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.
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).