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The enzyme FabH catalyzes the initial step of fatty acid biosynthesis via a type II fatty acid synthase. The pivotal role of this essential enzyme combined with its unique structural features and ubiquitous occurrence in bacteria has made it an attractive new target for the development of antibacterial and antiparasitic compounds. Predictive hologram quantitative structure activity relationship (HQSAR) model was developed for a series of benzoylamino benzoic acid derivatives acting as FabH inhibitor. The best HQSAR model was generated using atoms and bond types as fragment distinction and 4-7 as fragment size showing cross-validated q2 value of 0.678 and conventional r2 value of 0.920. The predictive ability of the model was validated by an external test set of 6 compounds giving satisfactory predictive r2 value of 0.82. The contribution maps obtained from this model were used to explain the individual atomic contributions to the overall activity. It was confirmed from the contribution map that both ring A and ring C play a vital role for activity. Moreover hydroxyl substitution in the ortho position of ring A is favorable for better inhibitory activity. Therefore the information derived from the contribution map can be used to design potent FabH inhibitors.