I would use pymol.

would you like to create an alignment of residues that contact the ligand from your three proteins?

Yes Trevor,

I have to align the contacting residues. But prior to that I would like to align each ligand in all three PDBs and than check if any correlation in contacting residues is present or not.

Thanks dear

In PyMOL, you can use the Pair Fitting option in the Wizard menu to define atom pairs in the ligand which then can be fit to eachother. Before defining pairs make sure the selection mode is"Atoms" in the lower right panel of PyMOL. Since you have 3 models you will have to choose one as the reference and fit the other two to that.

Hope this helps.

Thanx Dr Pijning,

I will try that.

Agree with Dr. Tjaard Pijning