The criterion of maximum overlap with the Huzinaga’s MINI basis functions as well as the ‘‘physical’’ orthogonalization concept are used to rationalize the standard atomic charges calculated within repre- sentation of extended basis sets and to compare charge distributions calculated using different basis sets. The generalization of ‘‘physical’’ orthogonalization approach on natural orbitals is introduced and briefly discussed. Numerical results fully validate the presented methodology identifying the newly proposed atomic charges as an interesting alternative to classical Mulliken’s and Löwdin’s population analyses