# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 12:10:38 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-4-oxidanylidene-3~{H}-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(ccc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 QBQ  QBQ  '[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-4-oxidanylidene-3~{H}-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  49  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QBQ
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
 QBQ  O3   O  O     0  -0.666  43.6571  -17.0664  -77.1917
 QBQ  C4   C  CR15  0  -0.032  39.5183  -13.7323  -80.8328
 QBQ  C5   C  CH1   0   0.204  40.5854  -11.8771  -79.5105
 QBQ  O4   O  O2    0  -0.686  41.3128  -16.7096  -76.3346
 QBQ  C6   C  CH1   0  -0.048  42.2762  -12.7876  -78.1890
 QBQ  N1   N  N     0  -0.519  39.4373  -10.3241  -81.7354
 QBQ  C7   C  CH2   0  -0.200  42.3221  -14.3071  -78.1094
 QBQ  C8   C  CH1   0  -0.037  41.2446  -12.1449  -77.2609
 QBQ  N2   N  NR5   0  -0.551  39.8324  -12.3991  -80.6133
 QBQ  C9   C  CH1   0  -0.031  39.9987  -12.2170  -78.1403
 QBQ  O5   O  OH1   0  -0.704  38.9629  -17.4089  -75.9693
 QBQ  C10  C  CR6   0   0.502  38.0143  -11.9659  -83.6391
 QBQ  O6   O  O     0  -0.662  40.4101  -16.7301  -73.8898
 QBQ  N3   N  NR16  0  -0.724  38.1683  -10.5774  -83.6939
 QBQ  O7   O  O2    0  -0.697  39.5912  -15.0507  -75.7189
 QBQ  O8   O  OH1   0  -0.722  39.7101  -13.4897  -73.8441
 QBQ  C    C  CR6   0   0.683  38.8490   -9.8185  -82.7863
 QBQ  O    O  O2    0  -0.496  41.8846  -12.4297  -79.5108
 QBQ  C1   C  CR56  0   0.541  39.3125  -11.6578  -81.6258
 QBQ  C2   C  CR56  0  -0.199  38.6535  -12.5198  -82.4947
 QBQ  C3   C  CR15  0  -0.415  38.7959  -13.8412  -81.9779
 QBQ  O1   O  O2    0  -0.578  42.7305  -14.6540  -76.7801
 QBQ  O11  O  OH1   0  -0.666  41.5258  -10.7913  -77.0252
 QBQ  O12  O  OH1   0  -0.676  38.9591  -11.3569  -77.8195
 QBQ  O13  O  O     0  -0.480  37.3899  -12.5499  -84.5126
 QBQ  O2   O  OH1   0  -0.714  43.2608  -15.9387  -74.8401
 QBQ  P    P  P     0   1.508  42.8548  -16.1733  -76.3472
 QBQ  P1   P  P     0   1.478  40.0924  -16.5289  -75.3060
 QBQ  P2   P  P     0   1.522  38.6488  -14.0263  -74.8831
 QBQ  H7   H  HCR5  0   0.287  39.8455  -14.5043  -80.1554
 QBQ  H    H  HCH1  0   0.262  40.6255  -10.7926  -79.6465
 QBQ  H1   H  HCH1  0   0.273  43.2800  -12.3958  -77.9952
 QBQ  H9   H  HCH2  0   0.235  41.3443  -14.7457  -78.3263
 QBQ  H8   H  HCH2  0   0.278  43.0355  -14.6959  -78.8385
 QBQ  H2   H  HCH1  0   0.247  41.1397  -12.7000  -76.3224
 QBQ  H3   H  HCH1  0   0.225  39.6527  -13.2595  -78.1521
 QBQ  H11  H  HOH1  0   0.517  38.8978  -18.3117  -75.6255
 QBQ  H16  H  HNR6  0   0.422  37.7298  -10.1140  -84.4791
 QBQ  H12  H  HOH1  0   0.515  39.4401  -12.7017  -73.3507
 QBQ  H5   H  HNH2  0   0.409  39.5066   -7.9480  -82.4410
 QBQ  H4   H  HNH2  0   0.411  38.6267   -8.1096  -83.8929
 QBQ  H6   H  HCR5  0   0.257  38.4157  -14.7559  -82.4029
 QBQ  H14  H  HOH1  0   0.458  42.3321  -10.7344  -76.5025
 QBQ  H15  H  HOH1  0   0.462  38.4856  -11.7622  -77.0763
 QBQ  H10  H  HOH1  0   0.515  43.5586  -16.7281  -74.3661
