Nystose, O-beta-D-fructofuranosyl-(2-->1)-O-beta-D-fructofuranosyl-(2-->1)- beta-D-fructofuranosyl alpha-D-glucopyranoside, was modeled with the rigid-residue program PFOS and with MM3. The three furanose rings of crystalline nystose trihydrate all are within the 1 kcal.mol-1 contour on an MM3 energy surface that was calculated with a dielectric constant of 4. The calculations showed that in the extended conformation found in the crystal, there was a small influence of the remainder of the residues on the conformation of any given disaccharide segment. Even accounting for intramolecular, interresidue forces, however, the central inulobiose and the sucrose linkages appear to be distorted. These discrepancies are apparently due to crystal packing forces and, for the sucrose linkage, miscalculation of the energy of an overlapping exoanomeric effect, as indicated by studies of a model miniature crystal. The different conformations of the central and terminal inulobiose linkages in the crystal show that conformations in higher oligosaccharides will not always correspond to the global minima on conformational maps for isolated disaccharides.