# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:59:41 2022
#   Inital geometry file: a 144 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S)-5-(formylamino)-3,4-dihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@H](OC[C@@H]1NC=O)O[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
 WQD  WQD  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S)-5-(formylamino)-3,4-dihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WQD
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
 WQD  C21  C  CH2    0  -0.173  -12.8285  -33.1639  -4.9497
 WQD  C22  C  CR15   0  -0.012  -12.7035  -34.6495  -5.2147
 WQD  C24  C  CR15   0  -0.061  -10.8346  -35.6183  -4.1168
 WQD  C28  C  CR16   0  -0.518   -7.8394  -33.4805  -6.4148
 WQD  C05  C  CH1    0   0.249  -10.2264  -31.1409   0.4298
 WQD  C06  C  CH1    0   0.001   -9.9167  -31.0915   1.9267
 WQD  C07  C  CH1    0   0.045  -10.9733  -30.2888   2.6770
 WQD  C08  C  CH1    0  -0.183  -11.1461  -28.9087   2.0220
 WQD  C09  C  CH2    0  -0.213  -11.4147  -29.0985   0.5375
 WQD  C23  C  CR15   0  -0.052  -12.3534  -35.4977  -3.9941
 WQD  C25  C  CR15   0   0.204  -10.6771  -35.7191  -5.6318
 WQD  C27  C  CR16   0   0.082   -9.0211  -33.9635  -5.9999
 WQD  C29  C  CR6    0   0.566   -6.8759  -34.3688  -7.0157
 WQD  C31  C  CR6    0   0.729   -8.5197  -36.2001  -6.6898
 WQD  N11  N  NH1    0  -0.582   -9.9934  -28.0558   2.2216
 WQD  N26  N  NR6    0  -0.568   -9.3771  -35.2786  -6.1188
 WQD  N30  N  NR16   0  -0.734   -7.3210  -35.6799  -7.1048
 WQD  O02  O  OP    -1  -0.783  -10.2463  -33.4043  -1.5262
 WQD  O03  O  O      0  -0.766  -12.7229  -33.7610  -0.7538
 WQD  O04  O  O2     0  -0.619  -11.3699  -31.9138   0.2384
 WQD  O10  O  O2     0  -0.485  -10.3827  -29.8451  -0.0782
 WQD  O13  O  O      0  -0.489  -10.6333  -27.0896   4.1837
 WQD  O14  O  OH1    0  -0.661  -10.5555  -30.2152   4.0161
 WQD  O15  O  OH1    0  -0.667   -9.8145  -32.4141   2.3868
 WQD  O16  O  O2     0  -0.753  -12.1375  -31.7442  -2.1535
 WQD  O18  O  O      0  -0.784  -12.5796  -30.2976  -4.1403
 WQD  O19  O  OP    -1  -0.781  -10.1084  -30.8883  -3.5238
 WQD  O20  O  O2     0  -0.628  -11.6075  -32.6575  -4.4629
 WQD  O32  O  O      0  -0.471   -8.7860  -37.3760  -6.8197
 WQD  O33  O  O      0  -0.456   -5.7710  -34.0616  -7.4203
 WQD  O34  O  O      0  -0.495  -11.6759  -34.9080  -6.1803
 WQD  O35  O  OH1    0  -0.657  -10.2888  -36.7550  -3.5064
 WQD  O36  O  OH1    0  -0.671  -12.9618  -36.7591  -4.1445
 WQD  P01  P  P      0   1.381  -11.5750  -32.8684  -1.0959
 WQD  P17  P  P      0   1.375  -11.5536  -31.2465  -3.6098
 WQD  H1   H  HCH2   0   0.228  -13.1163  -32.6544  -5.8752
 WQD  H2   H  HCH2   0   0.217  -13.6496  -33.0271  -4.2373
 WQD  H3   H  HCR5   0   0.253  -13.6630  -34.9789  -5.6286
 WQD  H4   H  HCR5   0   0.268  -10.3730  -34.7036  -3.7369
 WQD  H5   H  HCR6   0   0.287   -7.6043  -32.4335  -6.3014
 WQD  H6   H  HCH1   0   0.238   -9.3718  -31.5626  -0.1075
 WQD  H7   H  HCH1   0   0.216   -8.9539  -30.5692   2.0328
