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Тhe adequacy of chemical property predictions strongly depends on the structure representation, including the proper treatment of the tautomeric and isomeric forms. A combination of an in-house developed open-source tool for automatic generation of tautomers, Ambit-Tautomer, based on H-atom shift rules and standard quantum chemical (DFT) calculations is used for a detailed investigation of the possible geometric isomers, conformers and tautomers of unsubstituted and <i>para</i>-substituted phenylhydrazones, systems with experimentally observed unusual <i>para</i>-substituent effects on the intramolecular hydrogen bond (IMHB) for <i>E</i>-isomers of the compounds. The computational results show that the energetically preferred <i>E</i>-isomers are characterized by stronger IMHBs than the corresponding <i>Z</i>-isomers. The HN–N=C–C=N molecular fragment in the <i>E</i>-configurations is less sensitive to the substitution effect than the HN–N=C–C=O fragment in the isomers with <i>Z</i>-configuration. A probable reason for this decreased sensitivity of <i>E-</i>isomers to phenyl ring substitution is the more efficient conjugation and charge distribution in the HN–N=C–C=N fragment.