# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 27 19:45:06 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2R,3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl {(2R,3S,5R)-3-hydroxy-5-[(5R)-5-methyl-2,4-dioxotetrahydropyrimidin-1(2H)-yl]tetrahydrofuran-2-yl}methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]3O[C@H](C)C(=O)[C@H](O)[C@H]3O)O2)C(=O)NC1=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
 T6K  T6K  '(2R,3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl {(2R,3S,5R)-3-hydroxy-5-[(5R)-5-methyl-2,4-dioxotetrahydropyrimidin-1(2H)-yl]tetrahydrofuran-2-yl}methyl dihydrogen diphosphate (non-preferred name)'  ligand  59  35  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T6K
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
 T6K  C01  C  C      0   0.380  -6.5995  -1.9781   0.8642
 T6K  C02  C  CH1    0  -0.084  -5.3266  -2.4170   0.1532
 T6K  C03  C  CH3    0  -0.687  -5.5951  -2.6506  -1.3334
 T6K  O04  O  O2     0  -0.488  -4.2470  -1.5377   0.3868
 T6K  C05  C  CH1    0   0.311  -4.5090  -0.1658   0.2334
 T6K  O06  O  O2     0  -0.629  -3.3244   0.4907   0.5102
 T6K  P07  P  P      0   1.327  -2.5017   1.1739  -0.7627
 T6K  O08  O  O      0  -0.782  -2.2238   0.1221  -1.7864
 T6K  O09  O  OP    -1  -0.789  -3.1788   2.4525  -1.1388
 T6K  O10  O  O2     0  -0.733  -1.1723   1.4667   0.1465
 T6K  P11  P  P      0   1.342  -0.0508   2.6096  -0.2283
 T6K  O12  O  O      0  -0.799   0.1242   2.7088  -1.7107
 T6K  O13  O  OP    -1  -0.787  -0.2941   3.8360   0.5924
 T6K  O14  O  O2     0  -0.620   1.1937   1.7546   0.4250
 T6K  C15  C  CH2    0  -0.159   2.4992   2.2484   0.2072
 T6K  C16  C  CH1    0   0.020   3.4419   1.6511   1.2225
 T6K  O17  O  O2     0  -0.495   3.5224   0.2516   1.0406
 T6K  C18  C  CH1    0   0.230   4.8083  -0.2305   1.3493
 T6K  C19  C  CH2    0  -0.552   5.7063   0.9971   1.5592
 T6K  C20  C  CH1    0   0.020   4.8684   2.1848   1.0901
 T6K  O21  O  OH1    0  -0.670   4.9980   3.3476   1.8710
 T6K  N22  N  NT     0  -0.519   5.2165  -1.1847   0.3389
 T6K  C23  C  CH2    0  -0.299   5.5280  -2.5548   0.7132
 T6K  C24  C  CH1    0  -0.417   4.9521  -3.5342  -0.2938
 T6K  C25  C  CH3    0  -0.655   3.4220  -3.5632  -0.2796
 T6K  C26  C  C      0   0.554   5.4430  -3.1676  -1.6693
 T6K  O27  O  O      0  -0.438   5.6107  -3.9578  -2.5725
 T6K  N28  N  NH1    0  -0.715   5.6535  -1.8247  -1.8472
 T6K  C29  C  C      0   0.734   5.3800  -0.7965  -0.9434
 T6K  O30  O  O      0  -0.482   5.3135   0.3499  -1.3433
 T6K  C31  C  CH1    0  -0.037  -5.5843   0.2686   1.2216
 T6K  O32  O  OH1    0  -0.664  -5.1458  -0.0678   2.5116
 T6K  C33  C  CH1    0  -0.124  -6.8789  -0.4797   0.9204
 T6K  O34  O  OH1    0  -0.653  -7.3525  -0.0656  -0.3406
 T6K  O35  O  O      0  -0.381  -7.3883  -2.7882   1.2891
 T6K  H1   H  HCH1   0   0.277  -5.0283  -3.3699   0.5977
 T6K  H2   H  HCH3   0   0.241  -5.9259  -1.7515  -1.8495
 T6K  H3   H  HCH3   0   0.251  -4.6871  -3.0124  -1.8151
 T6K  H4   H  HCH3   0   0.244  -6.3654  -3.4115  -1.4589
 T6K  H5   H  HCH1   0   0.206  -4.8678   0.0490  -0.7842
