We assess transformation matrices in the combined quantum mechanical and molecular mechanical method based on generalized hybrid orbitals (GHO). In addition to the previous ones, we examine a restrained transformation matrix based on the assumption that all coefficients of the p-hybridized orbitals are uniform and each hybridized orbital points toward a vertex of a tetrahedron. It is clearly shown that the new implementation improves the accuracy of the GHO method reducing the error concerning the Pauli repulsion about auxiliary orbitals. (C) 2009 Elsevier B.V. All rights reserved.