Home » DataWarrior » Bug Reports » Indolizidine stereochemistry (Chiral molecules are seen as undefined configuration)
Indolizidine stereochemistry [message #2075] Fri, 05 January 2024 11:31 Go to next message
Messages: 1
Registered: January 2024
Junior Member

when drawing molecules containing an indolizidine core, structures are labeled "unknown chirality" and the nitrogen atom displayed in purple even if all stereocenters are defined.

As an example, you may want to use (-)-Swainsonin.

Drawing a wedge or hashed bond sprouting from the nitrogen will change the label to "this enantiomer", however in my opinion this bond type does not make sense at this position.

Best regards,
Re: Indolizidine stereochemistry [message #2076 is a reply to message #2075] Fri, 05 January 2024 13:46 Go to previous message
thomas is currently offline  thomas
Messages: 674
Registered: June 2014
Senior Member

many thanks for the observation. This is indeed a bug, because the nitrogen atom was wrongly considered having a fixed pyramidal geometry due to the bi-cyclic structure. That will be fixed in the next update...

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