We characterize structures and electronic excitation of domains from a bacteriophytochrome-based infrared fluorescent protein carrying a covalently bound biliverdin chromophore using the quantum mechanics/molecular mechanics methods. We show that geometry optimization at the density functional theory level and application of the extended multiconfigurational quasidegenerate perturbation theory in quantum subsystems allows us to achieve high calculation accuracy for the model systems mimicking the red-adsorbing and the farred-adsorbing protein forms. Specifically, discrepancies between experimental and theoretical excitation energies are less than 0.05 eV (similar to 20 nm) for the Q-band in both protein forms.