Electron transport through a single molecule is determined not only by intrinsic properties of the molecule but also by the configuration of the molecule with respect to the lead electrodes. Here, we show how electron transport through a single H2TPP molecule is modulated by the configuration change. The Coulomb stability diagram of a single H2TPP molecule transistor exhibited a few different patterns in different measurement scans. Furthermore, the sample exhibited a negative differential resistance, the magnitude of which changed together with the pattern of the Coulomb stability diagram. Such a behavior can be explained by rotation of the molecule with anisotropic molecular orbitals in the gap electrodes induced by electrical stresses. Moreover, we found that energy separations between molecular orbitals are also affected by the rotation, confirming that metal-molecule interface configuration renormalizes electronic levels in the molecule.