Calculating calories- calling all health and science jellies...

Please read the question as I’m not asking how many calories are in certain foods or anything like that. Here’s my concern:

My understanding is, that the main components of food are: carbohydrates, protein, and fat. That said, I also understand that 1 gram of carbohydrates = 4 calories, 1 gram of protein = 4 calories, and 1 gram of fat = 9 calories.

That being the case, if you know a donut has 35 grams of carbohydrates, 1 gram of protein, and 10 grams of fat you can say (with relative accuracy) that the donut in question amounts to approximately 234 calories. Often this formula gives you the exact number of calories that the food’s packaging states.

Here’s the deal though- many foods deviate from this formula slightly to moderately. Meaning- if you simply use the formula I just laid out, you sometimes get a slightly different number of calories than the food packaging might list. Sometimes this number is as much as 5 or even 10% off- statistically, that’s significant.

My guess is that there is a reason for this. e.g. You deduct calories for fiber or something the food has. So, the question really is, why the discrepancy and how do you really, scientifically, calculate the calories in food once you know its components and their proportions?

Bonus question: Alcohol (beer, wine, etc.) has calories but this formula fails miserably to calculate them as they have some carbohydrates but virtually no protein or fat. Is this because the alcohol turns to sugar as we metabolize it? Is there a formula for understanding the calories in alcoholic drinks?