Atomically precise monolayer protected clusters are molecules comprising a few-atom cluster core of a noble metal, typically Au or Ag, surrounded by a protective layer of ligands, exhibiting many special optical, electrical, catalytic, and magnetic properties, and are emerging as important materials in biology, medicine, catalysis, energy conversion and storage, and sensing. The structural diversity of these clusters or aspicules, as we definitively term them, meaning shielded molecules, combining the Greek word aspis (shield) with molecule, is rapidly increasing due to new compositions and modification routes such as ligand-exchange, alloying, or supramolecular functionalization. We present a structural analysis of the most stable cluster of this kind, Au25(SR)18, and propose a Borromean rings diagram for the cluster, showing its topological configuration of three interlocked (Au8S6)-rings. This simplified two-dimensional diagram is used to represent its structure and modifications via ligand or metal atom substitution uniquely. We enumerate and name its isomers with two-ligand or metal atom substituents. Among the several structural insights obtained, the identification of the Borromean rings-interlocked configuration in Au25(SR)18 may explain its high geometric stability and indicate a possible general unified structural viewpoint for these clusters without the division between core and staple motifs. On the basis of our structural analysis, we developed a structure-based nomenclature system that can be applied to both describe and understand the structure and modifications of gold thiolate clusters, AuM(SR)N, and is adaptable to the general case of MM(X)N (M, metal and X, ligand). The application of structural analysis and diagrams to Au38(SR)24 and Au102(SR)44, revealing the possible formation of the cluster core by stacking or growth of rings of metal atoms, is also presented. © 2015 American Chemical Society.