Estimating current when voltage drops > voltage input
First of all, in your initial calculation, you assumed that the LED will drop 2V no matter what current is flowing through it. In practice its voltage will vary depending on the current. If you have a data sheet for the LED, it should specify the current vs. voltage for the LED over some reasonable range. In your simulated circuit, you put 3 LEDs in series across a 5V source.  Assuming the LEDs are identical, then each one will drop 1/3 of 5V or 1.67 volts which is what your simulator shows. However the current depends on the actual current/voltage characteristics of your LED. The simulator probably assumed some generic model and came up with a current of 823 uA. That is not unreasonable for an LED operating well below its rated voltage but the exact value, as already mentioned, depends on the particular characteristics of your LED. This is true in general when operating devices above or below their ratings.