Somebody must have taken the coordinates of the Pentagon wall with a GPS
before the
day of the crash, then he could have made a flightplan ready to be loaded on
the FMC
of the 757 or 767 with the face of the pentagon wall as last point, then
engage the fsnav, and the plane will have follow it. The pilot had the
altitude and speed only to care about.
It is not so difficult to do.

I mean taking off with the full load of fuel, cargo and pax, manually
aiming to the point - unmarked on any aerial map, like a SID/STAR or
even an intersection - where you can approach the Pentagon like you
would do a runway without colliding against a building first ?

I've tried and, even with the autogen set on average density, I've
always failed. So I can't even imagine with high density autogen
buildings.