Abstract <p>Electronic excitation energies and dipole moments have been computed using multiconfiguration CASSCF method further corrected to the second order perturbation theory XMCQDPT2 for a molecular-cluster modeling the active site of (6–4) photolyase containing а thymine–thymine (6–4) photoproduct. A set of models is considered in which the excitation energies change in a wide range since anionic phosphate groups of the photoproduct and cofactor flavin adenine dinucleotide (FADH^–) are included in the models. The results demonstrate that an account for solvent effects using a PCM model reproduces the screening of the negative charges of the phosphate groups by the environment of the active site. The limits of the two-state model for estimating the electronic coupling matrix elements of the electron transfer reactions are investigated. The electronic coupling matrix elements may become overestimated due to the presence of a bright excited state in the flavin excitation spectrum.</p>