# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 10:08:36 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@@H](C[S](O)(=O)=O)O[C@H](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)[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
 USQ  USQ  '[(2S,3S,4S,5R,6R)-6-{[(R)-{[(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-yl]methanesulfonic acid (non-preferred name)'  ligand  60  39  .  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_USQ
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
 USQ  N1    N  NR6    0  -0.566  72.5077  102.2317  25.3826
 USQ  C2    C  CR6    0   0.728  73.6081  103.0586  25.5013
 USQ  N3    N  NR16   0  -0.734  73.6479  103.7878  26.6617
 USQ  C4    C  CR6    0   0.566  72.7372  103.7878  27.7094
 USQ  C5    C  CR16   0  -0.521  71.6134  102.9139  27.4855
 USQ  C6    C  CR16   0   0.072  71.5508  102.1864  26.3592
 USQ  O2    O  O      0  -0.472  74.4794  103.1418  24.6617
 USQ  O4    O  O      0  -0.456  72.9266  104.4782  28.6925
 USQ  C1D   C  CH1    0   0.169  72.3949  101.3556  24.2245
 USQ  C2D   C  CH1    0  -0.034  72.5118   99.8650  24.5700
 USQ  O2D   O  OH1    0  -0.653  73.8264   99.4214  24.6973
 USQ  C3D   C  CH1    0  -0.071  71.7057   99.2240  23.4380
 USQ  C4D   C  CH1    0  -0.041  70.6152  100.2692  23.1775
 USQ  O4D   O  O2     0  -0.492  71.1390  101.5246  23.6297
 USQ  O3D   O  OH1    0  -0.668  72.5181   98.9601  22.3122
 USQ  C5D   C  CH2    0  -0.159  69.2846   99.9887  23.8479
 USQ  O5D   O  O2     0  -0.632  69.4616  100.0072  25.2416
 USQ  PA    P  P      0   1.378  68.2977   99.5254  26.3045
 USQ  O1A   O  O      0  -0.778  68.5668  100.2930  27.5556
 USQ  O2A   O  OP    -1  -0.779  66.9578   99.5249  25.6426
 USQ  O3A   O  O2     0  -0.758  68.7030   97.9418  26.4975
 USQ  PB    P  P      0   1.373  70.1753   97.2633  26.7788
 USQ  O1B   O  O      0  -0.776  71.0247   98.1275  27.6526
 USQ  O2B   O  OP    -1  -0.764  70.7013   96.7251  25.4844
 USQ  O3B   O  O2     0  -0.622  69.6723   96.0233  27.7507
 USQ  C1'   C  CH1    0   0.256  68.6455   95.1404  27.4119
 USQ  C2'   C  CH1    0   0.010  68.4191   94.1809  28.5764
 USQ  C3'   C  CH1    0  -0.004  69.6134   93.2517  28.7212
 USQ  C4'   C  CH1    0   0.019  69.9190   92.5401  27.4059
 USQ  C5'   C  CH1    0   0.026  70.0530   93.5714  26.2753
 USQ  C6'   C  CH2    0  -0.679  70.0935   92.9966  24.8637
 USQ  O2'   O  OH1    0  -0.667  68.1673   94.9277  29.7376
 USQ  O3'   O  OH1    0  -0.674  69.3031   92.3308  29.7432
 USQ  O4'   O  OH1    0  -0.705  71.0896   91.8008  27.6271
 USQ  O5'   O  O2     0  -0.503  68.8990   94.4046  26.2555
 USQ  S     S  S      0   1.399  71.5613   92.0595  24.4003
 USQ  O1S   O  OS     0  -0.740  72.7193   92.9023  24.7376
 USQ  O2S   O  OS    -1  -0.761  71.5088   90.8000  25.2009
 USQ  O3S   O  OS     0  -0.739  71.4013   91.7988  22.9623
 USQ  HN3   H  HNR6   0   0.422  74.4570  104.3885  26.7616
 USQ  H5    H  HCR6   0   0.285  70.8317  102.8403  28.2259
 USQ  H6    H  HCR6   0   0.353  70.7191  101.5229  26.1707
 USQ  H1D   H  HCH1   0   0.267  73.1963  101.6468  23.5395
 USQ  H2D   H  HCH1   0   0.265  72.0097   99.6581  25.5186
