An integral equation for rigid-body molecules with respect to site-density distribution function under arbitrary external fields is derived by the density-functional theory. Using a grand canonical partition function of molecular systems, we extend original Percus' idea to molecular fluids. The extended Percus' idea provides a relation between the site-site pair distribution function and site-density distribution function under an external field composed of the site-site interaction potentials of a molecule fixed at the origin. The site-density integral equation combined with the extended Percus' relation to molecular fluids gives a closure relation of reference interaction site model equation. The site-site pair distribution functions of homonuclear diatomic Lennard-Jones fluids obtained by the integral equation agree well with those of Monte Carlo simulation.