Modeling the interaction of proteins with small ligands, in particularly, for the goals of drug design is traditionally performed using molecular mechanics or classical molecular dynamics methods with force field parameters. Application of quantum-based simulation tools is also growing, but is still far from the routine use. In this work, we describe quantumbased simulations for a molecular system, which can hardly be handled at the classical level. Specifically, we characterize a reactant complex of a flavin-dependent enzyme RutA from Escherichia coli with the molecular oxygen and uracil.