A detailed theoretical study of the electronic and transport properties of a single atom transistor, where a single phosphorus atom is embedded within a single crystal transistor architecture, is presented. Using a recently reported deterministic single-atom transistor as a reference, the electronic structure of the device is represented atomistically with a tight-binding model, and the channel modulation is simulated self-consistently with a Thomas-Fermi method. The multi-scale modeling approach used allows confirmation of the charging energy of the one-electron donor charge state and explains how the electrostatic environments of the device electrodes affects the donor confinement potential and hence extent in gate voltage of the two-electron charge state. Importantly, whilst devices are relatively insensitive to dopant ordering in the highly doped leads, a ∼1% variation of the charging energy is observed when a dopant is moved just one lattice spacing within the device. The multi-scale modeling method presented here lays a strong foundation for the understanding of single-atom device structures: essential for both classical and quantum information processing.