# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 14:12:55 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: (2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(2-oxopropyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)C[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 UD6  UD6  '(2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(2-oxopropyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  65  39  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UD6
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.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 UD6  N1    N  NR6    0  -0.578  -5.2306  -0.7229  -0.3422
 UD6  C2    C  CR6    0   0.748  -4.9515  -0.7012   1.0136
 UD6  O2    O  O      0  -0.462  -4.3350   0.1884   1.5558
 UD6  N3    N  NR16   0  -0.734  -5.4374  -1.7757   1.7136
 UD6  C4    C  CR6    0   0.567  -6.1666  -2.8545   1.2387
 UD6  O4    O  O      0  -0.464  -6.5348  -3.7347   1.9941
 UD6  C5    C  CR16   0  -0.511  -6.4096  -2.7960  -0.1808
 UD6  C6    C  CR16   0   0.098  -5.9345  -1.7604  -0.8892
 UD6  PA    P  P      0   1.348   0.2375   1.8149   0.9507
 UD6  PB    P  P      0   1.361   2.2372  -0.0893   1.9464
 UD6  C1'   C  CH1    0   0.294   4.3086  -0.7812   0.4625
 UD6  O1'   O  O2     0  -0.633   2.9238  -0.5652   0.5241
 UD6  O1A   O  OP    -1  -0.770   1.1218   2.4892  -0.0526
 UD6  C1B   C  CR15   0   0.240  -4.7400   0.3294  -1.2207
 UD6  O1B   O  O      0  -0.780   2.9565   1.1146   2.4675
 UD6  C2'   C  CH1    0  -0.317   4.8754  -0.0199  -0.7417
 UD6  O2'   O  OH1    0  -0.658  -6.4947   1.9386  -1.4392
 UD6  O2A   O  O      0  -0.799  -0.1811   2.5332   2.1947
 UD6  C2B   C  CR15   0  -0.059  -5.2132   1.7484  -0.9090
 UD6  O2B   O  OP    -1  -0.782   2.0180  -1.2846   2.8173
 UD6  C3'   C  CH1    0   0.074   4.4010  -0.6895  -2.0301
 UD6  O3'   O  OH1    0  -0.671   4.9857  -0.0283  -3.1256
 UD6  O3A   O  O2     0  -0.734   0.7805   0.3086   1.3154
 UD6  C3B   C  CR15   0  -0.039  -4.1138   2.5625  -1.6013
 UD6  O3B   O  OH1    0  -0.670  -4.3295   2.6138  -2.9889
 UD6  C4'   C  CH1    0  -0.032   4.7397  -2.1806  -2.0157
 UD6  O4'   O  OH1    0  -0.674   6.1408  -2.3185  -2.0666
 UD6  C4B   C  CR15   0  -0.026  -2.8790   1.7107  -1.3287
 UD6  O4B   O  O      0  -0.485  -3.3473   0.3626  -1.2138
 UD6  C5'   C  CH1    0  -0.002   4.1320  -2.8077  -0.7603
 UD6  O5'   O  O2     0  -0.494   4.5913  -2.1462   0.4014
 UD6  C5B   C  CH2    0  -0.142  -2.1374   2.1500  -0.0823
 UD6  O5B   O  O2     0  -0.618  -1.0973   1.2354   0.1764
 UD6  C6'   C  CH2    0  -0.174   4.4757  -4.2759  -0.6298
 UD6  O6'   O  OH1    0  -0.667   3.7343  -4.8314   0.4299
 UD6  C7'   C  C      0   0.415   5.0570   2.2420   0.4511
 UD6  O7'   O  O      0  -0.429   6.0256   1.8725   1.0811
