# Please go to the end to see rules of defining an atom ============================================================================================ Defination begin ============================================================================================ -------------------------------------------------------------------------------------------- WILDATOM XX C N O S P WILDATOM XA O S WILDATOM XB N P WILDATOM XC F Cl Br I WILDATOM XD S P -------------------------------------------------------------------------------------------- f1 f2 f3 f4 f5 f6 f7 f8 f9 -------------------------------------------------------------------------------------------- //3-membered ring atom ATD cx * 6 4 * * [RG3] & //4-membered ring atom ATD cy * 6 4 * * [RG4] & //other sp3 C ATD c3 * 6 4 & //C=O or C=S ATD c * 6 3 * * [2DL] (XA1) & ATD c * 6 3 * * [1DB,0DL] (XA1) & ATD c * 6 3 * * [3sb] (XA1) & ATD cz * 6 3 * * * (N3,N3,N3) & //pure aromatic atom that can form an aromatic single bond ATD cp * 6 3 * * [AR1,1RG6] (XX[AR1],XX[AR1],XX[AR1]) & //pure aromatic atom ATD ca * 6 3 * * [AR1] & // sp2 C of conjugated ring systems ATD cc * 6 3 * * [sb,db,AR2] (C3(C3)) & ATD cc * 6 3 * * [sb,db,AR2] (C3(C2)) & ATD cc * 6 3 * * [sb,db,AR2] (C3(XB2)) & ATD cc * 6 3 * * [sb,db,AR2] (XB2(XB2)) & ATD cc * 6 3 * * [sb,db,AR2] (XB2(C2)) & ATD cc * 6 3 * * [sb,db,AR2] (XB2(C3)) & ATD cc * 6 3 * * [sb,db,AR2] (C3[sb']) & ATD cc * 6 3 * * [sb,db,AR2] (XB2[sb']) & ATD cc * 6 3 * * [sb,db,AR2] (XD3[sb',db]) & ATD cc * 6 3 * * [sb,db,AR2] (XD4[sb',db]) & ATD cc * 6 3 * * [sb,db,AR3] (C3(C3)) & ATD cc * 6 3 * * [sb,db,AR3] (C3(C2)) & ATD cc * 6 3 * * [sb,db,AR3] (C3(XB2)) & ATD cc * 6 3 * * [sb,db,AR3] (XB2(XB2)) & ATD cc * 6 3 * * [sb,db,AR3] (XB2(C2)) & ATD cc * 6 3 * * [sb,db,AR3] (XB2(C3)) & ATD cc * 6 3 * * [sb,db,AR3] (C3[sb']) & ATD cc * 6 3 * * [sb,db,AR3] (XB2[sb']) & ATD cc * 6 3 * * [sb,db,AR3] (XD3[sb',db]) & ATD cc * 6 3 * * [sb,db,AR3] (XD4[sb',db]) & ATD cc * 6 3 * * [sb,db,AR2] & ATD cc * 6 3 * * [sb,db,AR3] & // sp2 C of conjugated chain systems ATD ce * 6 3 * * [sb,db] (C3[SB']) & ATD ce * 6 3 * * [sb,db] (C2[SB']) & ATD ce * 6 3 * * [sb,db] (XB2[SB']) & ATD ce * 6 3 * * [sb,db] (XD3[SB',db]) & ATD ce * 6 3 * * [sb,db] (XD4[SB',db]) & //sp2 carbon in a 3-membered ring ATD cu * 6 3 * * [RG3] & //sp2 carbon in a 4-membered ring ATD cv * 6 3 * * [RG4] & //other sp2 C ATD c2 * 6 3 & // sp C of conjugated systems ATD cg * 6 2 * * [sb,tb] (C2[SB']) & ATD cg * 6 2 * * [sb,tb] (C3[SB']) & ATD cg * 6 2 * * [sb,tb] (N1[SB']) & ATD cg * 6 2 * * [sb,tb] (XB2[SB']) & // other sp C ATD c1 * 6 2 & ATD c1 * 6 1 & ATD hn * 1 1 * * * (N) & ATD ho * 1 1 * * * (O) & ATD hs * 1 1 * * * (S) & ATD hp * 1 1 * * * (P) & ATD hx * 1 1 * * * (C(N4)) & ATD hw * 1 1 * * * (O(H1)) & ATD h3 * 1 1 * 3 * (C4) & ATD h2 * 1 1 * 2 * (C4) & ATD h1 * 1 