This paper reports on a novel application of a ligand field model for the detection of the local molecular structure of a coordination complex. By diagonalizing the complete energy matrices of the electron-electron repulsion, the ligand field and the spin-orbit coupling for the d(5) configuration ion in a trigonal ligand field, the local distortion structure of the (MnO6)(10-) coordination complex for Mn2+ ions doped into CaCO3, have been investigated. Both the second-order zero-field splitting parameter b(2)(0) and the fourth-order zero-field splitting parameter b(4)(0) are taken simultaneously in the structural investigation. From the electron paramagnetic resonance (EPR) calculations, the local structure distortion, Delta R=- 0.169 angstrom to - 0.156 angstrom, Delta theta = 0.996 to 1.035 for Mn2+ ions in calcite single crystal, Delta R= -0.185 angstrom to - 0.171 angstrom, Delta theta = 3.139 degrees to 3.184 degrees for Mn2+ ions in travertines, and Delta R= - 0.149 angstrom to - 0.102 angstrom, Delta theta = 0.791 degrees to 3.927 degrees for Mn2+ ions in shells are determined, respectively. These results elucidate a microscopic origin of various ligand field parameters which are usually used empirically for the interpretation of EPR and optical absorption experiments. It is found that the theoretical results of the EPR and optical absorption spectra for Mn2+ ions in CaCO3 are in good agreement with the experimental findings. Moreover, to understand the detailed physical and chemical properties of the doped CaCO3, the theoretical values of the fourth-order zero-field splitting parameters b(4)(0) for Mn2+ ions in travertines and shells are reported first.