# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 03:00:06 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2S,3R,4S,5R,6R)-6-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@@H]1O)C(O)=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
 UGB  UGB  '(2S,3R,4S,5R,6R)-6-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid'  ligand  56  37  .  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_UGB
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
 UGB  N1    N  NR6    0  -0.567   4.5338  -0.6137   0.7713
 UGB  C2    C  CR6    0   0.734   5.3580  -1.5596   1.3484
 UGB  O2    O  O      0  -0.479   6.2471  -1.2856   2.1275
 UGB  N3    N  NR16   0  -0.732   5.0913  -2.8505   0.9765
 UGB  C4    C  CR6    0   0.567   4.1178  -3.3068   0.0998
 UGB  O4    O  O      0  -0.468   4.0075  -4.4969  -0.1334
 UGB  C5    C  CR16   0  -0.527   3.3041  -2.2509  -0.4447
 UGB  C6    C  CR16   0   0.074   3.5414  -0.9752  -0.0958
 UGB  PA    P  P      0   1.350   0.4996   1.6829  -1.3559
 UGB  PB    P  P      0   1.354  -2.3173   1.2209  -0.9764
 UGB  C1'   C  CH1    0   0.254  -4.1260   0.4130   0.7686
 UGB  O1A   O  OP    -1  -0.773   1.1566   0.3683  -1.6591
 UGB  O1B   O  OP    -1  -0.779  -2.2216   0.3537  -2.1882
 UGB  C1D   C  CH1    0   0.215   4.7688   0.7936   1.0783
 UGB  C2'   C  CH1    0  -0.019  -4.2535  -0.3943   2.0640
 UGB  O2'   O  OH1    0  -0.674  -3.2946  -0.0174   3.0231
 UGB  O2A   O  O      0  -0.796   0.1850   2.6344  -2.4667
 UGB  O2B   O  O      0  -0.792  -3.0704   2.5128  -0.9892
 UGB  C2D   C  CH1    0  -0.043   5.5074   1.5496  -0.0241
 UGB  O2D   O  OH1    0  -0.652   6.8827   1.3391   0.0872
 UGB  C3'   C  CH1    0   0.027  -4.0772  -1.8787   1.7762
 UGB  O3'   O  OH1    0  -0.678  -4.2727  -2.6633   2.9289
 UGB  O3A   O  O2     0  -0.734  -0.7972   1.4724  -0.3807
 UGB  O3B   O  O2     0  -0.630  -2.8061   0.3212   0.3193
 UGB  C3D   C  CH1    0  -0.037   5.0498   2.9849   0.2549
 UGB  O3D   O  OH1    0  -0.669   5.7486   3.5345   1.3413
 UGB  C4'   C  CH1    0   0.000  -5.0630  -2.3210   0.7053
 UGB  O4'   O  OH1    0  -0.708  -6.3667  -2.2998   1.2254
 UGB  C4D   C  CH1    0  -0.031   3.5959   2.7558   0.6495
 UGB  O4D   O  O2     0  -0.492   3.5423   1.4433   1.2215
 UGB  C5'   C  CH1    0  -0.139  -4.9192  -1.4191  -0.5218
 UGB  O5'   O  O2     0  -0.507  -5.0429  -0.0424  -0.1783
 UGB  C5D   C  CH2    0  -0.160   2.6762   2.8652  -0.5529
 UGB  O5D   O  O2     0  -0.618   1.3766   2.4606  -0.1947
 UGB  C6'   C  C      0   0.437  -5.9968  -1.6682  -1.6068
 UGB  H5    H  HCR6   0   0.285   2.4985  -2.4846  -1.1234
 UGB  H6    H  HCR6   0   0.350   2.9121  -0.1869  -0.4914
 UGB  H1'   H  HCH1   0   0.228  -4.3949   1.4596   0.9519
 UGB  H1D   H  HCH1   0   0.269   5.3472   0.8165   2.0050
 UGB  HO2'  H  HOH1   0   0.456  -3.5575   0.8221   3.4118
 UGB  H2D   H  HCH1   0   0.251   5.1274   1.2323  -1.0042
 UGB  HO2D  H  HOH1   0   0.470   7.3049   1.5975  -0.7385
