The relaxation transformation of the nanoelectromechanical system (NEMS) of nanobots in the face-center-cubic (fcc) structure of 4d-transition metals (Ru, Rh, Pd) is considered in this paper. The objects of study are 256-atom cube-shaped clusters with fcc lattices limited by planes of (100) at a temperature of 298 K and zero pressure. These clusters have transitioned to the entangled two-electron coherent excited state of the nanobot quantum NEMS under the soft X-ray attosecond pulse. The calculation of interaction energy inside nanobots are performed by the nonlocal density-functional theory method with the orbital envelope approximation. It is shown that residual energy accumulation in the nanobots is the result of NEMS self-organization though special intermediate nonequilibrium quasistationary states with specific one- and two-particle distributions. The nanobot quantum NEMS is formed by two-electron excitation process during an attosecond absorption of the primary pulse. At the first stage of relaxation, the nanobot is expanded while keeping one and two-particle distribution of nuclei. For all the metals (Ru, Rh, Pd), the first mode of spontaneous nanobot self-organization while transitioning into a cuboid with convex-concave faces occurs in the first picosecond. The second mode of nanobot selforganization occurs after tens of picoseconds due to a coherent shear transformation of nanobot bulk and boundary parts. It remains resistant to energy fluctuations. Energy stored in nanobots corresponds to soft X-ray energy quanta 950 eV (Ru₂₅₆), 1058 eV (Rh₂₅₆) и 425 eV (Pd₂₅₆).