First-principle computations were carried out on the conformational space of trans and cis peptide bond isomers of HCO-Thr-NH2. Using the concept of multidimensional conformational analysis (MDCA), geometry optimizations were performed at the B3LYP/6-31G(d) level of theory, and single-point energies as well as thermodynamic functions were calculated at the G3MP2B3 level of theory for the corresponding optimized structures. Two backbone Ramachandran-type potential energy surfaces (PESs) were computed, one each for the cis and trans isomers, keeping the side chain at the fully extended orientation (chi(1) = chi(2) = anti). Similarly, two side chain PESs for the cis and trans isomers were generated for the (phi = psi = anti) orientation corresponding to approximately the, L backbone conformation. Besides correlating the relative Gibbs free energy of the various stable conformations with the number of stabilizing hydrogen bonds, the process of trans f cis isomerization is discussed in terms of intrinsic stabilities as measured by the computed thermodynamic functions.