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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
U8U U8U "5-METHYLAMINOMETHYL-2-THIOURIDINE-5'-MONOPHOSPHATE" RNA 40 24 .
data_comp_U8U
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
U8U N1 N NR6 0 0.456 2.604 0.086
U8U C2 C CR6 0 -0.243 3.482 0.893
U8U S2 S S1 0 -0.585 3.147 2.492
U8U N3 N NR16 0 -0.702 4.628 0.326
U8U C4 C CR6 0 -1.010 4.692 -1.034
U8U O4 O O 0 -1.713 5.625 -1.431
U8U C5 C CR6 0 -0.489 3.685 -1.852
U8U C6 C CR16 0 0.217 2.651 -1.267
U8U C C CH2 0 -0.704 3.683 -3.351
U8U N N NT1 0 -1.872 2.910 -3.775
U8U CA C CH3 0 -2.017 2.849 -5.229
U8U "C1'" C CH1 0 1.434 1.622 0.664
U8U "O2'" O OH1 0 0.295 0.217 2.288
U8U "C2'" C CH1 0 0.783 0.271 0.955
U8U "O3'" O OH1 0 2.734 -0.969 1.833
U8U "C3'" C CH1 0 1.909 -0.731 0.698
U8U "C4'" C CH1 0 2.694 -0.043 -0.428
U8U "O4'" O O2 0 2.469 1.381 -0.260
U8U "C5'" C CH2 0 2.312 -0.443 -1.832
U8U "O5'" O O2 0 3.116 0.299 -2.782
U8U P P P 0 2.851 0.085 -4.360
U8U OP1 O O 0 3.891 0.929 -5.073
U8U OP2 O OP -1 1.433 0.562 -4.609
U8U OP3 O OP -1 3.026 -1.401 -4.611
U8U HN3 H H 0 -0.808 5.342 0.817
U8U H6 H H 0 0.529 1.955 -1.816
U8U HC1 H H 0 0.092 3.310 -3.781
U8U HC2 H H 0 -0.805 4.606 -3.662
U8U HN1 H H 0 -1.779 2.078 -3.472
U8U HA1 H H 0 -2.746 2.241 -5.461
U8U HA2 H H 0 -1.187 2.524 -5.629
U8U HA3 H H 0 -2.216 3.740 -5.577
U8U "H1'" H H 0 1.825 1.991 1.490
U8U "HO2'" H H 0 -0.142 -0.503 2.395
U8U "H2'" H H 0 0.043 0.108 0.320
U8U "HO3'" H H 0 3.048 -0.233 2.117
U8U "H3'" H H 0 1.529 -1.586 0.368
U8U "H4'" H H 0 3.651 -0.223 -0.310
U8U "H5'" H H 0 1.353 -0.254 -1.982
U8U "H5''" H H 0 2.461 -1.413 -1.952
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
U8U N1 C2 SINGLE n 1.371 0.0118 1.371 0.0118
U8U N1 C6 SINGLE n 1.367 0.0104 1.367 0.0104
U8U N1 "C1'" SINGLE n 1.492 0.0124 1.492 0.0124
U8U C2 S2 DOUBLE n 1.663 0.0164 1.663 0.0164
U8U C2 N3 SINGLE n 1.356 0.0100 1.356 0.0100
U8U N3 C4 SINGLE n 1.390 0.0129 1.390 0.0129
U8U C4 O4 DOUBLE n 1.232 0.0120 1.232 0.0120
U8U C4 C5 SINGLE n 1.388 0.0157 1.388 0.0157
U8U C5 C6 DOUBLE n 1.379 0.0100 1.379 0.0100
U8U C5 C SINGLE n 1.512 0.0119 1.512 0.0119
U8U C N SINGLE n 1.463 0.0131 1.463 0.0131
U8U N CA SINGLE n 1.463 0.0141 1.463 0.0141
U8U "C1'" "C2'" SINGLE n 1.527 0.0119 1.527 0.0119
U8U "C1'" "O4'" SINGLE n 1.406 0.0103 1.406 0.0103
U8U "O2'" "C2'" SINGLE n 1.420 0.0122 1.420 0.0122
U8U "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134
U8U "O3'" "C3'" SINGLE n 1.422 0.0100 1.422 0.0100
U8U "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100
U8U "C4'" "O4'" SINGLE n 1.449 0.0100 1.449 0.0100
U8U "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100
U8U "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166
U8U "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178
U8U P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192
U8U P OP2 SINGLE n 1.517 0.0192 1.517 0.0192
U8U P OP3 SINGLE n 1.517 0.0192 1.517 0.0192
U8U N3 HN3 SINGLE n 1.016 0.0100 0.873 0.0200
U8U C6 H6 SINGLE n 1.082 0.0130 0.940 0.0112
U8U C HC1 SINGLE n 1.089 0.0100 0.979 0.0148
