In the paper, mobility isothermal — isochoric kinetic processes of Fe, Co, Ni atoms mobile quantum NEMS self-organization are investigated with computer simulation. The kinetic processes depend on the type of electronic interatomic bonds in different kinematic modes. Self-organization process is simulated for closed systems of atoms in nanopores by synthetic sampling (the Monte Carlo method). A summary of the problem statement and methods of calculation are presented. The objects of study are the NEMS 50 atoms of the iron group (Fe50, Co50, Ni50), placed randomly with a discreteness step 0.02 nm at initial time in nanopore cubic edge with length of 10.00 nm. NEMS relaxation is performed at normal temperature T = 293 K with consideration of the interatomic bonds total energy calculated by the nonlocal density functional. The evolution takes 100,000 steps, which corresponds to the order of one nanosecond duration. Computer experiments on the Monte Carlo method show different modes of self-organization in mobility with strong and weak displacement correlations of atoms NEMS. During the self-organization of the first type, a stable, compact cluster of atoms NEMS with higher binding energy is formed. In the latter case, some fractal islet clusters with lower binding energy are synthesized. Also, atoms NEMS self-organization details of dependencies on their grades and types of electronic bonds are revealed. It is shown that these two chemical factors are subsidiary to a type of NEMS self -organization in comparison with the change of the kinematic regime of Fe group atoms corporate mobility.