Functionalized metal nanoparticles (NPs) have been proposed as promising radiosensitizing agents for more efficient radiotherapy treatment using photons and ion beams. Radiosensitizing properties of NPs may depend on many different parameters (such as size, composition, and density) of the metal core, the organic coatings, and the molecular environment. A systematic exploration of each of these parameters on the atomistic level remains a formidable and costly experimental task, but it can be addressed by means of advanced computational modeling. This paper describes a detailed computational procedure for construction and atomistic-level characterization of radiosensitizing metal NPs in explicit molecular media. The procedure is general and is extensible to many different combinations of the core, coating, and environment. As an illustrative and experimentally relevant case study, we consider nanometer-sized gold NPs coated with thiol-poly(ethylene glycol)-amine molecules of different length and surface density and solvated in water at ambient conditions. The radial distribution of different atoms in the coatings as well as distribution and structural properties of water around the coated NPs are analyzed and linked to radiosensitizing properties of the NPs. It is revealed that the structure of the coating layer on the solvated NPs depends strongly on the surface density of ligands. At surface densities below ∼3 molecules/nm2 the coating represents a mixture of different conformation states, whereas elongated "brush"-like structures are formed at higher densities of ligands. The water content in denser coatings is significantly lower at distances from 1 nm up to 3 nm from the gold surface depending on the length of ligand molecules. Such dense and thick coatings may suppress the production of hydroxyl radicals by low-energy electrons emitted from the metal NPs and thus diminish their radiosensitizing properties. The presented computational framework provides precise information for a quantitative atomistic-level description of the structural properties of coated metal NPs in biologically relevant environments and so may form a basis for future developments to achieve a more realistic description of irradiation-driven chemistry effects in the vicinity of coated metal NPs.