The stacking energies between natural nucleobases and a universal base of 3-nitropyrrole (3-NP) were calculated by use of two theoretically independent quantum chemical methods, namely, molecular orbital (MO) and density function theory (DFT) calculations. The parameters required for molecular mechanics calculation of 3-NP were obtained by use of a software of Direct Force Field and used to evaluate the stacking energy of the complexes formed between 3-NP and canonical four nucleobases. Dependence of the twist angle between the two stacked bases on the stacking energy was studied in great detail.