 T6K  H8   H  HCH2   0   0.213   2.8477   1.9988  -0.8012
 T6K  H9   H  HCH2   0   0.210   2.5459   3.3393   0.3132
 T6K  H10  H  HCH1   0   0.219   3.0784   1.8801   2.2361
 T6K  H11  H  HCH1   0   0.243   4.7715  -0.8125   2.2744
 T6K  H12  H  HCH2   0   0.256   5.9051   1.1077   2.6271
 T6K  H13  H  HCH2   0   0.266   6.6662   0.9110   1.0526
 T6K  H14  H  HCH1   0   0.228   5.0853   2.3998   0.0401
 T6K  H15  H  HOH1   0   0.456   5.8170   3.7846   1.6215
 T6K  H16  H  HCH2   0   0.270   6.6105  -2.6925   0.7983
 T6K  H17  H  HCH2   0   0.275   5.1013  -2.7512   1.6949
 T6K  H18  H  HCH1   0   0.296   5.3322  -4.5305  -0.0623
 T6K  H19  H  HCH3   0   0.237   2.9924  -2.5877  -0.5095
 T6K  H20  H  HCH3   0   0.251   3.0371  -4.2817  -1.0019
 T6K  H21  H  HCH3   0   0.251   3.0695  -3.8583   0.7086
 T6K  H22  H  HNH1   0   0.415   5.8750  -1.5139  -2.7847
 T6K  H23  H  HCH1   0   0.244  -5.7557   1.3469   1.1018
 T6K  H24  H  HOH1   0   0.459  -5.7596   0.3085   3.1501
 T6K  H25  H  HCH1   0   0.263  -7.6157  -0.2860   1.7114
 T6K  H26  H  HOH1   0   0.468  -8.2543  -0.3823  -0.4572

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
 T6K  O08  P07  deloc   1.494  0.020  1.494
 T6K  O34  C33  single  1.409  0.020  1.409
 T6K  O12  P11  deloc   1.496  0.020  1.496
 T6K  O32  C31  single  1.403  0.020  1.403
 T6K  C33  C01  single  1.525  0.020  1.525
 T6K  C33  C31  single  1.525  0.020  1.525
 T6K  O13  P11  deloc   1.496  0.020  1.496
 T6K  P07  O06  single  1.663  0.020  1.663
 T6K  P07  O09  deloc   1.495  0.020  1.495
 T6K  P07  O10  single  1.637  0.020  1.637
 T6K  O06  C05  single  1.382  0.020  1.382
 T6K  C25  C24  single  1.530  0.020  1.530
 T6K  O35  C01  double  1.208  0.020  1.208
 T6K  C01  C02  single  1.523  0.020  1.523
 T6K  C31  C05  single  1.524  0.020  1.524
 T6K  P11  O10  single  1.645  0.020  1.645
 T6K  P11  O14  single  1.645  0.020  1.645
 T6K  O27  C26  double  1.212  0.020  1.212
 T6K  C05  O04  single  1.405  0.020  1.405
 T6K  C02  O04  single  1.412  0.020  1.412
 T6K  C02  C03  single  1.529  0.020  1.529
 T6K  C26  C24  single  1.506  0.020  1.506
 T6K  C26  N28  single  1.371  0.020  1.371
 T6K  C24  C23  single  1.518  0.020  1.518
 T6K  O14  C15  single  1.413  0.020  1.413
 T6K  N28  C29  single  1.396  0.020  1.396
 T6K  C23  N22  single  1.454  0.020  1.454
 T6K  C15  C16  single  1.509  0.020  1.509
 T6K  C19  C20  single  1.527  0.020  1.527
 T6K  C19  C18  single  1.535  0.020  1.535
 T6K  N22  C29  single  1.350  0.020  1.350
 T6K  N22  C18  single  1.448  0.020  1.448
 T6K  C29  O30  double  1.216  0.020  1.216
 T6K  C20  C16  single  1.529  0.020  1.529
 T6K  C20  O21  single  1.407  0.020  1.407
 T6K  C18  O17  single  1.408  0.020  1.408
 T6K  C16  O17  single  1.414  0.020  1.414
 T6K  C02  H1   single  0.970  0.020  1.090
 T6K  C03  H2   single  0.970  0.020  1.090
 T6K  C03  H3   single  0.970  0.020  1.090
 T6K  C03  H4   single  0.970  0.020  1.090
 T6K  C05  H5   single  0.970  0.020  1.090
 T6K  C15  H8   single  0.970  0.020  1.090
