Using a noncontact atomic force microscope, we track and manipulate the position of single electrons confined to atomic structures engineered from silicon dangling bonds on the hydrogen terminated silicon surface. An attractive tip surface interaction mechanically manipulates the equilibrium position of a surface silicon atom, causing rehybridization that stabilizes a negative charge at the dangling bond. This is applied to controllably switch the charge state of individual dangling bonds. Because this mechanism is based on short range interactions and can be performed without applied bias voltage, we maintain both site-specific selectivity and single-electron control. We extract the short range forces involved with this mechanism by subtracting the long range forces acquired on a dimer vacancy site. As a result of relaxation of the silicon lattice to accommodate negatively charged dangling bonds, we observe charge configurations of dangling bond structures that remain stable for many seconds at 4.5 K. Subsequently, we use charge manipulation to directly prepare the ground state and metastable charge configurations of dangling bond structures composed of up to six atoms.