Chemical table file

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 applications that are not yet V3000-capable.

The contents of a Molfile of L-Alanine

L-Alanine	Title line (can be blank but line must exist)	Header Block (3 lines)
ABCDEFGH09071717443D	Program / file timestamp line (Name of source program and a file timestamp)
Exported	Comment line (can be blank but line must exist)
6 5 0 0 1 0 3 V2000	Counts line	Connection table
-0.6622 0.5342 0.0000 C 0 0 2 0 0 0 0.6622 -0.3000 0.0000 C 0 0 0 0 0 0 -0.7207 2.0817 0.0000 C 1 0 0 0 0 0 -1.8622 -0.3695 0.0000 N 0 3 0 0 0 0 0.6220 -1.8037 0.0000 O 0 0 0 0 0 0 1.9464 0.4244 0.0000 O 0 5 0	Atom block (1 line for each atom): x, y, z (in angstroms), element, etc.
1 2 1 0 0 0 1 3 1 1 0 0 1 4 1 0 0 0 2 5 2 0 0 0 2 6 1 0 0 0	Bond block (1 line for each bond): 1st atom, 2nd atom, type, etc.
M CHG 2 4 1 6 -1 M ISO 1 3 13	Properties block
M END	END line (NOTE: some programs don't like a blank line before M END)	END

The Bond Block is made up of bond lines, one line per bond, with the following format:

111 222 ttt sss xxx rrr ccc

where the values are described in the following table:

The extended (V3000) molfile consists of a regular molfile “no structure” followed by a single molfile appendix that contains the body of the connection table (Ctab). The following figure shows both an alanine structure and the extended molfile corresponding to it.

Note that the “no structure” is flagged with the “V3000” instead of the “V2000” version stamp. There are two other changes to the header in addition to the version:

• The number of appendix lines is always written as 999, regardless of how many there actually are. (All current readers will disregard the count and stop at M END.)

• The “dimensional code” is maintained more explicitly. Thus “3D” really means 3D, although “2D” will be interpreted as 3D if any non-zero Z-coordinates are found.

Unlike the V2000 molfile, the V3000 extended Rgroup molfile has the same header format as a non-Rgroup molfile.

L-Alanine	Description	Header block
GSMACCS-II07189510252D 1 0.00366 0.00000 0	Header with timestamp
Figure 1, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992	Comment line
0 0 0 0 0 999 V3000	V2000-compatibility line
M V30 BEGIN CTAB		Connection table
M V30 COUNTS 6 5 0 0 1	Counts line
M V30 BEGIN ATOM M V30 1 C -0.6622 0.5342 0 0 CFG=2 M V30 2 C 0.6622 -0.3 0 0 M V30 3 C -0.7207 2.0817 0 0 MASS=13 M V30 4 N -1.8622 -0.3695 0 0 CHG=1 M V30 5 O 0.622 -1.8037 0 0 M V30 6 O 1.9464 0.4244 0 0 CHG=-1 M V30 END ATOM	Atom block
M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 1 3 CFG=1 M V30 3 1 1 4 M V30 4 2 2 5 M V30 5 1 2 6 M V30 END BOND	Bond block
M V30 END CTAB M END

A counts line is required, and must be first. It specifies the number of atoms, bonds, 3D objects, and Sgroups. It also specifies whether or not the CHIRAL flag is set. Optionally, the counts line can specify molregno. This is only used when the regno exceeds 999999 (the limit of the format in the molfile header line). The format of the counts line is:

M V30 COUNTS na nb nsg n3d chiral

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 format, and SDF files actually wrap the molfile (MDL Molfile) format. Multiple records are delimited by lines consisting of four dollar signs ($$). A key feature of this 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-line 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.

There are other, less commonly used formats of the family:

• RXNFile - for representing a single chemical reaction;
• RDFile - for representing a list of records with associated data. Each record can contain chemical structures, reactions, textual and tabular data;
• RGFile - for representing the Markush structures (deprecated, Molfile V3000 can represent Markush structures);
• XDFile - for representing chemical information in XML format.