The N-15{F-19} REDOR NMR spectra of two fluorolumazines complexed to the 1-MDa beta(60) capsid of lumazine synthase have been obtained at 20.3 and 50.7 MHz. Distances from CF3 groups of the ligands to six side- and main-chain nitrogens have been measured. These distances were used in combination with the X-ray crystal coordinates of wild-type lumazine synthase, complexed to a related substrate ligand, in a series of distance-restrained molecular dynamics simulations. The result is a model of the binding site of lumazine synthase that has sufficient detail to predict the absolute configuration at C-7 of complexed 7-hydroxy-8-D-ribityl-6,7-bis(trifluoromethyl)-7,8-dihydropteridine-2,4(1H,3H)-dione, a fluorinated analogue of an unstable, hypothetical intermediate in the reactions catalyzed by both lumazine synthase and riboflavin synthase.