Theoretical calculations are carried out to understand the geometric and electronic properties of the 4-nitro-2,5-bis(4-mercaptophenylethynyl)phenylamine molecule, which has been demonstrated to behave like a resonant tunneling diode under an external bias voltage. Results from density functional and Hartree-Fock theory show conflicting planar and nonplanar ground-state geometries, respectively. To underscore the effect of the molecular conformation on the electronic structure of the molecular devices, the potential energy surface of this molecule was calculated under the rigid rotor model. The results suggest that even a small perturbation can lead to a significant increase in the energy gaps between the highest occupied and lowest unoccupied energy levels. The electronic transport behavior in this molecule is analyzed from the electronic structure and spatial orientations of the molecular orbitals.