 T6K  C15  H9   single  0.970  0.020  1.090
 T6K  C16  H10  single  0.970  0.020  1.090
 T6K  C18  H11  single  0.970  0.020  1.090
 T6K  C19  H12  single  0.970  0.020  1.090
 T6K  C19  H13  single  0.970  0.020  1.090
 T6K  C20  H14  single  0.970  0.020  1.090
 T6K  O21  H15  single  0.850  0.020  0.980
 T6K  C23  H16  single  0.970  0.020  1.090
 T6K  C23  H17  single  0.970  0.020  1.090
 T6K  C24  H18  single  0.970  0.020  1.090
 T6K  C25  H19  single  0.970  0.020  1.090
 T6K  C25  H20  single  0.970  0.020  1.090
 T6K  C25  H21  single  0.970  0.020  1.090
 T6K  N28  H22  single  0.860  0.020  1.020
 T6K  C31  H23  single  0.970  0.020  1.090
 T6K  O32  H24  single  0.850  0.020  0.980
 T6K  C33  H25  single  0.970  0.020  1.090
 T6K  O34  H26  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
 T6K  O35  C01  C33  121.75  3.000
 T6K  O35  C01  C02  121.12  3.000
 T6K  C33  C01  C02  116.98  3.000
 T6K  H1   C02  O04  105.49  3.000
 T6K  H1   C02  C03  108.08  3.000
 T6K  O04  C02  C03  112.98  3.000
 T6K  H1   C02  C01  106.84  3.000
 T6K  C03  C02  C01  110.57  3.000
 T6K  O04  C02  C01  112.48  3.000
 T6K  H4   C03  H3   107.83  3.000
 T6K  H4   C03  H2   107.90  3.000
 T6K  H3   C03  H2   108.55  3.000
 T6K  H4   C03  C02  110.04  3.000
 T6K  H3   C03  C02  109.53  3.000
 T6K  H2   C03  C02  112.86  3.000
 T6K  C05  O04  C02  116.58  3.000
 T6K  H5   C05  C31  108.31  3.000
 T6K  H5   C05  O06  111.84  3.000
 T6K  C31  C05  O06  109.85  3.000
 T6K  H5   C05  O04  110.63  3.000
 T6K  C31  C05  O04  109.82  3.000
 T6K  O06  C05  O04  106.38  3.000
 T6K  P07  O06  C05  117.77  3.000
 T6K  O10  P07  O09  110.77  3.000
 T6K  O10  P07  O08  110.82  3.000
 T6K  O09  P07  O08  120.94  3.000
 T6K  O10  P07  O06   92.87  3.000
 T6K  O09  P07  O06  108.66  3.000
 T6K  O08  P07  O06  109.11  3.000
 T6K  P11  O10  P07  123.47  3.000
 T6K  O14  P11  O13  109.35  3.000
 T6K  O14  P11  O12  109.85  3.000
 T6K  O13  P11  O12  120.56  3.000
 T6K  O14  P11  O10   93.68  3.000
 T6K  O13  P11  O10  109.50  3.000
 T6K  O12  P11  O10  110.59  3.000
 T6K  C15  O14  P11  117.14  3.000
 T6K  H9   C15  H8   107.58  3.000
 T6K  H9   C15  C16  107.58  3.000
 T6K  H8   C15  C16  109.30  3.000
 T6K  H9   C15  O14  111.84  3.000
 T6K  H8   C15  O14  110.86  3.000
 T6K  C16  C15  O14  109.59  3.000
 T6K  H10  C16  C20  108.38  3.000
 T6K  H10  C16  O17  110.07  3.000
 T6K  C20  C16  O17  106.34  3.000
 T6K  H10  C16  C15  109.32  3.000
 T6K  O17  C16  C15  109.93  3.000
 T6K  C20  C16  C15  112.74  3.000
 T6K  C18  O17  C16  111.28  3.000
 T6K  H11  C18  N22  104.42  3.000
 T6K  H11  C18  C19  109.24  3.000
 T6K  N22  C18  C19  117.21  3.000
 T6K  H11  C18  O17  109.70  3.000
 T6K  N22  C18  O17  109.27  3.000
 T6K  C19  C18  O17  106.89  3.000
 T6K  H13  C19  H12  107.61  3.000
 T6K  H13  C19  C20  113.72  3.000
 T6K  H12  C19  C20  108.75  3.000
 T6K  H13  C19  C18  112.88  3.000
 T6K  H12  C19  C18  108.74  3.000
 T6K  C20  C19  C18  105.00  3.000
 T6K  H14  C20  O21  110.62  3.000
 T6K  H14  C20  C19  109.82  3.000
 T6K  O21  C20  C19  114.94  3.000
