Microwave s11 simulation of a 3d model LC resonator and antenna Yes, ADS, but I'll tell you in terms of Microwave Office, which is what I use. Much more integrated than ADS.
I have done resonator measurements and simulation such as these, but typically you would use a two port (S21) measurement with two loop probes, as you will get much more dynamic range than a reflection measurement. You need very weak coupling to measure the unloaded Q of the resonator, and you probably won't get that with a 1 port measurement, and get an accurate measurement..
Your loop probes must be electrically small and operating below their self resonance, which it looks as if they are, given the geometry.
You haven't stated the boundary conditions; open or closed. Your say it is in a box, but I assume you mean embedded in a brick of dielectric, which has the sides open to free space, rather than in a conducting box.
So you can simulate it in 2.5D, which for MWO would be Axiem (the ADS equivalent is Momentum). You are on an infinite substrate, of multiple dielectric layers, with top and bottom boundaries. The boundaries can be open (sheet resistance of 377 Ohm/square), or conducting. You need to get the open boundaries 1/4 wavelength away (i.e. out of the reactive near field) from you circuitry. This looks to be a UHF resonator, so that can be quite far away, compared to the thin layer between the parallel plate capacitor. This is drastic size difference is not an issue for 2.5D simulator since you only mesh the conductors, not the volume, which is why you start there before moving to 3D. If you need conducting side boundaries, surround it with vias, but again, I assume this is open boundary. You would use differential ports (+/-) to drive the probe, or a gap port.
Another 2.5D in MWO is EMSight; ADS does not have an equivalent. Now you are in a box with conducting sidewalls, and can still set the top and bottom boundaries. Sonnet is very similar. The advantage is you get much more dynamic range with the closed boundary, but you are in a box. The mesh is also on a grid, whereas open boundary is gridless, though sonnet has some conformal meshing tricks.
For 3D, the MWO simulator is Analyst. The ADS equivalent is EMPro (I think). Now you can set arbitrary boundary conditions; open & short (E and H), and PML. You still need to get 1/4 wavelength away for open and PML, but not restricted to an infinite substrate. Though now you need to mesh the volume, including tiny volume between the capacitor plates.
If you are in a conducting box, you can use eigenmode analysis with Analyst, dispensing with the driven probes to solve the resonant modes within the box.
CST has a characteristic mode analysis, which I believe is an open boundary eigenmode analysis.
All of these programs support DXF import, though you ought to be re-drawing it in the native environment, so you can parameterize it.