We report the detailed computational study of several perchlorinated cyclohexasilane (Si6Cl12)-based inverse sandwich compounds. It was found that regardless of the donor ligand size and charge, for example, Cl- and CN- anions or neutral HCN and NCPh nitriles, their coordination to the puckered Si6Cl12 ring results in its flattening. The NBO and CDA studies of the complexes showed that coordination occurs due to hybridization of low-lying antibonding σ*(Si-Cl) and σ*(Si-Si) unoccupied molecular orbitals (UMOs) of Si6Cl12 and occupied molecular orbitals (OMOs) of donor molecules (predominantly lone-pair-related), resulting in donor-to-ring charge transfer accompanied by complex stabilization and ring flattening. It is known that the Si6 ring distortion results from vibronic coupling of OMO and UMO pairs (pseudo-Jahn-Teller effect, PJT). Consequently, the Si6 ring flattening most probably occurs due to suppression of the PJT effect in all of the studied compounds. In this paper, the stabilization energy E(2) associated with donor-acceptor charge transfer (delocalization) was estimated using NBO analysis for [Si6Cl12·2Cl]2-, [Si6Cl12·2(NC)]2-, Si6Cl12·2(NCH), and Si6Cl12·2(NCPh). It was found that the polarizability of the donor might significantly affect the stabilization energy value (Cl- > CN- > HCN). For the neutral complexes, the E(2) value is correlated with the charge on the nitrogen atoms. All of these factors, that is, specific donor E(2) value, charge transfer, complex MO energy diagrams, and so on, should be taken into account when choosing the ligands suitable for forming Si-based 1D compounds and other nanoscale materials.