PDB database structure containing small molecules with certain pattern not working in protein_ligand notebook

[quantaosun]

protein_ligand.ipynb will not work for some certain heteroaromatic rings containing small molecules, for example, if anyone tries to simulate PDB 6LUD, it will not work, due to a wrong reduce process by pybel with two extra H atoms added to the ring, broken the aromatic ring. This looks like to me an pybel (open babel bug) but if anyone more familiar with this could help, would be great, thanks!

I have no idea what is the pattern of the small molecules would trigger this bug, but seems C=N/C=O in the ring (not every case) are likely to be the reason. I have encountered this for several times.