caffeine.pdb · 55 lines
HEADER SMALL MOLECULE CAFFEINE
COMPND CAFFEINE (1,3,7-TRIMETHYLXANTHINE)
HET CAF A 1 24
HETNAM CAF CAFFEINE
FORMUL 1 CAF C8 H10 N4 O2
HETATM 1 N1 CAF A 1 0.499 1.710 -0.000 1.00 0.00 N
HETATM 2 C2 CAF A 1 1.669 0.975 -0.000 1.00 0.00 C
HETATM 3 O2 CAF A 1 2.700 1.627 -0.000 1.00 0.00 O
HETATM 4 N3 CAF A 1 1.639 -0.399 -0.000 1.00 0.00 N
HETATM 5 C4 CAF A 1 0.440 -1.088 -0.000 1.00 0.00 C
HETATM 6 C5 CAF A 1 -0.766 -0.367 -0.000 1.00 0.00 C
HETATM 7 C6 CAF A 1 -0.731 1.068 -0.000 1.00 0.00 C
HETATM 8 O6 CAF A 1 -1.794 1.667 -0.000 1.00 0.00 O
HETATM 9 N7 CAF A 1 -1.786 -1.314 -0.000 1.00 0.00 N
HETATM 10 C8 CAF A 1 -1.145 -2.542 -0.000 1.00 0.00 C
HETATM 11 N9 CAF A 1 0.151 -2.428 -0.000 1.00 0.00 N
HETATM 12 C10 CAF A 1 0.545 3.179 -0.000 1.00 0.00 C
HETATM 13 H10A CAF A 1 1.583 3.510 0.000 1.00 0.00 H
HETATM 14 H10B CAF A 1 0.043 3.559 0.890 1.00 0.00 H
HETATM 15 H10C CAF A 1 0.043 3.559 -0.890 1.00 0.00 H
HETATM 16 C11 CAF A 1 2.903 -1.149 -0.000 1.00 0.00 C
HETATM 17 H11A CAF A 1 2.691 -2.218 0.000 1.00 0.00 H
HETATM 18 H11B CAF A 1 3.478 -0.892 0.890 1.00 0.00 H
HETATM 19 H11C CAF A 1 3.478 -0.892 -0.890 1.00 0.00 H
HETATM 20 C12 CAF A 1 -3.225 -1.066 -0.000 1.00 0.00 C
HETATM 21 H12A CAF A 1 -3.408 0.009 0.000 1.00 0.00 H
HETATM 22 H12B CAF A 1 -3.670 -1.510 0.890 1.00 0.00 H
HETATM 23 H12C CAF A 1 -3.670 -1.510 -0.890 1.00 0.00 H
HETATM 24 H8 CAF A 1 -1.664 -3.489 -0.000 1.00 0.00 H
CONECT 1 2 7 12
CONECT 2 1 4 3
CONECT 3 2
CONECT 4 2 5 16
CONECT 5 4 6 11
CONECT 6 5 7 9
CONECT 7 6 1 8
CONECT 8 7
CONECT 9 10 6 20
CONECT 10 11 9 24
CONECT 11 5 10
CONECT 12 1 13 14 15
CONECT 13 12
CONECT 14 12
CONECT 15 12
CONECT 16 4 17 18 19
CONECT 17 16
CONECT 18 16
CONECT 19 16
CONECT 20 9 21 22 23
CONECT 21 20
CONECT 22 20
CONECT 23 20
CONECT 24 10
ENDround 1 of 2
Caffeine again, bond for bond, in two rounds.
modelqwen/qwen3.8-max-0902taskpdb-caffeine@v1date2026-09-21rounds2 of 8 allowedcost$0.4734thinkingmediumtokens595,179 in, 28,157 out, of which 16,537 reasoningtime11 min 20 s
C8H10N4O2decided by a number, from the filepass
Fused purine coredecided by a number, from the filepass
Methyls on N1, N3, N7decided by a number, from the filepass
Carbonyls at C2 and C6decided by a number, from the filepass
Flat rings, real bond lengthsdecided by a number, from the filepass
There is no post about this one, since only some results need one, so the picture, the source and the scoring are here instead.
run 1 · 6r · $0.6292Textbook caffeine, flat to within a thousandth of an ångström.
run 2 · 1r · $0.5944Right on the first render, then still checking it when the clock ran out.
run 3 · 1r · $0.3614Right on the first render, and it stopped there.same prompt, other modelsall 9 runs on A caffeine molecule in 3D →
Write a PDB file with 3D coordinates for a caffeine molecule, hydrogens included.Frozen at v1. This model got this and nothing else.
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. How it is scored, and this run's files on GitHub.