 UD6  C8'   C  CH3    0  -0.784   4.3781   3.5550   0.7126
 UD6  C9'   C  CH2    0  -0.584   4.4855   1.4514  -0.6976
 UD6  H5    H  HCR6   0   0.294  -6.9605  -3.5861  -0.6661
 UD6  H6    H  HCR6   0   0.329  -6.0926  -1.6979  -1.9565
 UD6  H1'   H  HCH1   0   0.234   4.8035  -0.4335   1.3733
 UD6  H1B   H  HCR5   0   0.250  -5.1167   0.0573  -2.2135
 UD6  H2'   H  HCH1   0   0.244   5.9653  -0.1044  -0.6874
 UD6  HO2'  H  HOH1   0   0.469  -6.9154   2.6692  -0.9757
 UD6  H2B   H  HCR5   0   0.267  -5.1883   1.9440   0.1650
 UD6  H3'   H  HCH1   0   0.212   3.3048  -0.6129  -2.0771
 UD6  HO3'  H  HOH1   0   0.449   4.5674  -0.3486  -3.9309
 UD6  H3B   H  HCR5   0   0.247  -4.0195   3.5688  -1.1723
 UD6  HO3B  H  HOH1   0   0.448  -5.2596   2.8246  -3.1349
 UD6  H4'   H  HCH1   0   0.228   4.2665  -2.6531  -2.8903
 UD6  HO4'  H  HOH1   0   0.455   6.3572  -3.2170  -2.3305
 UD6  H4B   H  HCR5   0   0.251  -2.1903   1.7587  -2.1784
 UD6  H5'   H  HCH1   0   0.217   3.0393  -2.7256  -0.8482
 UD6  H5B   H  HCH2   0   0.210  -1.7609   3.1614  -0.2801
 UD6  H5BA  H  HCH2   0   0.219  -2.8129   2.2167   0.7747
 UD6  H6'   H  HCH2   0   0.201   4.2388  -4.7621  -1.5864
 UD6  H6'A  H  HCH2   0   0.197   5.5548  -4.3911  -0.4655
 UD6  HO6'  H  HOH1   0   0.454   3.9868  -5.7549   0.5150
 UD6  H8'   H  HCH3   0   0.238   4.8520   4.0975   1.5287
 UD6  H8'A  H  HCH3   0   0.244   4.4022   4.1732  -0.1875
 UD6  H8'B  H  HCH3   0   0.285   3.3290   3.3687   0.9426
 UD6  H9'   H  HCH2   0   0.276   4.8440   1.9534  -1.6036
 UD6  H9'A  H  HCH2   0   0.285   3.4011   1.5774  -0.7031
 UD6  HN3   H  HNR6   0   0.426  -5.2346  -1.7636   2.7060

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.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 UD6  C2   N1    single  1.384  0.020  1.384
 UD6  N1   C6    single  1.368  0.020  1.368
 UD6  N1   C1B   single  1.456  0.020  1.456
 UD6  N3   C2    single  1.371  0.020  1.371
 UD6  O2   C2    double  1.211  0.020  1.211
 UD6  N3   C4    single  1.386  0.020  1.386
 UD6  O4   C4    double  1.217  0.020  1.217
 UD6  C4   C5    single  1.441  0.020  1.441
 UD6  C5   C6    double  1.342  0.020  1.342
 UD6  C5   H5    single  0.930  0.020  1.080
 UD6  C6   H6    single  0.930  0.020  1.080
 UD6  O2A  PA    deloc   1.496  0.020  1.496
 UD6  O5B  PA    single  1.648  0.020  1.648
 UD6  PA   O1A   deloc   1.498  0.020  1.498
 UD6  PA   O3A   single  1.642  0.020  1.642
 UD6  O3A  PB    single  1.637  0.020  1.637
 UD6  O1B  PB    deloc   1.496  0.020  1.496
 UD6  PB   O1'   single  1.649  0.020  1.649
 UD6  PB   O2B   deloc   1.495  0.020  1.495
 UD6  O1'  C1'   single  1.403  0.020  1.403
 UD6  C1'  O5'   single  1.395  0.020  1.395
 UD6  C1'  C2'   single  1.533  0.020  1.533
