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where list i contains the receptor atoms belonging to the neighbor list of atom i. The electrostatic neighbor list includes all the receptor atoms of the van der Waals neighbor list and one atom for every charged residue whose charge center is within a distance of 13 A, from the closest binding site residue. Supplementing the van der Waals neighbor list with a monopole approximation of distant charged residues dramatically reduces the error originating from the long range electrostatic interactions.

Fragment desolvation The fragment intramolecular energy in solution is calculated with the GB formula as described in Reference 13:

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