Inorganic nanoparticles, including metals, semiconductors and metal oxides, comprise a common set of structures exhibiting an inorganic core ‘passivated’ by an organic shell. Ligated inorganic nanoparticles currently provoke widespread fundamental interest in their structural, optical and magnetic properties, which differ fundamentally from bulk counterparts. These nanomaterials are already finding applications in biology, medicine, solar energy, and display panels. 1-6 Conjugating inorganic nanoparticles with organic (biological) material for applications in nanobiology and nanomedicine creates significant challenges for controlling the effects on the environment, particularly regarding toxicity. Chemical reactions of almost identical substances can lead to drastically different outcomes in a biological environment. As a simplistic example one can consider the case of ethanol vs. methanol. Ethanol (CH3CH2OH) can be consumed by humans while even a small dose of methanol (CH3OH) can be fatal, yet the difference between the molecular formulas of these substances is just the smallest meaningful hydrocarbon unit CH2. This illuminates the fact that minute differences in the size and structure of molecular compounds can have drastically different end effects in a biological environment due to the way the compounds start to react with the environment. In recent years, gold nanoparticles covered by ligands that make them water-soluble have become a popular target for research in nanobiology and nanomedicine. 1,2 In most cases up to now, colloidal nanoparticles (5 nm and larger) have been used for sensing and photothermal applications. However, this class of gold-based nanomaterials still has large uncertainties regarding the atomic composition of the nanoparticle surface and particularly the metal-ligand interface. A simple example illuminates the facts. The density of atoms in the fcc lattice of macrosocopic gold metal is about 59 atoms/nm3. This means that a spherical colloidal gold nanoparticle with radius of 5 nm has about 3850 atoms. Even in a sample of extremely narrow range of diameters ranging from 5.25 nm to 4.75 nm (+/- 5% of the mean) the particles will have anywhere between 3300 and 4750 atoms, and their surface area can differ up to 20%. It is clear that such particles are not suitable for applications that would need molecularly precise size, structure and shape of the metal nanoparticle and precise knowledge of the composition of its organic surface. In 1994, Brust, Schiffrin and coworkers published a landmark synthesis recipe on how to prepare thiol(ate)-stabilized small gold nanoparticles of about 2 nm in size. 7 This paper started a completely new field which has now matured to studies of several “atom-precise” or “molecularly precise” gold-thiolate compounds for which molecular formulas Aux(SR)y can be written and the substances in most cases have a good ambient stability allowing for storage and later use.8 Atomic structures of the gold core and the thiolate layer have been resolved for many of these compounds, opening doors for detailed density functional theory (DFT) simulations of their properties. This Perspective discusses developments in understanding the structure and properties of one of such compounds, which can be used for site-specific (or “molecularly precise”) targeting of capsid proteins on a viral surface.