 UD6  C1'  H1'   single  0.970  0.020  1.090
 UD6  O4B  C1B   single  1.393  0.020  1.393
 UD6  C1B  C2B   single  1.528  0.020  1.528
 UD6  C1B  H1B   single  0.970  0.020  1.090
 UD6  C3'  C2'   single  1.528  0.020  1.528
 UD6  C9'  C2'   single  1.523  0.020  1.523
 UD6  C2'  H2'   single  0.970  0.020  1.090
 UD6  C2B  O2'   single  1.400  0.020  1.400
 UD6  O2'  HO2'  single  0.850  0.020  0.980
 UD6  C2B  C3B   single  1.533  0.020  1.533
 UD6  C2B  H2B   single  0.970  0.020  1.090
 UD6  C3'  C4'   single  1.529  0.020  1.529
 UD6  C3'  O3'   single  1.407  0.020  1.407
 UD6  C3'  H3'   single  0.970  0.020  1.090
 UD6  O3'  HO3'  single  0.850  0.020  0.980
 UD6  C4B  C3B   single  1.525  0.020  1.525
 UD6  O3B  C3B   single  1.405  0.020  1.405
 UD6  C3B  H3B   single  0.970  0.020  1.090
 UD6  O3B  HO3B  single  0.850  0.020  0.980
 UD6  C5'  C4'   single  1.529  0.020  1.529
 UD6  C4'  O4'   single  1.409  0.020  1.409
 UD6  C4'  H4'   single  0.970  0.020  1.090
 UD6  O4'  HO4'  single  0.850  0.020  0.980
 UD6  O4B  C4B   single  1.432  0.020  1.432
 UD6  C4B  C5B   single  1.515  0.020  1.515
 UD6  C4B  H4B   single  0.970  0.020  1.090
 UD6  C5'  C6'   single  1.514  0.020  1.514
 UD6  C5'  O5'   single  1.414  0.020  1.414
 UD6  C5'  H5'   single  0.970  0.020  1.090
 UD6  C5B  O5B   single  1.409  0.020  1.409
 UD6  C5B  H5B   single  0.970  0.020  1.090
 UD6  C5B  H5BA  single  0.970  0.020  1.090
 UD6  C6'  O6'   single  1.407  0.020  1.407
 UD6  C6'  H6'   single  0.970  0.020  1.090
 UD6  C6'  H6'A  single  0.970  0.020  1.090
 UD6  O6'  HO6'  single  0.850  0.020  0.980
 UD6  C8'  C7'   single  1.501  0.020  1.501
 UD6  C9'  C7'   single  1.507  0.020  1.507
 UD6  C7'  O7'   double  1.213  0.020  1.213
 UD6  C8'  H8'   single  0.970  0.020  1.090
 UD6  C8'  H8'A  single  0.970  0.020  1.090
 UD6  C8'  H8'B  single  0.970  0.020  1.090
 UD6  C9'  H9'   single  0.970  0.020  1.090
 UD6  C9'  H9'A  single  0.970  0.020  1.090
 UD6  N3   HN3   single  0.860  0.020  1.020

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
 UD6  C1B   N1   C6    118.71  3.000
 UD6  C1B   N1   C2    120.77  3.000
 UD6  C6    N1   C2    120.49  3.000
 UD6  N3    C2   O2    121.84  3.000
 UD6  O2    C2   N1    123.57  3.000
 UD6  N3    C2   N1    114.59  3.000
 UD6  HN3   N3   C4    116.76  3.000
 UD6  HN3   N3   C2    114.82  3.000
 UD6  C4    N3   C2    128.42  3.000
 UD6  C5    C4   O4    126.14  3.000
 UD6  C5    C4   N3    113.24  3.000
 UD6  O4    C4   N3    120.63  3.000
 UD6  H5    C5   C6    120.57  3.000
 UD6  H5    C5   C4    119.97  3.000
 UD6  C6    C5   C4    119.45  3.000
 UD6  H6    C6   C5    120.95  3.000
 UD6  H6    C6   N1    115.24  3.000
 UD6  C5    C6   N1    123.81  3.000