U8U C HC2 SINGLE n 1.089 0.0100 0.979 0.0148
U8U N HN1 SINGLE n 1.036 0.0160 0.890 0.0200
U8U CA HA1 SINGLE n 1.089 0.0100 0.977 0.0113
U8U CA HA2 SINGLE n 1.089 0.0100 0.977 0.0113
U8U CA HA3 SINGLE n 1.089 0.0100 0.977 0.0113
U8U "C1'" "H1'" SINGLE n 1.089 0.0100 0.986 0.0200
U8U "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
U8U "C2'" "H2'" SINGLE n 1.089 0.0100 0.988 0.0200
U8U "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
U8U "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200
U8U "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200
U8U "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200
U8U "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 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
U8U C2 N1 C6 120.521 1.80
U8U C2 N1 "C1'" 118.374 3.00
U8U C6 N1 "C1'" 121.105 1.78
U8U N1 C2 S2 120.641 1.58
U8U N1 C2 N3 118.551 1.50
U8U S2 C2 N3 120.808 1.50
U8U C2 N3 C4 121.850 1.81
U8U C2 N3 HN3 119.601 1.52
U8U C4 N3 HN3 118.549 2.42
U8U N3 C4 O4 118.399 1.50
U8U N3 C4 C5 117.583 1.50
U8U O4 C4 C5 124.018 1.64
U8U C4 C5 C6 119.418 1.50
U8U C4 C5 C 120.689 1.80
U8U C6 C5 C 119.893 1.50
U8U N1 C6 C5 122.076 2.78
U8U N1 C6 H6 119.173 1.52
U8U C5 C6 H6 118.751 1.50
U8U C5 C N 113.751 2.91
U8U C5 C HC1 108.858 1.50
U8U C5 C HC2 108.858 1.50
U8U N C HC1 108.790 1.50
U8U N C HC2 108.790 1.50
U8U HC1 C HC2 107.826 1.50
U8U C N CA 112.615 2.70
U8U C N HN1 108.101 1.98
U8U CA N HN1 108.144 3.00
U8U N CA HA1 109.627 1.50
U8U N CA HA2 109.627 1.50
U8U N CA HA3 109.627 1.50
U8U HA1 CA HA2 109.279 1.79
U8U HA1 CA HA3 109.279 1.79
U8U HA2 CA HA3 109.279 1.79
U8U N1 "C1'" "C2'" 112.110 1.66
U8U N1 "C1'" "O4'" 108.278 1.50
U8U N1 "C1'" "H1'" 109.209 1.50
U8U "C2'" "C1'" "O4'" 106.204 2.50
U8U "C2'" "C1'" "H1'" 109.914 1.68
U8U "O4'" "C1'" "H1'" 109.395 1.50
U8U "C2'" "O2'" "HO2'" 109.104 3.00
U8U "C1'" "C2'" "O2'" 111.164 2.38
U8U "C1'" "C2'" "C3'" 104.443 2.26
U8U "C1'" "C2'" "H2'" 110.518 1.74
U8U "O2'" "C2'" "C3'" 112.463 2.73
U8U "O2'" "C2'" "H2'" 110.259 1.63
U8U "C3'" "C2'" "H2'" 110.255 2.04
U8U "C3'" "O3'" "HO3'" 108.744 3.00
U8U "C2'" "C3'" "O3'" 112.463 2.73
U8U "C2'" "C3'" "C4'" 102.352 1.50
U8U "C2'" "C3'" "H3'" 110.255 2.04
U8U "O3'" "C3'" "C4'" 111.281 2.46
U8U "O3'" "C3'" "H3'" 110.380 1.67
U8U "C4'" "C3'" "H3'" 110.452 2.54
U8U "C3'" "C4'" "O4'" 105.508 1.50
U8U "C3'" "C4'" "C5'" 116.008 1.52
U8U "C3'" "C4'" "H4'" 109.363 1.86
U8U "O4'" "C4'" "C5'" 109.123 1.50
U8U "O4'" "C4'" "H4'" 108.642 1.50
U8U "C5'" "C4'" "H4'" 108.268 1.50
U8U "C1'" "O4'" "C4'" 109.926 1.50
U8U "C4'" "C5'" "O5'" 109.342 1.50
U8U "C4'" "C5'" "H5'" 109.624 1.50
U8U "C4'" "C5'" "H5''" 109.624 1.50
U8U "O5'" "C5'" "H5'" 109.845 1.50
U8U "O5'" "C5'" "H5''" 109.845 1.50
U8U "H5'" "C5'" "H5''" 108.472 1.50
U8U "C5'" "O5'" P 118.783 1.50
U8U "O5'" P OP1 105.808 2.07
U8U "O5'" P OP2 105.808 2.07
U8U "O5'" P OP3 105.808 2.07
U8U OP1 P OP2 112.864 1.69
U8U OP1 P OP3 112.864 1.69
U8U OP2 P OP3 112.864 1.69
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
U8U C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6
U8U C2e-nyu0 "C4'" "O4'" "C1'" "C2" 340.700 6.300 1
