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In the title compound, C(5)H(8)N(3)O(+)·ClO(4) (-)·C(5)H(7)N(3)O·H(2)O, each perchlorate anion is paired with a protonated cationic 2-amino-6-methyl-pyrimidin-4(1H)-one and another non-protonated entity of the same organic pyrimidinone. The crystal structure is stabilized by N-H⋯O(org), N-H⋯O(water), N-H⋯O(ClO4), O-H⋯O(ClO4), N-H⋯N and C-H⋯O(ClO4) hydrogen bonds between the anions, organic entities and water mol-ecules. Inter-molecular π-π stacking inter-actions between neighbouring organic rings are observed with a face-to-face distance of 3.776 (2) Å, and O-H⋯O hydrogen bonds link the perchlorate anions and the water mol-ecules into chains along the b-axis direction. The perchlorate anion and the inter-stitial water mol-ecule are disordered over two mutually incompatible positions with a common occupancy ratio of 0.678 (16):0.322 (16).

2-Amino-4-methyl-6-oxo-3,6-dihydropyrimidin-1-ium perchlorate–2-amino-6-methylpyrimidin-4(1H)-one–water (1/1/1)