A colorie is a calorie (in the sense that a unit of energy is a unit of energy); however, there are some (I don't have science to cite, so I won't say it is factual) people that say fructose is worse for you than glucose (the two monosaccharides). Here's an interesting article you can read: http://www.eatingrules.com/2011/05/introduction-to-sugar/

In this sense, a calorie is not a calorie - but to be precise it's more that different sources of calories have different side-effects on the body when converted INTO energy/calorie.

Now to grains (specifically wheat-based products): gluten. The single reason why people in my athletic sphere (CrossFit) avoid wheat products as a source of calories when training is because of gluten (and sometimes yeast - as it does stimulate candida growth).

Gluten can cause all sorts of problems that aren't related to the calorie intake - diseases, obesity, inflammation, etc...

(I won't cite anything here for that because the information is widely available and in many books - although there are still "studies" that would say this information is bunk)

I consume around 4-5k calories per-day as part of my training. As long as you use it, the calories aren't bad for you but the source of the calories must be clean.