Connection table format

Specification

Note

Reference

The molfile is identified by the extension mol and the structure data format is identified by sdf. Both V2000 and V3000 connection tables can be read.

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

Extensions

No extension implemented to the original format.

Missing Features

The following features are currently not supported:

  • Not all modifiers are supported for the connection table
  • SDF key-value pair annotations are dropped
  • 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.