The atom-centered charges and polarizabilities are derived based on amino-acid-based fragments, as shown in Figure . The parameters of a given fragment thus intrinsically include, by virtue of the wave-function optimization, polarization among sites that are present in the fragment, i.e., the amino-acid residue itself and part of the backbone of the neighboring residues through the capping groups. Thus, to avoid double-counting of polarization effects, when two neighboring fragments interact, it is appropriate to exclude those interactions accordingly. This interaction scheme is compatible (by design) with the one used for MFCC-based potentials, thus allowing a mixed representation of protein systems.