Abstract: Different partial charge distribution methodologies (Mulliken, Löwdin, Hirshfeld, Natural Population Analysis, Merz–Kollman Electrostatic Potential) were used for charge determination in manganese and zinc Schiff base complexes that are isostructural analogs. Chemical reliable clusters were chosen on the ground of experimental X-ray data. Packing effect on charges was found to be negligible. All calculation employed non hybrid ab-initio GGA PBE density functional method with conjunction of different basis sets to show small influence of basis set incompleteness. On the ground of chemical bonding theory Hishfeld partial charge definition was found to be most reliable in different situation – different spin states, H–bonding, molecular crystal and clusters.