The electron density distributions of a small dipeptide molecule, glycyl-L-threonine dihydrate whose structure has recently been determined using accurate single-crystal X-ray diffraction to a resolution of 0.43 , have been studied theoretically at the semiempirical level and Hartree-Fock level employing varying sizes of basis sets up to the valence triple-zeta plus polarization level. Both theoretical structure factors and dynamic deformation maps are computed using the electronic wavefunctions derived in vacuo using MO methods. General agreement between theory and experiment is good and improves when larger basis sets are employed. The dynamic theoretical structure factors calculated at the HF/6-311G** level for all the experimentally observed reflection angles fit the experimental ones better with about a 0.01 decrease in the R_w value compared to the Independent Atom Model (IAM). The semiempirical MNDO density performs consistently better than the minimal basis Hartree-Fock density, but is shown to be slightly inferior to the Hartree-Fock density employing split-valence basis sets. The partial atomic charges are also computed and compared to experimental charges derived from the kappa refinement procedure.