Stereoinformation in SDF/Mol V3000 Files

Q

How Stereoinformation is stored in in SDF/Mol V3000 files?

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A

Similar to SDF/Mol V2000, stereoinformation can be stored in SDF/Mol V3000 files in 3 ways: 0D, 2D, and 3D.

  • 0D: Stereoinformation in 0 dimension is defined by parity at atom lines as "CFG=n" options.
  • 2D: Stereoinformation in 2 dimension is defined by wedge, hatch or wiggly bond styles at bond lines as "CFG=n" options.
  • 3D: Stereoinformation in 3 dimension is defined by the x, y and z 3D coordinates at atom lines.

Here is the same molecule L-Alanine with a chiral center (Tetrahedral Stereocenter) stored in a SDF/Mol V3000 file, L-Alanine.sd3:

L-Alanine
FYICenter.com
Stereoinformation in SDF/Mol V3000
  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 6 5 0 0 1
M  V30 BEGIN ATOM
M  V30 1 C -0.6622 0.5342 0 0 CFG=2
M  V30 2 C 0.6622 -0.3 0 0
M  V30 3 C -0.7207 2.0817 0 0 MASS=13
M  V30 4 N -1.8622 -0.3695 0 0 CHG=1
M  V30 5 O 0.622 -1.8037 0 0
M  V30 6 O 1.9464 0.4244 0 0 CHG=-1
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 1 3 CFG=1
M  V30 3 1 1 4
M  V30 4 2 2 5
M  V30 5 1 2 6
M  V30 END BOND
M  V30 END CTAB
M  END

The molecule structure is displayed below:

L-Alanine with Chiral Center
L-Alanine with Chiral Center

Open Babel can also be used to read and write SDF/Mol V3000 files.

Here is the command to read a SDF/Mol V3000 file and write in SDF/Mol V2000 format. The conversion keeps both 0D and 2D Stereoinformation.

herong$ obabel -i sdf L-Alanine.sd3 -o sdf 
L-Alanine
 OpenBabel02032119432D
Stereoinformation in SDF/Mol V3000
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.6622    0.5342    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6622   -0.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7207    2.0817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8622   -0.3695    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.6220   -1.8037    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9464    0.4244    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  1  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
M  ISO  1   3  13
M  CHG  2   4   1   6  -1
M  END
$$$$
1 molecule converted

Here is the command to read a SDF/Mol V2000 file and write in SDF/Mol V3000 format.

fyicenter$ obabel L-Alanine.sdf -o sdf -x3
L-Alanine
 OpenBabel02032111532D
123456789012345678901234567890123456789012345678901234567890                                                         
  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 6 5 0 0 1
M  V30 BEGIN ATOM
M  V30 1 C -0.6622 0.5342 0 0
M  V30 2 C 0.6622 -0.3 0 0
M  V30 3 C -0.7207 2.0817 0 0 MASS=13
M  V30 4 N -1.8622 -0.3695 0 0 CHG=1
M  V30 5 O 0.622 -1.8037 0 0
M  V30 6 O 1.9464 0.4244 0 0 CHG=-1
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 1 3 CFG=1
M  V30 3 1 1 4
M  V30 4 2 2 5
M  V30 5 1 2 6
M  V30 END BOND
M  V30 END CTAB
M  END
$$$$
1 molecule converted

Open Babel keeps the 2D Stereoinformation correctly. But it fails to added CFG=2 in atom line #1, because it was given in the input SDF/Mol V2000 file:

fyicenter$ cat L-Alanine.sdf
L-Alanine
CTFile Formats, 2003
123456789012345678901234567890123456789012345678901234567890
  6  5  0  0  1  0              3 V2000
   -0.6622    0.5342    0.0000 C   0  0  2  0  0  0
    0.6622   -0.3000    0.0000 C   0  0  0  0  0  0
   -0.7207    2.0817    0.0000 C   1  0  0  0  0  0
   -1.8622   -0.3695    0.0000 N   0  3  0  0  0  0
    0.6220   -1.8037    0.0000 O   0  0  0  0  0  0
    1.9464    0.4244    0.0000 O   0  5  0  0  0  0
  1  2  1  0  0  0
  1  3  1  1  0  0
  1  4  1  0  0  0
  2  5  2  0  0  0
  2  6  1  0  0  0 
M  CHG  2   4   1   6  -1
M  ISO  1   3  13
M  END

 

Stereochemistry with JSME (Molecule Editor in JavaScript)

Open Babel Options on SDF/Mol Files

Stereochemistry, Chirality, Parity

⇑⇑ SDF/Mol File FAQ

2021-02-06, 124👍, 0💬