 USQ  HO2'  H  HOH1   0   0.442  74.1697   99.2542  23.8106
 USQ  H3D   H  HCH1   0   0.284  71.2871   98.2668  23.7502
 USQ  H4D   H  HCH1   0   0.257  70.4193  100.3347  22.1005
 USQ  HO3'  H  HOH1   0   0.456  72.6905   99.7703  21.8194
 USQ  H5'1  H  HCH2   0   0.218  68.9188   99.0219  23.4847
 USQ  H5'2  H  HCH2   0   0.225  68.5580  100.7465  23.5374
 USQ  H1'   H  HCH1   0   0.238  67.7214   95.6901  27.2015
 USQ  H2'   H  HCH1   0   0.213  67.5440   93.5699  28.3046
 USQ  H3'   H  HCH1   0   0.207  70.4965   93.8476  28.9970
 USQ  H4'   H  HCH1   0   0.191  69.0655   91.8830  27.1654
 USQ  H5'   H  HCH1   0   0.227  70.9541   94.1718  26.4394
 USQ  H6'1  H  HCH2   0   0.283  70.0423   93.8264  24.1553
 USQ  H6'2  H  HCH2   0   0.270  69.2331   92.3465  24.6845
 USQ  HO2A  H  HOH1   0   0.449  67.9904   94.3090  30.4534
 USQ  HO3A  H  HOH1   0   0.449  70.0758   91.7751  29.8874
 USQ  HO4'  H  HOH1   0   0.450  71.2789   91.2711  26.8240

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
 USQ  N1   C2    single  1.382  0.020  1.382
 USQ  N1   C6    single  1.368  0.020  1.368
 USQ  N1   C1D   single  1.457  0.020  1.457
 USQ  C2   N3    single  1.371  0.020  1.371
 USQ  C2   O2    double  1.213  0.020  1.213
 USQ  N3   C4    single  1.388  0.020  1.388
 USQ  N3   HN3   single  0.860  0.020  1.020
 USQ  C4   C5    single  1.441  0.020  1.441
 USQ  C4   O4    double  1.216  0.020  1.216
 USQ  C5   C6    double  1.342  0.020  1.342
 USQ  C5   H5    single  0.930  0.020  1.080
 USQ  C6   H6    single  0.930  0.020  1.080
 USQ  C1D  C2D   single  1.535  0.020  1.535
 USQ  C1D  O4D   single  1.400  0.020  1.400
 USQ  C1D  H1D   single  0.970  0.020  1.090
 USQ  C2D  O2D   single  1.393  0.020  1.393
 USQ  C2D  C3D   single  1.530  0.020  1.530
 USQ  C2D  H2D   single  0.970  0.020  1.090
 USQ  O2D  HO2'  single  0.850  0.020  0.980
 USQ  C3D  C4D   single  1.533  0.020  1.533
 USQ  C3D  O3D   single  1.413  0.020  1.413
 USQ  C3D  H3D   single  0.970  0.020  1.090
 USQ  C4D  O4D   single  1.434  0.020  1.434
 USQ  C4D  C5D   single  1.516  0.020  1.516
 USQ  C4D  H4D   single  0.970  0.020  1.090
 USQ  O3D  HO3'  single  0.850  0.020  0.980
 USQ  C5D  O5D   single  1.405  0.020  1.405
 USQ  C5D  H5'1  single  0.970  0.020  1.090
 USQ  C5D  H5'2  single  0.970  0.020  1.090
 USQ  O5D  PA    single  1.648  0.020  1.648
 USQ  PA   O1A   deloc   1.492  0.020  1.492
 USQ  PA   O2A   deloc   1.494  0.020  1.494
 USQ  PA   O3A   single  1.646  0.020  1.646
 USQ  O3A  PB    single  1.645  0.020  1.645
 USQ  PB   O1B   deloc   1.494  0.020  1.494
 USQ  PB   O2B   deloc   1.497  0.020  1.497
 USQ  PB   O3B   single  1.654  0.020  1.654
 USQ  O3B  C1'   single  1.396  0.020  1.396
 USQ  C1'  C2'   single  1.526  0.020  1.526
 USQ  C1'  O5'   single  1.394  0.020  1.394
 USQ  C1'  H1'   single  0.970  0.020  1.090
 USQ  C2'  C3'   single  1.520  0.020  1.520
 USQ  C2'  O2'   single  1.403  0.020  1.403
 USQ  C2'  H2'   single  0.970  0.020  1.090
 USQ  C3'  C4'   single  1.526  0.020  1.526
 USQ  C3'  O3'   single  1.410  0.020  1.410
 USQ  C3'  H3'   single  0.970  0.020  1.090
 USQ  C4'  C5'   single  1.536  0.020  1.536
