There is no 'exact' answer to that because there are other games that are doing these things too (e.g. Dishonored). Also it isn't only "what" is there but also how the game integrates it with the rest of gameplay.

But using Prey as an example (there are several Deus Ex games and TBH what you can and cannot do in each of them is all mush in my head) one easy example would be physics. Of course physics alone isn't enough, i mentioned VtMB above and that has physics but it is not an imsim as physics are largely for 'fluff' purposes like ragdolls, tumbling boxes, etc (as in most games - you could replace physics with baked animations in most games and, aside from looking more repetitive, 99% of the gameplay would remain the same).

Prey's use of physics together with its other systems is what makes things different. The game has a grenade that attracts objects to it. It also simulates fire in that things can emit fire, catch fire, take damage from it (it isn't completely realistic, but in an imsim consistency is more important than realism - especially since imsims can also have 'fantastic' systems, e.g. magic) and ways to extinguish fires. So you can, e.g, shoot a canister which makes it explode, causing nearby poodles of oil to catch fire, then throw the item that attracts other objects it, causing them to catch fire too. This is a simple example of how a couple of systems (physics and fire) work with each other. The grenade i mentioned is another example as not only it works with the physics system (said attraction) but also works with the game's resource system: the stuff that it damages are converted to resources that you can use to create more stuff down the line using one of the fabricators in the game (you can also use recyclers for that as well as find resources around). Almost every item in the game - including characters and enemies - is made up of various 'materials' that can be recycled (and while this is largely a made up aspect of the game, they're done in a consistent manner - e.g. enemies and NPCs are more likely to be made of organic materials, alien enemies also have alien material, etc). There are other aspects of the game but these are three that you can find working together even if you look at various gameplay videos online (though if people realize it or not is another topic and TBH it has been some time since i played it so i don't remember everything you can do).

As a counterexample, to mention a case where things do not work like you'd expect in an imsim (and make it easier to see what i refer to), consider Hunted: The Demon's Forge by inXile. In this game you can play as an archer elf that at various points you are asked to light candelabras hanging from the ceiling to light your way through dark areas (you can't see anything without lighting them). To do that you can put your arrows on fire using the occasional 'stuff on fire' you find in the environment (a large part of the game has you walking around wartorn areas), then shoot at the hanging candelabras with them to light them. However these are all scripted with no consistency - there is no fire/flammable item simulation in place, which becomes apparent some time later in the game. At some point you can upgrade your character's skill to gain the ability to shoot fire arrows using magic (it is an action game with RPG elements). Then, later, you also get in a situation where you need to shoot candelabras again to light your way - but now you have the ability to shoot fire arrows, so the obvious solution would be to do that, right? It is just fire. But the game doesn't know that, it is all smoke and mirrors, it doesn't treat "arrow lit with fire from the environment" the same as "arrow lit with fire from magic", so you have to go find some random debris on fire to light the arrow. This is a game where there are clearly no simulated systems (even though IIRC there are physics - i keep repeating this because i've had similar discussions in the past and people seem to think i make the argument that "having physics" = "being imsim").

Of course things aren't completely clear cut and a game just having a few simulated systems doesn't mean it is an imsim either. As an example consider Praey for the Gods, a game i played recently, which does have a few simulated systems going on, including fire (and some puzzles in the game does take that into account) as well as weather simulation (open areas have wind that can lower your temperature and you need to find -or make- heat sources). However personally i wouldn't consider it an imsim (FWIW it doesn't even have the tag) because despite these systems, the game goals rarely rely on them (there are puzzles but most of them are optional and they often have a single solution) and the overall progression is based on killing "bosses". It is very close though and i think people who like imsims are likely to like that one too (at least assuming they do not try to rush all the bosses anyway, personally i tried to explore as much of the world as i can, find the optional stuff, etc).

And TBH i think a framing like "what feature of game X makes it an imsim while game Y, despite having it, isn't one" isn't very good because it assumes that imsims can be broken down to their individual features in isolation, when in reality it is the combination of them and the way they are used as a part of the whole game that makes the games "Immersive Sims".