Diffusion coefficient depends on temperature, pressure, reduced mass of colliding particles and collision cross section. The presented method is designed to calculate the diffusion coefficient in loose systems containing molecules with relatively complicated colliding trajectories. It is a combination of the Chapman-Enskog theory and the molecular dynamics calculation. The Chapman-Enskog theory provides the relation between the diffusion coefficient and the collision cross section which is the result of multiple integration of the scattering angle of all possible initial conditions of the collision. The scattering angle is obtained by numerical integration of the Newton’s equation of motion with previously selected initial conditions. The proposed method has been verified for the simple system of a lead atom diffusion in rare gases and the results were compared to those of two other theoretical methods.