A computational analysis has been carried out to determine the configurational preference of a pair of 5-( trans -4-heptylcyclohexyl)-2-(4-cyanophenyl) pyrimidine (HCCPP) molecules with respect to translatory and orientational motions. The CNDO/2 method has been employed to evaluate the net atomic charge and atomic dipole components at each atomic centre of the molecule. Configuration energy has been computed using Rayleigh-Schrodinger perturbation method. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at phase transition temperature using Maxwell-Boltzmann formula. An attempt has been made to identify the most probable configuration at phase transition temperature. Further, the flexibility of various configuration has been studied in terms of variation of probability due to small departures from the most probable configuration. On the basis of stacking, in-plane, and terminal interaction energy calculations, all possible geometrical arrangements of a molecular pair have been considered. An attempt has been made to identify the most probable configuration at phase transition temperature.