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Jungfraujoch/image_analysis/structure_refinement/monomers/SAM.cif
T
leonarski_f 00662c4110 Refinement: common cofactors and modified RNA nucleotides in the embedded dictionary; heme iron restrained from LINK records 
The embedded CCP4 Monomer Library subset grows from 62 to 84 compounds:
- the modified tRNA/rRNA nucleotides PSU, 5MC, 1MA, OMG, OMC, OMU, H2U, M2G, 7MG, 2MG, 5MU (RNA group,
  joined by the library's backbone link "p");
- the cofactors NAD, NAI, NAP, NDP, FAD, FMN, HEM, HEC, SAM, SAH, and dioxygen (OXY). CMO is left out:
  its dictionary has C-O at 1.25 A, where bound CO is near 1.15 A.
links_and_mods.cif gains the links these compounds use: HEC-CYS1/HEC-CYS2 (heme C thioethers),
CYS-HEMB/CYS-HEMC, CYS-FAD and HIS-FAD1/2, with their modifications.

AddMetalLinks now takes a metal atom of any residue, not only a one-atom ion, so a heme iron's LINK records
to His NE2 / Met SD / water become bonds at the library's metal-site distances; the site's coordination counts
the metal's bonds in its own dictionary (a heme's four pyrrole N) as well as the records. A metal within a
ligand is also a metal for the repulsions (1.9 A to N, O, S) and its dictionary bonds are kept with the metal
bonds. Note HEC.cif's own Fe-N(pyrrole) ideal is 1.90 A (HEM: 2.04 A), so a cytochrome c reports a metal-bond
rmsd near 0.1 A.

Test RefinementRestraints_deposited_ligands builds the topology of eleven deposited models cut down to the
ligand and its surroundings (tests/test_data/ligands, 66 KB, from PDB 1EHZ, 8BKH, 6K9I, 2W3V, 5VML, 6F3P,
8CON, 3TK0, 7TCD, 6W4H, 5EPE): every ligand restrained, bond rmsd < 0.03 A, the RNA backbone bonded to each
modified nucleotide, the heme Fe-His bonds, and the HEC thioethers. rugnux --mode refine on the full entries
against their deposited structure factors: R-free within +-0.003 of the build where these were held fixed,
ligand bond rmsd vs the dictionary from 0.004-0.058 A down to 0.002-0.042 A. rugnux grows by 425 KiB.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit f4d407c8de6cb462320edb21a70665350e436d28)
2026-10-26 13:56:29 +01:00

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data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
SAM SAM S-ADENOSYLMETHIONINE NON-POLYMER 50 27 .
data_comp_SAM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
SAM N N NT3 1 -27.592 29.068 46.677
SAM CA C CH1 0 -28.803 28.395 46.134
SAM C C C 0 -29.252 27.303 47.112
SAM O O O 0 -28.390 26.481 47.482
SAM OXT O OC -1 -30.447 27.315 47.469
SAM CB C CH2 0 -28.507 27.780 44.760
SAM CG C CH2 0 -29.706 27.205 44.008
SAM SD S S3 1 -30.917 28.471 43.547
SAM CE C CH3 0 -32.145 27.508 42.679
SAM "C5'" C CH2 0 -30.019 29.269 42.194
SAM "C4'" C CH1 0 -29.862 30.762 42.411
SAM "O4'" O O2 0 -29.159 30.988 43.651
SAM "C3'" C CH1 0 -29.042 31.494 41.354
SAM "O3'" O OH1 0 -29.880 31.908 40.281
SAM "C2'" C CH1 0 -28.448 32.677 42.130
SAM "O2'" O OH1 0 -29.235 33.845 42.037
SAM "C1'" C CH1 0 -28.400 32.173 43.575
SAM N9 N NR5 0 -27.055 31.878 44.061
SAM C8 C CR15 0 -26.399 32.530 45.075
SAM N7 N NRD5 0 -25.203 32.054 45.314
SAM C5 C CR56 0 -25.057 31.017 44.404
SAM C6 C CR6 0 -24.001 30.114 44.153
SAM N6 N NH2 0 -22.853 30.119 44.825
SAM N1 N NRD6 0 -24.177 29.196 43.169
SAM C2 C CR16 0 -25.338 29.196 42.495
