The two attached PDB files differ in that one has a hydrogen on N17 and the other doesn't.
But, with openbabel-2.3.1, I get the same InChI key twomack@fs1:~/projects/grade-inchi-2% obabel 4PC.grade_PDB_ligand.pdb -oinchi -xK GPLPRFCWPJTQND-IVZWLZJFSA-N 1 molecule converted twomack@fs1:~/projects/grade-inchi-2% obabel 4PD.grade_PDB_ligand.pdb -oinchi -xK GPLPRFCWPJTQND-IVZWLZJFSA-N 1 molecule converted I think this is a bug. Tom
4PC.grade_PDB_ligand.pdb
Description: Binary data
4PD.grade_PDB_ligand.pdb
Description: Binary data
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