[Biopython] aligning a bound ligand from one PDB complex to a reference structure?

[R. K. Belew]

Sorry, this is a [repost from 
BioStars](https://www.biostars.org/p/195014/); no response there(:

PDB:4DMN is a HIV-1 integrase structure with a bound ligand (PDB:0L9). 
i want to bring this ligand into alignment with another, reference 
structure PDB:3AO1.

i can do alignments of the two structures, and i can identify the 
ligand's heteroatoms by checking the residue.get_full_id() tags.  but 
there are obviously no CA atoms to associated with the ligand to use as 
references for `Superimposer` to use for alignment.  So i figure i need 
to do it in two steps: first align the two structures, then use the 
transform found by `Superimposer` on the ligand.

but i don't know how to do the second bit?

PS:  poking at PyMOL,  i seem to be able to do what i want using its 
`matrix_copy` command:

     extract 4dmn_0L9, 4dmn and organic
     align 4dmn////CA, 3ao1////CA
     matrix_copy 4dmn, 4dmn_0L9

but i want to do it in bioPython!

thanks for any hints, Rik