 USQ  C4'  O4'   single  1.402  0.020  1.402
 USQ  C4'  H4'   single  0.970  0.020  1.090
 USQ  C5'  C6'   single  1.525  0.020  1.525
 USQ  C5'  O5'   single  1.423  0.020  1.423
 USQ  C5'  H5'   single  0.970  0.020  1.090
 USQ  C6'  S     single  1.802  0.020  1.802
 USQ  C6'  H6'1  single  0.970  0.020  1.090
 USQ  C6'  H6'2  single  0.970  0.020  1.090
 USQ  O2'  HO2A  single  0.850  0.020  0.980
 USQ  O3'  HO3A  single  0.850  0.020  0.980
 USQ  O4'  HO4'  single  0.850  0.020  0.980
 USQ  S    O1S   deloc   1.471  0.020  1.471
 USQ  S    O2S   deloc   1.493  0.020  1.493
 USQ  S    O3S   deloc   1.470  0.020  1.470

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
 USQ  C1D   N1   C6    119.57  3.000
 USQ  C1D   N1   C2    119.34  3.000
 USQ  C6    N1   C2    121.04  3.000
 USQ  O2    C2   N3    121.91  3.000
 USQ  O2    C2   N1    123.63  3.000
 USQ  N3    C2   N1    114.46  3.000
 USQ  HN3   N3   C4    116.72  3.000
 USQ  HN3   N3   C2    114.97  3.000
 USQ  C4    N3   C2    128.30  3.000
 USQ  O4    C4   C5    126.25  3.000
 USQ  O4    C4   N3    120.53  3.000
 USQ  C5    C4   N3    113.22  3.000
 USQ  H5    C5   C6    120.33  3.000
 USQ  H5    C5   C4    119.97  3.000
 USQ  C6    C5   C4    119.69  3.000
 USQ  H6    C6   C5    121.00  3.000
 USQ  H6    C6   N1    115.74  3.000
 USQ  C5    C6   N1    123.26  3.000
 USQ  H1D   C1D  O4D   111.05  3.000
 USQ  H1D   C1D  C2D   110.11  3.000
 USQ  O4D   C1D  C2D   106.34  3.000
 USQ  H1D   C1D  N1    106.33  3.000
 USQ  O4D   C1D  N1    109.56  3.000
 USQ  C2D   C1D  N1    113.53  3.000
 USQ  H2D   C2D  C3D   108.70  3.000
 USQ  H2D   C2D  O2D   107.09  3.000
 USQ  C3D   C2D  O2D   115.54  3.000
 USQ  H2D   C2D  C1D   110.14  3.000
 USQ  C3D   C2D  C1D   101.55  3.000
 USQ  O2D   C2D  C1D   113.69  3.000
 USQ  HO2'  O2D  C2D   107.86  3.000
 USQ  H3D   C3D  O3D   106.55  3.000
 USQ  H3D   C3D  C4D   111.97  3.000
 USQ  O3D   C3D  C4D   113.64  3.000
 USQ  H3D   C3D  C2D   110.98  3.000
 USQ  O3D   C3D  C2D   111.38  3.000
 USQ  C4D   C3D  C2D   102.41  3.000
 USQ  H4D   C4D  C5D   106.78  3.000
 USQ  H4D   C4D  O4D   108.83  3.000
 USQ  C5D   C4D  O4D   110.07  3.000
 USQ  H4D   C4D  C3D   109.55  3.000
 USQ  C5D   C4D  C3D   115.03  3.000
 USQ  O4D   C4D  C3D   106.47  3.000
 USQ  C4D   O4D  C1D   110.87  3.000
 USQ  HO3'  O3D  C3D   110.68  3.000
 USQ  H5'2  C5D  H5'1  107.17  3.000
 USQ  H5'2  C5D  O5D   110.84  3.000
 USQ  H5'1  C5D  O5D   112.49  3.000
 USQ  H5'2  C5D  C4D   109.21  3.000
 USQ  H5'1  C5D  C4D   108.04  3.000
 USQ  O5D   C5D  C4D   109.01  3.000
 USQ  PA    O5D  C5D   123.16  3.000
 USQ  O3A   PA   O2A   105.80  3.000
 USQ  O3A   PA   O1A   110.62  3.000
 USQ  O2A   PA   O1A   122.22  3.000
 USQ  O3A   PA   O5D   100.55  3.000
 USQ  O2A   PA   O5D   110.34  3.000
 USQ  O1A   PA   O5D   105.25  3.000
 USQ  PB    O3A  PA    129.57  3.000
 USQ  O3B   PB   O2B   110.20  3.000
 USQ  O3B   PB   O1B   105.24  3.000
 USQ  O2B   PB   O1B   120.92  3.000
 USQ  O3B   PB   O3A    97.90  3.000
 USQ  O2B   PB   O3A   108.35  3.000
 USQ  O1B   PB   O3A   111.73  3.000
 USQ  C1'   O3B  PB    123.73  3.000
 USQ  H1'   C1'  O5'   105.01  3.000
 USQ  H1'   C1'  C2'   109.69  3.000