 UD6  O5B   PA   O3A    92.84  3.000
 UD6  O3A   PA   O2A   110.38  3.000
 UD6  O5B   PA   O2A   109.44  3.000
 UD6  O3A   PA   O1A   111.49  3.000
 UD6  O5B   PA   O1A   108.77  3.000
 UD6  O2A   PA   O1A   120.40  3.000
 UD6  O3A   PB   O2B   106.77  3.000
 UD6  O2B   PB   O1B   120.73  3.000
 UD6  O3A   PB   O1B   111.51  3.000
 UD6  O2B   PB   O1'   109.43  3.000
 UD6  O1B   PB   O1'   109.41  3.000
 UD6  O3A   PB   O1'    96.21  3.000
 UD6  H1'   C1'  O5'   104.83  3.000
 UD6  H1'   C1'  C2'   109.21  3.000
 UD6  O5'   C1'  C2'   112.12  3.000
 UD6  H1'   C1'  O1'   111.18  3.000
 UD6  C2'   C1'  O1'   108.84  3.000
 UD6  O5'   C1'  O1'   110.64  3.000
 UD6  C1'   O1'  PB    119.55  3.000
 UD6  H1B   C1B  O4B   110.73  3.000
 UD6  H1B   C1B  C2B   107.99  3.000
 UD6  O4B   C1B  C2B   106.65  3.000
 UD6  H1B   C1B  N1    104.55  3.000
 UD6  C2B   C1B  N1    116.34  3.000
 UD6  O4B   C1B  N1    110.56  3.000
 UD6  H2'   C2'  C9'   109.16  3.000
 UD6  H2'   C2'  C3'   108.50  3.000
 UD6  C9'   C2'  C3'   111.62  3.000
 UD6  H2'   C2'  C1'   106.91  3.000
 UD6  C9'   C2'  C1'   111.24  3.000
 UD6  C3'   C2'  C1'   109.26  3.000
 UD6  HO2'  O2'  C2B   108.73  3.000
 UD6  H2B   C2B  C3B   109.43  3.000
 UD6  H2B   C2B  O2'   111.66  3.000
 UD6  C3B   C2B  O2'   114.41  3.000
 UD6  H2B   C2B  C1B   111.10  3.000
 UD6  C3B   C2B  C1B   100.31  3.000
 UD6  O2'   C2B  C1B   109.42  3.000
 UD6  H3'   C3'  C4'   106.80  3.000
 UD6  H3'   C3'  O3'   110.38  3.000
 UD6  C4'   C3'  O3'   111.93  3.000
 UD6  H3'   C3'  C2'   108.37  3.000
 UD6  O3'   C3'  C2'   108.76  3.000
 UD6  C4'   C3'  C2'   110.53  3.000
 UD6  HO3'  O3'  C3'   108.33  3.000
 UD6  PB    O3A  PA    127.08  3.000
 UD6  H3B   C3B  C4B   111.88  3.000
 UD6  H3B   C3B  O3B   111.44  3.000
 UD6  C4B   C3B  O3B   108.74  3.000
 UD6  H3B   C3B  C2B   111.83  3.000
 UD6  O3B   C3B  C2B   110.81  3.000
 UD6  C4B   C3B  C2B   101.73  3.000
 UD6  HO3B  O3B  C3B   107.79  3.000
 UD6  H4'   C4'  C5'   107.78  3.000
 UD6  H4'   C4'  O4'   110.90  3.000
 UD6  C5'   C4'  O4'   112.63  3.000
 UD6  H4'   C4'  C3'   108.41  3.000
 UD6  O4'   C4'  C3'   108.39  3.000
 UD6  C5'   C4'  C3'   108.63  3.000
 UD6  HO4'  O4'  C4'   108.99  3.000
 UD6  H4B   C4B  C5B   108.53  3.000
 UD6  H4B   C4B  O4B   108.02  3.000
 UD6  C5B   C4B  O4B   111.53  3.000
 UD6  H4B   C4B  C3B   110.25  3.000
 UD6  C5B   C4B  C3B   112.42  3.000
 UD6  O4B   C4B  C3B   105.99  3.000
 UD6  C4B   O4B  C1B   110.43  3.000
 UD6  H5'   C5'  C6'   107.76  3.000
 UD6  H5'   C5'  O5'   110.71  3.000
 UD6  C6'   C5'  O5'   108.01  3.000
 UD6  H5'   C5'  C4'   107.38  3.000
 UD6  O5'   C5'  C4'   110.71  3.000
 UD6  C6'   C5'  C4'   112.23  3.000
 UD6  C5'   O5'  C1'   115.33  3.000
 UD6  H5BA  C5B  H5B   107.29  3.000
