After finding the ligands within the protein:ligand complexes, try some of the following exercises:

• Display the ligands as space-filling models and try to orient the ligands alone so that they match the highlighted ligands within the complex.
• View each complex from the same angle, then return to the table of ligands to see if you can orient them they way they all bind to HIV-protease. Then try to determine areas where size/shape seem to be important based on commonalities between the ligands.
• Continue examining your oriented ligands for functionality that they have in common in their bound orientation (hydrogen bond acceptors or donors in approximately the same location...).