One important element of molecular structure is partial planar structures, such as those arising from π-conjugation, including carbon-carbon double bonds in alkenes, peptide bonds, and aromatic rings. However, constraining only bond lengths and angles, as in the previously introduced FB-ENM, is insufficient to fix such planar structures. To address this, the present study extracts the atomic groups forming planar structures in all reference structures and fixes the planar structures by strongly constraining all atom pairs within each of these groups. If atoms 1, 2, 3, and 4, which are included in the same plane and sequentially linked by bonds, have a trans conformation in some reference structures and a cis conformation in other reference structures with respect to their dihedral angle, the plane containing atoms 1, 2, and 3 and the plane containing atoms 2, 3, and 4 are considered different planes.