# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 21 19:42:09 2020
#   Inital geometry file: a 174 line input string
#   Ligand name: [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-methyl-3,5-bis(oxidanyl)-4-[[(3~{R})-3-oxidanylbutanoyl]amino]oxan-2-yl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)CC(=O)N[C@H]1[C@H](O)[C@@H](C)O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@@H]1O
#
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
 QUH  QUH  '[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-methyl-3,5-bis(oxidanyl)-4-[[(3~{R})-3-oxidanylbutanoyl]amino]oxan-2-yl] hydrogen phosphate'  ligand  72  41  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QUH
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
 QUH  O1   O  O      0  -0.508   3.5522   2.0314   1.8160
 QUH  C1   C  C      0   0.563   4.6900   2.1089   1.3719
 QUH  C2   C  CH2    0  -0.590   5.7764   2.8643   2.1096
 QUH  C3   C  CH1    0   0.050   5.3194   4.2470   2.5417
 QUH  O2   O  OH1    0  -0.671   4.9884   4.9529   1.3604
 QUH  C4   C  CH3    0  -0.687   6.3970   4.9619   3.3418
 QUH  N1   N  NH1    0  -0.627   5.0818   1.5293   0.2274
 QUH  C5   C  CH1    0  -0.153   4.2528   0.6776  -0.5856
 QUH  C6   C  CH1    0   0.051   4.2580   1.1465  -2.0384
 QUH  O3   O  OH1    0  -0.662   3.7110   2.4403  -2.0866
 QUH  C7   C  CH1    0   0.013   3.4544   0.1778  -2.9147
 QUH  C8   C  CH3    0  -0.700   3.5717   0.5009  -4.3901
 QUH  O4   O  O2     0  -0.499   3.9236  -1.1571  -2.7477
 QUH  C9   C  CH1    0   0.017   4.7424  -0.7735  -0.5198
 QUH  O5   O  OH1    0  -0.697   4.8371  -1.2647   0.7815
 QUH  C10  C  CH1    0   0.239   3.8870  -1.6483  -1.4485
 QUH  O6   O  O2     0  -0.628   2.5436  -1.6903  -1.0310
 QUH  P1   P  P      0   1.363   2.0304  -2.7159   0.1534
 QUH  O7   O  OP    -1  -0.788   2.3921  -2.0943   1.4796
 QUH  O8   O  O      0  -0.778   2.4470  -4.1117  -0.1693
 QUH  O9   O  O2     0  -0.726   0.4534  -2.4661  -0.1721
 QUH  P2   P  P      0   1.348  -0.7924  -3.2825   0.5299
 QUH  O10  O  O      0  -0.790  -0.2997  -4.0610   1.7068
 QUH  O11  O  OP    -1  -0.787  -1.5891  -3.9418  -0.5499
 QUH  O12  O  O2     0  -0.619  -1.5725  -1.9275   1.0367
 QUH  C11  C  CH2    0  -0.158  -2.8924  -2.0742   1.5186
 QUH  C12  C  CH1    0   0.013  -3.3923  -0.7418   2.0175
 QUH  C13  C  CH1    0   0.025  -4.7844  -0.8299   2.6439
 QUH  O13  O  OH1    0  -0.668  -4.6470  -1.0957   4.0170
 QUH  C14  C  CH2    0  -0.561  -5.3879   0.5350   2.3104
 QUH  C15  C  CH1    0   0.219  -4.5677   1.0477   1.1222
 QUH  O14  O  O2     0  -0.489  -3.4960   0.1678   0.9367
 QUH  N2   N  NR6    0  -0.567  -5.2869   1.1991  -0.1408
 QUH  C16  C  CR16   0   0.059  -5.2377   2.4021  -0.7966
 QUH  C17  C  CR6    0  -0.185  -5.8320   2.6482  -1.9765
 QUH  C18  C  CH3    0  -0.707  -5.7653   3.9717  -2.6645
 QUH  C19  C  CR6    0   0.558  -6.5654   1.5675  -2.6036
 QUH  O15  O  O      0  -0.455  -7.1544   1.6464  -3.6664
