The OrbNet Denali dataset is a comprehensive training collection used to develop OrbNet Denali, a ML-enhanced semiempirical method for electronic structure calculations. It includes over 2.3 million molecular geometries with corresponding energy labels calculated at the DFT and semi-empirical levels. Based on ChEMBL27 database, it covers a wide range of organic molecules, including various protonation states, tautomers, non-covalent interactions, and common salts. The dataset features key elements (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I) essential to biological and organic systems.