Stereoinformation Presentation in SDF/Mol File

Q

How Stereoinformation Is Presented in SDF/Mol and SDF/Mol V3000 Files?

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A

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:

  • Tetrahedral central atom with 4 different neighboring atoms.
  • Tetrahedral central atom with neighboring atoms that have different stereo environments.
  • Atoms N, P and S in ring have parity, if they are bridgehead atoms.
  • Atom N has parity in a 3 membered ring.

2. Local Parity - Local Parity is assigned to atoms in 2 cases:

  • Atom that has number of implicit and explicit H < 3.
  • Atom that has number implicit H < 2.

3. Allene-like Parity - Allene-like Parity is assigned to atoms in 2 cases:

  • There are equal numbers of double bonds in each side of the central atom.
  • there are at least two different ligands on both terminal atoms.

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.

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

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:

  • The "chiral flag", the 5th number, in the counter line. In this example, "chiral flag" is "1" indicating that there are chiral centers in the molecule.
  • The "parity code", the 7th number, in an atom line. In this example, atom #1 has a "parity code" of "2" indicating that it's an even parity.
  • The "stereo code", the 4th number, in a bond line. In this example, bound #2 has a "stereo code" of "1" indicating that the bound is pointing up towards the viewer.

Note that SDF/Mol file format is capable to support stereoinformation in 3 ways: 0D, 2D, and 3D.

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

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

What Is Stereochemistry

Stereochemistry, Chirality, Parity

⇑⇑ SDF/Mol File FAQ

2021-03-21, 145👍, 0💬