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The accurate prediction of suitable chiral stationary phases (CSPs) for resolving the enantiomers of a given compound poses a significant challenge in chiral chromatography. Previous attempts at developing machine learning models for structure-based CSP prediction have primarily relied on 1D SMILES strings\footnote{The simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings.} or 2D graphical representations of molecular structures, and have met with only limited success. In this study, we apply the recently developed 3D molecular conformation representation learning algorithm, which uses rapid conformational analysis and point clouds of atom positions in 3D space, enabling efficient chemical structure-based machine learning. By harnessing the power of the rapid 3D molecular representation learning and a dataset comprising over 300,000 chromatographic enantioseparation records sourced from the literature, our models afford notable improvements for the chemical structure-based choice of appropriate CSP for enantioseparation, paving the way for more efficient and informed decision-making in the field of chiral chromatography.