Can the body really get as much energy AND building material as the nutrition content declaration says?

Suppose you eat a food that, according to its nutrient content declaration, provides X grams of protein, etc, etc, and Y calories of energy. When you eat that food, the energy in the X grams of protein is included in Y, right? But what if your body uses the protein for building material and not for energy? Then do you still get Y calories of energy? I mean, the same protein molecules can't be used for both energy AND building material, can they? But, on the other hand, if Y _doesn't_ include

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