The geometric configuration of carbonic anhydrase II inhibitor molecule was optimized by means of Gaussian 03 quantum chemistry calculational program package to obtain the 3D-hydrogen-suppressed molecular graph, the standard orientation of the atomic groups in a molecule and the single point energies of the molecule, and this 3D-hydrogen-suppressed molecular graph is simulate into a space frame element system to solve the fundamental frequencyω₀ of the molecular system. The the fundamental frequencyω₀ is a dynamic structure characterstic parameters of the molecular system to get for this paper as the parameters of the 3D-QSAR model along with the nodal sequence number N_Xm in the first ring circuit structure, the phyletic number N_e of elements in the assistant group and the absolute value E₀ of molecular single point energies. The multiple correlation coefficient r²＞0.99, the standard deviation s＜0.14, the mean deviation is less than 0.112.

Key words: carbonic anhydrase II inhibitor, chemical-bond space element, molecular structure inherent frequency, 3D-QSAR