As shown in the panels in Fig. , the constructed model comprises the chromophore in the cisneutral form, and the side chain of His145 (protonated at Nε) and Glu222 in the neutral form. This choice matches best the observed absorption spectra of the protein . This model serves as an initial template of the full-protein structure in the ON-state for simulations described in this work. We shall cite below geometry parameters optimized for the structures in the ground electronic state obtained in the QM/MM calculations with the NWChem software package .