Abstract The effective π-electron Hamiltonian for the excited molecule has been derived from the singly excited configuration interaction method (SECI) considering Σ-Π interaction. In this paper, the zero-differential overlap (ZDO) approximation has been employed. Then, in SECI scheme, π-π* and σ-σ* configurations interact through the exchange type MO-integrals over π- and σ-MO’s. As the result, only the excited singlet states are modified by Σ-Π interaction. So that the triplet states remain unchanged by this type of interaction. When the ZDO approximation is employed, the effective electron interaction over AO’s, \ ildeγμν, can be derived. It is found that \ ildeγμν’s are represented approximately in terms of topological matrix, so named ‘bond index matrix’.