A comprehensive theoretical investigation has been performed to study the six most stable complexes of isolated, mono, and hexahydrated 6-selenoguanine tautomers. The ground state geometries are studied at the density-functional theory and Møller–Plesset Perturbation theory implementing the 6-311++G (2d, 2p) basis set. The intermolecular distances between the water molecule and the acceptor atom of 6-selenoguanine is about 0.6 Å longer for hydrogen bonds involving selenium atom. The relative Gibbs free energy of the 6-selenoguanine tautomers favors the selenone tautomer. The majority of the stable monohydrated complexes are the one in which the oxygen atom of water accepts the acidic N7-H proton while donating a proton to the carbonyl selenium atom of 6-selenoguanine; the interaction toward N7-H being stronger than that with the selenium site. The amino group planarity has been found to be increased in the hydrated complexes. The examination of molecular orbital reveals a moderate band gap between the donor and acceptor atoms of isolated and hydrated complexes. An excellent linear correlation is found to exist between electron density and laplacian of electron density with hydrogen-bond length through atoms in molecule analysis. The natural bond orbital analysis shows a maximum charge transfer of 0.060e for selenium acceptors and around 0.025e for selenium donors.