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The design of single flux-quantum (SFQ) circuits requires well-defined inductances. In many cases these are created by irregular geometries and a computer-aided design tool is necessary for inductance calculations. This becomes a challenging task in cases where no ground plane is used and thus three-dimensional calculations are required. For this purpose, InductEx was developed and verified successfully for simple structures. In this work we take the next step and demonstrate the applicability of InductEx to the design of rapid single flux-quantum (RSFQ) cells. We use InductEx for inductance modeling as an integral part of the design cycle for an RSFQ cell with flux quantum transfer via mutual inductance and for a DC-reprogrammable logic circuit with similar inductive coupling. The relation between coupling factor and self-inductance is optimized in the circuit layout. All coupling structures are duplicated in SQUID modulation test circuits to measure and verify calculation accuracy. We find excellent agreement between the calculated and measured inductance values. Furthermore, the operational area of the basic cell is determined and compared with similar investigations reported earlier. Based on this comparison we conclude that InductEx is a valuable inductance design tool, and that mutual coupling in structures using ground plane holes and RSFQ-compatible self-inductances can be modeled and designed reliably.