 USQ  O5'   C1'  C2'   109.16  3.000
 USQ  H1'   C1'  O3B   110.47  3.000
 USQ  O5'   C1'  O3B   113.67  3.000
 USQ  C2'   C1'  O3B   108.76  3.000
 USQ  H2'   C2'  O2'   110.91  3.000
 USQ  H2'   C2'  C3'   107.98  3.000
 USQ  O2'   C2'  C3'   112.79  3.000
 USQ  H2'   C2'  C1'   106.16  3.000
 USQ  O2'   C2'  C1'   108.88  3.000
 USQ  C3'   C2'  C1'   109.91  3.000
 USQ  H3'   C3'  O3'   110.41  3.000
 USQ  H3'   C3'  C4'   107.92  3.000
 USQ  O3'   C3'  C4'   111.36  3.000
 USQ  H3'   C3'  C2'   108.86  3.000
 USQ  O3'   C3'  C2'   107.17  3.000
 USQ  C4'   C3'  C2'   111.11  3.000
 USQ  H4'   C4'  O4'   111.47  3.000
 USQ  H4'   C4'  C5'   107.87  3.000
 USQ  O4'   C4'  C5'   113.41  3.000
 USQ  H4'   C4'  C3'   108.09  3.000
 USQ  O4'   C4'  C3'   106.08  3.000
 USQ  C5'   C4'  C3'   109.80  3.000
 USQ  H5'   C5'  O5'   110.38  3.000
 USQ  H5'   C5'  C6'   108.87  3.000
 USQ  O5'   C5'  C6'   103.25  3.000
 USQ  H5'   C5'  C4'   109.24  3.000
 USQ  O5'   C5'  C4'   109.42  3.000
 USQ  C6'   C5'  C4'   115.51  3.000
 USQ  H6'2  C6'  H6'1  107.98  3.000
 USQ  H6'2  C6'  S     106.83  3.000
 USQ  H6'1  C6'  S     105.45  3.000
 USQ  H6'2  C6'  C5'   110.80  3.000
 USQ  H6'1  C6'  C5'   108.23  3.000
 USQ  S     C6'  C5'   117.11  3.000
 USQ  HO2A  O2'  C2'   107.84  3.000
 USQ  HO3A  O3'  C3'   107.99  3.000
 USQ  HO4'  O4'  C4'   108.47  3.000
 USQ  C5'   O5'  C1'   116.42  3.000
 USQ  O3S   S    O2S   111.78  3.000
 USQ  O3S   S    O1S   114.29  3.000
 USQ  O2S   S    O1S   112.82  3.000
 USQ  O3S   S    C6'   104.78  3.000
 USQ  O2S   S    C6'   105.79  3.000
 USQ  O1S   S    C6'   106.51  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
 USQ  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 USQ  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 USQ  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 USQ  CONST_04  C1D   N1   C2   N3    180.00   0.0  0
 USQ  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 USQ  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 USQ  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 USQ  CONST_08  C1D   N1   C2   O2      0.00   0.0  0
 USQ  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 USQ  Var_01    O1S   S    C6'  C5'   -51.02  30.0  3
 USQ  Var_02    O1A   PA   O5D  C5D  -152.63  30.0  3
 USQ  Var_03    O1B   PB   O3A  PA     35.37  30.0  3
 USQ  Var_04    H5'1  C5D  O5D  PA    -50.77  30.0  1

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
 USQ  chir_01  C1D  N1   C2D  O4D  negativ
 USQ  chir_02  C2D  O2D  C3D  C1D  positiv
 USQ  chir_03  C3D  O3D  C2D  C4D  negativ
 USQ  chir_04  C4D  O4D  C3D  C5D  negativ
 USQ  chir_07  C1'  O3B  C2'  O5'  positiv
 USQ  chir_08  C2'  O2'  C1'  C3'  negativ
 USQ  chir_09  C3'  O3'  C2'  C4'  positiv
 USQ  chir_10  C4'  O4'  C5'  C3'  positiv
 USQ  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
 USQ  plan-1  N1   0.020
 USQ  plan-1  C2   0.020
 USQ  plan-1  N3   0.020
 USQ  plan-1  C4   0.020
 USQ  plan-1  C5   0.020
 USQ  plan-1  C6   0.020
 USQ  plan-1  O2   0.020
 USQ  plan-1  O4   0.020
 USQ  plan-1  C1D  0.020
 USQ  plan-1  HN3  0.020
 USQ  plan-1  H5   0.020
 USQ  plan-1  H6   0.020

