leonarski_f
e58453a693
A restraint dictionary carried in the binary, so refinement reads nothing from disk and needs no CLIBD_MON: the 20 amino acids and MSE, the DNA/RNA nucleotides, ATP/ADP/AMP/GTP/GDP/GMP, DMSO, PEG fragments (PEG, PGE, PG4, 1PE), GOL, EDO, SO4, PO4, ACT, MPD, water and common ions - copied verbatim from the CCP4 Monomer Library (LGPL-3.0) - plus links_and_mods.cif cut down to the links and modifications those compounds can take (peptide, cis-peptide, proline, N-methyl, disulfide, nucleic-acid backbone, termini, metal-Cys/His) and ener_lib.cif cut to its atom-type table. monomers/update_monomers.py holds the compound list and regenerates the subset; CMake embeds every .cif of the directory as string pieces under MSVC's literal limit; EmbeddedMonomerLibrary() parses them from memory into a gemmi::MonLib once per process. About 0.7 MB of text in the binary. gemmi v0.7.5's monlib.cpp, topo.cpp and riding_h.cpp vendored verbatim (prepare_topology). Licence text in licenses/, rows and a note in THIRD_PARTY_NOTICES.md. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 38034718052c4a300691393b5b817f476c83dfc2)
313 lines
19 KiB
Plaintext
313 lines
19 KiB
Plaintext
#
|
|
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
|
|
GTP GTP "GUANOSINE-5'-TRIPHOSPHATE" NON-POLYMER 44 32 .
|
|
#
|
|
data_comp_GTP
|
|
#
|
|
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
|
|
GTP PG P P 0 4.560 31.688 21.477
|
|
GTP O1G O O 0 4.404 32.256 22.874
|
|
GTP O2G O OP -1 4.031 32.621 20.405
|
|
GTP O3G O OP -1 4.007 30.282 21.352
|
|
GTP O3B O O2 0 6.154 31.567 21.217
|
|
GTP PB P P 0 7.014 30.840 20.078
|
|
GTP O1B O O 0 7.367 29.484 20.548
|
|
GTP O2B O OP -1 6.320 31.011 18.784
|
|
GTP O3A O O2 0 8.339 31.740 20.070
|
|
GTP PA P P 0 8.640 33.246 19.616
|
|
GTP O1A O O 0 8.465 33.336 18.144
|
|
GTP O2A O OP -1 7.853 34.171 20.471
|
|
GTP "O5'" O O2 0 10.195 33.377 19.964
|
|
GTP "C5'" C CH2 0 10.583 33.182 21.348
|
|
GTP "C4'" C CH1 0 12.036 33.553 21.524
|
|
GTP "O4'" O O2 0 12.846 32.727 20.657
|
|
GTP "C3'" C CH1 0 12.389 35.007 21.180
|
|
GTP "O3'" O OH1 0 13.296 35.538 22.138
|
|
GTP "C2'" C CH1 0 13.016 34.892 19.786
|
|
GTP "O2'" O OH1 0 13.937 35.921 19.490
|
|
GTP "C1'" C CH1 0 13.732 33.549 19.908
|
|
GTP N9 N NR5 0 14.014 32.895 18.629
|
|
GTP C8 C CR15 0 13.089 32.464 17.714
|
|
GTP N7 N NRD5 0 13.617 31.910 16.650
|
|
GTP C5 C CR56 0 14.986 31.978 16.880
|
|
GTP C6 C CR6 0 16.070 31.533 16.074
|
|
GTP O6 O O 0 16.021 30.976 14.968
|
|
GTP N1 N NR16 0 17.307 31.793 16.676
|
|
GTP C2 C CR6 0 17.480 32.406 17.902
|
|
GTP N2 N NH2 0 18.744 32.578 18.332
|
|
GTP N3 N NRD6 0 16.461 32.825 18.660
|
|
GTP C4 C CR56 0 15.250 32.581 18.093
|
|
GTP "H5'" H H 0 10.452 32.234 21.605
|
|
GTP "H5''" H H 0 10.026 33.747 21.941
|
|
GTP "H4'" H H 0 12.287 33.371 22.464
|
|
GTP "H3'" H H 0 11.567 35.560 21.142
|
|
GTP "HO3'" H H 0 14.015 35.710 21.778
|
|
GTP "H2'" H H 0 12.311 34.844 19.092