U8U C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1
U8U C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1
U8U C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1
U8U C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1
U8U C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6
U8U C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1
U8U C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1
U8U C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1
U8U C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1
U8U C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1
U8U alpha "C5'" "O5'" P OP3 -60.000 10.00 3
U8U beta P "O5'" "C5'" "C4'" 180.000 10.00 3
U8U epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3
U8U gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3
U8U sp2_sp2_3 S2 C2 N1 C6 180.000 5.0 2
U8U sp2_sp2_21 C5 C6 N1 C2 0.000 5.0 2
U8U sp3_sp3_46 "C1'" "C2'" "O2'" "HO2'" 180.000 10.0 3
U8U sp2_sp2_7 S2 C2 N3 C4 180.000 5.0 2
U8U sp2_sp2_11 O4 C4 N3 C2 180.000 5.0 2
U8U sp2_sp2_16 O4 C4 C5 C 0.000 5.0 2
U8U sp2_sp2_19 C C5 C6 N1 180.000 5.0 2
U8U sp2_sp3_8 C4 C5 C N -90.000 10.0 6
U8U sp3_sp3_32 C5 C N CA -60.000 10.0 3
U8U sp3_sp3_37 HA1 CA N C 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
U8U chir_1 "C1'" "O4'" N1 "C2'" negative
U8U chir_2 "C2'" "O2'" "C1'" "C3'" negative
U8U chir_3 "C3'" "O3'" "C4'" "C2'" positive
U8U chir_4 "C4'" "O4'" "C3'" "C5'" negative
U8U chir_5 P "O5'" OP2 OP3 both
U8U chir_6 N C CA HN1 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
U8U plan-1 "C1'" 0.020
U8U plan-1 C2 0.020
U8U plan-1 C6 0.020
U8U plan-1 N1 0.020
U8U plan-2 C2 0.020
U8U plan-2 N1 0.020
U8U plan-2 N3 0.020
U8U plan-2 S2 0.020
U8U plan-3 C2 0.020
U8U plan-3 C4 0.020
U8U plan-3 HN3 0.020
U8U plan-3 N3 0.020
U8U plan-4 C4 0.020
U8U plan-4 C5 0.020
U8U plan-4 N3 0.020
U8U plan-4 O4 0.020
U8U plan-5 C 0.020
U8U plan-5 C4 0.020
U8U plan-5 C5 0.020
U8U plan-5 C6 0.020
U8U plan-6 C5 0.020
U8U plan-6 C6 0.020
U8U plan-6 H6 0.020
U8U plan-6 N1 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
U8U SMILES ACDLabs 10.04 O=C1NC(=S)N(C=C1CNC)C2OC(C(O)C2O)COP(=O)(O)O
U8U SMILES_CANONICAL CACTVS 3.341 CNCC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=S)NC1=O
U8U SMILES CACTVS 3.341 CNCC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=S)NC1=O
U8U SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CNCC1=CN(C(=S)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
U8U SMILES "OpenEye OEToolkits" 1.5.0 CNCC1=CN(C(=S)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
U8U InChI InChI 1.03 InChI=1S/C11H18N3O8PS/c1-12-2-5-3-14(11(24)13-9(5)17)10-8(16)7(15)6(22-10)4-21-23(18,19)20/h3,6-8,10,12,15-16H,2,4H2,1H3,(H,13,17,24)(H2,18,19,20)/t6-,7-,8-,10-/m1/s1
U8U InChIKey InChI 1.03 LVNQROXSHGRCLA-FDDDBJFASA-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
U8U acedrg 243 "dictionary generator"
U8U acedrg_database 11 "data source"
U8U rdkit 2017.03.2 "Chemoinformatics tool"
U8U refmac5 5.8.0238 "optimization tool"
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