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. Author manuscript; available in PMC: 2021 Jul 14.
Published in final edited form as: J Chem Theory Comput. 2020 Jun 12;16(7):4655–4668. doi: 10.1021/acs.jctc.0c00111

Figure 1.

Figure 1.

Thermodynamic cycle for proton binding. RH and R represent protonated and deprotonated forms of the residue, respectively, in the solvent environment as a model compound (upper) or in the protein environment (lower). The superscripts are used to highlight that the polarization of residue R/RH is different in the protein and solvent. With the additive force fields these polarizations are the same.