What Is SDF/Mol V3000 file format?

SDF (Structural Data File) V3, also call Mol V3000 file, or Molfile V3, is the improved version of SDF file format.

SDF V3000 was developed and published by Molecular Design Limited (MDL) and became the the most widely used standard for importing and exporting information on molecules.

Here is an example of SDF V3000 file, Molecule-FYI-001.sd3, of a single molecule:

FYI-001
FYICenter.com
123456789012345678901234567890123456789012345678901234567890
 0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 13 14 0 0 0
M  V30 BEGIN ATOM
M  V30 1 N 0.84 -0.16 0 0
M  V30 2 N 1.48 0.43 0 0
M  V30 3 N 0.09 0.27 0 0
M  V30 4 C 1.11 1.21 0 0
M  V30 5 C 0.27 1.12 0 0
M  V30 6 C 0.84 -1.03 0 0
M  V30 7 C 1.53 1.99 0 0
M  V30 8 Cl 1.07 2.74 0 0
M  V30 9 C 1.59 -1.46 0 0
M  V30 10 C 0.08 -1.46 0 0
M  V30 11 C 1.59 -2.33 0 0
M  V30 12 C 0.07 -2.32 0 0
M  V30 13 C 0.84 -2.76 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 2 1
M  V30 2 1 3 1
M  V30 3 1 6 1
M  V30 4 2 4 2
M  V30 5 2 5 3
M  V30 6 1 7 4
M  V30 7 1 4 5
M  V30 8 1 9 6
M  V30 9 2 10 6
M  V30 10 1 8 7
M  V30 11 2 11 9
M  V30 12 1 12 10
M  V30 13 1 13 11
M  V30 14 2 13 12
M  V30 END BOND
M  V30 END CTAB
M  END
>  <Comment>
This is a SDF example.

$$$$

As a reference, here is the same molecule written in SDF file format:

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.

$$$$

For detailed specifications of SDF V3000 and SDF file formats, see "CTfile Formats" at download.accelrys.com/freeware/ctfile-formats/.

 

⇒ Tools for SDF/Mol V3000 File Format

⇐ Introduction to SDF/Mol V3000 File Format

⇑ Introduction to SDF/Mol V3000 File Format

⇑⇑ SDF/Mol File FAQ