The phase estimation algorithm is crucial for computing the ground-state energy of a molecular electronic Hamiltonian on a quantum computer. Its efficiency depends on the overlap between the Hamiltonian's ground state and an initial state, which tends to decay exponentially with system size. We showcase a practical orbital optimization scheme to alleviate this issue. Applying our method to four iron-sulfur molecules, we achieve a notable enhancement, up to 2 orders of magnitude, compared to localized orbitals. Furthermore, our approach yields improved overlaps in cytochrome P450 enzyme models.