All protein ligand interactions take place in bulk environment. It is important to predict how water molecules in the binding pocket affect their interactions. Thus, a number of tools, including WATsite, Waterdock, Schrodinger Watermap, OpenEYE SZMAP and WaterLap, were developed for this purpose which become very useful for lead optimization.

However, most of the commercial tools in this area are unbelievably expensive and most users actually use them only for foreseeing 1 or 2 projects. As a free open source tool, WATsite (http://people.pharmacy.purdue.edu/~mlill/software/watsite) gives us reliable water fingerprint diagram of protein-ligand interactions in PYMOL.

Reference:

Bingjie Hu, Markus A. Lill. WATsite: Hydration site prediction program with PyMOL interface. Computational Chemistry (2014), 89(6) 670, DOI: 10.1002/jcc.23616 

Figure 1.  settings in Pymol

Figure 2.  Visualization results in Pymol

Figure 3.  hydration energy values of each water molecule in Pymol panel