SAM N3 N NRD6 0 -26.395 29.994 42.645
SAM C4 C CR56 0 -26.195 30.896 43.625
SAM HN1 H H 0 -27.310 29.714 46.100
SAM HN2 H H 0 -26.921 28.461 46.790
SAM H3 H H 0 -27.781 29.453 47.481
SAM HA H H 0 -29.519 29.065 46.056
SAM HB1 H H 0 -27.851 27.065 44.879
SAM HB2 H H 0 -28.094 28.464 44.200
SAM HG1 H H 0 -30.155 26.532 44.561
SAM HG2 H H 0 -29.394 26.764 43.189
SAM HE1 H H 0 -32.772 28.106 42.242
SAM HE2 H H 0 -32.619 26.946 43.314
SAM HE3 H H 0 -31.707 26.952 42.015
SAM "H5'1" H H 0 -30.506 29.113 41.356
SAM "H5'2" H H 0 -29.133 28.858 42.111
SAM "H4'" H H 0 -30.759 31.175 42.468
SAM "H3'" H H 0 -28.320 30.910 41.010
SAM "HO3'" H H 0 -29.420 32.372 39.739
SAM "H2'" H H 0 -27.528 32.871 41.805
SAM "HO2'" H H 0 -28.800 34.500 42.358
SAM "H1'" H H 0 -28.805 32.854 44.158
SAM H8 H H 0 -26.773 33.252 45.550
SAM HN61 H H 0 -22.410 29.370 44.938
SAM HN62 H H 0 -22.544 30.872 45.153
SAM H2 H H 0 -25.416 28.540 41.820
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.aromatic
_chem_comp_bond.value_dist_nucleus
_chem_comp_bond.value_dist_nucleus_esd
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
SAM N CA SINGLE n 1.488 0.0100 1.488 0.0100
SAM CA C SINGLE n 1.533 0.0100 1.533 0.0100
SAM CA CB SINGLE n 1.532 0.0100 1.532 0.0100
SAM C O DOUBLE n 1.247 0.0187 1.247 0.0187
SAM C OXT SINGLE n 1.247 0.0187 1.247 0.0187
SAM CB CG SINGLE n 1.516 0.0200 1.516 0.0200
SAM CG SD SINGLE n 1.807 0.0171 1.807 0.0171
SAM SD CE SINGLE n 1.786 0.0143 1.786 0.0143
SAM SD "C5'" SINGLE n 1.807 0.0171 1.807 0.0171
SAM "C5'" "C4'" SINGLE n 1.516 0.0120 1.516 0.0120
SAM "C4'" "O4'" SINGLE n 1.446 0.0100 1.446 0.0100
SAM "C4'" "C3'" SINGLE n 1.528 0.0117 1.528 0.0117
SAM "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100
SAM "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100
SAM "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100
SAM "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100
SAM "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100
SAM "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100
SAM N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100
SAM N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101
SAM C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100
SAM N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100
SAM C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100
SAM C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100
SAM C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100
SAM C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100
SAM N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100
SAM C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100
SAM N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100
SAM N HN1 SINGLE n 1.036 0.0160 0.911 0.0200
SAM N HN2 SINGLE n 1.036 0.0160 0.911 0.0200
SAM N H3 SINGLE n 1.036 0.0160 0.911 0.0200
SAM CA HA SINGLE n 1.089 0.0100 0.985 0.0200
SAM CB HB1 SINGLE n 1.089 0.0100 0.978 0.0200
SAM CB HB2 SINGLE n 1.089 0.0100 0.978 0.0200
SAM CG HG1 SINGLE n 1.089 0.0100 0.981 0.0150
SAM CG HG2 SINGLE n 1.089 0.0100 0.981 0.0150
SAM CE HE1 SINGLE n 1.089 0.0100 0.971 0.0165
SAM CE HE2 SINGLE n 1.089 0.0100 0.971 0.0165
SAM CE HE3 SINGLE n 1.089 0.0100 0.971 0.0165
SAM "C5'" "H5'1" SINGLE n 1.089 0.0100 0.981 0.0150
SAM "C5'" "H5'2" SINGLE n 1.089 0.0100 0.981 0.0150
