We present a new model of intermolecular interactions taking into account the anharmonic coupling between the tunneling inter-conformation molecular mode and the long-range crystalline displacement. The coupling of the anharmonic phonon modes and local mode disordering causes the non-centrosymmetry in the electrostatic potential distribution. Symmetry of the molecular disorder has a point group C-3 The model is explained within a framework of tunneling soft mode conception and including molecular dynamics ab initio molecular dynamics simulations. The optical second harmonic generation (SHG) sensitive to local potential non-centrosymmetry is used as an experimental method for detection of manifestation the intermolecular disordering. The results are considered to be general importance for systems with electron-phonon anharmonic ordering, which is common to many organic materials.