•The efficient post-multicomponent synthesis of the chloride salt of 1-(3,6-dihydropyrimidin-2-yl)urea hydrated based on Biginelli´s products is described.•The structure of the compound was confirmed by single crystal X-ray analysis in conjunction with HRMS, FTIR and NMR spectroscopy techniques.•Intermolecular interactions were examined using X-ray diffraction results and compared with those obtained by Hirshfeld surface analysis.•Hirshfeld surfaces and 2D fingerprint plots were used to clarify intermolecular interactions in the crystal lattice of the title compound. The postmulticomponent synthesis and crystal structure of 1-(3,6-dihydropyrimidin-2-yl)urea salt, 5-(ethoxycarbonyl)-4-methyl-6-phenyl-2-ureido-3,6-dihydropyrimidin-1-ium chloride monohydrate, C15H21O4N4+·ClH2O; structurally related to dihydropyrimidinon-2-ylurea-type RNA-binding ligands is reported. The structure of this new type of hydrated organic salt was investigated by FT-IR, NMR and HRMS methods, and its structure was unambiguous confirmed using X-ray single crystal diffraction techniques. X-ray diffraction analysis show that this material crystallizes in the monoclinic space group P21/c (N°14), Z = 4 with the 3,6-dihydropyrimidin-1-ium ring in a pucked-boat conformation attached to the ester group in an s−trans relationship. The molecular structure and crystal packing are stabilized by intermolecular N − H···O, O − H···O, and N − H···Cl hydrogen bonds formed an infinite three-dimensional (3D) network. Furthermore, the Hirshfeld surface analysis confirms that the most important contributions for the crystal packing are the C − H···H (52.5%), C − H···C (17.8%), C − H···O (15.4%) and N − H···Cl (5.80%) surface contacts. Display omitted