SAM "C4'" "H4'" SINGLE n 1.089 0.0100 0.989 0.0197
SAM "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200
SAM "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
SAM "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200
SAM "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
SAM "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200
SAM C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170
SAM N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200
SAM N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200
SAM C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
SAM CA N HN1 110.062 1.93
SAM CA N HN2 110.062 1.93
SAM CA N H3 110.062 1.93
SAM HN1 N HN2 109.028 2.41
SAM HN1 N H3 109.028 2.41
SAM HN2 N H3 109.028 2.41
SAM N CA C 109.241 1.50
SAM N CA CB 110.906 1.50
SAM N CA HA 108.487 1.50
SAM C CA CB 109.344 1.50
SAM C CA HA 108.824 1.50
SAM CB CA HA 109.670 1.50
SAM CA C O 117.124 1.50
SAM CA C OXT 117.124 1.50
SAM O C OXT 125.752 1.50
SAM CA CB CG 113.808 1.88
SAM CA CB HB1 108.666 1.50
SAM CA CB HB2 108.666 1.50
SAM CG CB HB1 108.557 1.50
SAM CG CB HB2 108.557 1.50
SAM HB1 CB HB2 107.698 1.50
SAM CB CG SD 108.220 3.00
SAM CB CG HG1 109.481 1.50
SAM CB CG HG2 109.481 1.50
SAM SD CG HG1 108.504 1.57
SAM SD CG HG2 108.504 1.57
SAM HG1 CG HG2 108.193 1.50
SAM CG SD CE 102.026 1.83
SAM CG SD "C5'" 98.345 1.79
SAM CE SD "C5'" 102.487 1.89
SAM SD CE HE1 109.268 1.50
SAM SD CE HE2 109.268 1.50
SAM SD CE HE3 109.268 1.50
SAM HE1 CE HE2 109.605 1.50
SAM HE1 CE HE3 109.605 1.50
SAM HE2 CE HE3 109.605 1.50
SAM SD "C5'" "C4'" 111.142 2.46
SAM SD "C5'" "H5'1" 108.544 1.50
SAM SD "C5'" "H5'2" 108.544 1.50
SAM "C4'" "C5'" "H5'1" 109.065 1.50
SAM "C4'" "C5'" "H5'2" 109.065 1.50
SAM "H5'1" "C5'" "H5'2" 107.808 1.50
SAM "C5'" "C4'" "O4'" 109.393 1.53
SAM "C5'" "C4'" "C3'" 115.549 1.59
SAM "C5'" "C4'" "H4'" 109.003 1.50
SAM "O4'" "C4'" "C3'" 105.508 1.50
SAM "O4'" "C4'" "H4'" 109.115 1.50
SAM "C3'" "C4'" "H4'" 109.143 1.50
SAM "C4'" "O4'" "C1'" 109.426 1.50
SAM "C4'" "C3'" "O3'" 110.985 2.41
SAM "C4'" "C3'" "C2'" 102.352 1.50
SAM "C4'" "C3'" "H3'" 110.624 1.81
SAM "O3'" "C3'" "C2'" 111.581 2.83
SAM "O3'" "C3'" "H3'" 110.380 1.67
SAM "C2'" "C3'" "H3'" 110.504 1.75
SAM "C3'" "O3'" "HO3'" 108.744 3.00
SAM "C3'" "C2'" "O2'" 112.782 2.45
SAM "C3'" "C2'" "C1'" 101.239 1.50
SAM "C3'" "C2'" "H2'" 110.596 1.51
SAM "O2'" "C2'" "C1'" 111.715 2.69
SAM "O2'" "C2'" "H2'" 110.448 1.97
SAM "C1'" "C2'" "H2'" 110.636 1.70
SAM "C2'" "O2'" "HO2'" 109.103 2.13
SAM "O4'" "C1'" "C2'" 106.047 1.50
SAM "O4'" "C1'" N9 108.477 1.50
SAM "O4'" "C1'" "H1'" 109.807 1.50
SAM "C2'" "C1'" N9 113.824 1.50
SAM "C2'" "C1'" "H1'" 109.015 1.50
SAM N9 "C1'" "H1'" 109.561 1.50
SAM "C1'" N9 C8 126.848 1.91
SAM "C1'" N9 C4 127.459 1.80
SAM C8 N9 C4 105.693 1.50
SAM N9 C8 N7 113.469 1.50
SAM N9 C8 H8 123.206 1.50
SAM N7 C8 H8 123.326 1.50
SAM C8 N7 C5 104.739 1.50
SAM N7 C5 C6 132.250 1.50
SAM N7 C5 C4 110.483 1.50
SAM C6 C5 C4 117.267 1.50
SAM C5 C6 N6 123.792 1.50
SAM C5 C6 N1 117.409 1.50
SAM N6 C6 N1 118.799 1.50
SAM C6 N6 HN61 119.723 1.50
SAM C6 N6 HN62 119.723 1.50
SAM HN61 N6 HN62 120.554 1.88
SAM C6 N1 C2 118.521 1.50
SAM N1 C2 N3 129.332 1.50
SAM N1 C2 H2 115.313 1.50
SAM N3 C2 H2 115.355 1.50
SAM C2 N3 C4 110.982 1.50
SAM N9 C4 C5 105.616 1.50
SAM N9 C4 N3 127.895 1.50
SAM C5 C4 N3 126.489 1.50