 QUH  N3   N  NR16   0  -0.733  -6.5528   0.3822  -1.8913
 QUH  C20  C  CR6    0   0.741  -5.9437   0.1227  -0.6906
 QUH  O16  O  O      0  -0.472  -5.9963  -0.9705  -0.1677
 QUH  H1   H  HCH2   0   0.271   6.0389   2.2844   2.9987
 QUH  H2   H  HCH2   0   0.246   6.6880   2.9467   1.5110
 QUH  H3   H  HCH1   0   0.204   4.4341   4.1322   3.1802
 QUH  H4   H  HOH1   0   0.449   4.6294   5.8091   1.6132
 QUH  H5   H  HCH3   0   0.227   6.6386   4.4094   4.2506
 QUH  H6   H  HCH3   0   0.224   7.3141   5.0732   2.7602
 QUH  H7   H  HCH3   0   0.235   6.0623   5.9564   3.6431
 QUH  H8   H  HNH1   0   0.392   6.0446   1.6378  -0.0516
 QUH  H9   H  HCH1   0   0.261   3.2348   0.7395  -0.1941
 QUH  H10  H  HCH1   0   0.210   5.3009   1.1448  -2.3939
 QUH  H11  H  HOH1   0   0.455   4.0232   2.8787  -2.8830
 QUH  H12  H  HCH1   0   0.223   2.4001   0.2484  -2.6165
 QUH  H13  H  HCH3   0   0.229   4.6121   0.4762  -4.7204
 QUH  H14  H  HCH3   0   0.247   3.0034  -0.2107  -4.9893
 QUH  H15  H  HCH3   0   0.232   3.1699   1.4912  -4.6027
 QUH  H16  H  HCH1   0   0.224   5.7597  -0.8008  -0.9313
 QUH  H17  H  HOH1   0   0.451   3.9393  -1.4242   1.1549
 QUH  H18  H  HCH1   0   0.243   4.3057  -2.6608  -1.4920
 QUH  H21  H  HCH2   0   0.216  -3.5629  -2.4408   0.7332
 QUH  H22  H  HCH2   0   0.214  -2.9379  -2.7849   2.3530
 QUH  H23  H  HCH1   0   0.228  -2.6970  -0.3450   2.7718
 QUH  H24  H  HCH1   0   0.232  -5.3606  -1.6201   2.1538
 QUH  H25  H  HOH1   0   0.457  -5.5049  -1.3602   4.3613
 QUH  H26  H  HCH2   0   0.275  -6.4574   0.5016   2.1105
 QUH  H27  H  HCH2   0   0.267  -5.2343   1.2098   3.1542
 QUH  H28  H  HCH1   0   0.254  -4.1963   2.0518   1.3407
 QUH  H29  H  HCR6   0   0.317  -4.6743   3.1731  -0.2883
 QUH  H30  H  HCH3   0   0.247  -5.3180   3.8818  -3.6553
 QUH  H31  H  HCH3   0   0.247  -6.7588   4.4024  -2.7975
 QUH  H32  H  HCH3   0   0.247  -5.1680   4.6787  -2.0912
 QUH  H33  H  HNR6   0   0.425  -7.0508  -0.3999  -2.2986

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
 QUH  O15  C19  double  1.218  0.020  1.218
 QUH  N3   C19  single  1.383  0.020  1.383
 QUH  N3   C20  single  1.371  0.020  1.371
 QUH  C19  C17  single  1.449  0.020  1.449
 QUH  O16  C20  double  1.213  0.020  1.213
 QUH  C20  N2   single  1.376  0.020  1.376
 QUH  C17  C18  single  1.493  0.020  1.493
 QUH  C17  C16  double  1.344  0.020  1.344
 QUH  N2   C16  single  1.371  0.020  1.371
 QUH  N2   C15  single  1.461  0.020  1.461
 QUH  C15  O14  single  1.399  0.020  1.399
 QUH  C15  C14  single  1.532  0.020  1.532
 QUH  O8   P1   deloc   1.492  0.020  1.492
 QUH  O14  C12  single  1.416  0.020  1.416
 QUH  C14  C13  single  1.529  0.020  1.529
 QUH  P1   O7   deloc   1.509  0.020  1.509
 QUH  P1   O9   single  1.630  0.020  1.630
 QUH  P1   O6   single  1.649  0.020  1.649
 QUH  O9   P2   single  1.647  0.020  1.647
 QUH  C12  C13  single  1.529  0.020  1.529
 QUH  C12  C11  single  1.508  0.020  1.508
 QUH  C13  O13  single  1.405  0.020  1.405