1 * 1 * (C4) & ATD hc * 1 1 * * * (C4) & ATD h5 * 1 1 * 2 * (C3) & ATD h4 * 1 1 * 1 * (C3) & ATD ha * 1 1 & ATD f * 9 & ATD cl * 17 & ATD br * 35 & ATD i * 53 & // sp2 P of conjugated ring systems ATD pc * 15 2 * * [sb,db,AR2] (C3(C3)) & ATD pc * 15 2 * * [sb,db,AR2] (C3(C2)) & ATD pc * 15 2 * * [sb,db,AR2] (C3(XB2)) & ATD pc * 15 2 * * [sb,db,AR2] (XB2(C3)) & ATD pc * 15 2 * * [sb,db,AR2] (XB2(C2)) & ATD pc * 15 2 * * [sb,db,AR2] (XB2(XB2)) & ATD pc * 15 2 * * [sb,db,AR2] (C3[sb']) & ATD pc * 15 2 * * [sb,db,AR2] (C2[sb']) & ATD pc * 15 2 * * [sb,db,AR2] (XB2[sb']) & ATD pc * 15 2 * * [sb,db,AR2] (XD3[sb',db]) & ATD pc * 15 2 * * [sb,db,AR2] (XD4[sb',db]) & ATD pc * 15 2 * * [sb,db,AR3] (C3(C3)) & ATD pc * 15 2 * * [sb,db,AR3] (C3(C2)) & ATD pc * 15 2 * * [sb,db,AR3] (C3(XB2)) & ATD pc * 15 2 * * [sb,db,AR3] (XB2(C3)) & ATD pc * 15 2 * * [sb,db,AR3] (XB2(C2)) & ATD pc * 15 2 * * [sb,db,AR3] (XB2(XB2)) & ATD pc * 15 2 * * [sb,db,AR3] (C3[sb']) & ATD pc * 15 2 * * [sb,db,AR3] (C2[sb']) & ATD pc * 15 2 * * [sb,db,AR3] (XB2[sb']) & ATD pc * 15 2 * * [sb,db,AR3] (XD3[sb',db]) & ATD pc * 15 2 * * [sb,db,AR3] (XD4[sb',db]) & // sp2 P of conjugated chain systems ATD pb * 15 2 * * [AR1] & ATD pe * 15 2 * * [sb,db] (C3[sb']) & ATD pe * 15 2 * * [sb,db] (C2[SB']) & ATD pe * 15 2 * * [sb,db] (XA1[SB']) & ATD pe * 15 2 * * [sb,db] (XB2[SB']) & ATD pe * 15 2 * * [sb,db] (XD3[SB',DB]) & ATD pe * 15 2 * * [sb,db] (XD4[SB',DB]) & ATD p2 * 15 2 & ATD p2 * 15 1 & ATD px * 15 3 * * [db] (XB2[sb']) & ATD px * 15 3 * * [db] (C3[sb']) & ATD px * 15 3 * * [db] (XD3[sb',db]) & ATD px * 15 3 * * [db] (XD4[sb',db]) & ATD p4 * 15 3 * * [db] (XA1) & ATD p3 * 15 3 & ATD py * 15 4 * * [db] (XB2[sb']) & ATD py * 15 4 * * [db] (C3[sb']) & ATD py * 15 4 * * [db] (XD3[sb',db]) & ATD py * 15 4 * * [db] (XD4[sb',db]) & ATD p5 * 15 4 & ATD p5 * 15 5 & ATD p5 * 15 6 & ATD n * 7 3 * * * (C3(XA1)) & ATD n4 * 7 4 & ATD no * 7 3 * * * (O1,O1) & ATD na * 7 3 * * [AR1.AR2.AR3] & ATD nh * 7 3 * * * (XX[AR1.AR2.AR3]) & ATD nh * 7 3 * * * (C3[DB]) & ATD nh * 7 3 * * * (N2[DB]) & ATD nh * 7 3 * * * (P2[DB]) & ATD n3 * 7 3 & ATD nb * 7 2 * * [AR1] & // sp2 N of conjugated ring systems ATD nc * 7 2 * * [sb,db,AR2] (C3(C3)) & ATD nc * 7 2 * * [sb,db,AR2] (C3(C2)) & ATD nc * 7 2 * * [sb,db,AR2] (C3(XB2)) & ATD nc * 7 2 * * [sb,db,AR2] (XB2(C3)) & ATD nc * 7 2 * * [sb,db,AR2] (XB2(C2)) & ATD nc * 7 2 * * [sb,db,AR2] (XB2(XB2)) & ATD nc * 7 2 * * [sb,db,AR2] (C3[sb']) & ATD nc * 7 2 * * [sb,db,AR2] (XB2[sb']) & ATD nc * 7 2 * * [sb,db,AR2] (XD3[sb',db]) & ATD nc * 7 2 * * [sb,db,AR2] (XD4[sb',db]) & ATD nc * 7 2 * * [sb,db,AR3] (C3(C3)) & ATD nc * 7 2 * * [sb,db,AR3] (C3(C2)) & ATD nc * 7 2 * * [sb,db,AR3] (C3(XB2)) & ATD nc * 7 2 * * [sb,db,AR3] (XB2(C3)) & ATD nc * 7 2 * * [sb,db,AR3] (XB2(C2)) & ATD nc * 7 2 * * [sb,db,AR3] (XB2(XB2)) & ATD