Hi there, Attached is a crystal_ligand.mol2 for the ACE target from DUDE. I'd like to generate a number of conformers for this ligand. The trick is it has 2 amide bonds that I'd like to keep planar. As far as I can see neither MMFF nor UFF will keep those planar by default, at least not for this input file.
One way around it, is to find all the amide bonds by smarts matching. From that, find the hydrogen connected to N and add a DihedralConstraint on the 4 atoms before running the minimization. That's what conformers.py is attempting to do (basing on one of the test scripts). However, I still get non-planar amide bonds and I'm really confused as to why. I can filter them out manually with GetDihedralDeg(). Thanks for all the help (I'm using up all the rdkit credits this weekend ;) ) - Jan
crystal_ligand.mol2
Description: application/not-regular-file
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.rdMolTransforms import GetDihedralDeg
mol = Chem.MolFromMol2File("Downloads/crystal_ligand.mol2", removeHs=False)
patt = Chem.MolFromSmarts("[OX1]=CN")
amides = mol.GetSubstructMatches(patt)
constraints = []
for amide in amides:
print amide
amide = [mol.GetAtomWithIdx(idx) for idx in amide]
for a in amide: print a.GetSymbol()
carbon = [a for a in amide if a.GetSymbol() == "C"][0]
oxygen = [a for a in amide if a.GetSymbol() == "O"][0]
nitrogen = [a for a in amide if a.GetSymbol() == "N"][0]
# there may be a better way of finding the N-H hydrogen
hydrogens = [ b.GetBeginAtom() for b in nitrogen.GetBonds() if b.GetBeginAtom().GetSymbol() == "H"] + [ b.GetEndAtom() for b in nitrogen.GetBonds() if b.GetEndAtom().GetSymbol() == "H"]
assert(len(hydrogens)==1)
hydrogen = hydrogens[0]
constraints.append((hydrogen.GetIdx(), nitrogen.GetIdx(), carbon.GetIdx(), oxygen.GetIdx()))
confIds = AllChem.EmbedMultipleConfs(mol, 200)
prop = AllChem.MMFFGetMoleculeProperties(mol)
for confId in confIds:
ff = AllChem.MMFFGetMoleculeForceField(mol, prop, confId=confId)
for c in constraints:
ff.MMFFAddTorsionConstraint(c[0], c[1], c[2], c[3], False, -170, 170, 1.0e5)
print ff.Minimize(maxIts=2000)
Chem.MolToPDBFile(mol, "conformer_{}.pdb".format(confId), confId)
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