 WQD  H8   H  HCH1   0   0.217  -11.9385  -30.8097   2.5947
 WQD  H9   H  HCH1   0   0.274  -12.0140  -28.4095   2.4604
 WQD  H10  H  HCH2   0   0.254  -11.4470  -28.1328   0.0315
 WQD  H11  H  HCH2   0   0.237  -12.3913  -29.5728   0.3996
 WQD  H12  H  H      0   0.202   -8.8786  -26.7025   3.2323
 WQD  H13  H  HCR5   0   0.247  -12.6586  -35.0164  -3.0572
 WQD  H14  H  HCR5   0   0.265  -10.7893  -36.7573  -5.9517
 WQD  H15  H  HCR6   0   0.343   -9.7602  -33.3164  -5.5483
 WQD  H16  H  HNH1   0   0.404   -9.2339  -28.1093   1.5600
 WQD  H17  H  HNR6   0   0.422   -6.6829  -36.3506  -7.5156
 WQD  H19  H  HOH1   0   0.451  -11.2121  -29.7231   4.5194
 WQD  H20  H  HOH1   0   0.450   -9.5034  -32.3898   3.2968
 WQD  H22  H  HOH1   0   0.463  -10.0696  -36.5358  -2.5950
 WQD  H23  H  HOH1   0   0.443  -12.4532  -37.3910  -3.6220
 WQD  C12  C  C1     0   0.252   -9.8347  -27.2465   3.2764

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
 WQD  O33  C29  double  1.216  0.020  1.216
 WQD  N30  C29  single  1.387  0.020  1.387
 WQD  N30  C31  single  1.371  0.020  1.371
 WQD  O32  C31  double  1.213  0.020  1.213
 WQD  C29  C28  single  1.442  0.020  1.442
 WQD  C31  N26  single  1.382  0.020  1.382
 WQD  C28  C27  double  1.342  0.020  1.342
 WQD  N26  C27  single  1.368  0.020  1.368
 WQD  N26  C25  single  1.456  0.020  1.456
 WQD  O34  C25  single  1.399  0.020  1.399
 WQD  O34  C22  single  1.434  0.020  1.434
 WQD  C25  C24  single  1.527  0.020  1.527
 WQD  C22  C21  single  1.514  0.020  1.514
 WQD  C22  C23  single  1.527  0.020  1.527
 WQD  C24  O35  single  1.401  0.020  1.401
 WQD  C24  C23  single  1.529  0.020  1.529
 WQD  O18  P17  deloc   1.495  0.020  1.495
 WQD  O36  C23  single  1.409  0.020  1.409
 WQD  C21  O20  single  1.409  0.020  1.409
 WQD  O20  P17  single  1.650  0.020  1.650
 WQD  P17  O19  deloc   1.491  0.020  1.491
 WQD  P17  O16  single  1.646  0.020  1.646
 WQD  O16  P01  single  1.643  0.020  1.643
 WQD  P01  O03  deloc   1.494  0.020  1.494
 WQD  P01  O02  deloc   1.496  0.020  1.496
 WQD  P01  O04  single  1.653  0.020  1.653
 WQD  O10  C05  single  1.401  0.020  1.401
 WQD  O10  C09  single  1.415  0.020  1.415
 WQD  O04  C05  single  1.393  0.020  1.393
 WQD  C05  C06  single  1.529  0.020  1.529
 WQD  C09  C08  single  1.520  0.020  1.520
 WQD  C06  O15  single  1.404  0.020  1.404
 WQD  C06  C07  single  1.524  0.020  1.524
 WQD  C08  N11  single  1.448  0.020  1.448
 WQD  C08  C07  single  1.537  0.020  1.537
 WQD  N11  C12  single  1.339  0.020  1.339
 WQD  C07  O14  single  1.405  0.020  1.405
 WQD  C12  O13  double  1.219  0.020  1.219
 WQD  C21  H1   single  0.970  0.020  1.090
 WQD  C21  H2   single  0.970  0.020  1.090
 WQD  C22  H3   single  0.970  0.020  1.090
 WQD  C24  H4   single  0.970  0.020  1.090
 WQD  C28  H5   single  0.930  0.020  1.080
 WQD  C05  H6   single  0.970  0.020  1.090
 WQD  C06  H7   single  0.970  0.020  1.090
 WQD  C07  H8   single  0.970  0.020  1.090
