The pharmacophoric geometry for the inhibition of human fibroblast collagenase has been determined using a novel computational method. The inhibitors used in this study, which had from seven to 11 rotatable torsion angles, did not show any irreversible movement from the pharmacophore geometry during a 20 ps room temperature molecular dynamics simulation. A parallel NMR study confirmed two torsion angles and a key atom distance, and an X-ray crystallographic study of the protein-ligand complex established the model unequivocally. The X-ray structure showed that nine out of 11 torsion angles were within the range predicted by the pharmacophoric model. For one of the two remaining torsion angles it suggested two possible values, one of which corresponded to the X-ray structure, Molecular dynamics simulations starting from the computed active conformation suggested that both of these two torsion angles could have alternate values which included the X-ray value. The computational method described here is applicable to any general molecular superimposition problem which, in rational drug design, helps : (i) to visualize the similarities among the molecules of diverse structures; (ii) to determine the active conformation for inhibiting a certain biological system, which in turn can be used for developing SD-QSAR models; and (iii) to dock new ligands at the active site of an enzyme or a biological receptor where the conformational correspondence with the X-ray crystallographically solved ligand is not obvious. The method uses multiple distance matrices to represent the conformational flexibility and conformational diversity. The molecules may be fairly flexible, with 10-12 rotatable torsion angles. No prior assumption of active conformation is necessary during the fitting process; only a hypothesis of equivalent atoms is required to work with this method. The method suggests conformations which are within a predefined molecular mechanics energy value and indicates the possibility of multiple conformational solutions if the molecules are not sufficiently diverse or constrained.