Tripos Mol2 File Format

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SYBYL Atom Types


Code Definition Code Definition
C.3

carbon sp3

H

hydrogen

C.2

carbon sp2

H.spc

hydrogen in Single Point Charge (SPC) water model

C.1

carbon sp

H.t3p

hydrogen in Transferable intermolecular Potential (TIP3P) water model

C.ar

carbon aromatic

LP

lone pair

C.cat

carbocation (C+) used only in a guadinium group

Du

dummy atom

N.3

nitrogen sp3

Du.C

dummy carbon

N.2

nitrogen sp2

Any

any atom

N.1

nitrogen sp

Hal

halogen

N.ar

nitrogen aromatic

Het

heteroatom = N, O, S, P

N.am

nitrogen amide

Hev

heavy atom (non hydrogen)

N.pl3

nitrogen trigonal planar

Li

lithium

N.4

nitrogen sp3 positively charged

Na

sodium

O.3

oxygen sp3

Mg

magnesium

O.2

oxygen sp2

Al

aluminum

O.co2

oxygen in carboxylate and phosphate groups

Si

silicon

O.spc

oxygen in Single Point Charge (SPC) water model

K

potassium

O.t3p

oxygen in Transferable Intermolecular Potential (TIP3P) water model

Ca

calcium

S.3

sulfur sp3

Cr.th

chromium (tetrahedral)

S.2

sulfur sp2

Cr.oh

chromium (octahedral)

S.O

sulfoxide sulfur

Mn

manganese

S.O2

sulfone sulfur

Fe

iron

P.3

phosphorous sp3

Co.oh

cobalt (octahedral)

F

fluorine

Cu

copper

Cl

chlorine

Zn

zinc

Br

bromine

Se

selenium

I

iodine

Mo

molybdenum

 

 

Sn

tin



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