Regarding pharmacophore generation through hypogen

The pharmacophore generation in Discovey studio through Hypogen generates a maximum of five features ie a combination of  maximum five features is restricted in hypogen. There are  instances where the developement of five featured pharmacophore sometimes fail to differentiate between the active and inactive molecule due to numerous interaction  of the active molecule at the receptor site (or in other words more than five chemical functionalities in the active molecule are important). In that case manual addition of pharmacophore features to the developed pharmacophore may be a alternative but not a permanent solution. I am using DS2.0 in windows platform. How the above problem may be solved without maual customization? Is the above problem resoluted in DS 3.0?