The Geant4-based Monte Carlo model for Heavy-Ion Therapy (MCHIT) was extended to study the patterns of energy deposition at sub-micrometer distance from individual ion tracks. Dose distributions for low-energy (1)H, (4)He, (12)C and (16)O ions measured in several experiments are well described by the model in a broad range of radial distances, from 0.5 to 3000 nm. Despite the fact that such distributions are characterized by long tails, a dominant fraction of deposited energy (∼80%) is confined within a radius of about 10 nm. The probability distributions of clustered ionization events in nanoscale volumes of water traversed by (1)H, (2)H, (4)He, (6)Li, (7)Li, and (12)C ions are also calculated. A good agreement of calculated ionization cluster-size distributions with the corresponding experimental data suggests that the extended MCHIT can be used to characterize stochastic processes of energy deposition to sensitive cellular structures.