Connection Table Format (MOL/SDF)

Overview

Property Value
File extensions .mol, .sdf
Coordinate units Ångström
Supports periodicity No
Supports bonds Yes
Format hints mol, sdf

Specification

Note

Reference

The MDL connection table format stores molecular structures with bond connectivity information.

  • Molfile (.mol): Single molecule format
  • SDF (.sdf): Structure Data Format, can contain multiple molecules with additional properties

Both V2000 and V3000 connection table formats are supported.

Example

Caffeine molecule in mol format:

          11262021073D

 24  0  0     0  0            999 V2000
    1.0732    0.0488   -0.0757 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5137    0.0126   -0.0758 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3520    1.0959   -0.0753 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6190    0.7303   -0.0755 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5791   -0.6314   -0.0753 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3013   -1.1026   -0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9807   -2.4869   -0.0738 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8253   -2.9004   -0.0758 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1144   -3.3043   -0.0694 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4517   -2.8562   -0.0723 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3893   -3.6597   -0.0723 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6624   -1.4768   -0.0749 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0095   -0.9365   -0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9206   -4.7409   -0.0616 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7340    1.0879   -0.0750 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7124   -0.4570    0.8233 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7124   -0.4558   -0.9755 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9930    2.1176   -0.0748 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7653   -1.7263   -0.0759 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1486   -0.3218    0.8197 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1480   -0.3208   -0.9695 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8650   -5.0232   -0.0583 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4023   -5.1592    0.8284 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4002   -5.1693   -0.9478 H   0  0  0  0  0  0  0  0  0  0  0  0
M  END

Limitations

The following features are currently not supported:

  • Not all atom and bond modifiers are supported in the connection table
  • SDF key-value pair annotations are dropped during reading
  • Continuation lines in V3000 format are not supported

Note

Feel free to contribute support for missing features or bring missing features to our attention by opening an issue.