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Read Stereoinformation from Input
How stereoinformation is being read from input data by Open Babel?
✍: FYIcenter.com
Most molecule data files store stereoinformation in 3 ways:
0D, 2D, and 3D.
0D Stereoinformation in SMILES data format
0D Stereoinformation in SDF/MOL data format - Parity Code (1 for Odd, 2 for Even) is used to identify a chiral center and its local chirality in an atom line. For example, the following SDF/MOL file, L-Alanin-0D.sdf, specifies Parity Code of 1 (Odd) for the atom #1 for molecule L-Alanin.
L-Alanin FYICenter.com 0D Stereoinformation: Parity Code 6 5 0 0 1 0 0 0 0 0999 V2000 3.6373 2.1000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 1.4000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4249 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 2 3 1 0 0 0 0 4 2 1 0 0 0 0 5 4 2 0 0 0 0 6 4 1 0 0 0 0 M END
2D Stereoinformation in SDF/MOL data format - Stereo Code (1 for Up, 6 for Down) is used to identify the stereo direction in a bond line. For example, the following SDF/MOL file, L-Alanin-2D.sdf, specifies Stereo Code of 1 (Up) for the bond #1 for molecule L-Alanin.
L-Alanin FYICenter.com 2D Stereoinformation: Stereo Code 6 5 0 0 1 0 0 0 0 0999 V2000 3.6373 2.1000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 1.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 3 2 1 0 0 0 0 4 2 1 0 0 0 0 5 4 2 0 0 0 0 6 4 1 0 0 0 0 M END
3D Stereoinformation in SDF/MOL data format - Different z-values are used in 3D coordinates to identify Stereoinformation in atom lines. For example, the following SDF/MOL file, L-Alanin-3D.sdf, specifies a z-value of 1.0000 on atom #1 higher than z-values of other atoms for molecule L-Alanin.
L-Alanin FYICenter.com 3D Stereoinformation: z-value 6 5 0 0 1 0 0 0 0 0999 V2000 3.6373 2.1000 1.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 1.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 3 2 1 0 0 0 0 4 2 1 0 0 0 0 5 4 2 0 0 0 0 6 4 1 0 0 0 0 M END
For more information SDF/MOL file format, see SDF/Mol File FAQ.
⇒ Stereo Perception Performed by Open Babel
2022-11-16, 548👍, 0💬
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