We found a linear correlation between the theoretically predicted shifts and experimentally observed absorption spectra for various mutants of photoactive yellow protein, a photosensory receptor. Excitation energies of mutants were evaluated by the combination of the high level ab initio calculation for the chromophore inside and the low level ab initio calculation for the surrounding protein environment. Importantly, the electronic states of these two regions were treated both as variables and they are solved consistently to each other. The protein-chromophore interaction has been accurately reproduced by this method. (c) 2006 Elsevier B.V. All rights reserved.