Technical Abstract: Protoporphyrinogen oxidase (Protox) is the target site of a large number of commercial herbicides. Previous QSARs performed at a 2-dimensional (2-D) level reproduced the activity of individual data sets relatively well, but these models could not be used to predict the activity of structurally related derivatives. We developed a more reliable model by applying 3-dimensional (3-D) molecular techniques to a set of 31 phenyl ether (PE) analogues. Inhibitory activity at the molecular site of action was chosen because it circumvents the effects of uptake, translocation, and metabolism of the compounds occurring in whole plant studies. Increased predictability was achieved by aligning the diphenyl ether (DPE) analogues along the trifluoromethyl phenyl (q2=0.70) ring rather than along the nitrophenyl (q2=0.65) ring or along the centroids (q2=0.69). This new analysis differentiated between R and S enantiomers and allowed the prediction of the inhibitory activity of the natural diphenyl ether cyperine. The prediction model suggests that the binding of cyperine on the active site of Protox is stereospecific.