not finding H bond between HIS 95 NE2 and 6IC 202 N01 in 7rpz

[hstern2]

expected to find a hydrogen bond here? PLIP does not list HIS 95 in the list of H bond interactions

[snbolz]

PLIP uses OpenBabel to identify hydrogen bond donors and acceptors. In your example, both nitrogens that would be involved in the hydrogen bond are recognized as hydrogen bond acceptors but not donors. Without a donor, PLIP does not detect a hydrogen bond. Indeed, whether the nitrogen in the imidazole ring of histidine acts as a hydrogen bond donor depends on its tautomeric state. The observed behavior of PLIP is related to how OpenBabel handles the tautomeric states and protonation of the histidine imidazole ring.

In summary, PLIP works as expected in your case, as it does not detect a hydrogen bond between two acceptors. However, in one of the tautomeric states of histidine, there might be a hydrogen bond between histidine and 6IC. Since PLIP is open source, you have the option to modify the code to better fit your specific requirements or even contribute to improving protonation in PLIP. Alternatively, you could use a pre-protonated structure along with the --no-hydro flag (as mentioned in issue #108) to define the protonation state of the histidine side chain.