Mo-containing nitrogenase is the main enzyme that is able to take N-2 from the air and form ammonia. The active-site cofactor of the enzyme, termed FeMoco, is unique in nature. It has seven Fe and one Mo atoms connected by S bridges, with a C atom in the center of the cofactor. Another unusual feature is that it has a large homocitrate ligand known to be of importance for catalysis. In the present computational study, the role of the homocitrate ligand is investigated. It is found that a large structural change, which makes Mo-III five coordinated, is energetically favorable in the more reduced states. This is of probable importance for the nitrogenase mechanism.