<p>The electronic structure calculation of multi-molecular non-bonded interaction problem is of vital importance in various biological process, while performing the calculation on quantum computers appears to be challenging and remains largely unexplored. In this work, we study the ground state calculation of homogeneous and heterogeneous hydrogen bond system, i.e., water dimer and water–ammonia complex, under the framework of variational quantum eigensolver with hardware-efficient ansatz (HEA). Also, we propose a general modification scheme on HEA circuit by inverting the second half of the circuit. Our result suggests that it is possible to solve the electronic structure problem of those complicated non-bonded system with modified HEA. It improves the accuracy of ground state calculation, recovers the equilibrium geometry of molecules, and efficiently mitigates the barren plateau problem in HEA. Furthermore, the modified HEA is more capable of preserving the symmetry of Hamiltonian, including electron number, <i>z</i>-spin and total spin number, which are essential for the study of electronic structure.</p>