|
|
GTP "HO2'" H H 0 14.731 35.591 19.468
|
|
GTP "H1'" H H 0 14.596 33.678 20.425
|
|
GTP H8 H H 0 12.160 32.561 17.840
|
|
GTP HN1 H H 0 18.034 31.538 16.221
|
|
GTP HN21 H H 0 18.891 32.964 19.107
|
|
GTP HN22 H H 0 19.424 32.310 17.847
|
|
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
|
|
GTP PG O1G DOUBLE n 1.516 0.0200 1.516 0.0200
|
|
GTP PG O2G SINGLE n 1.516 0.0200 1.516 0.0200
|
|
GTP PG O3G SINGLE n 1.516 0.0200 1.516 0.0200
|
|
GTP PG O3B SINGLE n 1.620 0.0143 1.620 0.0143
|
|
GTP O3B PB SINGLE n 1.601 0.0108 1.601 0.0108
|
|
GTP PB O1B DOUBLE n 1.478 0.0100 1.478 0.0100
|
|
GTP PB O2B SINGLE n 1.478 0.0100 1.478 0.0100
|
|
GTP PB O3A SINGLE n 1.602 0.0126 1.602 0.0126
|
|
GTP O3A PA SINGLE n 1.600 0.0185 1.600 0.0185
|
|
GTP PA O1A DOUBLE n 1.485 0.0100 1.485 0.0100
|
|
GTP PA O2A SINGLE n 1.485 0.0100 1.485 0.0100
|
|
GTP PA "O5'" SINGLE n 1.598 0.0100 1.598 0.0100
|
|
GTP "O5'" "C5'" SINGLE n 1.445 0.0200 1.445 0.0200
|
|
GTP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
|
|
GTP "C4'" "O4'" SINGLE n 1.444 0.0100 1.444 0.0100
|
|
GTP "C4'" "C3'" SINGLE n 1.532 0.0100 1.532 0.0100
|
|
GTP "O4'" "C1'" SINGLE n 1.423 0.0100 1.423 0.0100
|
|
GTP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100
|
|
GTP "C3'" "C2'" SINGLE n 1.532 0.0103 1.532 0.0103
|
|
GTP "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100
|
|
GTP "C2'" "C1'" SINGLE n 1.528 0.0100 1.528 0.0100
|
|
GTP "C1'" N9 SINGLE n 1.462 0.0102 1.462 0.0102
|
|
GTP N9 C8 SINGLE y 1.371 0.0100 1.371 0.0100
|
|
GTP N9 C4 SINGLE y 1.383 0.0114 1.383 0.0114
|
|
GTP C8 N7 DOUBLE y 1.311 0.0104 1.311 0.0104
|
|
GTP N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100
|
|
GTP C5 C6 SINGLE y 1.418 0.0111 1.418 0.0111
|
|
GTP C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100
|
|
GTP C6 O6 DOUBLE n 1.240 0.0104 1.240 0.0104
|
|
GTP C6 N1 SINGLE y 1.394 0.0120 1.394 0.0120
|
|
GTP N1 C2 SINGLE y 1.374 0.0124 1.374 0.0124
|
|
GTP C2 N2 SINGLE n 1.341 0.0143 1.341 0.0143
|
|
GTP C2 N3 DOUBLE y 1.331 0.0119 1.331 0.0119
|
|
GTP N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100
|
|
GTP "C5'" "H5'" SINGLE n 1.089 0.0100 0.991 0.0200
|
|
GTP "C5'" "H5''" SINGLE n 1.089 0.0100 0.991 0.0200
|
|
GTP "C4'" "H4'" SINGLE n 1.089 0.0100 0.990 0.0200
|
|
GTP "C3'" "H3'" SINGLE n 1.089 0.0100 0.991 0.0200
|
|
GTP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.839 0.0200
|
|
GTP "C2'" "H2'" SINGLE n 1.089 0.0100 0.991 0.0200
|
|
GTP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.839 0.0200
|
|
GTP "C1'" "H1'" SINGLE n 1.089 0.0100 1.016 0.0200
|
|
GTP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0168
|
|
GTP N1 HN1 SINGLE n 1.016 0.0100 0.894 0.0200
|
|
GTP N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200
|
|
GTP N2 HN22 SINGLE n 1.016 0.0100 0.877 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
|
|
GTP O1G PG O2G 112.609 3.00
|
|
GTP O1G PG O3G 112.609 3.00
|
|
