We have carried out an analysis of the wave function data for three MHC-peptide complexes: HLA-DRbeta1*0101-HA, HLA-DRbeta1*0401-HA and HLA-DRbeta1*0401-Col. We used quantum chemistry computer programs to generate wave function coefficients for these complexes, from which we obtained both molecular and atomic orbital data for both pocket and peptide amino acids within each pocket region. From these discriminated data, interaction molecular orbitals (IMOs) were identified as those with large and similar atomic orbital coefficient contributions from both pocket and peptide amino acids. The present results correlate well with our previous research where only electrostatic moments were used to explore molecular component interactions. Furthermore, we show a quantum chemical methodology to produce more fine-grained results concerning amino acid behavior in the MHC-peptide interaction.