 QUH  O12  C11  single  1.413  0.020  1.413
 QUH  O12  P2   single  1.644  0.020  1.644
 QUH  O6   C10  single  1.407  0.020  1.407
 QUH  O1   C1   double  1.224  0.020  1.224
 QUH  P2   O10  deloc   1.495  0.020  1.495
 QUH  P2   O11  deloc   1.495  0.020  1.495
 QUH  C3   C4   single  1.521  0.020  1.521
 QUH  C3   O2   single  1.415  0.020  1.415
 QUH  C3   C2   single  1.519  0.020  1.519
 QUH  O5   C9   single  1.394  0.020  1.394
 QUH  C1   C2   single  1.515  0.020  1.515
 QUH  C1   N1   single  1.341  0.020  1.341
 QUH  C10  C9   single  1.536  0.020  1.536
 QUH  C10  O4   single  1.389  0.020  1.389
 QUH  C5   C9   single  1.533  0.020  1.533
 QUH  C5   N1   single  1.440  0.020  1.440
 QUH  C5   C6   single  1.527  0.020  1.527
 QUH  O4   C7   single  1.425  0.020  1.425
 QUH  C7   C6   single  1.534  0.020  1.534
 QUH  C7   C8   single  1.515  0.020  1.515
 QUH  C6   O3   single  1.405  0.020  1.405
 QUH  C2   H1   single  0.970  0.020  1.090
 QUH  C2   H2   single  0.970  0.020  1.090
 QUH  C3   H3   single  0.970  0.020  1.090
 QUH  O2   H4   single  0.850  0.020  0.980
 QUH  C4   H5   single  0.970  0.020  1.090
 QUH  C4   H6   single  0.970  0.020  1.090
 QUH  C4   H7   single  0.970  0.020  1.090
 QUH  N1   H8   single  0.860  0.020  1.020
 QUH  C5   H9   single  0.970  0.020  1.090
 QUH  C6   H10  single  0.970  0.020  1.090
 QUH  O3   H11  single  0.850  0.020  0.980
 QUH  C7   H12  single  0.970  0.020  1.090
 QUH  C8   H13  single  0.970  0.020  1.090
 QUH  C8   H14  single  0.970  0.020  1.090
 QUH  C8   H15  single  0.970  0.020  1.090
 QUH  C9   H16  single  0.970  0.020  1.090
 QUH  O5   H17  single  0.850  0.020  0.980
 QUH  C10  H18  single  0.970  0.020  1.090
 QUH  C11  H21  single  0.970  0.020  1.090
 QUH  C11  H22  single  0.970  0.020  1.090
 QUH  C12  H23  single  0.970  0.020  1.090
 QUH  C13  H24  single  0.970  0.020  1.090
 QUH  O13  H25  single  0.850  0.020  0.980
 QUH  C14  H26  single  0.970  0.020  1.090
 QUH  C14  H27  single  0.970  0.020  1.090
 QUH  C15  H28  single  0.970  0.020  1.090
 QUH  C16  H29  single  0.930  0.020  1.080
 QUH  C18  H30  single  0.970  0.020  1.090
 QUH  C18  H31  single  0.970  0.020  1.090
 QUH  C18  H32  single  0.970  0.020  1.090
 QUH  N3   H33  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
 QUH  N1   C1   C2   114.93  3.000
 QUH  N1   C1   O1   123.63  3.000
 QUH  C2   C1   O1   121.44  3.000
 QUH  H2   C2   H1   106.56  3.000
 QUH  H2   C2   C3   109.75  3.000
 QUH  H1   C2   C3   108.89  3.000
 QUH  H2   C2   C1   111.64  3.000
 QUH  H1   C2   C1   107.68  3.000
 QUH  C3   C2   C1   112.12  3.000
 QUH  H3   C3   C4   108.34  3.000
 QUH  H3   C3   O2   110.43  3.000
 QUH  C4   C3   O2   111.74  3.000
 QUH  H3   C3   C2   108.23  3.000
 QUH  O2   C3   C2   106.68  3.000
 QUH  C4   C3   C2   111.37  3.000
 QUH  H4   O2   C3   108.16  3.000
 QUH  H7   C4   H6   108.16  3.000
 QUH  H7   C4   H5   107.42  3.000
