Found out how to do this:
-- Search Berberiene
http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/BER
links -> downloaden pdb file (ideal), (representative)
(First I thought the ideal file would be best, but then recgonized that this does not neccessarily mean "ideal/perfect for analysis" but rather "ideal/simplified gas molecules". So the represdentative is probably better.
download receptor
http://www.rcsb.org/pdb/explore/explore.do?structureId=2Y1M
insert files .pdb. It compares the structures
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