Using this code, the amine nitrogen gets properly protonated, but the azide group gets disconnected from the molecule, one of the azide nitrogens disappears and the remaining ones get hydrogenated.
If I don't use SetAutomaticFormalCharge(), the azide is fine, but the amine doesn't get protonated.
I've tested writing the output molecules in Mol2 and PDB, and the missing nitrogen never gets written in the molecule.
Surprisingly, the both number of heavy atoms and the formula reported by OB does not change, meaning the nitrogen is still there, somewhere.
Is this a bug or am I doing something wrong?
Stefano Forli, PhD
Assistant Professor of Integrative
Structural and Computational Biology,
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.