Decomposition of 'free binding energy' per residue indicates if the residue contributes in favoring the complex formation in water against the clusters of monomers-waters in solution or other way around (i.e., favoring formation of clusters of monomers-waters against complex formation such as protein-ligand, protein-protein, etc., in water).  If the value is negative, then it favors complex formation in water, otherwise, if it is positive it does not stabilize complex formation but clusters of monomers-water formation (e.g., protein-water and ligand-water, but not protein-ligand complex.)

See also a recent reference:

Christopher J. Woods, Maturos Malaisree, Julien Michel, Ben Long, Simon McIntosh-Smith and Adrian J. Mulholland, Faraday Discuss., 2014, 169, 477-499.

Dear Prof. Hiqmet,

Thank you very much for the answer.

The entropy calculation using the normal mode analysis in Gibbs free energy calculations is not exactly right. You may consider recalculating the free energy using a quasi harmonic method and these values may change. It may become negative or smaller positive. Schiltter method yields results in a very fast way.

Thank you very much for the answer