Read Stereoinformation from Input with Open Babel

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∟Read Stereoinformation from Input with Open Babel

This section provides a quick introduction how stereochemistry information is stored in input molecule data in 3 ways: 0D, 2D, and 3D.

Most molecule data files store stereoinformation in 3 ways: 0D, 2D, and 3D.

0D: Stereoinformation in 0 dimension is defined by parity (or chirality) at atom level.
2D: Stereoinformation in 2 dimension is defined by bond style as wedges and hashes.
3D: Stereoinformation in 3 dimension is defined by atom's relative position 3D coordinates (x, y, z).

0D Stereoinformation in SMILES data format

"@" is used to identify a chiral center followed by 3 atoms in anti-clockwise order. For example: "N[C@H](C)C(=O)O" represents D-Alanin.
"@@" is used to identify a chiral center followed by 3 atoms in clockwise order. For example: "N[C@@H](C)C(=O)O" represents L-Alanin.
A molecule can have multiple chiral centers. For example, O[C@H]1CCCC[C@H]1O.
"/" and "\" are used to identify directional bonds next to a double bond to differentiate trans- and cis- conformations. For example, "F/C=C\F" and "F/C=C/F".

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
HerongYang.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
HerongYang.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
HerongYang.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