A calorie is a measure of heat given off by burning a substance.
This article shows the origin of the term in the context of nutrition https://academic.oup.com/jn/article/136/12/2957/4663943
One of the earlier uses of the term in a physiological metabolic context, as apposed to a physics context, was in a paper by a German scientist named J. R. Mayer. The Mayer quote shows an early use of the definition that comes up in nutrition classes.
"When substances endowed with considerable chemical affinity for each other combine chemically, much heat is developed during the process. We shall estimate the quantity of heat thus set free by the number of kilogrammes of water which it would heat 1°C. The quantity of heat necessary to raise 1 kilogramme of water 1 degree is called a unit of heat, Calorie. "
A calorie itself is not something you ingest, and there's no Dietary Reference Intake https://ods.od.nih.gov/Health_Information/Dietary_Reference_Intakes.aspx for it, unlike everything else on the nutrition facts label (maybe that's why it's in separate box).
It's a measure of energy generation, so it depends on the individual process of how it's generated, and I'm not sure if the FDA bases their label's numbers off of cellular metabolic data using digestive enzymes and gut flora, they might use something like a butane torch. It might be a good idea to take the calorie number as a reference point when considering your own metabolism, and not as an exact quantity. Many things can affect someone's metabolism, its efficiency and its rate, at cellular and molecular levels (and above and below probably).
If you're thinking in terms of this definition, anything that causes metabolic reaction that generates heat could be measured as a calorie. Ethanol burns in a lab, but whether or not it generates heat in your body when it's metabolized depends on its metabolic processes https://en.wikipedia.org/wiki/Ethanol_metabolism .
If you wanted to know what substances generate heat in the body in general, the answer might be in the field of bioenergetics https://en.wikipedia.org/wiki/Bioenergetics , but that would include cellular respiration as well as enzymatic processes as the wiki article says, so breathing and processing anything (including your own dead cells thru apoptosis, or any drug you take or xenobiotic substance that enters your body https://www.sciencedirect.com/science/article/pii/S1359644612000359) could be shown to have a caloric value. Nutritionists and food producers are mostly focused on the calories from catabolic metabolism http://www.cte.sfasu.edu/wp-content/uploads/2012/01/2_Principles_of_Digestion_and_Metabolism.html by specifically liver enzymes, of something absorbed through the intestines (different parts of the intestines absorb different things, and not all gets processed catabolically).
The food/nutrition industries' use of "calories" is a weirdly specific definition that presents a narrow view of bioenergetics -- bodies are way more complex and unique!
