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Charged conjugated linear chromophores provide basis for photosensitivity of biomolecules enabling significant variations of wavelength sensitivity, efficiency of double-bond isomerization or efficiency of radiative decay. Although great progress in characterization of the underlying molecular mechanisms has been achieved in recent years, rational engineering of biomolecules with desired photodynamic properties requires further elaborate studies of electronic effects. In particular, it is still unclear how optical properties are controlled by hydrogen bonds that stabilize the ionic chromophore within the protein. Photoactive yellow protein (PYP) is a well-established model system to study the role of intermolecular interactions experimentally and computationally. We investigated the impact of hydrogen bonding on optical properties and photoisomerization of the trans-pCTM- chromophore of PYP by employing, for the first time, highly accurate and robust ab initio XMCQDPT2 calculations to analyze geometries, energies, charge distributions and other properties. Overall, our results indicated that the influence of hydrogen bonds on charge transfer in the chromophore is due to electron correlation effects rather than electrostatic interactions. We described all computed variations of properties as resulting from the varied contributions of phenolic/quinonic electronic configurations, either closed-shell or biradicaloid (four configurations in total), characterized by transfer of the negative charge from one end of the pCTM- chromophore to the other. Our computational results explained a peculiar color tuning mechanism of PYP reported by Hoff et al (PNAS 2010, p. 5821) and volume-conserving isomerization described by Ihee et al (Nat. Chem. 2013, p. 212). We discussed the significance of the identified electronic mechanisms for other charged biological chromophores. In particular, our calculations indicated that color tuning in linear tetrapyrroles enabling red/far-red conversion in phytochromes is explained by a similar electronic mechanism as the color tuning of PYP.