Models simulating the catalytic diiron subcluster [FeFe](H) in Fe-only hydrogenases have often been designed for computational exploration of the catalytic mechanism of the formation and cleavage of dihydrogen. In this work, we extended the above models by explicitly considering the electron reservoir [4Fe-4S](H) which is linked to the diiron subcluster to form a whole H cluster (6Fe-6S] = [4Fe-4S](H) + [FeFe](H)). Large-scale density functional theory (DFT) computations on the complete H cluster, together with simplified models in which the [4Fe-S-4](H) subcluster is not directly involved in the reaction processes, have been performed to probe hydrogen activation on the Fe-only hydrogenases. A new intermediate state containing an Fep center dot center dot center dot H center dot center dot center dot CN two-electron three-center bond is identified as a key player in the H-2 formation/cleavage processes.