Sample Mol2 File
The lines of a .mol2 file for benzene have been numbered for easy reference during the following discussion.
1 # Name: benzene
2 # Creating user name: tom
3 # Creation time: Wed Dec 28 00:18:30 1988
4
5 # Modifying user name: tom
6 # Modification time: Wed Dec 28 00:18:30 1988
7
8 @<TRIPOS>MOLECULE
9 benzene
10 12 12 1 0 0
11 SMALL
12 NO_CHARGES
13
14
15 @<TRIPOS>ATOM
16 1 C1 1.207 2.091 0.000 C.ar 1 BENZENE 0.000
17 2 C2 2.414 1.394 0.000 C.ar 1 BENZENE 0.000
18 3 C3 2.414 0.000 0.000 C.ar 1 BENZENE 0.000
19 4 C4 1.207 -0.697 0.000 C.ar 1 BENZENE 0.000
20 5 C5 0.000 0.000 0.000 C.ar 1 BENZENE 0.000
21 6 C6 0.000 1.394 0.000 C.ar 1 BENZENE 0.000
22 7 H1 1.207 3.175 0.000 H 1 BENZENE 0.000
23 8 H2 3.353 1.936 0.000 H 1 BENZENE 0.000
24 9 H3 3.353 -0.542 0.000 H 1 BENZENE 0.000
25 10 H4 1.207 -1.781 0.000 H 1 BENZENE 0.000
26 11 H5 -0.939 -0.542 0.000 H 1 BENZENE 0.000
27 12 H6 -0.939 1.936 0.000 H 1 BENZENE 0.000
28 @<TRIPOS>BOND
29 1 1 2 ar
30 2 1 6 ar
31 3 2 3 ar
32 4 3 4 ar
33 5 4 5 ar
34 6 5 6 ar
35 7 1 7 1
36 8 2 8 1
37 9 3 9 1
38 10 4 10 1
39 11 5 11 1
40 12 6 12 1
41 @<TRIPOS>SUBSTRUCTURE
42 1 BENZENE 1 PERM 0 **** **** 0 ROOT
Comments
Lines 1,2,3,5 and 6 are comments. They are ignored by the MOL2 command and are provided only for your convenience. These lines are added by SYBYL when a .mol2 file is written out. They contain the molecule name and information about the time the molecule was created and last modified.
Blank Lines
Lines 4,7,13, and 14 are blank and will be ignored by the MOL2 command.
Record Type Indicators (RTI)
Lines 8, 15, 28, and 41 in the example are RTIs. They divide the file into 4 sections. A section begins with a RTI and ends at the next RTI or the end of the file. Each section contains a different type of information needed to reconstruct the molecule. In this example, section one (lines 8-14) contains information global to the molecule. The second section (lines 15-27) contains all the information about atoms in the molecule. Section three (lines 28-40) contains all the bond information and section four (lines 41 and 42) contains information necessary to reconstruct substructures.
Data Records
Lines 9-12, 16-27, 29-40, and 42 are all data records. The format of a data record depends on that section of the file in which it resides.
