The geometries and electronic structures of selenolate-protected Au nanoclusters, Au24(SeR)20 and Au20(SeR)16, and their thiolate analogues are theoretically investigated with DFT and SCS-MP2 methods, to elucidate the electronic structure of their unusual Au8 core and the reason why they have the unusual entangled "staple-like" chain ligands. The Au8 core is understood to be an [Au4](2+) dimer in which the [Au4](2+) species has a tetrahedral geometry with a closed-shell singlet ground state. The SCS-MP2 method successfully reproduced the distance between two [Au4](2+) moieties, but the DFT with various functionals failed it, suggesting that the dispersion interaction is crucial between these two [Au4](2+) moieties. The SCS-MP2-calculated formation energies of these nanocluster compounds indicate that the thiolate staple-like chain ligands are more stable than the selenolate ones, but the Au8 core more strongly coordinates with the selenolate staple-like chain ligands than with the thiolate ones. Though Au20(SeR)16 has not been reported yet, its formation energy is calculated to be large, suggesting that this compound can be synthesized as a stable species if the concentration of Au(SeR) is well adjusted. The aurophilic interactions between the staple-like chain ligands and between the Au8 core and the staple-like chain ligand play an important role for the stability of these compounds. Because of the presence of this autophilic interaction, Au24(SeR)20 is more stable than Au20(SeR)16 and the unusual entangled ligands are involved in these compounds.