Azide and protonation: disappearing nitrogen

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Azide and protonation: disappearing nitrogen

Stefano Forli
Hi,
I have a problem adding hydrogens (correcting for the pH) to molecules containing the azide group.
I'm attaching a script that reproduces the bug. Basically, the procedure I use is the following:

  mol.DeleteHydrogens()
  mol.UnsetFlag(ob.OB_PH_CORRECTED_MOL)
  mol.SetAutomaticFormalCharge(True)
  mol.AddHydrogens(False, True, 7.4)

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?

Thanks,

S


--

 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.

    tel: +1 (858)784-2055
    fax: +1 (858)784-2860
    email: [hidden email]
    http://www.scripps.edu/~forli/
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azide_issue.py (872 bytes) Download Attachment