 QBQ  H13  H  HOH1  0   0.514  36.8167  -15.1033  -74.4025
 QBQ  N    N  NH2   0  -0.832  38.8632   -8.4904  -82.9923
 QBQ  O10  O  O     0  -0.675  37.9942  -13.0598  -75.7843
 QBQ  O9   O  OH1   0  -0.719  37.6921  -14.9471  -74.0199

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
 QBQ  O13  C10  double    1.222  0.020  1.222
 QBQ  C10  N3   single    1.398  0.020  1.398
 QBQ  C10  C2   single    1.423  0.020  1.423
 QBQ  N3   C    single    1.365  0.020  1.365
 QBQ  N    C    single    1.344  0.020  1.344
 QBQ  C    N1   double    1.306  0.020  1.306
 QBQ  C2   C3   aromatic  1.426  0.020  1.426
 QBQ  C2   C1   aromatic  1.390  0.020  1.390
 QBQ  C3   C4   aromatic  1.358  0.020  1.358
 QBQ  C1   N1   single    1.344  0.020  1.344
 QBQ  C1   N2   aromatic  1.358  0.020  1.358
 QBQ  C4   N2   aromatic  1.387  0.020  1.387
 QBQ  N2   C5   single    1.434  0.020  1.434
 QBQ  C5   O    single    1.412  0.020  1.412
 QBQ  C5   C9   single    1.529  0.020  1.529
 QBQ  O    C6   single    1.424  0.020  1.424
 QBQ  C9   O12  single    1.387  0.020  1.387
 QBQ  C9   C8   single    1.527  0.020  1.527
 QBQ  C6   C7   single    1.522  0.020  1.522
 QBQ  C6   C8   single    1.529  0.020  1.529
 QBQ  C7   O1   single    1.433  0.020  1.433
 QBQ  C8   O11  single    1.402  0.020  1.402
 QBQ  O1   P    single    1.585  0.020  1.585
 QBQ  O3   P    double    1.468  0.020  1.468
 QBQ  P    O4   single    1.633  0.020  1.633
 QBQ  P    O2   single    1.578  0.020  1.578
 QBQ  O4   P1   single    1.606  0.020  1.606
 QBQ  O10  P2   double    1.475  0.020  1.475
 QBQ  O5   P1   single    1.578  0.020  1.578
 QBQ  O7   P1   single    1.615  0.020  1.615
 QBQ  O7   P2   single    1.624  0.020  1.624
 QBQ  P1   O6   double    1.465  0.020  1.465
 QBQ  P2   O8   single    1.579  0.020  1.579
 QBQ  P2   O9   single    1.584  0.020  1.584
 QBQ  C4   H7   single    0.930  0.020  1.080
 QBQ  C5   H    single    0.970  0.020  1.090
 QBQ  C6   H1   single    0.970  0.020  1.090
 QBQ  C7   H9   single    0.970  0.020  1.090
 QBQ  C7   H8   single    0.970  0.020  1.090
 QBQ  C8   H2   single    0.970  0.020  1.090
 QBQ  C9   H3   single    0.970  0.020  1.090
 QBQ  O5   H11  single    0.850  0.020  0.980
 QBQ  N3   H16  single    0.860  0.020  1.020
 QBQ  O8   H12  single    0.850  0.020  0.980
 QBQ  N    H5   single    0.890  0.020  1.040
 QBQ  N    H4   single    0.890  0.020  1.040
 QBQ  C3   H6   single    0.930  0.020  1.080
 QBQ  O11  H14  single    0.850  0.020  0.980
 QBQ  O12  H15  single    0.850  0.020  0.980
 QBQ  O2   H10  single    0.850  0.020  0.980
 QBQ  O9   H13  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
 QBQ  H7   C4   C3   129.33  3.000
 QBQ  H7   C4   N2   121.34  3.000
 QBQ  C3   C4   N2   109.32  3.000
 QBQ  H    C5   O    110.76  3.000
 QBQ  H    C5   C9   110.24  3.000
 QBQ  O    C5   C9   105.45  3.000
 QBQ  H    C5   N2   106.53  3.000
 QBQ  C9   C5   N2   114.01  3.000
 QBQ  O    C5   N2   109.91  3.000
 QBQ  P1   O4   P    133.29  3.000
 QBQ  H1   C6   O    109.05  3.000
 QBQ  H1   C6   C8   111.14  3.000
 QBQ  O    C6   C8   105.79  3.000
