We created five comparison analogues for each molecule. The same logic as in the previous experiment was applied (Figure ), resulting in a total of 80 1:1 comparisons between correct and incorrect molecules. Additionally, we performed a control experiment comparing every molecule with each other within the same category as done in Level 1. Figure presents a heatmap illustrating the percentages of correctly identified molecules in the 1:1 matching results, while Supplementary Figure shows the control results, displaying a consistent probability centered around 0.5. In this experiment, comparable accuracy to the level 1 decoys was achieved. This time MNova and ACD (91%) with EucDist-NN and HungDist-Trunc, respectively delivered the best performance, followed by DFT (86%) and ML (85%) using HungDist-NN. Here the same trends were observed as for Level 1. MinSum exhibited the weakest performance for all simulation techniques. In combination with peak truncation as padding strategy it gave the most optimal results. Zero-padding performed consistently weaker compared to the other padding strategies.