 T6K  H14  C20  C16  109.69  3.000
 T6K  O21  C20  C16  109.06  3.000
 T6K  C19  C20  C16  102.35  3.000
 T6K  H15  O21  C20  108.07  3.000
 T6K  C29  N22  C23  119.31  3.000
 T6K  C29  N22  C18  120.49  3.000
 T6K  C23  N22  C18  120.10  3.000
 T6K  H17  C23  H16  107.15  3.000
 T6K  H17  C23  C24  109.46  3.000
 T6K  H16  C23  C24  110.22  3.000
 T6K  H17  C23  N22  108.56  3.000
 T6K  H16  C23  N22  110.51  3.000
 T6K  C24  C23  N22  110.85  3.000
 T6K  H18  C24  C26  107.61  3.000
 T6K  H18  C24  C25  109.21  3.000
 T6K  C26  C24  C25  109.82  3.000
 T6K  H18  C24  C23  108.43  3.000
 T6K  C26  C24  C23  108.98  3.000
 T6K  C25  C24  C23  112.66  3.000
 T6K  H21  C25  H20  107.96  3.000
 T6K  H21  C25  H19  107.81  3.000
 T6K  H20  C25  H19  108.13  3.000
 T6K  H21  C25  C24  109.69  3.000
 T6K  H20  C25  C24  111.08  3.000
 T6K  H19  C25  C24  112.03  3.000
 T6K  N28  C26  O27  121.39  3.000
 T6K  N28  C26  C24  114.02  3.000
 T6K  O27  C26  C24  124.56  3.000
 T6K  H22  N28  C29  114.61  3.000
 T6K  H22  N28  C26  117.03  3.000
 T6K  C29  N28  C26  127.40  3.000
 T6K  O30  C29  N28  119.48  3.000
 T6K  O30  C29  N22  125.24  3.000
 T6K  N28  C29  N22  115.28  3.000
 T6K  H23  C31  C33  109.13  3.000
 T6K  H23  C31  O32  112.60  3.000
 T6K  C33  C31  O32  109.21  3.000
 T6K  H23  C31  C05  108.62  3.000
 T6K  C33  C31  C05  109.34  3.000
 T6K  O32  C31  C05  107.90  3.000
 T6K  H24  O32  C31  108.47  3.000
 T6K  H25  C33  O34  111.55  3.000
 T6K  H25  C33  C31  109.92  3.000
 T6K  O34  C33  C31  108.52  3.000
 T6K  H25  C33  C01  108.83  3.000
 T6K  C31  C33  C01  109.49  3.000
 T6K  O34  C33  C01  108.50  3.000
 T6K  H26  O34  C33  109.05  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
 T6K  CONST_01  N28  C29  N22  C18  180.00   0.0  0
 T6K  CONST_03  N28  C29  N22  C23    0.00   0.0  0
 T6K  CONST_04  C29  N28  C26  C24    0.00   0.0  0
 T6K  CONST_05  O30  C29  N22  C18    0.00   0.0  0
 T6K  CONST_06  O30  C29  N22  C23  180.00   0.0  0
 T6K  CONST_08  C29  N28  C26  O27  180.00   0.0  0
 T6K  CONST_09  H22  N28  C29  N22  180.00   0.0  0
 T6K  Var_01    H16  C23  N22  C18  -99.35  30.0  1
 T6K  Var_02    O08  P07  O06  C05  -56.23  30.0  2
 T6K  Var_03    C16  C15  O14  P11  161.00  30.0  3
 T6K  Var_04    O12  P11  O10  P07  -35.27  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
 T6K  chir_01  C02  C01  O04  C03  positiv
 T6K  chir_02  C05  O06  O04  C31  negativ
 T6K  chir_05  C16  C15  C20  O17  positiv
 T6K  chir_06  C18  O17  N22  C19  negativ
 T6K  chir_07  C20  O21  C16  C19  positiv
 T6K  chir_08  C24  C23  C26  C25  positiv
 T6K  chir_09  C31  O32  C33  C05  positiv
 T6K  chir_10  C33  O34  C31  C01  positiv

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
 T6K  plan-1  C01  0.020
 T6K  plan-1  C02  0.020
 T6K  plan-1  C33  0.020
 T6K  plan-1  O35  0.020
 T6K  plan-2  C18  0.020
 T6K  plan-2  N22  0.020
 T6K  plan-2  C23  0.020
 T6K  plan-2  C24  0.020
 T6K  plan-2  C26  0.020
 T6K  plan-2  O27  0.020
 T6K  plan-2  N28  0.020
 T6K  plan-2  C29  0.020
 T6K  plan-2  O30  0.020
 T6K  plan-2  H22  0.020

