The Q(y) excitation energies of the 96 chlorophyll molecules in photosystem I of Synechococcus elongatus, both in and out of their protein environments, were obtained by using the semiempirical INDO/S method and the crystal structure geometries. The dipole-dipole approximation was used to calculate the coupling between the Q(y) states of chlorophylls; in the case of closely separated chlorophylls INDO/S dimer calculations were used to determine the couplings. The effective Hamiltonian for chlorophyll Q(y) excitations was constructed, enabling tentative assignment of red chlorophylls and calculation of the absorption spectrum of PSI.