Best to charge the battery directly from the battery terminals in case there is a bad/loose connection somewhere between the engine bay and battery.

Bad engine to body ground wires are not uncommon on BMW models, the E46 and E38, E39 have this issue with the frame side often. More often in wet and snowy climates.

BMW technical literature directs to NOT EVER disconnect the battery and that the Intelligent Battery Sensor - IBS - must see all charge and discharge current.

E70 Training https://drive.google.com/folderview?...&usp=drive_web
BMW General Training https://drive.google.com/folderview?...&usp=drive_web

Luca Paindelli has amassed an incredible resource. To not take maximum benefit from it is foolish!

Well I got it started and left it idling while I looked for the ground cable, which i wasn't able to locate. I took off the plastic cover from passenger side and just saw the air pump. Do i have to take the wheel of to get to this cable?

While i was doing that, the car stopped. I checked the voltage and it was at 5v. Is my battery bad, not holding charge or you guys think it's the alternator?

Where did you check the voltage?

Stop starting the car before you damage some electronics. Charge the battery for 12 hours or more and sort out the ground strap before you start it again.

If you cant find the old ground strap just fit an extra one from a decent size bolt on the engine block to a decent size bolt on the chassis.

Nominal battery capacity is 100 AH, that's about 4 A for twenty-four hours. Even an AGM battery will be damaged by sulfation if left undercharged/discharged. An AGM will be damaged by charging voltage >14.7 VDC

Alright guys, i let the battery charge overnight and plugged it in this morning.
I put a ground jump from the engine to the chassis ground and it fired up right away. I will be getting a load test done on the battery today to make sure its still ok and i will be finding this ground wire so i can replace it. Passenger airbag light is on, lets see if that goes away after a bit. Clearing codes didnt help.

I read that the ground wire was on the passenger side but it wasn't there, now i read on Xoutpost that its on the driver side so i will check there.

If anyone has a pic of the location that be appreciated.
Thanks for all the help.

At least on the E46 and I think the E39 with the 6 cylinders the engine to body ground happens to be on the passenger side near the motor mount. Often you have to remove the lower engine cover to see them.

Not sure if the E53 is set up like the E46/E39, but usually you will find a frame rail connection near or just behind the strut tower. Look around the motor mount area to see if you can find the ground.

Here is a picture of the strap on an E39 which is a 2nd cousin of the E53 IMHO - Bimmerfest - BMW Forums - View Single Post - 2003 Ground Wire on shock tower?

Here is the post that had the same issue as mine and he states it was on drivers side.
http://www.xoutpost.com/bmw-sav-foru...-no-crank.html
Either case.. i should be ok with leaving this 4 gauge ground wire and it should be ok yes?

Update for anyone who has this issue in the future:

As stated before, the ground was the issue so adding a chassis ground solved the no crank issue. Turns out the battery was pretty drained out so i charged it overnight and got it load tested, it tested good so nothing is wrong with the battery.
The AutoZone employee also tested the alternator and said one part passed but other part didn't. I'm not sure what those parts mean but basically i was told the alternator wasn't charging the battery like it should be. No issues since all that and it starts right up. Maybe i will need to get the alternator rebuilt at some point if this happens again.
Next step is to replace the original ground wire when i have some time.