Kindling fluorescent protein (KFP) is an important member of the colored proteins family widely used as biomarkers in living cells. We apply quantum chemistry modeling of KFP properties by computing structure and spectra of a large molecular cluster mimicking the chromophore-containing pocket, assuming the protonated (neutral) form of the chromophore in the trans configuration. We provide evidence that this protein conformation accounts for the previously observed but unassigned absorption band at 445 nm. We demonstrate that the structure and charge of the amino acid residues nearest to the chromophore play a role in the shifts in the absorption wave length, thus underlying a strong role of intermolecular interactions when considering properties of the fluorescent proteins. © 2012 Wiley Periodicals, Inc.