 UGB  HO3'  H  HOH1   0   0.446  -3.6536  -2.3560   3.5990
 UGB  H3D   H  HCH1   0   0.251   5.1280   3.6211  -0.6371
 UGB  HO3D  H  HOH1   0   0.449   6.6801   3.3049   1.2392
 UGB  H4'   H  HCH1   0   0.202  -4.7803  -3.3379   0.3838
 UGB  HO4'  H  HOH1   0   0.439  -6.9079  -2.4223   0.4135
 UGB  H4D   H  HCH1   0   0.262   3.2813   3.4709   1.4157
 UGB  H5'   H  HCH1   0   0.222  -3.9361  -1.6051  -0.9722
 UGB  H5D   H  HCH2   0   0.233   2.6793   3.9098  -0.8839
 UGB  H5DA  H  HCH2   0   0.207   3.0754   2.2720  -1.3855
 UGB  HN3   H  HNR6   0   0.425   5.6963  -3.5491   1.3904
 UGB  H2'   H  HCH1   0   0.221  -5.2717  -0.2303   2.4398
 UGB  O'P   O  O      0  -0.568  -5.8314  -1.1015  -2.6907
 UGB  O'Q   O  OC    -1  -0.612  -6.9618  -2.4162  -1.2975
 UGB  H3'   H  HCH1   0   0.209  -3.0652  -2.0355   1.3732

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
 UGB  C1D  N1    single  1.459  0.020  1.459
 UGB  C6   N1    single  1.367  0.020  1.367
 UGB  N1   C2    single  1.381  0.020  1.381
 UGB  C2   O2    double  1.214  0.020  1.214
 UGB  C2   N3    single  1.370  0.020  1.370
 UGB  C4   N3    single  1.387  0.020  1.387
 UGB  C5   C4    single  1.440  0.020  1.440
 UGB  C4   O4    double  1.218  0.020  1.218
 UGB  C6   C5    double  1.344  0.020  1.344
 UGB  C5   H5    single  0.930  0.020  1.080
 UGB  C6   H6    single  0.930  0.020  1.080
 UGB  O2A  PA    deloc   1.496  0.020  1.496
 UGB  O3A  PA    single  1.636  0.020  1.636
 UGB  PA   O1A   deloc   1.501  0.020  1.501
 UGB  PA   O5D   single  1.650  0.020  1.650
 UGB  O2B  PB    deloc   1.495  0.020  1.495
 UGB  O3A  PB    single  1.652  0.020  1.652
 UGB  O3B  PB    single  1.652  0.020  1.652
 UGB  PB   O1B   deloc   1.493  0.020  1.493
 UGB  O'P  C6'   deloc   1.234  0.020  1.234
 UGB  C6'  O'Q   deloc   1.259  0.020  1.259
 UGB  O3B  C1'   single  1.397  0.020  1.397
 UGB  O5'  C1'   single  1.395  0.020  1.395
 UGB  C1'  C2'   single  1.532  0.020  1.532
 UGB  C1'  H1'   single  0.970  0.020  1.090
 UGB  C2D  C1D   single  1.527  0.020  1.527
 UGB  O4D  C1D   single  1.395  0.020  1.395
 UGB  C1D  H1D   single  0.970  0.020  1.090
 UGB  C3'  C2'   single  1.522  0.020  1.522
 UGB  C2'  O2'   single  1.408  0.020  1.408
 UGB  C2'  H2'   single  0.970  0.020  1.090
 UGB  O2'  HO2'  single  0.850  0.020  0.980
 UGB  C3D  C2D   single  1.532  0.020  1.532
 UGB  C2D  O2D   single  1.396  0.020  1.396
 UGB  C2D  H2D   single  0.970  0.020  1.090
 UGB  O2D  HO2D  single  0.850  0.020  0.980
 UGB  C4'  C3'   single  1.521  0.020  1.521
 UGB  C3'  O3'   single  1.408  0.020  1.408
 UGB  C3'  H3'   single  0.970  0.020  1.090
 UGB  O3'  HO3'  single  0.850  0.020  0.980
 UGB  C3D  O3D   single  1.404  0.020  1.404
 UGB  C3D  C4D   single  1.524  0.020  1.524
 UGB  C3D  H3D   single  0.970  0.020  1.090
 UGB  O3D  HO3D  single  0.850  0.020  0.980
 UGB  C5'  C4'   single  1.530  0.020  1.530
 UGB  C4'  O4'   single  1.404  0.020  1.404