 UD6  H5BA  C5B  O5B   110.60  3.000
 UD6  H5B   C5B  O5B   112.22  3.000
 UD6  H5BA  C5B  C4B   111.10  3.000
 UD6  H5B   C5B  C4B   106.67  3.000
 UD6  O5B   C5B  C4B   108.91  3.000
 UD6  C5B   O5B  PA    117.11  3.000
 UD6  H6'A  C6'  H6'   107.20  3.000
 UD6  H6'A  C6'  O6'   111.33  3.000
 UD6  H6'   C6'  O6'   111.55  3.000
 UD6  H6'A  C6'  C5'   109.75  3.000
 UD6  H6'   C6'  C5'   107.77  3.000
 UD6  O6'   C6'  C5'   109.16  3.000
 UD6  HO6'  O6'  C6'   107.91  3.000
 UD6  C9'   C7'  C8'   114.84  3.000
 UD6  C9'   C7'  O7'   122.60  3.000
 UD6  C8'   C7'  O7'   122.49  3.000
 UD6  H8'B  C8'  H8'A  106.97  3.000
 UD6  H8'B  C8'  H8'   110.24  3.000
 UD6  H8'A  C8'  H8'   109.03  3.000
 UD6  H8'B  C8'  C7'   108.82  3.000
 UD6  H8'A  C8'  C7'   109.97  3.000
 UD6  H8'   C8'  C7'   111.69  3.000
 UD6  H9'A  C9'  H9'   105.53  3.000
 UD6  H9'A  C9'  C7'   108.66  3.000
 UD6  H9'   C9'  C7'   105.41  3.000
 UD6  H9'A  C9'  C2'   111.45  3.000
 UD6  H9'   C9'  C2'   109.56  3.000
 UD6  C7'   C9'  C2'   115.59  3.000

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
 UD6  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 UD6  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 UD6  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 UD6  CONST_04  C1B  N1   C2   N3    180.00   0.0  0
 UD6  CONST_05  O4   C4   N3   C2    180.00   0.0  0
 UD6  CONST_06  C6   N1   C2   O2    180.00   0.0  0
 UD6  CONST_07  C1B  N1   C2   O2      0.00   0.0  0
 UD6  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 UD6  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 UD6  Var_01    C4B  C5B  O5B  PA    151.05  30.0  1
 UD6  Var_02    O3A  PB   O1'  C1'   167.94  30.0  2
 UD6  Var_03    C8'  C7'  C9'  C2'  -163.45  30.0  3
 UD6  Var_04    O2A  PA   O3A  PB    -77.27  30.0  2
 UD6  Var_05    H8'  C8'  C7'  O7'    -0.96  30.0  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
 UD6  chir_03  C1'  O1'  O5'  C2'  negativ
 UD6  chir_04  C1B  N1   O4B  C2B  positiv
 UD6  chir_05  C2'  C1'  C3'  C9'  negativ
 UD6  chir_06  C2B  O2'  C1B  C3B  negativ
 UD6  chir_07  C3'  C2'  C4'  O3'  positiv
 UD6  chir_08  C3B  O3B  C4B  C2B  positiv
 UD6  chir_09  C4'  C3'  C5'  O4'  positiv
 UD6  chir_10  C4B  O4B  C3B  C5B  negativ
 UD6  chir_11  C5'  C4'  C6'  O5'  negativ

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
 UD6  plan-1  N1   0.020
 UD6  plan-1  C2   0.020
 UD6  plan-1  O2   0.020
 UD6  plan-1  N3   0.020
 UD6  plan-1  C4   0.020
 UD6  plan-1  O4   0.020
 UD6  plan-1  C5   0.020
 UD6  plan-1  C6   0.020
 UD6  plan-1  C1B  0.020
 UD6  plan-1  H5   0.020
 UD6  plan-1  H6   0.020
 UD6  plan-1  HN3  0.020
 UD6  plan-2  C7'  0.020
 UD6  plan-2  O7'  0.020
 UD6  plan-2  C8'  0.020
 UD6  plan-2  C9'  0.020

