The enzyme has to be complementary to the transition state rather than to the substrate because, if an enzyme will be complementary to the enzyme the interactions between them will be so stable that the reaction cannot be carried forward. Thus, the modern notion of enzymatic catalysis was proposed, which stated that the enzyme should not be complementary to the substrate.
It has to be complementary to the transition state formed between the enzyme and substrate. The weak binding interactions resulting in the formation of enzyme-substrate transition complex between the substrate and enzyme. The enzyme-substrate transition complex has the strong interactions.
These strong interactions release the free energy that is also named as binding energy, which lowers the high activation energy barrier and hence forming the product. Enzyme complementarity to substrate lowers its potential to catalysis, whereas enzyme complementarity to transition state facilitates the enzyme catalysis. This is the reason that the enzyme found complementary to transition state instead of the substrate.