caffeine.pdb · 58 lines
HEADER CAFFEINE (1,3,7-TRIMETHYLXANTHINE)
COMPND CAFFEINE
HET CFF A 1 24 CAFFEINE
REMARK 3D ideal coordinates from the RCSB chemical component dictionary (CFF),
REMARK rigidly rotated so the fused-ring plane is the x-y plane.
REMARK All 24 atoms are present, including 10 hydrogens.
REMARK CONECT records encode bond order by repeating the bonded atom serial.
HETATM 1 N1 CFF A 1 1.047 1.312 -0.000 1.00 0.00 N
HETATM 2 C2 CFF A 1 -0.208 1.790 -0.000 1.00 0.00 C
HETATM 3 C10 CFF A 1 2.176 2.246 0.000 1.00 0.00 C
HETATM 4 C6 CFF A 1 1.285 -0.016 -0.001 1.00 0.00 C
HETATM 5 N3 CFF A 1 -1.276 0.971 -0.000 1.00 0.00 N
HETATM 6 O11 CFF A 1 -0.384 2.993 0.000 1.00 0.00 O
HETATM 7 C12 CFF A 1 -2.629 1.533 -0.000 1.00 0.00 C
HETATM 8 C4 CFF A 1 -1.098 -0.402 -0.000 1.00 0.00 C
HETATM 9 C5 CFF A 1 0.193 -0.911 0.005 1.00 0.00 C
HETATM 10 N9 CFF A 1 -1.934 -1.444 -0.000 1.00 0.00 N
HETATM 11 O13 CFF A 1 2.428 -0.437 -0.000 1.00 0.00 O
HETATM 12 N7 CFF A 1 0.068 -2.286 -0.000 1.00 0.00 N
HETATM 13 C8 CFF A 1 -1.251 -2.560 -0.000 1.00 0.00 C
HETATM 14 C14 CFF A 1 1.161 -3.261 -0.000 1.00 0.00 C
HETATM 15 H101 CFF A 1 1.800 3.269 0.001 1.00 0.00 H
HETATM 16 H102 CFF A 1 2.783 2.082 0.890 1.00 0.00 H
HETATM 17 H103 CFF A 1 2.783 2.083 -0.889 1.00 0.00 H
HETATM 18 H121 CFF A 1 -2.570 2.622 -0.000 1.00 0.00 H
HETATM 19 H122 CFF A 1 -3.162 1.198 -0.890 1.00 0.00 H
HETATM 20 H123 CFF A 1 -3.162 1.198 0.889 1.00 0.00 H
HETATM 21 H81 CFF A 1 -1.679 -3.552 0.000 1.00 0.00 H
HETATM 22 H141 CFF A 1 1.432 -3.503 -1.028 1.00 0.00 H
HETATM 23 H142 CFF A 1 2.024 -2.839 0.513 1.00 0.00 H
HETATM 24 H143 CFF A 1 0.839 -4.167 0.513 1.00 0.00 H
TER
CONECT 1 2 3 4
CONECT 2 1 5 6 6
CONECT 3 1 15 16 17
CONECT 4 1 9 11 11
CONECT 5 2 7 8
CONECT 6 2 2
CONECT 7 5 18 19 20
CONECT 8 5 9 9 10
CONECT 9 4 8 8 12
CONECT 10 8 13 13
CONECT 11 4 4
CONECT 12 9 13 14
CONECT 13 10 10 12 21
CONECT 14 12 22 23 24
CONECT 15 3
CONECT 16 3
CONECT 17 3
CONECT 18 7
CONECT 19 7
CONECT 20 7
CONECT 21 13
CONECT 22 14
CONECT 23 14
CONECT 24 14
ENDround 1 of 4
Right in four rounds, most of them spent renaming atoms to the standard ligand names.
modeldeepseek/deepseek-v4.1-flashtaskpdb-caffeine@v1date2026-09-22rounds4 of 8 allowedcost$0.0698thinkingmediumtokens1,548,297 in, 35,386 out, of which 25,318 reasoningtime7 min 9 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 · 3r · $0.0418The same five checks Qwen3.8 Max passed, right on the first render, for a fifteenth of the price.
run 2 · 1r · $0.0428Right on the first render.
run 3 · 4r · $0.0633Right on the first render and unchanged through four, until the clock ended it.
run 3 · 2r · $0.0317Right in two rounds, for three cents.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.