Editing ChargeCalculator:Technical details (section)

===Polarization and charge transfer===
EEM, as implemented in '''ACC''', works at the atomic level, and does not see the electronic structure. Nonetheless, due to the principle of electronegativity equalization, EEM allows electron density to spread across the molecule in a manner which depends on the nature of the atoms and the chemical environment created by the surrounding atoms. The degree to which this happens also depends on the ''charge definition'' and fitting algorithms used during the development of the EEM parameters (see also the [[ChargeCalculator:Theoretical_background | Theoretical background ]]).

This behavior means that atomic charges in a residue depend on the conformation of the residue, as well as the conformation of nearby residues. Moreover, the total charge on each residue may differ from the expected formal charge (-1, 0, +1) due to charge transfer to the surrounding residues, ligands, ions, water, etc. While this behavior is realistic, it may not be desired for some applications.