# original source: http://tripod.nih.gov/files/patty.rules, copied July 2015 # # CAT CATION, used for basic functionality; i.e., protonated # ANI ANION, used for acidic functionality; i.e., de-protonated # # POL POLAR, atom is neither an ANION nor a CATION and has a LP # and a polar H, or (due to tautomerization) can be a donor # or an acceptor. # # DON DONOR, an atom that is none of the above and has a polar H. # ACC ACCEPTOR, an atom that is none of the above and has an LP. # # HYD HYRDOPHOBIC, an atom that is none of the above and is an # accessible atom that has hydrophobic functionality # # OTH OTHER, an atom that falls in none of the above classes. * OTH # Default Rule [#8] ACC # O [#7] DON # N [#6,#14] HYD # C, Si [#16] HYD # S [#34] HYD # Se [#16] HYD # P [#33] HYD # As [#9D1,#17D1,#35D1,#53D1,#85D1] HYD # halogens [#9D0,#17D0,#35D0,#53D0,#85D0] ANI [OHD1] POL # hydroxide [OH2] POL # water (NEW) [#1] HYD # H [#1][#7] DON [NH0]#* ACC # :N# (sp) [ND2](*)=* ACC # =N- (sp2) [nH0] ACC # aomatic N - (sp2) [NH;D1]=* POL # HN=X [ND1]=* POL # N=N= (azide) [#7,#15,#33;D4] CAT # quaternary N,P,As # any nonconjugated sp3 N is a basic amine (except next # to conjugated a N) [#7D1]-* CAT [#7D2](-*)-* CAT [#7D3](-*)(-*)-* CAT [#7v4] CAT [#7D3]-N-*=* OTH [#7D3](-*)(-*)-N-*#* OTH # conjugated N's [#7D1]-*=* DON [#7D1]-*:* DON [#7D1]-*#* DON [#7H;D2]-*=* DON [#7H;D2]-*:* DON [#7H;D2]-*#* DON [#7;D3]-*=* OTH # conj & buried [#7;D3]-*:* OTH # [#7;D3](*=*)(-&!@*)*:* OTH [#7;D3]-*#* OTH # amidine # # N+H2 # // # CH3--C--:NH2 [#7D1]-C(-[#6])=[#7D1] CAT [#7D1]=C(-[#6])-[#7D1] CAT # changed to #7D1 [#7D1]-C(-S)=[#7D1] CAT [#7D1]=C(-S)-[#7D1] CAT # guanidinium N-C(=N)-N CAT N=C(-N)-N CAT # nitro [OD1]-N=[OD1] ACC [OD1]=N-[OD1] ACC # trisubstituted sp2 amines are cations with exceptions [#7,#15,#33;D3]=* CAT N([OD1])=[OD1] OTH # disbustituted sp amines and exceptions [N+;D2](=*)=* CAT # diazonium -[N+]# [N+;D2]#* CAT # #N- [N+;D2]#[CX1] OTH # isonitrile -N#C: [CX1]#[N+;D2] ACC # isonitrile :C#N- # trisubstituted oxygens, sulfurs and exceptions [#8,#16;D3] CAT # -O(-*)(-*) [#8,#16;D3](=*) CAT # =O- S=[#8,#16;X1] OTH # dative sulfoxides *-[#8,#16;X1] OTH # oxides,sulfides # misc anions [SD1]a ANI # phosphate/arsenate monoanion and S equialents # # O O # | | # P--O (-) and --P--O (-) # / [#8,#16,#34;X1]~[#15,#33;D3]~[#8,#16,#34;D1] ANI [#8,#16,#34;D1]~[#15,#33;D3]~[#8,#16,#34;X1] ANI [#8,#16,#34;X1]~[#15,#33;D4]~[#8,#16,#34;D1] ANI [#8,#16,#34;D1]~[#15,#33;D4]~[#8,#16,#34;X1] ANI [#15,#33;D3]([#8,#16,#34;X1])~[#8,#16,#34;D1] OTH [#15,#33;D3]([#8,#16,#34;D1])~[#8,#16,#34;X1] OTH [#15,#33;D4]([#8,#16,#34;X1])~[#8,#16,#34;D1] OTH [#15,#33;D4]([#8,#16,#34;D1])~[#8,#16,#34;X1] OTH # sulfite and selenite anion and S equivalents # # O O # | | # S--O (-) and O--S--O (-) # / | [#8,#16,#34;X1]~[#8,#16,#34;D3]~[#8,#16,#34;D1] ANI [#8,#16,#34;D1]~[#8,#16,#34;D3]~[#8,#16,#34;X1] ANI [#8,#16,#34;X1]~[#8,#16,#34;D4](~[#8,#16,#34;D1])~[#8,#16,#34;X1] ANI [#8,#16,#34;D1]~[#8,#16,#34;D4](~[#8,#16,#34;X1])~[#8,#16,#34;X1] ANI # muscimol anion (first O is ANI, N is ACC) # # *--* *--* # / | / | # (-) O-C O or O=C O # \\ / \ / # N: :N (-) [#8D1][#6]1=[#7][#8]**1 ANI [#7]1=[#6]([#8D1])**[#8]1 ANI [#8]=[#6]1[#7][#8]**1 ANI [#7]1[#6](=O)**[#8]1 ANI # tetrazole anion (all Ns are ANI) # # :N--N: (-) :N--N: # # || / || # :N C or :N C (aromatic) # \ / \\ / # N: (-) N: [nD2]1[nD2][nD2][nD2]c1 ANI [nD2]1[nD2][nD2]c[nD2]1 ANI [nD2]1[nD2]c[nD2][nD2]1 ANI [nD2]1c[nD2][nD2][nD2]1 ANI # diaminopyrimidine (ring Ns are POL) # # *==* # / \ # :N C--NH2 (aromatic) # \\ # # C--N: # / # NH2 [nD2]1c(N)[nD2]c(N)aa1 POL [nD2]1c(N)aa[nD2]c1(N) POL # make imidazole Ns both POL # # C==C C==C # / | / | # :N NH or HN N: (aromatic) # \\ / \ # # C C # # n1cncc1 POL # stabilized sulfonamides and phosphonamides # # O # | # a--S--NH2 # | # O [ND1]~[SD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) POL [ND1]~[PD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) POL [#8,#16,#34;D1]~[SD4](a)(~[#8,#16,#34;D1])~[ND1] ACC [#8,#16,#34;D1]~[PD4](a)(~[#8,#16,#34;D1])~[ND1] ACC [#8,#16,#34;D1]~[SD4](a)(~[#8,#16,#34;D1])~[ND2] ANI [#8,#16,#34;D1]~[PD4](a)(~[#8,#16,#34;D1])~[ND2] ANI [ND2]~[SD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) ANI # carbonyl-hydroxide tautaumers # # !O !O # | | # C C # / \\/ \\ # OH X O [OH]C(*)=*C=O POL O=C*=C(*)[OH] POL O=C-*:[#6](*)[OH] POL # carboxylates and S equivalents # # O # # # -C # \ # O (-) [#8,#16,#34;D1]C=[#8,#16,#34] ANI [#8,#16,#34]=C[#8,#16,#34;D1] ANI # *==* # / \ # * C==O (aromatic) # \\ / # C--C And 4 Cs away # / # OH [OH]c1cc(=O)aaa1 POL O=c1cc([OH])aaa1 POL [OH]c1ccc(=O)aa1 POL O=c1ccc([OH])aa1 POL # special ionizations of adjacent keto/enols [OD1]C=CC(=O)[O]* ANI [OD1]C=CC(=O)[N]* ANI O=C-CC(=O)[O]* ANI O=C-CC(=O)[N]* ANI OC=C-C(=O)C=CO ANI OC-C=C(-O)C=CO ANI # planar buried C bonded to electronegative atom [#6D3](=*)-[#7,#8] OTH [#6D3](:*)(:*)[#7,#8] OTH [#6D3](-*)(:*):[#7,#8] OTH [#6D3]=[#7,#8] OTH [#6D2](#*)-[#7,#8] OTH [#6D2](*)#[#7,#8] OTH [#6D2](=*)=[#7,#8] OTH [#16D2](#*)-[#7,#8] OTH # buried sp S [#16D2](*)#[#7,#8] OTH [#16D2](=*)=[#7,#8] OTH # misc fixups [ND2](=*)=* OTH # sp buried [ND2](*)#* OTH [#7,#15,#33;D4]=[S,O] OTH [ND3]P(=O) OTH [OD1]-n ACC n-[OD1] OTH