If the restricted singlet state DFT approximation is applied instead of the unrestricted version, the electronic structure cannot describe radical pairs. Figure illustrates the consequences of such modeling showing that the covalently bound adduct is formed after spontaneous binding oxygen to the C6 atom of flavin. It is not evident how the reactive species shown in Fig. and Fig. react with the uracil molecule given its position on the other side of the isoalloxazine ring; further cumbersome calculations are required to clarify the full reaction pathway. We only note that the main difference between the ROU and RO systems are due to uracil blocking water access to the C6 and N5 atoms of the flavin and to the oxygen atoms of O2 or subsequent HOO radical/group. Now we turn to the results of simulations in the area corresponding to the pocket-5 oxygen binding site. In this case, the QM subsystem included FMN, O2, uracil, the side chains of Trp139, Lys39, Glu143, Asn134 and several water molecules. The results for the QM/MM MD trajectory (Fig. Analyzing these results, we observe significant charge transfer to the oxygen molecule at many steps of the simulation. Such structures are characterized by: (i) close distances of oxygen to the flavin, (ii) close position of the Lys69 sidechain, (iii) proper position of the uracil that allows for hydrogen bonding network to stabilize the charge transfer. All these issues are observed in the 60-80 ps window (see Fig. , Fig. ). Here, we also model a possible reaction step toward the intermediate formed by flavin and oxygen. We again switched the trajectory at some frame to the restricted singlet spin state of the system. Figure shows that the covalently bound adduct is formed after binding oxygen to the C4a atom of flavin. Subsequent reactions may lead to the oxidation of uracil.