Conformational dynamics can define the function of organocatalysts. While the accepted mechanism of Schreiner's catalyst features a double hydrogen bond to the substrate that only forms with the anti-anti conformation of its central thiourea group, our electronic-structure theory study reveals that binding of the model substrate methyl vinyl ketone prefers syn-anti conformations. We find a new mechanism featuring π stacking interactions and highlight the need for extensive structure searches for flexible molecules, especially when aiming for structure-based design of catalytic activity.