What Is SDF (Structure Data File)

Molecule Tutorials - Herong's Tutorial Examples

∟What Is SDF (Structure Data File)

This section provides a quick introduction of the SDF (Structure Data File) format. An example of SDF file is also provided.

What Is SDF (Structure Data File)? - SDF is a file format to represent multiple chemical structure records and associated data fields. SDF was developed and published by Molecular Design Limited (MDL) and became the the most widely used standard for importing and exporting information on chemicals.

Here is an example of SDF file, Molecule-HY-001.sdf, of a single molecule:

HY-001
herongyang.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 SDF example 1.

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