And is there any program taking these factors into account? How to calculate the effect of phosphorylation on electrostatic, especially when it is located around the binding site and not included in PDB file?
If you study the Poission Boltzmann equation, you can observe the importance of ionic strength. The ionic strength and electrostatic properties are inversely proportional, and the change is non linear. pH has its own importance everywhere. Especially at binding sites, where the protonation states of the residues are considered, a small change in the pH can effect the affinity of drug/ligand.