The bare M and ligand-protected nanoparticles M(25)(SR) and M(13)(PR)(10)Cl (M = Au, Ag, Cu) are investigated using the density functional theory. There are strong interactions between the metal core atoms and the ligands. It is found that the electronic structures agree well with the Jellium model for gold and copper nanoparticles. The superatoms's S and P orbitals are shown. However for silver ones, as the adding of the ligands, the S orbital of the nanoparticle disappears. The binding energy of these nanoparticles are also obtained by our calculation. The Au nanoparticles are most stable, the Cu ones take second place, and the Ag ones are the third stable. Our results could be essential for further understanding of the properties of ligand-protected isolated superatoms.