 UGB  C4'  H4'   single  0.970  0.020  1.090
 UGB  O4'  HO4'  single  0.850  0.020  0.980
 UGB  C5D  C4D   single  1.518  0.020  1.518
 UGB  C4D  O4D   single  1.433  0.020  1.433
 UGB  C4D  H4D   single  0.970  0.020  1.090
 UGB  C6'  C5'   single  1.549  0.020  1.549
 UGB  C5'  O5'   single  1.424  0.020  1.424
 UGB  C5'  H5'   single  0.970  0.020  1.090
 UGB  O5D  C5D   single  1.407  0.020  1.407
 UGB  C5D  H5D   single  0.970  0.020  1.090
 UGB  C5D  H5DA  single  0.970  0.020  1.090
 UGB  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
 UGB  C1D   N1   C6   120.37  3.000
 UGB  C6    N1   C2   121.16  3.000
 UGB  C1D   N1   C2   118.45  3.000
 UGB  N3    C2   O2   121.99  3.000
 UGB  N3    C2   N1   114.57  3.000
 UGB  O2    C2   N1   123.43  3.000
 UGB  HN3   N3   C4   116.79  3.000
 UGB  HN3   N3   C2   115.02  3.000
 UGB  C4    N3   C2   128.19  3.000
 UGB  C5    C4   O4   126.38  3.000
 UGB  O4    C4   N3   120.40  3.000
 UGB  C5    C4   N3   113.22  3.000
 UGB  H5    C5   C6   120.05  3.000
 UGB  H5    C5   C4   120.06  3.000
 UGB  C6    C5   C4   119.88  3.000
 UGB  H6    C6   C5   119.56  3.000
 UGB  H6    C6   N1   117.45  3.000
 UGB  C5    C6   N1   122.97  3.000
 UGB  O5D   PA   O3A   93.58  3.000
 UGB  O5D   PA   O2A  109.54  3.000
 UGB  O3A   PA   O2A  110.96  3.000
 UGB  O5D   PA   O1A  108.81  3.000
 UGB  O3A   PA   O1A  110.78  3.000
 UGB  O2A   PA   O1A  119.95  3.000
 UGB  O3B   PB   O3A   94.15  3.000
 UGB  O3B   PB   O2B  109.17  3.000
 UGB  O3A   PB   O2B  109.57  3.000
 UGB  O3B   PB   O1B  109.83  3.000
 UGB  O3A   PB   O1B  108.79  3.000
 UGB  O2B   PB   O1B  121.81  3.000
 UGB  H1'   C1'  O5'  105.32  3.000
 UGB  H1'   C1'  O3B  110.38  3.000
 UGB  O5'   C1'  O3B  112.41  3.000
 UGB  H1'   C1'  C2'  109.97  3.000
 UGB  O5'   C1'  C2'  110.33  3.000
 UGB  O3B   C1'  C2'  108.42  3.000
 UGB  H1D   C1D  O4D  111.62  3.000
 UGB  H1D   C1D  C2D  110.23  3.000
 UGB  O4D   C1D  C2D  105.59  3.000
 UGB  H1D   C1D  N1   106.49  3.000
 UGB  O4D   C1D  N1   109.21  3.000
 UGB  C2D   C1D  N1   113.79  3.000
 UGB  H2'   C2'  C3'  108.53  3.000
 UGB  H2'   C2'  O2'  111.01  3.000
 UGB  C3'   C2'  O2'  108.12  3.000
 UGB  H2'   C2'  C1'  106.74  3.000
 UGB  O2'   C2'  C1'  112.24  3.000
 UGB  C3'   C2'  C1'  110.15  3.000
 UGB  HO2'  O2'  C2'  108.84  3.000
 UGB  H2D   C2D  C3D  109.26  3.000
 UGB  H2D   C2D  O2D  111.63  3.000
 UGB  C3D   C2D  O2D  114.90  3.000
 UGB  H2D   C2D  C1D  109.51  3.000
 UGB  O2D   C2D  C1D  110.14  3.000
 UGB  C3D   C2D  C1D  100.83  3.000
 UGB  HO2D  O2D  C2D  108.86  3.000
 UGB  H3'   C3'  C4'  107.26  3.000
 UGB  H3'   C3'  O3'  110.37  3.000
 UGB  C4'   C3'  O3'  108.93  3.000
 UGB  H3'   C3'  C2'  108.34  3.000
 UGB  O3'   C3'  C2'  111.87  3.000
 UGB  C4'   C3'  C2'  109.97  3.000
 UGB  HO3'  O3'  C3'  107.62  3.000
 UGB  PB    O3A  PA   122.27  3.000
 UGB  C1'   O3B  PB   119.74  3.000
 UGB  H3D   C3D  C4D  111.42  3.000
