AM1 semi-empirical and ab initio calculations were performed on certain synthetic polyamide conjugates of the aglycone of the minor groove binding antibiotic calicheamicin. Geometry optimized conformations and heats of formation were obtained. The binding of the optimized conformations of the drug to both alternating and non-alternating (AT)_n and to (G)_n·(C)_n sequences were studied and the energies of binding were compared to each other. The results can be utilized in the design of novel enediyne-based drugs.