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If one adopts atom-centered polarizable dipole approximation, the Fock matrix elements involving dipole-electron interactions must be evaluated. In refs 18 and 43, these integrals were approximately evaluated after expansion of the dipole into a set of six point charges.
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note
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In all the bR structures which we examined so far (refs 30 and 48-50), there are seven aromatic residues (W86A, W138A, W182A, W189A, Y83A, Y185A, and F208A) surrounding the chromophore and no significant difference in their side chain orientations. Therefore, the use of the structures other than 2BRD would not affect the main conclusion of this study, insisting the dominant role of these residues in causing the opsin shift of bR.
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