caffeine.pdb · 65 lines
HEADER CAFFEINE 01-JAN-25 CFF
TITLE 1,3,7-TRIMETHYL-1H-PURINE-2,6(3H,7H)-DIONE (CAFFEINE), C8H10N4O2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CAFFEINE;
COMPND 3 CHAIN: 500;
SOURCE MOL_ID: 1;
KEYWDS PURINE ALKALOID, XANTHINE, METHYLXANTHINE
EXPDTA THEORETICAL MODEL
AUTHOR GENERATED
REVDAT 1 01-JAN-25 0
HET CFF 24
HETNAM CFF CAFFEINE
FORMUL 1 CFF C8 H10 N4 O2
HETATM 1 N1 CFF 500 0.436 1.682 0.000 1.00 0.00 N
HETATM 2 C2 CFF 500 -0.934 1.682 0.000 1.00 0.00 C
HETATM 3 O2 CFF 500 -1.549 2.747 0.000 1.00 0.00 O
HETATM 4 N3 CFF 500 -1.619 0.495 0.000 1.00 0.00 N
HETATM 5 C4 CFF 500 -0.934 -0.691 0.000 1.00 0.00 C
HETATM 6 C5 CFF 500 0.436 -0.691 0.000 1.00 0.00 C
HETATM 7 C6 CFF 500 1.121 0.495 0.000 1.00 0.00 C
HETATM 8 O6 CFF 500 2.351 0.495 0.000 1.00 0.00 O
HETATM 9 N7 CFF 500 0.862 -2.004 0.000 1.00 0.00 N
HETATM 10 C8 CFF 500 -0.279 -2.743 0.000 1.00 0.00 C
HETATM 11 N9 CFF 500 -1.361 -2.004 0.000 1.00 0.00 N
HETATM 12 H8 CFF 500 -0.293 -3.823 0.000 1.00 0.00 H
HETATM 13 C10 CFF 500 1.161 2.938 0.000 1.00 0.00 C
HETATM 14 H101 CFF 500 1.038 3.428 0.966 1.00 0.00 H
HETATM 15 H102 CFF 500 0.771 3.583 -0.787 1.00 0.00 H
HETATM 16 H103 CFF 500 2.219 2.747 -0.178 1.00 0.00 H
HETATM 17 C11 CFF 500 -3.069 0.495 0.000 1.00 0.00 C
HETATM 18 H111 CFF 500 -3.433 0.144 0.966 1.00 0.00 H
HETATM 19 H112 CFF 500 -3.433 -0.165 -0.787 1.00 0.00 H
HETATM 20 H113 CFF 500 -3.433 1.507 -0.178 1.00 0.00 H
HETATM 21 C12 CFF 500 2.229 -2.488 0.000 1.00 0.00 C
HETATM 22 H121 CFF 500 2.454 -2.941 -0.966 1.00 0.00 H
HETATM 23 H122 CFF 500 2.351 -3.232 0.787 1.00 0.00 H
HETATM 24 H123 CFF 500 2.910 -1.656 0.178 1.00 0.00 H
TER 25 CFF 500
CONECT 1 2 7 13
CONECT 2 1 3 3 4
CONECT 3 2 2
CONECT 4 2 5 17
CONECT 5 4 6 6 11
CONECT 6 5 5 7 9
CONECT 7 1 6 8 8
CONECT 8 7 7
CONECT 9 6 10 21
CONECT 10 9 11 11 12
CONECT 11 5 10 10
CONECT 12 10
CONECT 13 1 14 15 16
CONECT 14 13
CONECT 15 13
CONECT 16 13
CONECT 17 4 18 19 20
CONECT 18 17
CONECT 19 17
CONECT 20 17
CONECT 21 9 22 23 24
CONECT 22 21
CONECT 23 21
CONECT 24 21
MASTER 0 0 1 0 0 0 0 0 24 1 24 0
ENDround 1 of 6

Textbook caffeine, flat to within a thousandth of an ångström.
modelqwen/qwen3.8-max-0902taskpdb-caffeine@v1date2026-09-14rounds6 of 8 allowedcost$0.6292thinkingmediumtokens1,091,788 in, 30,828 out, of which 18,709 reasoningtime11 min 59 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
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.


