Finding
Every check passes!
The prompt, v1, frozen
Write a PDB file with 3D coordinates for a caffeine molecule, hydrogens included.
| check · how it is decided | Qwen3.8 Max |
|---|---|
| C8H10N4O2measured · Atom records counted by element: 8 C, 10 H, 4 N, 2 O. 24 atoms in total. | ✓ pass |
| Fused purine coremeasured · A 6-ring and a 5-ring found in the bond graph, sharing exactly two atoms. | ✓ pass |
| Methyls on N1, N3, N7measured · Each CH3 carbon traced to the nitrogen it is bonded to. | ✓ pass |
| Carbonyls at C2 and C6measured · Both terminal oxygens traced to their ring carbon. | ✓ pass |
| Flat rings, real bond lengthsmeasured · Out-of-plane RMS of each ring, and every heavy-atom bond length. | ✓ pass |
Ground truth: Caffeine, C8H10N4O2: a purine core, a six-membered ring fused to a five-membered ring across two shared carbons, methyls on N1, N3 and N7, carbonyl oxygens at C2 and C6, and the whole ring system flat. Every model on this task.
What six rounds looked like
So how did it get there? Mostly by arguing with itself:
The angle between dv and axis: cos = -cos(th) = -0.334 → 109.5°. But the measured angle N7-C12-H is the angle at C12 between the vectors C12→N7 (=axis) and C12→H (=dv) [...] Measured is 70.5 → dot = +0.334 [...] unless axis is defined as nrm(sub(C,N)) = C - N normalized → pointing from N to C! sub(a,b) = a-b. sub(C,N) = C-N → vector from N to C. Oops: I named it axis = nrm(sub(C, N)), but this is the direction N→C.
What's jagged here
Nothing failed, so there is no failure type here. The PDB file is under the picture if you want to open it and count the atoms yourself.