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
SAM sp3_sp3_25 C CA N HN1 180.000 10.0 3
SAM sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3
SAM sp3_sp3_83 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3
SAM sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3
SAM sp3_sp3_88 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3
SAM sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3
SAM sp3_sp3_91 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3
SAM sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3
SAM sp2_sp3_7 C8 N9 "C1'" "O4'" 150.000 10.0 6
SAM const_14 N7 C8 N9 "C1'" 180.000 10.0 2
SAM const_26 C5 C4 N9 "C1'" 180.000 10.0 2
SAM const_17 N9 C8 N7 C5 0.000 10.0 2
SAM const_20 C6 C5 N7 C8 180.000 10.0 2
SAM sp2_sp3_1 O C CA N 0.000 10.0 6
SAM sp3_sp3_34 N CA CB CG 180.000 10.0 3
SAM const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2
SAM const_21 N9 C4 C5 N7 0.000 10.0 2
SAM sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2
SAM const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2
SAM const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2
SAM const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2
SAM const_12 N9 C4 N3 C2 180.000 10.0 2
SAM sp3_sp3_43 CA CB CG SD 180.000 10.0 3
SAM sp3_sp3_52 CB CG SD CE 180.000 10.0 3
SAM sp3_sp3_58 HE1 CE SD CG 180.000 10.0 3
SAM sp3_sp3_64 "C4'" "C5'" SD CG 180.000 10.0 3
SAM sp3_sp3_70 "O4'" "C4'" "C5'" SD 180.000 10.0 3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
SAM chir_1 CA N C CB positive
SAM chir_2 SD "C5'" CG CE positive
SAM chir_3 "C4'" "O4'" "C5'" "C3'" positive
SAM chir_4 "C3'" "O3'" "C4'" "C2'" positive
SAM chir_5 "C2'" "O2'" "C1'" "C3'" negative
SAM chir_6 "C1'" "O4'" N9 "C2'" negative
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
SAM plan-1 "C1'" 0.020
SAM plan-1 C2 0.020
SAM plan-1 C4 0.020
SAM plan-1 C5 0.020
SAM plan-1 C6 0.020
SAM plan-1 C8 0.020
SAM plan-1 H2 0.020
SAM plan-1 H8 0.020
SAM plan-1 N1 0.020
SAM plan-1 N3 0.020
SAM plan-1 N6 0.020
SAM plan-1 N7 0.020
SAM plan-1 N9 0.020
SAM plan-2 C 0.020
SAM plan-2 CA 0.020
SAM plan-2 O 0.020
SAM plan-2 OXT 0.020
SAM plan-3 C6 0.020
SAM plan-3 HN61 0.020
SAM plan-3 HN62 0.020
SAM plan-3 N6 0.020
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
SAM SMILES ACDLabs 10.04 "[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O"
SAM SMILES_CANONICAL CACTVS 3.341 C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
SAM SMILES CACTVS 3.341 C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SAM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
SAM SMILES "OpenEye OEToolkits" 1.5.0 C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
SAM InChI InChI 1.03 InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
SAM InChIKey InChI 1.03 MEFKEPWMEQBLKI-FCKMPRQPSA-N
loop_
_pdbx_chem_comp_description_generator.comp_id
_pdbx_chem_comp_description_generator.program_name
_pdbx_chem_comp_description_generator.program_version
_pdbx_chem_comp_description_generator.descriptor
SAM acedrg 243 "dictionary generator"
SAM acedrg_database 11 "data source"
SAM rdkit 2017.03.2 "Chemoinformatics tool"
SAM refmac5 5.8.0238 "optimization tool"
loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
_chem_comp_alias.atom_id_standard
SAM peptide HN1 H
SAM peptide HN2 H2
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