Collections:
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, 1225👍, 0💬
Popular Posts:
Where to find FAQ (Frequently Asked Questions) on Open Babel, Chemistry Toolbox? I want to learn mor...
What are tools that support the SDF/Mol V3000 file format? There are a number of online or standalon...
How to Install Open Babel binary package on Windows computers? The easiest option to install Open Ba...
What information is displayed in each area on PyMol Screen? Once PyMol is started, you should see tw...
How to add hydrogen atoms to molecule data during data conversion? Most molecules contains many hydr...