MNDO calculations were carried out to determine reactant complexes and transition states of the $S_N2$ reactions of $CH_3X;+;Y^-;{ o};CH_3Y;+;X^-$ where X = F, Cl, CN and Y = CN, OH, F, Cl. The leaving group ability was found to vary inversely with the activation barrier, which in turn was mainly ascribable to the deformation energies accompanied with bond stretching of C-X bond and inversion of $CH_3$ group. The nucleophilicity was shown to be in the order $Cl^->F^->OH^->CN^-$ but the effect on the activation barrier was relatively small compared with that of the leaving group. The bond breaking and bond formation indices and energy decomposition analysis showed that the TS for the reaction of $CH_3$Cl occurs in the early stage of the reaction coordinate relative to that of $CH_3$F. It has been shown that the potential energy surface (PES) diagrams approach can only accommodate thermodynamic effects but fails to correlate intrinsic kinetic effects on the TS structure.