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The geometry and vibrational behavior of selenocysteine [NiFeSe] hydrogenase isolated from <i>Desulfovibrio vulgaris</i> Hildenborough have been investigated using a hybrid quantum mechanical (QM)/ molecular mechanical (MM) approach. Structural models have been built based on the three conformers identified in the recent crystal structure resolved at 1.3 &#197; from X-ray crystallography. In the models, a diamagnetic Ni²⁺ atom was modeled in combination with both Fe²⁺ and Fe³⁺ to investigate the effect of iron oxidation on geometry and vibrational frequency of the nonproteic ligands, CO and CN-, coordinated to the Fe atom. Overall, the QM/MM optimized geometries are in good agreement with the experimentally resolved geometries. Analysis of computed vibrational frequencies, in comparison with experimental Fourier-transform infrared (FTIR) frequencies, suggests that a mixture of conformers as well as Fe²⁺ and Fe³⁺ oxidation states may be responsible for the acquired vibrational spectra.