Molecular geometries and electronic structures of manganese binuclear complexes, [(H2O)3(O–)Mn(bis-μ-oxo-O2)Mn(OH2)4]q+ (q = 2 or 3), which are model complexes of the S3 state in the Kok cycle of OEC, were examined using hybrid density functional theory and broken symmetry method. The complexes of q = 2 and 3, which have a Mn–O bond, correspond to those derived from Mn2(II,III) and Mn2(III,III) at the S0 state of the Kok cycle. The conformers with the Mn–O bond axial to the Mn2O2 core are lower in energy than those with the equatorial Mn–O bond. The equatorial Mn–O bonds are assigned as Mn(III)–O˙− and Mn(IV)–O˙− for M2(II,III) and M2(III,III) series, respectively. The axial Mn–O bonds are Mn(IV)
O2− for M2(II,III) and Mn(IV)–O˙− for Mn2(III,III). The characters of Mn–O orbitals are π-orbitals composed of d–p interactions. The conformer with the axial Mn(IV)
O2− derived from M2(II,III) at S0 is thermochemically unstable, leading to proton transfer to give two OHs in the complex, while the axial Mn(IV)–O˙− from Mn2(III,III) at S0 is stable without the proton transfer. The magnetic interactions between two Mn ions and O were also examined by estimations of effective exchange integrals.