 UGB  H3D   C3D  O3D  111.49  3.000
 UGB  C4D   C3D  O3D  109.47  3.000
 UGB  H3D   C3D  C2D  111.93  3.000
 UGB  C4D   C3D  C2D  101.03  3.000
 UGB  O3D   C3D  C2D  111.04  3.000
 UGB  HO3D  O3D  C3D  107.79  3.000
 UGB  H4'   C4'  C5'  106.59  3.000
 UGB  H4'   C4'  O4'  111.09  3.000
 UGB  C5'   C4'  O4'  112.06  3.000
 UGB  H4'   C4'  C3'  107.88  3.000
 UGB  O4'   C4'  C3'  109.67  3.000
 UGB  C5'   C4'  C3'  109.41  3.000
 UGB  HO4'  O4'  C4'  101.73  3.000
 UGB  H4D   C4D  C5D  109.47  3.000
 UGB  H4D   C4D  O4D  107.96  3.000
 UGB  C5D   C4D  O4D  111.08  3.000
 UGB  H4D   C4D  C3D  110.94  3.000
 UGB  O4D   C4D  C3D  106.07  3.000
 UGB  C5D   C4D  C3D  111.23  3.000
 UGB  C4D   O4D  C1D  110.65  3.000
 UGB  H5'   C5'  C6'  107.97  3.000
 UGB  H5'   C5'  O5'  109.92  3.000
 UGB  C6'   C5'  O5'  105.30  3.000
 UGB  H5'   C5'  C4'  108.28  3.000
 UGB  O5'   C5'  C4'  111.61  3.000
 UGB  C6'   C5'  C4'  113.68  3.000
 UGB  C5'   O5'  C1'  114.98  3.000
 UGB  H5DA  C5D  H5D  106.57  3.000
 UGB  H5DA  C5D  O5D  111.93  3.000
 UGB  H5D   C5D  O5D  110.71  3.000
 UGB  H5DA  C5D  C4D  109.97  3.000
 UGB  H5D   C5D  C4D  107.83  3.000
 UGB  O5D   C5D  C4D  109.70  3.000
 UGB  C5D   O5D  PA   116.57  3.000
 UGB  C5'   C6'  O'Q  117.16  3.000
 UGB  C5'   C6'  O'P  116.61  3.000
 UGB  O'Q   C6'  O'P  126.23  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
 UGB  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 UGB  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 UGB  CONST_03  C1D  N1   C2   N3    180.00   0.0  0
 UGB  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 UGB  CONST_05  O4   C4   N3   C2    180.00   0.0  0
 UGB  CONST_06  C1D  N1   C2   O2      0.00   0.0  0
 UGB  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 UGB  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 UGB  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 UGB  Var_01    C4D  C5D  O5D  PA   -145.61  30.0  3
 UGB  Var_02    O2B  PB   O3B  C1'    32.39  30.0  3
 UGB  Var_03    O2A  PA   O3A  PB     45.29  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
 UGB  chir_03  C1'  O3B  O5'  C2'  negativ
 UGB  chir_04  C1D  N1   C2D  O4D  negativ
 UGB  chir_05  C2'  O2'  C1'  C3'  negativ
 UGB  chir_06  C2D  C1D  C3D  O2D  negativ
 UGB  chir_07  C3'  C2'  C4'  O3'  positiv
 UGB  chir_08  C3D  O3D  C4D  C2D  positiv
 UGB  chir_09  C4'  O4'  C3'  C5'  positiv
 UGB  chir_10  C4D  C3D  C5D  O4D  negativ
 UGB  chir_11  C5'  O5'  C4'  C6'  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
 UGB  plan-1  N1   0.020
 UGB  plan-1  C2   0.020
 UGB  plan-1  O2   0.020
 UGB  plan-1  N3   0.020
 UGB  plan-1  C4   0.020
 UGB  plan-1  O4   0.020
 UGB  plan-1  C5   0.020
 UGB  plan-1  C6   0.020
 UGB  plan-1  C1D  0.020
 UGB  plan-1  H5   0.020
 UGB  plan-1  H6   0.020
 UGB  plan-1  HN3  0.020
 UGB  plan-2  C5'  0.020
 UGB  plan-2  C6'  0.020
 UGB  plan-2  O'P  0.020
 UGB  plan-2  O'Q  0.020

