It is considered the quantum-chemical approach in the electron structure modeling of the active centers of the metal-containing fermentative bionanocomplexes, resulting in the using of the central tenets of the following theories: the method of the valence bonds, the crystal field theory, the ligands field theory, the elements of the symmetry theory and the groups theory. It is demonstrated that the interaction of the central ions with the ligands is carried out by the donor-acceptor mechanism: the ions provide for the connection the vacant orbitals and the ligands - the unshared electrons pairs, one of the coordination bond is functional, using for the interaction with substrates. The active centers structure is defined by the central ions and the ligands nature. The active center as a whole is considered as the bionanocomplex, relating to the certain symmetry group. It is given the algorithm for the construction of the quantum-chemical active centers models. It is proposed that from the quantum-chemical point of view the functional mechanism of the bionanocomplexes is universal and, in the final, it is reduced to the acceptance and the less of the functional electron in the molecular antibonding orbitals of the complex that induces the active center transition from one state to another. It is explained the electron distribution on the molecular orbitals, the electron-conformational transitions, the active centers changes at it functioning, the role of it protein surrounding on a basis of the conception «protein - machine». It is discussed, as an example, the quantum-chemical model of the ferroporphyrin active centers, containing Fe(II) or Fe(III) central ions.