(overlap-ligands imol-ligand imol-ref chain-id-ref resno-ref)
returns a rotation+translation operator which can be applied to other molecules (and maps). Here, imol-ligand is the molecule number of the ligand (which is presumed to be a a molecule on its own - Coot simply takes the first residue that it finds). imol-ref chain-id-ref resno-ref collectively describe the target position for the moving imol-ligand molecule.
The convenience function
(overlay-my-ligands imol-mov chain-id-mov resno-mov imol-ref chain-id-ref resno-ref)
wraps overlap-ligands.
The GUI for the function can be found under
Extensions -> Modelling -> Supperpose Ligands...