Quantum computers are expected to perform full-configuration interaction calculations with less computational resources compared to classical ones, thanks to the use of quantum phase estimation (QPE) algorithms. However, only a limited number of QPE-based quantum chemical calculations have been reported even for numerical simulations on a classical computer, and the practical workflow for the QPE computation has not yet been established. In this paper, we report the QPE simulations of the electronic ground and the π-π* excited singlet state of benzene and its chloro- and nitro-derivatives as the representative industrially important systems, with the aid of GPGPU acceleration of quantum circuit simulations. We adopted the pseudo-natural orbitals obtained from the MP2 calculation as the basis for the wave function expansion, the CISD calculation within the active space to find the main electronic configurations to be included in the input wave function of the excited state, and the technique to reduce the truncation error of the calculated total energies. The proposed computational workflow is easily applicable to other molecules and can be a standard approach for performing QPE-based quantum chemical calculations of practical molecules.