The nuclear magnetic resonance (NMR) frequency of a single qubit structure of Kane’s solid-state quantum computer is investigated by using the perturbation theory. With higher-order excited states (up to 3d modes) included in our calculation, the perturbation frequencies and energies are obtained numerically. To compute for arbitrary A gate geometries, the perturbation potential inside the qubit structure is determined through an electromagnetic simulation method. Calculations show that the potential distributions for realistic A gate geometries are far from linear ones. Our results show that the A gate voltage has a much more effective control over the NMR frequency of the phosphorus nucleus than that previously shown. Using our method, arbitrary A gate structures of any shapes or geometries can be engineered for the realization of a solid-state scalable quantum computer. We also investigate an alternative A gate structure using SiGe as the insulation barrier. Our study shows that this A gate structure offers a much more efficient utilization of the control voltage than the original A gate structure using SiO2 as the insulation barrier.