The effect of interactions of Li+, Na+ and K+ cations with two configuration of the A–G mispairs, AantiGanti and AsynGanti, on the geometries and hydrogen bond energies have been studied at the MP2/6-311++G(d,p) level of theory. For each ion type, the most stable complex in AantiGanti and AsynGanti configurations are related to binding cation to N3 atom of guanine and N1 atom of adenine, respectively. The AantiGanti configuration is higher in the absolute values of binding energy than the AsynGanti configuration, indicating that AantiGanti configuration is more stable than AsynGanti ones. The results indicate that the strength of hydrogen bonds depends on the type and position of cations in considered systems. The values of hydrogen bonding energies estimated by the EML formula in AantiGanti mismatch are higher than AsynGanti case. The influences of cations binding in hydrogen bond strength are confirmed by the results of natural bond orbital (NBO) and atoms in molecules (AIM) analyses