The structure of the oxygen evolving complex (OEC) of photosystem II (PSII) was recently analyzed by crystallography at 1.95 angstrom resolution using X-ray free electron laser (XFEL), but the positions of hydrogen atoms were not determined. We have examined the XFEL structure theoretically under the assumption off our protonation cases. The spin densities obtained by the high-spin UB3LYP revealed that a partial internal reduction of the high-valent Mn ions in the CaMn4O4X(H2O)(3)Y cluster occurs for the O-(5)(=X) = O2- case, entailing its protonation (X = OH-) in the XFEL structure. (C) 2015 Elsevier B.V. All rights reserved.