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In the title compound, [Co(C8H5N5O3)(C12H8N2)(H2O)]·3H2O, a tridentate 2-amino-7-methyl-4-oxidopteridine-6-carboxyl­ate ligand, a bidentate ancillary 1,10-phenanthroline (phen) ligand and a water mol­ecule complete a distorted octa­hedral geometry around the CoII atom. The pterin ligand forms two chelate rings. The phen and pterin ring systems are nearly perpendicular [dihedral angle = 85.15 (8)°]. N—H...O, O—H...N and O—H...O hydrogen bonds link the complex mol­ecules and lattice water mol­ecules into a layer parallel to (001). π–π stacking contacts (involving phen–phen and pteridine–pteridine) are also observed [centroid–centroid distances = 3.670 (2), 3.547 (2), 3.698 (2) and 3.349 (2) Å].
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