The electronic spectra of three rhombic type I blue copper proteins, nitrite reductase, pseudoazurin, and cucumber basic protein, have been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2, method). The six lowest excitations have been calculated and assigned with an error of less than 1800 cm(-1). The singly occupied orbital in the ground-state forms a strongly covalent antibond between the copper ion and the thiolate group of the cysteine ligand with a mixture of sigma and pi character. This is in contrast to the axial type 1 copper protein plastocyanin which has an almost pure Cu-S-Cys pi interaction. The two brightest fines in the absorption spectrum originate from transitions to the corresponding sigma (similar to 460 nm) and pi (similar to 600 nm) bonding orbitals. The relative intensity of these two lines is determined by the character of the ground-state orbital. It is possible to obtain a structure closely similar to the one found in nitrite reductase by geometry optimizations with the hybrid density functional B3LYP method in vacuum. It is a tetragonal structure with bands of mainly sigma character to the four ligands like normal square-planar Cu(II) complexes, but the cysteine thiolate,group donates much charge to the copper ion and thereby makes the structure strongly distorted toward a tetrahedron. Both this structure and a trigonal pi-bonded structure, which also can be obtained for all complexes and is an excellent model of plastocyanin, are equilibrium structures (although usually not with the same ligand models). They have virtually the same energy (within similar to 7 kJ/mol), and the barrier between them is low. Therefore, small differences in the structure and electrostatics of different proteins may lead to stabilization of one or the other of the structures. The results indicate that axial type 1 proteins have a trigonal structure with an almost pure Cu-S-Cys pi bond, whereas rhombic type I proteins have tetragonal structures with a significant a character in this bond. Type 1.5 and 2 copper-cysteinate proteins arise when the tetragonal structure becomes more flattened than in nitrite reductase, probably by the inclusion of stronger (type 1.5) and more (type 2) ligands.