nc * 7 2 * * [sb,db,AR3] (C3[sb']) & ATD nc * 7 2 * * [sb,db,AR3] (XB2[sb']) & ATD nc * 7 2 * * [sb,db,AR3] (XD3[sb',db]) & ATD nc * 7 2 * * [sb,db,AR3] (XD4[sb',db]) & // sp2 N of conjugated chain systems ATD ne * 7 2 * * [sb,db] (C2[SB']) & ATD ne * 7 2 * * [sb,db] (C3[SB']) & ATD ne * 7 2 * * [sb,db] (XA1[SB']) & ATD ne * 7 2 * * [sb,db] (XB2[SB']) & ATD ne * 7 2 * * [sb,db] (XD3[SB',db]) & ATD ne * 7 2 * * [sb,db] (XD4[SB',db]) & ATD n1 * 7 2 * * [2db] & ATD n1 * 7 2 * * [tb,sb] & ATD n2 * 7 2 & ATD n1 * 7 1 & ATD o * 8 1 & ATD oh * 8 2 1 & ATD oh * 8 2 2 & ATD oh * 8 3 1 & ATD oh * 8 3 2 & ATD oh * 8 3 3 & ATD os * 8 2 & ATD os * 8 3 & ATD os * 8 & ATD s * 16 1 & ATD s2 * 16 2 * * [DB] & ATD s2 * 16 2 * * [TB] & ATD sh * 16 2 1 & ATD sh * 16 2 2 & ATD ss * 16 2 & ATD sx * 16 3 * * [db] (XB2[sb']) & ATD sx * 16 3 * * [db] (C3[sb']) & ATD sx * 16 3 * * [db] (XD3[sb',db]) & ATD sx * 16 3 * * [db] (XD4[sb',db]) & ATD s4 * 16 3 & ATD sy * 16 4 * * [db] (XB2[sb']) & ATD sy * 16 4 * * [db] (C3[sb']) & ATD sy * 16 4 * * [db] (XD3[sb',db]) & ATD sy * 16 4 * * [db] (XD4[sb',db]) & ATD s6 * 16 4 & ATD s6 * 16 5 & ATD s6 * 16 6 & ATD He * 2 & ATD Li * 3 & ATD Be * 4 & ATD B * 5 & ATD Ne * 10 & ATD Na * 11 & ATD Mg * 12 & ATD Al * 13 & ATD Si * 14 & ATD Ar * 18 & ATD K * 19 & ATD Ca * 20 & ATD Sc * 21 & ATD Ti * 22 & ATD V * 23 & ATD Cr * 24 & ATD Mn * 25 & ATD Fe * 26 & ATD Co * 27 & ATD Ni * 28 & ATD Cu * 29 & ATD Zn * 30 & ATD Ga * 31 & ATD Ge * 32 & ATD As * 33 & ATD Se * 34 & ATD Kr * 36 & ATD Rb * 37 & ATD Sr * 38 & ATD Y * 39 & ATD Zr * 40 & ATD Nb * 41 & ATD Mo * 42 & ATD Tc * 43 & ATD Ru * 44 & ATD Rh * 45 & ATD Pd * 46 & ATD Ag * 47 & ATD Cd * 48 & ATD In * 49 & ATD Sn * 50 & ATD Sb * 51 & ATD Te * 52 & ATD Xe * 54 & ATD Cs * 55 & ATD Ba * 56 & ATD La * 57 & ATD Ce * 58 & ATD Pr * 59 & ATD Nd * 60 & ATD Pm * 61 & ATD Sm * 62 & ATD Eu * 63 & ATD Gd * 64 & ATD Tb * 65 & ATD Dy * 66 & ATD Ho * 67 & ATD Er * 68 & ATD Tm * 69 & ATD Yb * 70 & ATD Lu * 71 & ATD Hf * 72 & ATD Ta * 73 & ATD W * 74 & ATD Re * 75 & ATD Os * 76 & ATD Ir * 77 & ATD Pt * 78 & ATD Au * 79 & ATD Hg * 80 & ATD Tl * 81 & ATD Pb * 82 & ATD Bi * 83 & ATD Po * 84 & ATD At * 85 & ATD Rn * 86 & ATD Fr * 87 & ATD Ra * 88 & ATD Ac * 89 & ATD Th * 90 & ATD Pa * 91 & ATD U * 92 & ATD Np * 93 & ATD Pu * 94 & ATD Am * 95 & ATD Cm * 96 & ATD Bk * 97 & ATD Cf * 98 & ATD Es * 99 & ATD Fm * 100 & ATD Md * 101 & ATD No * 102 & ATD Lr * 103 & ATD Rf * 104 & ATD Db * 105 & ATD Sg * 106 & ATD Bh * 107 & ATD Hs * 108 & ATD Mt * 109 & ATD Ds * 103 & ATD LP * 0 1 & ATD lp * 0 1 & ATD DU & -------------------------------------------------------------------------------------------- ============================================================================================ ============================================================================================ Field descriptions ============================================================================================ f1 ATD, which stands for atom type defination, ATD should always in the first three columns f2 Atom type name, can be letters or numbers f3 Residue names, which means this description is only applied to atoms in special residues f4 Atomic number f5 Number of attached atoms f6 Number of attached hydrogen atoms f7 For hydrogen, number of the electron-withdrawal atoms connected to the atom that the hydrogen attached f8 atomic property f9 Chemical enviornment definations ============================================================================================ Specific symbols ============================================================================================ * Ignore this field & End of defination . "or" operation in the ring and aromatity descriptions ============================================================================================ Predefined words ============================================================================================ EW Electron-withdraw atom AA Amino acid residue NA Nucleric acid BIO AA + NA AR1 Pure aromatic atom (such as benzene and pyridine) AR2 Atom in a planar ring, usually the ring has two continous single bonds and at least two double bonds AR3 Atom in a planar ring, which has one or several double bonds formed between non-ring atoms and the ring atoms AR4 Atom other than AR1, AR2, AR3 and AR5. AR5 Pure aliphatic atom in a ring, which is made of sp3 carbon RG Ring (from 3-membered to nine-membered) RG3 3-membered ring RG4 4-membered ring RG5 5-membered ring RG6 6-membered ring RG7 7-membered ring RG8 8-membered ring RG9 9-membered ring NR non-ring atom SB Single bond DB Double bond TB Triple bond AB Aromatic bond DL Delocalized bond (9 in AM1-BCC) sb Single bond, including aromtaic single, delocalized bond (9 in AM1-BCC) db Double bond, including aromatic double tb Triple bond ' Bond type (SB sb etc) followed by ' means the current atom forms this kind of bond with the immediately precessor in a chain of atoms For example, (XD3[SB',db]) means the current atom XD3 has a double bond with the atom in defination '' Bond type (SB sb etc) followed by '' means the current atom does not form this kind of bond with the immediately precessor in a chain of atoms ============================================================================================ Miscellaneous ============================================================================================ 1. maximum line length is 500 characters 2. no space in the atomic property string 3. no space in the chemical environment string 4. no filed missing before & 5. the defination order is crucial, special atom types should defined before the more general ones