 QUH  H6   C4   H5   108.03  3.000
 QUH  H7   C4   C3   110.87  3.000
 QUH  H6   C4   C3   111.28  3.000
 QUH  H5   C4   C3   110.93  3.000
 QUH  H8   N1   C5   117.20  3.000
 QUH  H8   N1   C1   117.94  3.000
 QUH  C5   N1   C1   124.69  3.000
 QUH  H9   C5   C9   109.63  3.000
 QUH  H9   C5   C6   109.07  3.000
 QUH  C9   C5   C6   109.30  3.000
 QUH  H9   C5   N1   107.49  3.000
 QUH  C6   C5   N1   110.71  3.000
 QUH  C9   C5   N1   110.60  3.000
 QUH  H10  C6   C7   108.10  3.000
 QUH  H10  C6   O3   111.02  3.000
 QUH  C7   C6   O3   110.97  3.000
 QUH  H10  C6   C5   108.04  3.000
 QUH  O3   C6   C5   108.30  3.000
 QUH  C7   C6   C5   110.36  3.000
 QUH  H11  O3   C6   108.78  3.000
 QUH  H12  C7   O4   110.16  3.000
 QUH  H12  C7   C8   108.97  3.000
 QUH  O4   C7   C8   106.77  3.000
 QUH  H12  C7   C6   107.90  3.000
 QUH  C8   C7   C6   112.41  3.000
 QUH  O4   C7   C6   110.62  3.000
 QUH  H15  C8   H14  107.08  3.000
 QUH  H15  C8   H13  108.24  3.000
 QUH  H14  C8   H13  108.40  3.000
 QUH  H15  C8   C7   110.82  3.000
 QUH  H14  C8   C7   110.84  3.000
 QUH  H13  C8   C7   111.32  3.000
 QUH  C10  O4   C7   115.60  3.000
 QUH  H16  C9   C10  105.98  3.000
 QUH  H16  C9   O5   106.15  3.000
 QUH  C10  C9   O5   113.67  3.000
 QUH  H16  C9   C5   107.66  3.000
 QUH  C10  C9   C5   109.59  3.000
 QUH  O5   C9   C5   113.28  3.000
 QUH  H17  O5   C9   110.42  3.000
 QUH  H18  C10  O6   110.41  3.000
 QUH  H18  C10  C9   109.71  3.000
 QUH  O6   C10  C9   111.67  3.000
 QUH  H18  C10  O4   106.21  3.000
 QUH  C9   C10  O4   110.44  3.000
 QUH  O6   C10  O4   108.24  3.000
 QUH  P1   O6   C10  121.92  3.000
 QUH  O9   P1   O8   111.75  3.000
 QUH  O9   P1   O7   110.15  3.000
 QUH  O8   P1   O7   120.58  3.000
 QUH  O9   P1   O6    93.57  3.000
 QUH  O7   P1   O6   107.49  3.000
 QUH  O8   P1   O6   109.86  3.000
 QUH  P2   O9   P1   124.82  3.000
 QUH  O12  P2   O11  109.47  3.000
 QUH  O11  P2   O10  120.98  3.000
 QUH  O12  P2   O10  110.06  3.000
 QUH  O11  P2   O9   108.29  3.000
 QUH  O10  P2   O9   110.15  3.000
 QUH  O12  P2   O9    94.69  3.000
 QUH  C11  O12  P2   117.58  3.000
 QUH  H22  C11  H21  107.64  3.000
 QUH  H22  C11  C12  107.88  3.000
 QUH  H21  C11  C12  109.26  3.000
 QUH  H22  C11  O12  111.43  3.000
 QUH  H21  C11  O12  111.22  3.000
 QUH  C12  C11  O12  109.32  3.000
 QUH  H23  C12  O14  109.75  3.000
 QUH  H23  C12  C13  108.38  3.000
 QUH  O14  C12  C13  106.44  3.000
 QUH  H23  C12  C11  109.63  3.000
 QUH  C13  C12  C11  112.73  3.000
 QUH  O14  C12  C11  109.83  3.000
 QUH  H24  C13  C14  109.82  3.000
 QUH  H24  C13  O13  110.65  3.000
 QUH  C14  C13  O13  114.86  3.000
 QUH  H24  C13  C12  109.73  3.000
 QUH  O13  C13  C12  108.80  3.000
 QUH  C14  C13  C12  102.62  3.000
 QUH  H25  O13  C13  108.34  3.000
 QUH  H27  C14  H26  107.42  3.000
 QUH  H27  C14  C15  108.50  3.000
 QUH  H26  C14  C15  113.20  3.000
 QUH  H27  C14  C13  109.13  3.000
 QUH  H26  C14  C13  113.60  3.000
