In QM/MM MD calculations for the RutA-FMN-O2-uracil system, with the oxygen molecule in pocket-1, the QM part included the FMN, O2 and uracil moieties and the Asn134, Thr105 sidechains. Simulations were carried out for triplet spin state of the system due to the ground electronic state of O2. Correspondingly, the unrestricted DFT approach was used in QM/MM calculations of energies and forces.