GTP O1G PG O3B 106.004 3.00
|
|
GTP O2G PG O3G 112.609 3.00
|
|
GTP O2G PG O3B 106.004 3.00
|
|
GTP O3G PG O3B 106.004 3.00
|
|
GTP PG O3B PB 132.613 3.00
|
|
GTP O3B PB O1B 108.634 3.00
|
|
GTP O3B PB O2B 108.634 3.00
|
|
GTP O3B PB O3A 100.990 3.00
|
|
GTP O1B PB O2B 119.776 1.50
|
|
GTP O1B PB O3A 108.634 3.00
|
|
GTP O2B PB O3A 108.634 3.00
|
|
GTP PB O3A PA 133.108 3.00
|
|
GTP O3A PA O1A 109.053 3.00
|
|
GTP O3A PA O2A 109.053 3.00
|
|
GTP O3A PA "O5'" 100.137 3.00
|
|
GTP O1A PA O2A 118.805 3.00
|
|
GTP O1A PA "O5'" 109.340 2.31
|
|
GTP O2A PA "O5'" 109.340 2.31
|
|
GTP PA "O5'" "C5'" 116.362 1.50
|
|
GTP "O5'" "C5'" "C4'" 109.454 1.61
|
|
GTP "O5'" "C5'" "H5'" 109.882 1.50
|
|
GTP "O5'" "C5'" "H5''" 109.882 1.50
|
|
GTP "C4'" "C5'" "H5'" 109.589 1.50
|
|
GTP "C4'" "C5'" "H5''" 109.589 1.50
|
|
GTP "H5'" "C5'" "H5''" 108.471 1.50
|
|
GTP "C5'" "C4'" "O4'" 109.154 1.50
|
|
GTP "C5'" "C4'" "C3'" 115.288 1.50
|
|
GTP "C5'" "C4'" "H4'" 108.351 1.59
|
|
GTP "O4'" "C4'" "C3'" 105.318 1.50
|
|
GTP "O4'" "C4'" "H4'" 109.120 1.50
|
|
GTP "C3'" "C4'" "H4'" 109.322 2.54
|
|
GTP "C4'" "O4'" "C1'" 109.502 2.85
|
|
GTP "C4'" "C3'" "O3'" 110.713 3.00
|
|
GTP "C4'" "C3'" "C2'" 102.593 1.50
|
|
GTP "C4'" "C3'" "H3'" 110.577 3.00
|
|
GTP "O3'" "C3'" "C2'" 111.671 3.00
|
|
GTP "O3'" "C3'" "H3'" 110.541 2.08
|
|
GTP "C2'" "C3'" "H3'" 110.454 1.85
|
|
GTP "C3'" "O3'" "HO3'" 109.389 3.00
|
|
GTP "C3'" "C2'" "O2'" 112.677 3.00
|
|
GTP "C3'" "C2'" "C1'" 101.406 1.50
|
|
GTP "C3'" "C2'" "H2'" 110.788 1.91
|
|
GTP "O2'" "C2'" "C1'" 110.814 3.00
|
|
GTP "O2'" "C2'" "H2'" 110.904 1.50
|
|
GTP "C1'" "C2'" "H2'" 110.342 1.91
|
|
GTP "C2'" "O2'" "HO2'" 109.217 3.00
|
|
GTP "O4'" "C1'" "C2'" 106.114 1.65
|
|
GTP "O4'" "C1'" N9 108.577 1.50
|
|
GTP "O4'" "C1'" "H1'" 109.833 2.53
|
|
GTP "C2'" "C1'" N9 113.380 2.77
|
|
GTP "C2'" "C1'" "H1'" 109.222 1.50
|
|
GTP N9 "C1'" "H1'" 109.411 1.50
|
|
GTP "C1'" N9 C8 127.058 3.00
|
|
GTP "C1'" N9 C4 126.955 2.94
|
|
GTP C8 N9 C4 105.987 1.50
|
|
GTP N9 C8 N7 113.721 1.50
|
|
GTP N9 C8 H8 122.935 1.50
|
|
GTP N7 C8 H8 123.345 1.50
|
|
GTP C8 N7 C5 103.926 1.50
|
|
GTP N7 C5 C6 129.926 1.50
|
|
GTP N7 C5 C4 110.770 1.50
|
|
GTP C6 C5 C4 119.304 1.50
|
|
GTP C5 C6 O6 128.237 1.50
|
|
GTP C5 C6 N1 111.514 1.50
|
|
GTP O6 C6 N1 120.248 1.50
|
|
GTP C6 N1 C2 125.452 1.50
|
|
GTP C6 N1 HN1 117.160 2.45
|
|
GTP C2 N1 HN1 117.387 2.97
|
|
GTP N1 C2 N2 116.657 1.50
|
|
GTP N1 C2 N3 123.538 1.50
|
|
GTP N2 C2 N3 119.805 1.50
|
|
GTP C2 N2 HN21 119.712 3.00
|
|
GTP C2 N2 HN22 119.712 3.00
|
|
GTP HN21 N2 HN22 120.576 3.00
|
|
GTP C2 N3 C4 111.926 1.50
|
|
GTP N9 C4 C5 105.596 1.50
|
|
GTP N9 C4 N3 126.138 1.50
|
|
GTP C5 C4 N3 128.265 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
|
|
GTP sp3_sp3_27 PB O3B PG O1G 60.000 10.0 3
|
|
GTP sp3_sp3_40 "C4'" "C5'" "O5'" PA 180.000 10.0 3
|
|
GTP sp3_sp3_43 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3
|
|
GTP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3
