Water has been found to interact with the redox site of rubredoxin by molecular dynamics simulations, resonance Raman spectroscopy, and X-ray crystallographic structure determination. Since this should have a large effect on its electron-transfer properties, the nature of this interaction is important to characterize. Here, the interaction of [Fe(SCH3)(4)](2-), a redox site analogue for reduced rubredoxin, with a water molecule was investigated using ab initio calculations. Two different conformations of the analogue and different orientations of the incoming water were examined. Geometry optimizations at the unrestricted Hartree-Fock and second-order Moller-Plesset levels reveal hydrogen bonds donated from the water molecule to the sulfurs of the analogue. Calculated binding energies, which are similar at all computational levels even after correcting for basis set superposition error, indicate that the orientation in which each hydrogen of the water interacts with a separate sulfur is preferred to that in which a single hydrogen points toward the analogue. In addition, an enthalpically unfavorable trigonal-bipyramidal type adduct was found in which the water oxygen interacts directly with the iron but only at the lowest computational level. Atom-centered partial charges, by both Mulliken＇s and electrostatic potential fitting methods, and geometries of the redox site show only slight changes upon complexation. This indicates that both electronic and geometric polarization of the analogue by the water was small, although there was some localized electronic polarization of the sulfurs near the incoming water. On the other hand, both electronic and geometric polarization of the water by the analogue were seen: the dipole moment of the water molecule increased by about 20% over that for an isolated water, with about one-quarter of this increase attributed to a more acute H-O-H angle. These results are also important in modeling the interaction of the water and the redox site in classical molecular dynamics simulations of rubredoxin and other iron-sulfur proteins.