 QUH  C15  C14  C13  104.86  3.000
 QUH  H28  C15  N2   104.18  3.000
 QUH  H28  C15  O14  110.13  3.000
 QUH  N2   C15  O14  109.12  3.000
 QUH  H28  C15  C14  109.54  3.000
 QUH  O14  C15  C14  107.61  3.000
 QUH  N2   C15  C14  116.19  3.000
 QUH  C15  O14  C12  111.03  3.000
 QUH  C20  N2   C16  120.84  3.000
 QUH  C16  N2   C15  119.12  3.000
 QUH  C20  N2   C15  119.96  3.000
 QUH  H29  C16  C17  120.82  3.000
 QUH  H29  C16  N2   114.80  3.000
 QUH  C17  C16  N2   124.39  3.000
 QUH  C19  C17  C18  118.97  3.000
 QUH  C18  C17  C16  123.17  3.000
 QUH  C19  C17  C16  117.86  3.000
 QUH  H32  C18  H31  107.91  3.000
 QUH  H32  C18  H30  107.87  3.000
 QUH  H31  C18  H30  107.18  3.000
 QUH  H32  C18  C17  110.94  3.000
 QUH  H31  C18  C17  111.43  3.000
 QUH  H30  C18  C17  111.33  3.000
 QUH  N3   C19  O15  120.63  3.000
 QUH  N3   C19  C17  114.32  3.000
 QUH  O15  C19  C17  125.05  3.000
 QUH  H33  N3   C20  115.12  3.000
 QUH  H33  N3   C19  116.76  3.000
 QUH  C20  N3   C19  128.12  3.000
 QUH  O16  C20  N3   121.93  3.000
 QUH  O16  C20  N2   123.62  3.000
 QUH  N3   C20  N2   114.46  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
 QUH  CONST_01  N3   C20  N2   C15  180.00   0.0  0
 QUH  CONST_02  C19  N3   C20  N2     0.00   0.0  0
 QUH  CONST_03  N3   C20  N2   C16    0.00   0.0  0
 QUH  CONST_04  C20  N3   C19  C17    0.00   0.0  0
 QUH  CONST_05  O16  C20  N2   C15    0.00   0.0  0
 QUH  CONST_06  O16  C20  N2   C16  180.00   0.0  0
 QUH  CONST_07  O16  C20  N3   C19  180.00   0.0  0
 QUH  CONST_08  C20  N3   C19  O15  180.00   0.0  0
 QUH  CONST_09  H33  N3   C20  N2   180.00   0.0  0
 QUH  CONST_10  C5   N1   C1   O1     0.00   0.0  0
 QUH  CONST_11  C5   N1   C1   C2   180.00   0.0  0
 QUH  CONST_12  H8   N1   C1   O1   180.00   0.0  0
 QUH  Var_01    H30  C18  C17  C16  121.03  30.0  3
 QUH  Var_02    O8   P1   O6   C10  -52.82  30.0  1
 QUH  Var_03    C12  C11  O12  P2   176.18  30.0  3
 QUH  Var_04    C3   C2   C1   O1   -48.69  30.0  3
 QUH  Var_05    O12  P2   O9   P1   125.70  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
 QUH  chir_01  C3   C4   O2   C2   negativ
 QUH  chir_02  C5   N1   C9   C6   positiv
 QUH  chir_03  C6   O3   C7   C5   positiv
 QUH  chir_04  C7   O4   C6   C8   negativ
 QUH  chir_05  C9   O5   C10  C5   negativ
 QUH  chir_06  C10  O6   O4   C9   negativ
 QUH  chir_09  C12  O14  C13  C11  negativ
 QUH  chir_10  C13  O13  C12  C14  positiv
 QUH  chir_11  C15  O14  N2   C14  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
 QUH  plan-1  O1   0.020
 QUH  plan-1  C1   0.020
 QUH  plan-1  C2   0.020
 QUH  plan-1  N1   0.020
 QUH  plan-1  C5   0.020
 QUH  plan-1  H8   0.020
 QUH  plan-2  C15  0.020
 QUH  plan-2  N2   0.020
 QUH  plan-2  C16  0.020
 QUH  plan-2  C17  0.020
 QUH  plan-2  C18  0.020
 QUH  plan-2  C19  0.020
 QUH  plan-2  O15  0.020
 QUH  plan-2  N3   0.020
 QUH  plan-2  C20  0.020
 QUH  plan-2  O16  0.020
 QUH  plan-2  H29  0.020
 QUH  plan-2  H33  0.020

