring Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1] Thioketone: [#6][CX3](=[SX1])[#6] # does not include thioxo-groups connected to a (hetero-) aromatic ring Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])] # nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])] Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H] Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])] # ether, not ester or amide; does not hit isoxazole # I.3.2. Two Single Bonds to Hetero Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] # does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc. Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6] # Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H] Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])] Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H] Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] # hits chloromethylenethers and other reactive alkylating agents Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] # includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] # also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] # Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] # Combination of the last two patterns Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H] # I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar) Chloroalkene: [ClX1][CX3]=[CX3] Fluoroalkene: [FX1][CX3]=[CX3] Bromoalkene: [BrX1][CX3]=[CX3] Iodoalkene: [IX1][CX3]=[CX3] Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3] # no phenols Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H] # no 1,2-diphenols, ketenacetals, ... Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3] # finds also endiodiethers, but not enolesters, no aromats Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])] Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3] # does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3] Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3] # I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives) # ------------------------------ Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1] Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1] Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1] Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1] Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1] # all of the above # The following contains all simple carboxylic combinations of O, N, S, & Hal - # - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...) # Cyclic structures (including aromats) like lactones, lactames, ... got their own # definitions. Structures where both heteroatoms are part of an aromatic ring # (oxazoles, imidazoles, ...) were excluded. Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])] # includes carboxylate anions Carboxylic_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])] # does not hit anhydrides or lactones Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])] # may also be aromatic Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1]) # anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6] # includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])] # hits both tautomeric forms, as well as anions Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])] Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])] # may also be aromatic Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])] Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])] Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1] Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])] Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])] Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])] Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] # does not hit lactames Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2] Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])] Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])] Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] # cyclic amides, may also be aromatic Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) # may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) # everything else than H or C at central N Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1]) # can be deprotonated Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] # does not hit thiolactames Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] # cyclic thioamides, may also be aromatic Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])] # may also be part of a ring / aromatic Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])] # only basic amidines, not as part of aromatic ring (e.g. imidazole) Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])] Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])] # does not hit anhydrides of carboxylic acids withs hydroxamic acids Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] # not cyclic Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] # the enamide-form of lactames. may be aromatic like 2-hydroxypyridine Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] # esters of the above structures. no anhydrides. Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] # no oxazoles and similar Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] # not cyclic Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] # the enamide-form of thiolactames. may be aromatic like 2-thiopyridine Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] # thioesters of the above structures. no anhydrides. Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] # no thioxazoles and similar Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])] # only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])] # one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] # not cyclic Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] # may also be aromatic # may be ring, aromatic, substituted with carbonyls, hetero, ... # (everything else would get too complicated) Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])] # hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ... Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-] # N may be alkylated, but not part of an amide (as in peptides), ionic forms are included # includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C # N may not be aromatic as in 1H-pyrrole-2-carboxylic acid Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-] Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] # finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-] # finds C-terminal amino acids Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] # finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond. Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6] # hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues) Ketene: [CX3]=[CX2]=[OX1] Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3] # includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be Nitrile: [NX1]#[CX2] # includes cyanhydrines Isonitrile: [CX1-]#[NX2+] Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I] # may be part of a ring, even aromatic Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])] Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])] Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1] # I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives) # ----------------------------- Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])] # may be part of a ring, even aromatic Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1] Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])] # unstable Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6] Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])] # may be part of a ring, even aromatic Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1] Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])] Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])] # no check whether part of imide, biuret, etc. Aromatic structures are only hit if # both N share no double bonds, like in the dioxo-form of uracil Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])] Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])] # O may be substituted. no check whether further amide-like bonds are present. Aromatic # structures are only hit if single bonded N shares no additional double bond, like in # the 1-hydroxy-3-oxo form of uracil Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])] Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+] # also hits guanidinium salts. v3 and v4 to avoid nitroamidines Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-] # quite unstable, unlikely to be found. Also hits salts Urethan: [#7X3][#6](=[OX1])[#8X2][#6] # also hits when part of a ring, no check whether the last C is part of carbonyl Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3] Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1] Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1] Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1] Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1] Isocyanate: [NX2]=[CX2]=[OX1] Cyanate: [OX2][CX2]#[NX1] Isothiocyanate: [NX2]=[CX2]=[SX1] Thiocyanate: [SX2][CX2]#[NX1] Carbodiimide: [NX2]=[CX2]=[NX2] Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I] # halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more # stable as for example C(OCH3)4) # I.6 Aromatics # ------------- # I know that this classification is not very logical, arylamines are found under I.2 ... Phenol: [OX2H][c] 1,2-Diphenol: [OX2H][c][c][OX2H] Arylchloride: [Cl][c] Arylfluoride: [F][c] Arylbromide: [Br][c] Aryliodide: [I][c] Arylthiol: [SX2H][c] Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])] # N may be substituted with H or C, but not carbonyl or similar # aromatic atom is always C, not S or P (these are not planar when substituted) Oxoarene: [c]=[OX1] Thioarene: [c]=[SX1] Hetero_N_basic_H: [nX3H1+0] # as in pyrole. uncharged to exclude pyridinium ions Hetero_N_basic_no_H: [nX3H0+0] # as in N-methylpyrole. uncharged to exclude pyridinium ions Hetero_N_nonbasic: [nX2,nX3+] # as in pyridine, pyridinium Hetero_O: [o] Hetero_S: [sX2] # X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic # (is not planar because of lonepair at S) Heteroaromatic: [a;!c] # Part II: N, S, P, Si, B # ======================= # II.1 Nitrogen # ------------- Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])] # hits nitrous acid, its anion, esters, and other O-substituted derivatives Thionitrite: [SX2][NX2]=[OX1] Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])] # hits nitric acid, its anion, esters, and other O-substituted derivatives Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] # hits nitro groups attached to C,N, ... but not nitrates Nitroso: [NX2](=[OX1])[!#7;!#8] # no nitrites, no nitrosamines Azide: [NX1]~[NX2]~[NX2,NX1] # hits both mesomeric forms, also anion Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1] Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])] Diazonium: [#6][NX2+]#[NX1] Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1] Nitrosamide: [NX2](=[OX1])N-*=O # includes nitrososulfonamides N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] # Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate. Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])] # no hydrazides Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6] Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])] # no discrimination between O-, N-, and O,N-substitution # II.2 Sulfur # ----------- Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])] # can't be aromatic, thus S and not #16 Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])] Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])] # can't be aromatic, thus S and not #16 Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] # includes anions Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6] # everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative # than sulfur, but this should be very very rare, anyway) #### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])] Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])] Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1] Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6] # includes all of the above and many more # for comparison: this is what "all sulfonic derivatives but not the ones above" would look like: # [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])] Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])] Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1] Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6] Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])] Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])] Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1] Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6] # II.3 Phosphorous # ---------------- Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])] # similar to amine, but less restrictive: includes also amide- and aminal-analogues Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])] Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])] # similar to Ammonium Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])] # conventions for the following acids and derivatives: # acids find protonated and deprotonated acids # esters do not find mixed anhydrides ( ...P-O-C(=O)) # derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O, # thus including acids and esters) Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] # includes anions Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6] # all of the above and much more Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] # includes anions Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6] Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])] Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6] Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6] Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])] Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])] Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6] # II.4 Silicon # ------------ Quart_silane: [SiX4]([#6])([#6])([#6])[#6] # four C-substituents. non-reactive, non-toxic, in experimental phase for drug development Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])] # has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to # the free positions at Si, thus Hs had to be added implicitly Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6] # reagents for inserting protection groups Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6] # mostly acid-labile protection groups such as trimethylsilyl-ethers Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6] Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6] Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6] # four substituent which are neither C nor H # II.5 Boron # ---------- Trialkylborane: [BX3]([#6])([#6])[#6] # also carbonyls allowed Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6] # includes acids, esters, amides, ... H-substituent at B is very rare. Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6] # # includes acids, esters, amides, ... Borohydride: [BH1,BH2,BH3,BH4] # at least one H attached to B Quaternary_boron: [BX4] # mostly borates (negative charge), in complex with Lewis-base # Part III: Some Special Patterns # =============================== # III.1 Chains # ------------ # some simple chains # III.2 Rings # ----------- Aromatic: a Heterocyclic: [!#6;!R0] # may be aromatic or not Epoxide: [OX2r3]1[#6r3][#6r3]1 # toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione) NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1 # toxic/reactive according to Maybridge's garbage filter Spiro: [D4R;$(*(@*)(@*)(@*)@*)] # at least two different rings can be found which are sharing just one atom. # these two rings can be connected by a third ring, so it matches also some # bridged systems, like morphine Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])] # two different rings sharing exactly two atoms Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])] # part of two or more rings, not spiro, not annelated -> finds bridgehead atoms, # but only if they are not annelated at the same time - otherwise impossible (?) # to distinguish from non-bridgehead annelated atoms # some basic ring-patterns (just size, no other information): # III.3 Sugars and Nucleosides/Nucleotides, Steroids # -------------------------------------------------- # because of the large variety of sugar derivatives, different patterns can be applied. # The choice of patterns and their combinations will depend on the contents of the database # e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the # desired restriction Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)] # 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents. Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] # 5 or 6-membered ring containing one O and an acetal-like bond at postion 2. Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)] # combination of the two above Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)] # 5 or 6-membered cyclic hemi-acetal Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] # 5 or 6-membered cyclic hemi-acetal Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] # 5 or 6-membered cyclic hemi-acetal ##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]) # pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!) ##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]) # pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!) # III.4 Everything else... # ------------------------ Conjugated_double_bond: *=*[*]=,#,:[*] Conjugated_tripple_bond: *#*[*]=,#,:[*] Cis_double_bond: */[D2]=[D2]\* # only one single-bonded substituent on each DB-atom. no aromats. # only found when character of DB is explicitely stated. Trans_double_bond: */[D2]=[D2]/* # analog Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))] # should hits all combinations of two acids Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6] Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])] # Halogen which is not mono-substituted nor an anion, e.g. chlorate. # Most of these cases should be also filtered by Halogen_on_hetero. Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1]) # C with three F attached, connected to anything which is not another halogen C_ONS_bond: [#6]~[#7,#8,#16] # probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter ## Mixture: (*).(*) # two or more seperate parts, may also be salt # component-level grouping is not yet supported in Open Babel Version 2.0 Charged: [!+0] Anion: [-1,-2,-3,-4,-5,-6,-7] Kation: [+1,+2,+3,+4,+5,+6,+7] Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7]) # two or more seperate components with opposite charges ##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7]) # both negative and positive charges somewhere within the same molecule. 1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)] # 1,3 migration of H allowed. Includes keto/enol and amide/enamide. # Aromatic rings must stay aromatic - no keto form of phenol 1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)] Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1] # taken from http://www.daylight.com/support/contrib/smarts/content.html Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])] # the classical case: C=C near carbonyl, nitrile, nitro, or similar # Oxo-heteroaromats and similar are not included. Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1]) # Michael-like acceptor, see Mitsunobu reaction # H-Bond_donor: # H-Bond_acceptor: # Pos_ionizable: # Neg_ionizable: # Unlikely_ions: # O+,N-,C+,C-, ... CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)] # C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed. # pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded. # hits also CH-acidic_strong CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])] # same as above (without pentadiene), but carbonyl or similar on two or three sides Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)] # Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string # depictmach does not find oxonium, sulfonium, or sulfoxides! # Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)] # Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string # "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0