What Is SDF/Mol file format?

SDF (Structural Data File), also call Mol file, or Molfile, is a text file to represent one or multiple molecule Structures and their associated properties.

SDF was developed and published by Molecular Design Limited (MDL) and became the the most widely used standard for importing and exporting information on molecules.

There are 2 versions of SDF/Mol file formats: V2000 released in 1996 and V3000 released in 2001. V3000 version is a better replacement of V2000. But V2000 is still widely used and it is the default SDF/Mol for most tools.

Here is an example of SDF/Mol V2000 file, Molecule-FYI-001.sdf, of a single molecule:

FYI-001
FYICenter.com
123456789012345678901234567890123456789012345678901234567890
 13 14  0  0  0  0  0  0  0  0  0     0
    0.8400   -0.1600    0.0000 N   0  0     0  0  0  0  0  0
    1.4800    0.4300    0.0000 N   0  0     0  0  0  0  0  0
    0.0900    0.2700    0.0000 N   0  0     0  0  0  0  0  0
    1.1100    1.2100    0.0000 C   0  0     0  0  0  0  0  0
    0.2700    1.1200    0.0000 C   0  0     0  0  0  0  0  0
    0.8400   -1.0300    0.0000 C   0  0     0  0  0  0  0  0
    1.5300    1.9900    0.0000 C   0  0     0  0  0  0  0  0
    1.0700    2.7400    0.0000 Cl  0  0     0  0  0  0  0  0
    1.5900   -1.4600    0.0000 C   0  0     0  0  0  0  0  0
    0.0800   -1.4600    0.0000 C   0  0     0  0  0  0  0  0
    1.5900   -2.3300    0.0000 C   0  0     0  0  0  0  0  0
    0.0700   -2.3200    0.0000 C   0  0     0  0  0  0  0  0
    0.8400   -2.7600    0.0000 C   0  0     0  0  0  0  0  0
  2  1  1  0  2  0  0
  3  1  1  0  2  0  0
  4  2  2  0  2  0  0
  5  3  2  0  2  0  0
  6  1  1  0  2  0  0
  7  4  1  0  2  0  0
  8  7  1  0  2  0  0
  9  6  1  0  1  0  0
 10  6  2  0  1  0  0
 11  9  2  0  1  0  0
 12 10  1  0  1  0  0
 13 12  2  0  1  0  0
  4  5  1  0  2  0  0
 13 11  1  0  1  0  0
M  END
>  <Comment>
This is a SDF example.

$$$$

⇒ SDF/Mol V2000 File Format Specification

⇐ Introduction to SDF/Mol File Format

⇑ Introduction to SDF/Mol File Format

⇑⇑ SDF/Mol File FAQ