Tripos MOL2 Molecule File Format


Sample

    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 MOL2 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 MOL2.

    Record Type Indicators (RTI)

      Lines 8, 15, 28, and 41 are RTIs. They divide the mol2 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 mol2 file in which it resides.