-SO2 in the ligand group makes interaction (Salt bridge/Hbond) with protein but not captured by plip.

[aniketsh]

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[fkaiserbio]

Could you please give more details? Ideally the PDB file you used and the exact specification of the bond you are expecting PLIP to detect.

[ljmartin]

Sorry to hijack this issue but I came here for the same thing. Here's a repro (PDB: 4NIE). One might expect a hydrogen bond to arginine (ARG120) and or backbone nitrogen (of LEU40) from the sulfone, although maybe that's arguable? Both of these are present in the RCSB ligand interaction visualiser: https://www.rcsb.org/3d-view/4NIE?preset=ligandInteraction&sele=NBH

Happy to try contributing something myself if you could point me to the area of the code.

#imports:
from plip.structure.preparation import PDBComplex
from plip.exchange.report import BindingSiteReport

import prody
prody.confProDy(verbosity='none')


#load pdb using prody:
pdbid = '4NIE'
chA = prody.parsePDB(pdbid, chain='A',verbose=False)
prody.writePDB('temp.pdb', chA)

#analyse binding site of drug-like ligand:
my_mol = PDBComplex()
my_mol.load_pdb('./temp.pdb') # Load the PDB file into PLIP class

ligname = 'NBH'

my_mol.analyze()
for key, value in my_mol.interaction_sets.items():
    if ligname in key:
        intrxn = value

#print hbonds. Note, no interaction with arginine is present.
bsr = BindingSiteReport(intrxn)
print(bsr.hbond_info)

output. Notice no ARG or LEU:

[(377, 'PHE', 'A', 601, 'NBH', 'A', False, '2.07', '3.04', '168.46', False, 1988, 'Nam', 909, 'O2', (24.272, -4.851, -10.765), (27.161, -5.19, -11.658))]

Also thanks for PLIP! It's awesome!!

PS - note that if you put 4NIE into the web server, a different arginine will be shown. ARG120 is absent, even though the side chain is closer, because it is not recognised as a bonding residue.

[ljmartin]

apologies if this is a double post, I lost a post somewhere...

the 'simple' definition of HBA used by OpenBabel is here: https://github.com/openbabel/openbabel/blob/08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b/src/atom.cpp#L1730 this uses a blanket definition for all oxygens.

Arguably this is incorrect, and SO2 oxygens should not be hydrogen bond acceptors. The updated definition is here: https://github.com/openbabel/openbabel/blob/08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b/src/atom.cpp#L1779

If anyone prefers to use the simple definition, then they need to swap at.OBAtom.IsHbondAcceptor to at.OBAtom.IsHbondAcceptorSimple in here https://github.com/pharmai/plip/blob/b481cf70870f6f100037551861cef32adef99105/plip/structure/preparation.py#L509

    def find_hba(self, all_atoms):
        """Find all possible hydrogen bond acceptors"""
        data = namedtuple('hbondacceptor', 'a a_orig_atom a_orig_idx type')
        a_set = []
        for atom in filter(lambda at: at.OBAtom.IsHbondAcceptor(), all_atoms):
            if atom.atomicnum not in [9, 17, 35, 53] and atom.idx not in self.altconf:  # Exclude halogen atoms
                a_orig_idx = self.Mapper.mapid(atom.idx, mtype=self.mtype, bsid=self.bsid)
                a_orig_atom = self.Mapper.id_to_atom(a_orig_idx)
                a_set.append(data(a=atom, a_orig_atom=a_orig_atom, a_orig_idx=a_orig_idx, type='regular'))
        a_set = sorted(a_set, key=lambda x: x.a_orig_idx)
        return a_set

[fkaiserbio]

Thanks for pointing this out and your detailed investigation! Might be even something to include as a command line option for advanced users.