Abstract: Provided is a computer model generated from a data array, computer readable storage media encoded with the model, and computers comprising the model, wherein the model is derived from atomic structure coordinates of a FMN riboswitch or a lysine riboswitch. Further provided is a pharmacophore having a spatial arrangement of atoms defined by the binding pocket identified in the model, along with a compound defined by the pharmacophore. Also further provided are methods for rational drug design based on the atomic structure data, and compounds identified by the rational drug design process.