Chem3D Users Manual - CambridgeSoft

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7 2 10 1
8 3 6 1
9 3 11 1
10 3 12 1
11 4 5 1
12 4 13 1
13 4 14 1
14 5 6 1
15 5 15 1
16 5 16 1
17 6 17 1
18 6 18 1
19 7 19 1
0 MOL
The following illustration shows the components of
the SYBYL Output File from Chem3D for C(6)
and Bond 3 of Cyclohexanol.
Number
of Atoms
Number
of Bonds
Number
of Features
19 MOL
Atom
ID
19 MOL
Bond
Number
0 MOL
Molecule
Name
Cyclohexanol 0
6 1 -1.3959 -0.4449 0.7768C
Atom
Type
X
Coord
Y
Coord
3 1 7 1
From-Atom To-Atom Bond
Type
Z
Coord
Center
The format for SYBYL MOL files is as follows:
1. The first record in the SYBYL MOL File
contains the number of atoms in the model, the
word “MOL”, the name of the molecule, and
the center of the molecule.
2. The atom records (lines 2–20 in the
cyclohexanol example) contain the Atom ID in
column 1, followed by the Atom Type in
column 2, and the X, Y and Z Cartesian
coordinates of that atom in columns 3–5.
3. The first record after the last atom records
contains the number of bonds in the molecule,
followed by the word “MOL”.
4. The bond records (lines 22–40 in the
cyclohexanol example) contain the Bond
Number in column 1, followed by the Atom
ID of the atom where the bond starts (the
“From-Atom”) in column 2 and the Atom ID
of the atom where the bond stops (the “To-
Atom”) in column 3. The last column in the
bond records is the bond type. Finally the last
line in the file is the Number of Features
266• File Formats CambridgeSoft
Protein Data Bank Files