cocoa bean vs Theobroma cacao

cocoa bean and Theobroma cacao both are nouns.

Word	Noun	Adjective	Verb	Adverb
cocoa bean	Yes	No	No	No
Theobroma cacao	Yes	No	No	No

As nouns, Theobroma cacao is a hypernym of cocoa bean; that is, Theobroma cacao is a word with a broader meaning than cocoa bean:

cocoa bean: seed of the cacao tree; ground roasted beans are source of chocolate
Theobroma cacao: tropical American tree producing cacao beans

Other hypernyms of cocoa bean include cacao, cacao tree, chocolate tree.

cocoa bean (noun)	Theobroma cacao (noun)
seed of the cacao tree; ground roasted beans are source of chocolate	tropical American tree producing cacao beans