Methods, systems and apparatus for implementing a target two-qubit quantum logic gate on a first qubit and second qubit using a tunable qubit coupler. In one aspect, a method includes generating a control signal for the target two-qubit quantum logic gate according to a control model, wherein the control model comprises a controlled-Z operator and a swap operator that are non-orthogonal; and applying the control signal to the first qubit, second qubit and tunable qubit coupler.