As shown in Fig. , the oxygen molecule is localized almost equally close to the N5 and C6 atoms of flavin. Fig. illustrates that the O2 molecule is stably located in this pocket; this conclusion holds for both complexes, ROU and RO, that is with or without uracil molecule present in the system. At this point, we speculate about subsequent chemical transformations in the system. As mentioned above, when the oxygen molecule comes close enough to the isoalloxazine ring, the electron transfer (coupled with the proton transfer) might occur, resulting in creation of the reactive oxygen species capable to interact with flavin. We model this step by switching the trajectory at some QM/MM MD frame to the singlet spin state of the system. In the case of the unrestricted singlet state DFT approximation, the resulting electronic structure of the system can describe the radical pair FMN and OOH, as shown in Fig. . This structure remains stable along QM/MM MD trajectories, and the Asn134 amino acid residue is very important to stabilize the HOO radical. Interestingly, the average N5(flavin)-O(O2) distance is very short (2.64 Å) and exhibits low variation (±0.09 Å), We note that in this singlet radical pair configuration, the N5-O distance is somewhat close (2.64 Å) to the value 2.09 Å, suggested upon the interpretation of experimental density in the PDB ID 6TEG and 6SGG structures.