Filename extension .mol Type of format chemical file format | Internet media type chemical/x-mdl-molfile | |
Chemical table file is a family of text-based chemical file formats that describe molecules and chemical reactions. One format, for example, lists each atom in a molecule, the x-y-z coordinates of that atom, and the bonds among the atoms.
Contents
File formats
There are several file formats in the family.
The formats were created by MDL Information Systems (MDL), which was acquired by Symyx Technologies then merged with Accelrys Corp., and now called BIOVIA, a subsidiary of Dassault Systemes of Dassault Group
Molfile
An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule.
The molfile consists of some header information, the Connection Table (CT) containing atom info, then bond connections and types, followed by sections for more complex information.
The molfile is sufficiently common that most, if not all, cheminformatics software systems/applications are able to read the format, though not always to the same degree. It is also supported by some computational software such as Mathematica.
The current de facto standard version is molfile V2000; although, more recently, the V3000 format has been circulating widely enough to present a potential compatibility issue for those not yet V3000-capable.
BIOVIA publishes a specification of their Connection-Table formats, which include Molfile and SD formats.
Following are the contents of a Molfile of benzene created in ChemSketch, as seen in a text editor (Note: According to the official molfile specification, the '$$$$' notation applied only to the SDF file – not to the molfile, so ChemSketch molfiles will not always function properly.):
benzene
ACD/Labs0812062058
6 6 0 0 0 0 0 0 0 0 1 V2000
1.9050 -0.7932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9050 -2.1232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7531 -0.1282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7531 -2.7882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3987 -0.7932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3987 -2.1232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 1 2 0 0 0 0
4 2 2 0 0 0 0
5 3 1 0 0 0 0
6 4 1 0 0 0 0
6 5 2 0 0 0 0
M END
$$$$
SDF
SDF is one of a family of chemical-data file formats developed by MDL; it is intended especially for structural information. "SDF" stands for structure-data file, and SDF files actually wrap the molfile (MDL Molfile) format. Multiple compounds are delimited by lines consisting of four dollar signs ($$$$). A feature of the SDF format is its ability to include associated data.
Associated data items are denoted as follows:
> <Unique_ID>
XCA3464366
> <ClogP>
5.825
> <Vendor>
Sigma
> <Molecular Weight>
499.611
Multiple-lines data items are also supported. The MDL SDF-format specification requires that a hard-carriage-return character be inserted if a single line of any text field exceeds 200 characters. This requirement is frequently violated in practice, as many SMILES and InChI strings exceed that length.
Other formats of the family
There are other, less commonly used formats of the family: