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R/S (Right/Left) Hand Stereo Centers
Right/Left Hand Stereo Centers?
✍: FYIcenter.com
In chemstry study, a stereo center a labeled as R (Rectus, Right in Latin) Hand or S (Sinister, Left in Latin) according to the following rules.
1. Assign precedence ranks to its 4 neighboring branches, as #1, #2, #3, and #4. Neighboring branch with #1 has the highest rank.
2. Determine R/S-hand.
With the R/S-Hand Stereo Centers definitions describbe above, we can figure out the algorithm used by Open Babel to determine the wedge/hash bonds.
Case 1: Without Implicit Hydrogen Neighbors
For example, the following pictures shows a pair of R-Hand (on the right) and S-Hand (on the left) stereo centers without implicit Hydrogen neighbors. Note that it is the lowest rank atom getting changed into a Hash or Wedge bond to present the stereo center.
If you specify the S-Hand stereo center with downward bond on atom F in the SDF file shown below, Open Babel will correct with upward bond on atom C.
Without Implicit Hydrogen Neighbors FYIcenter.com 5 4 0 0 0 0 0 0 0 0999 V2000 1.1887 1.0905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1887 2.4905 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 2.5229 0.6663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3108 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.8301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 6 0 0 0 1 3 1 0 0 0 0 1 4 1 0 0 0 0 1 5 1 0 0 0 0 M END
Case 2: With an Implicit Hydrogen Neighber
For example, the following pictures shows a pair of R-Hand (on the right) and S-Hand (on the left) stereo centers with an implicit Hydrogen neighbor.
⇒ Custom Wedge/Hash with SVG output
⇐ Wedge/Hash Bond Changed by Open Babel
2021-12-02, 1467🔥, 0💬
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