You can build the model from whatever: Draw it with a GUI, query your server infrastructure, analyze binaries, collect it from databases, parse it from documentation, process your issues, etc. The important points is to merge all the information into a single model.
You cannot represent this model on a screen in any meaningful way. Instead you can only get certain "views" into it to understand an aspect or answer specific questions.
Does it exist today? Many tools and processes have been developed to achieve it. For example, "Model-based systems engineering" is a very formal approach. I have yet to see it realized in practice though.
I'm pretty sure it isn't a single tool or process though. By definition it integrates with nearly everything and that means a lot of customization. You won't get it get it off the shelf.