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Stereoinformation Presentation in SDF/Mol File
How Stereoinformation Is Presented in SDF/Mol and SDF/Mol V3000 Files?
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Ideally stereoinformation should be stored in atom's
coordinates, since SDF/Mol files support x, y, and z,
3-dimensional coordinates.
However, not all software supports 3-dimensional coordinates. So SDF/Mol file uses 3 types of parities to store stereoinformation.
1. Global Parity - Global or General Parity is assigned to atoms in 4 cases:
2. Local Parity - Local Parity is assigned to atoms in 2 cases:
3. Allene-like Parity - Allene-like Parity is assigned to atoms in 2 cases:
Here is the structure of molecule L-Alanine with a chiral center (Tetrahedral Stereocenter) as shown in the SDF/Mol documentation (CTFile Formats, 2003). Each atom in the structure is labelled with an index number. The chiral center is located at atom number 1.
The SDF/Mol file, L-Alanine.sdf, for the above molecule is given below:
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
According to the SDF/Mol file documentation, stereoinformation for the above molecule are represented in 3 places:
Note that SDF/Mol file format is capable to support stereoinformation in 3 ways: 0D, 2D, and 3D.
In the above example, stereoinformation is actually redundantly defined in 2 ways, 0D and 2D, in the same SDF/Mol file.
⇒ Parity and Stereo with Open Babel
2021-03-21, 631👍, 0💬
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