Graph[MapIndexed[Labeled[#2[[1]],#1,Center]&,ChemicalData["Caffeine","VertexTypes"]],ChemicalData["Caffeine","EdgeRules"],VertexSize->Large,ImageSize->500,VertexCoordinates->ChemicalData["Caffeine","VertexCoordinates"],GraphStyle->"SimpleLink",DirectedEdges->False]