|
|
GTP sp3_sp3_56 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3
|
|
GTP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3
|
|
GTP sp3_sp3_61 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3
|
|
GTP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3
|
|
GTP sp3_sp3_64 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3
|
|
GTP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3
|
|
GTP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6
|
|
GTP const_18 N7 C8 N9 "C1'" 180.000 0.0 2
|
|
GTP const_30 C5 C4 N9 "C1'" 180.000 0.0 2
|
|
GTP const_21 N9 C8 N7 C5 0.000 0.0 2
|
|
GTP const_24 C6 C5 N7 C8 180.000 0.0 2
|
|
GTP const_sp2_sp2_4 N7 C5 C6 O6 0.000 0.0 2
|
|
GTP const_25 N9 C4 C5 N7 0.000 0.0 2
|
|
GTP const_sp2_sp2_7 O6 C6 N1 C2 180.000 0.0 2
|
|
GTP const_11 N2 C2 N1 C6 180.000 0.0 2
|
|
GTP sp2_sp2_33 N1 C2 N2 HN21 180.000 5.0 2
|
|
GTP const_14 N2 C2 N3 C4 180.000 0.0 2
|
|
GTP const_16 N9 C4 N3 C2 180.000 0.0 2
|
|
GTP sp3_sp3_30 PG O3B PB O1B 60.000 10.0 3
|
|
GTP sp3_sp3_32 PA O3A PB O3B -60.000 10.0 3
|
|
GTP sp3_sp3_36 PB O3A PA O1A 60.000 10.0 3
|
|
GTP sp3_sp3_37 "C5'" "O5'" PA O3A 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
|
|
GTP chir_1 PB O3A O3B O2B both
|
|
GTP chir_2 PA O3A "O5'" O2A both
|
|
GTP chir_3 "C4'" "O4'" "C3'" "C5'" negative
|
|
GTP chir_4 "C3'" "O3'" "C4'" "C2'" positive
|
|
GTP chir_5 "C2'" "O2'" "C1'" "C3'" negative
|
|
GTP chir_6 "C1'" "O4'" N9 "C2'" negative
|
|
GTP chir_7 PG O3B O2G O3G both
|
|
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
|
|
GTP plan-1 "C1'" 0.020
|
|
GTP plan-1 C4 0.020
|
|
GTP plan-1 C5 0.020
|
|
GTP plan-1 C6 0.020
|
|
GTP plan-1 C8 0.020
|
|
GTP plan-1 H8 0.020
|
|
GTP plan-1 N3 0.020
|
|
GTP plan-1 N7 0.020
|
|
GTP plan-1 N9 0.020
|
|
GTP plan-2 C2 0.020
|
|
GTP plan-2 C4 0.020
|
|
GTP plan-2 C5 0.020
|
|
GTP plan-2 C6 0.020
|
|
GTP plan-2 HN1 0.020
|
|
GTP plan-2 N1 0.020
|
|
GTP plan-2 N2 0.020
|
|
GTP plan-2 N3 0.020
|
|
GTP plan-2 N7 0.020
|
|
GTP plan-2 N9 0.020
|
|
GTP plan-2 O6 0.020
|
|
GTP plan-3 C2 0.020
|
|
GTP plan-3 HN21 0.020
|
|
GTP plan-3 HN22 0.020
|
|
GTP plan-3 N2 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
|
|
GTP SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O"
|
|
GTP InChI InChI 1.03 "InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1"
|
|
GTP InChIKey InChI 1.03 XKMLYUALXHKNFT-UUOKFMHZSA-N
|
|
GTP SMILES_CANONICAL CACTVS 3.370 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O"
|
|
GTP SMILES CACTVS 3.370 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O"
|
|
GTP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N"
|
|
GTP SMILES "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)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
|
|
GTP acedrg 271 "dictionary generator"
|
|
GTP acedrg_database 12 "data source"
|
|
GTP rdkit 2019.09.1 "Chemoinformatics tool"
|
|
GTP refmac5 5.8.0405 "optimization tool"
|