/usr/share/pdb2pqr/pdb2pka/ is in pdb2pqr 2.1.0+dfsg-1.
This file is owned by root:root, with mode 0o755.
..
/usr/share/pdb2pqr/pdb2pka/NEWligand_topology.py
/usr/share/pdb2pqr/pdb2pka/__init__.py
/usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
/usr/share/pdb2pqr/pdb2pka/apbs.py
/usr/share/pdb2pqr/pdb2pka/charge_mon.py
/usr/share/pdb2pqr/pdb2pka/example.py
/usr/share/pdb2pqr/pdb2pka/inputgen_pKa.py
/usr/share/pdb2pqr/pdb2pka/ligand_topology.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/
/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/ligff.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/lookuptable.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/peoe_PDB2PQR.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/templates.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/trial_templates.py
/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
/usr/share/pdb2pqr/pdb2pka/pKa_base.py
/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
/usr/share/pdb2pqr/pdb2pka/pMC_mult.py
/usr/share/pdb2pqr/pdb2pka/pka_help.py
/usr/share/pdb2pqr/pdb2pka/pka_old.py
/usr/share/pdb2pqr/pdb2pka/pka_routines.py
/usr/share/pdb2pqr/pdb2pka/prepare_pKa_ligand.py
/usr/share/pdb2pqr/pdb2pka/substruct/
/usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
/usr/share/pdb2pqr/pdb2pka/substruct/__init__.py