Kaolinite as a remarkable industrial raw material has notable structural features despite its simple chemical composition (Al2O3·2SiO2·2H2O). We report here a systematic development of a coordination chemical model for the [6Al-6(OH)] honeycomb-like unit of kaolinite's octahedral sheet, which was proposed to be the adsorption site for small molecules from earlier studies. The coordination environment of the Al(3+) ions was completed with outer sphere groups from both octahedral and tetrahedral sheets. Dangling bonds were terminated by additional Al(3+) and Si(4+) ions with hydroxide and oxide groups from the second coordination sphere versus simple protonation. A cage of Na(+) and Mg(2+) ions rendered the computational model to be charge neutral. In this exfoliated kaolinite model, the inner hydroxide groups and the adjacent Al(3+) ions have compositionally the most complete environments with respect to the crystal structure. Thus, their atomic positions were used as a benchmark for the level of theory dependence of the optimized structures. We evaluated the performance of a representative set of density functionals, basis sets, point-charges, identified pitfalls and caveats. Importantly, the structural changes during optimization of periodic and cluster models suggest pliability for the exfoliated kaolinite layers, which is influenced by the external chemical environment.