 WQD  C08  H9   single  0.970  0.020  1.090
 WQD  C09  H10  single  0.970  0.020  1.090
 WQD  C09  H11  single  0.970  0.020  1.090
 WQD  C12  H12  single  0.930  0.020  1.080
 WQD  C23  H13  single  0.970  0.020  1.090
 WQD  C25  H14  single  0.970  0.020  1.090
 WQD  C27  H15  single  0.930  0.020  1.080
 WQD  N11  H16  single  0.860  0.020  1.020
 WQD  N30  H17  single  0.860  0.020  1.020
 WQD  O14  H19  single  0.850  0.020  0.980
 WQD  O15  H20  single  0.850  0.020  0.980
 WQD  O35  H22  single  0.850  0.020  0.980
 WQD  O36  H23  single  0.850  0.020  0.980

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
 WQD  H2   C21  H1   107.12  3.000
 WQD  H2   C21  O20  112.34  3.000
 WQD  H1   C21  O20  110.65  3.000
 WQD  H2   C21  C22  107.35  3.000
 WQD  H1   C21  C22  109.29  3.000
 WQD  O20  C21  C22  109.98  3.000
 WQD  H3   C22  O34  108.61  3.000
 WQD  H3   C22  C23  109.62  3.000
 WQD  O34  C22  C23  105.90  3.000
 WQD  H3   C22  C21  106.78  3.000
 WQD  C23  C22  C21  115.08  3.000
 WQD  O34  C22  C21  110.73  3.000
 WQD  H4   C24  O35  111.29  3.000
 WQD  H4   C24  C25  110.90  3.000
 WQD  O35  C24  C25  109.80  3.000
 WQD  H4   C24  C23  109.01  3.000
 WQD  O35  C24  C23  114.59  3.000
 WQD  C25  C24  C23  100.80  3.000
 WQD  H5   C28  C29  119.74  3.000
 WQD  H5   C28  C27  120.56  3.000
 WQD  C29  C28  C27  119.70  3.000
 WQD  H6   C05  O10  105.40  3.000
 WQD  H6   C05  O04  111.09  3.000
 WQD  O10  C05  O04  111.83  3.000
 WQD  H6   C05  C06  109.57  3.000
 WQD  O04  C05  C06  108.57  3.000
 WQD  O10  C05  C06  110.35  3.000
 WQD  H7   C06  O15  110.60  3.000
 WQD  H7   C06  C07  108.00  3.000
 WQD  O15  C06  C07  112.66  3.000
 WQD  H7   C06  C05  106.67  3.000
 WQD  C07  C06  C05  111.00  3.000
 WQD  O15  C06  C05  107.76  3.000
 WQD  H8   C07  O14  110.93  3.000
 WQD  H8   C07  C08  107.13  3.000
 WQD  O14  C07  C08  113.11  3.000
 WQD  H8   C07  C06  108.79  3.000
 WQD  O14  C07  C06  106.90  3.000
 WQD  C08  C07  C06  109.93  3.000
 WQD  H9   C08  N11  107.93  3.000
 WQD  H9   C08  C09  107.96  3.000
 WQD  N11  C08  C09  110.42  3.000
 WQD  H9   C08  C07  109.17  3.000
 WQD  N11  C08  C07  112.37  3.000
 WQD  C09  C08  C07  108.89  3.000
 WQD  H11  C09  H10  107.39  3.000
 WQD  H11  C09  O10  111.55  3.000
 WQD  H10  C09  O10  106.67  3.000
 WQD  H11  C09  C08  109.56  3.000
 WQD  H10  C09  C08  110.35  3.000
 WQD  O10  C09  C08  111.22  3.000
 WQD  H13  C23  O36  111.35  3.000
 WQD  H13  C23  C24  112.32  3.000
 WQD  O36  C23  C24  110.49  3.000
 WQD  H13  C23  C22  112.05  3.000
 WQD  O36  C23  C22  108.24  3.000
 WQD  C24  C23  C22  101.98  3.000
 WQD  H14  C25  O34  111.29  3.000
 WQD  H14  C25  N26  106.34  3.000
 WQD  O34  C25  N26  109.32  3.000
 WQD  H14  C25  C24  110.05  3.000
 WQD  O34  C25  C24  106.09  3.000
 WQD  N26  C25  C24  113.83  3.000
 WQD  H15  C27  N26  115.72  3.000
 WQD  H15  C27  C28  121.04  3.000
 WQD  N26  C27  C28  123.25  3.000
 WQD  O33  C29  N30  120.58  3.000
 WQD  N30  C29  C28  113.24  3.000
