The intriguing ability of phytochromes to photoconvert between red-absorbing (Pr) and far-red-absorbing (Pfr) states depends on key interactions between a bilin chromophore and protein matrix. However, both the identification of the chemical nature and quantification of chromophore-protein interactions have not been yet fully investigated by experiments or extensive computations. Here, we presented a powerful and straightforward approach based on the fragment molecular orbital method to identify the nature and quantify the strength of the noncovalent interactions at a fully quantum mechanical level between the biliverdin (BV) chromophore and protein matrix of the Deinococcus radiodurans phytochrome (DrBphP) in the Pr state. By using pair interaction energy decomposition analysis approach, the pyrrole water, Asp207, and Glu27 were detected as key residues for the stabilization of the pyrrole rings of the BV chromophore through the formation of six H-bonds. Furthermore, the conserved Arg254 and His260 were also identified as essential residues in the conformational stability of both propionic side chains B and C. Moreover, new interactions were identified in the chromophore-binding pocket, two nonclassical H-bonds (CH/O interactions) between Asp207 and Tyr263, and an OH/π interaction between Tyr263 and ring D of the BV chromophore, which might have photochemical relevance.