How can I align a generated ligand (from SMILES) to a ligand in a PDB?

Question

[brett.spurrier]

I have a ligand that exists in its own PDB (reference PDB). I have then generated another (structurally similar, but not exact) ligand from SMILES, and written that to a PDB.

I am trying to find out how to superimpose the generated ligand onto the reference PDB, but I am having trouble finding a simple way to do this. This is a step that is part of a pipeline, so I need to be able to do it via command line, however, the tool I use can be flexible. I have been looking at rdkit, but am having trouble with that (the number of atoms don't match since the ligand compounds are similar, and not identical). It looks like PyMol can do this, but I don't know how to do it from the command line.

Does anyone have any idea how to superimpose two PDB ligands from two PDB files?

UPDATE:

The ligand generated from SMILES ligand energy minimized so it does have proper 3d coordinates.

Answer 1

[brett.spurrier]

I think I hav found an answer using OpenBabel.

obfit "Oc1ccc(cc1O)C1Nc2cccc3cccc(N1)c23" fixed.pdb moving.pdb > new_aligned.pdb

Where the smiles pattern matches my moving.pdb (which is where my generated conformers came from).