 WQD  O33  C29  C28  126.17  3.000
 WQD  O32  C31  N30  121.84  3.000
 WQD  O32  C31  N26  123.68  3.000
 WQD  N30  C31  N26  114.48  3.000
 WQD  H16  N11  C12  117.36  3.000
 WQD  H16  N11  C08  118.55  3.000
 WQD  C12  N11  C08  123.99  3.000
 WQD  C31  N26  C27  121.04  3.000
 WQD  C27  N26  C25  119.61  3.000
 WQD  C31  N26  C25  119.35  3.000
 WQD  H17  N30  C31  114.98  3.000
 WQD  H17  N30  C29  116.73  3.000
 WQD  C31  N30  C29  128.28  3.000
 WQD  P01  O04  C05  122.20  3.000
 WQD  C09  O10  C05  114.31  3.000
 WQD  H19  O14  C07  108.81  3.000
 WQD  H20  O15  C06  108.04  3.000
 WQD  P17  O16  P01  130.92  3.000
 WQD  P17  O20  C21  120.97  3.000
 WQD  C25  O34  C22  110.63  3.000
 WQD  H22  O35  C24  108.45  3.000
 WQD  H23  O36  C23  107.52  3.000
 WQD  O16  P01  O04   99.61  3.000
 WQD  O04  P01  O03  104.81  3.000
 WQD  O16  P01  O03  107.05  3.000
 WQD  O04  P01  O02  109.20  3.000
 WQD  O03  P01  O02  122.30  3.000
 WQD  O16  P01  O02  111.35  3.000
 WQD  O20  P17  O19  105.48  3.000
 WQD  O19  P17  O18  122.21  3.000
 WQD  O20  P17  O18  109.69  3.000
 WQD  O19  P17  O16  111.43  3.000
 WQD  O20  P17  O16  100.80  3.000
 WQD  O18  P17  O16  105.22  3.000
 WQD  H12  C12  O13  122.36  3.000
 WQD  H12  C12  N11  111.72  3.000
 WQD  O13  C12  N11  125.91  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
 WQD  CONST_01  C31  N30  C29  C28    0.00   0.0  0
 WQD  CONST_02  N30  C31  N26  C25  180.00   0.0  0
 WQD  CONST_03  N30  C31  N26  C27    0.00   0.0  0
 WQD  CONST_04  N26  C31  N30  C29    0.00   0.0  0
 WQD  CONST_05  O32  C31  N26  C25    0.00   0.0  0
 WQD  CONST_06  O32  C31  N26  C27  180.00   0.0  0
 WQD  CONST_07  O32  C31  N30  C29  180.00   0.0  0
 WQD  CONST_08  O33  C29  N30  C31  180.00   0.0  0
 WQD  CONST_09  H17  N30  C29  C28  180.00   0.0  0
 WQD  CONST_10  O13  C12  N11  C08    0.00   0.0  0
 WQD  CONST_11  H16  N11  C12  O13  180.00   0.0  0
 WQD  Var_01    C08  C09  O10  C05   61.35  30.0  1
 WQD  Var_02    O16  P01  O04  C05  -83.18  30.0  1
 WQD  Var_03    O18  P17  O20  C21  -34.83  30.0  3
 WQD  Var_04    H1   C21  O20  P17   80.41  30.0  2

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
 WQD  chir_01  C22  O34  C21  C23  positiv
 WQD  chir_02  C24  O35  C23  C25  positiv
 WQD  chir_03  C05  O10  O04  C06  positiv
 WQD  chir_04  C06  O15  C05  C07  negativ
 WQD  chir_05  C07  O14  C06  C08  positiv
 WQD  chir_06  C08  N11  C07  C09  positiv
 WQD  chir_07  C23  C22  C24  O36  positiv
 WQD  chir_08  C25  O34  N26  C24  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
 WQD  plan-1  C08  0.020
 WQD  plan-1  N11  0.020
 WQD  plan-1  O13  0.020
 WQD  plan-1  H12  0.020
 WQD  plan-1  H16  0.020
 WQD  plan-1  C12  0.020
 WQD  plan-2  C28  0.020
 WQD  plan-2  C25  0.020
 WQD  plan-2  C27  0.020
 WQD  plan-2  C29  0.020
 WQD  plan-2  C31  0.020
 WQD  plan-2  N26  0.020
 WQD  plan-2  N30  0.020
 WQD  plan-2  O32  0.020
 WQD  plan-2  O33  0.020
 WQD  plan-2  H5   0.020
 WQD  plan-2  H15  0.020
 WQD  plan-2  H17  0.020

