Using a hydrogen molecule as a test system we demonstrate how to compute the effective potential according to the formalism of the new density functional theory (DFT), in which the basic variable is the set of spherically averaged densities instead of the total density, used in the traditional DFT. The effective potential together the external potential, nuclear Coulomb potential, can be substituted in the Schrodinger like differential equation to obtain the spherically averaged electron density of the system. In the new method instead of one three-dimensional low symmetry equation one has to solve as many spherically symmetric equations as there are atoms in the system.