 QBQ  H1   C6   C7   108.69  3.000
 QBQ  C8   C6   C7   114.09  3.000
 QBQ  O    C6   C7   107.92  3.000
 QBQ  C1   N1   C    114.07  3.000
 QBQ  H8   C7   H9   108.00  3.000
 QBQ  H8   C7   O1   110.30  3.000
 QBQ  H9   C7   O1   109.98  3.000
 QBQ  H8   C7   C6   109.89  3.000
 QBQ  H9   C7   C6   111.30  3.000
 QBQ  O1   C7   C6   107.38  3.000
 QBQ  H2   C8   O11  111.36  3.000
 QBQ  H2   C8   C9   113.04  3.000
 QBQ  O11  C8   C9   107.82  3.000
 QBQ  H2   C8   C6   111.81  3.000
 QBQ  O11  C8   C6   111.86  3.000
 QBQ  C9   C8   C6   100.43  3.000
 QBQ  C1   N2   C5   125.15  3.000
 QBQ  C5   N2   C4   126.20  3.000
 QBQ  C1   N2   C4   108.66  3.000
 QBQ  H3   C9   O12  110.79  3.000
 QBQ  H3   C9   C8   107.94  3.000
 QBQ  O12  C9   C8   116.69  3.000
 QBQ  H3   C9   C5   108.80  3.000
 QBQ  C8   C9   C5   101.10  3.000
 QBQ  O12  C9   C5   110.92  3.000
 QBQ  H11  O5   P1   114.76  3.000
 QBQ  O13  C10  C2   128.18  3.000
 QBQ  C2   C10  N3   111.64  3.000
 QBQ  O13  C10  N3   120.18  3.000
 QBQ  H16  N3   C    118.53  3.000
 QBQ  H16  N3   C10  115.95  3.000
 QBQ  C    N3   C10  125.52  3.000
 QBQ  P2   O7   P1   128.77  3.000
 QBQ  H12  O8   P2   115.11  3.000
 QBQ  N    C    N3   116.92  3.000
 QBQ  N    C    N1   120.07  3.000
 QBQ  N3   C    N1   122.98  3.000
 QBQ  C6   O    C5   110.56  3.000
 QBQ  C2   C1   N2   107.99  3.000
 QBQ  N2   C1   N1   124.53  3.000
 QBQ  C2   C1   N1   127.48  3.000
 QBQ  C3   C2   C1   107.50  3.000
 QBQ  C1   C2   C10  118.31  3.000
 QBQ  C3   C2   C10  134.19  3.000
 QBQ  H6   C3   C2   127.46  3.000
 QBQ  H6   C3   C4   126.01  3.000
 QBQ  C2   C3   C4   106.52  3.000
 QBQ  P    O1   C7   120.52  3.000
 QBQ  H14  O11  C8   108.44  3.000
 QBQ  H15  O12  C9   106.50  3.000
 QBQ  H10  O2   P    115.19  3.000
 QBQ  O2   P    O1    97.96  3.000
 QBQ  O2   P    O4   106.53  3.000
 QBQ  O1   P    O4   104.06  3.000
 QBQ  O2   P    O3   119.95  3.000
 QBQ  O4   P    O3   108.72  3.000
 QBQ  O1   P    O3   117.97  3.000
 QBQ  O7   P1   O6   116.11  3.000
 QBQ  O6   P1   O5   119.00  3.000
 QBQ  O7   P1   O5   100.42  3.000
 QBQ  O6   P1   O4   116.02  3.000
 QBQ  O7   P1   O4   100.08  3.000
 QBQ  O5   P1   O4   102.24  3.000
 QBQ  O9   P2   O10  116.48  3.000
 QBQ  O9   P2   O8   104.18  3.000
 QBQ  O10  P2   O8   118.54  3.000
 QBQ  O9   P2   O7   105.33  3.000
 QBQ  O8   P2   O7    99.38  3.000
 QBQ  O10  P2   O7   110.89  3.000
 QBQ  H4   N    H5   115.91  3.000
 QBQ  H4   N    C    120.58  3.000
 QBQ  H5   N    C    117.10  3.000
 QBQ  H13  O9   P2   115.13  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
 QBQ  CONST_01  C1   C2   C3  C4      0.00   0.0  0
 QBQ  CONST_02  C2   C1   N2  C4      0.00   0.0  0
 QBQ  CONST_03  C3   C2   C1  N2      0.00   0.0  0
 QBQ  CONST_04  C2   C3   C4  N2      0.00   0.0  0
 QBQ  CONST_05  C3   C4   N2  C1      0.00   0.0  0
 QBQ  CONST_06  C2   C1   N2  C5    180.00   0.0  0
 QBQ  CONST_07  N1   C1   N2  C5      0.00   0.0  0
 QBQ  CONST_08  C3   C4   N2  C5    180.00   0.0  0
 QBQ  CONST_09  C10  N3   C   N1      0.00   0.0  0
 QBQ  CONST_10  C1   N1   C   N3      0.00   0.0  0
 QBQ  CONST_11  C2   C10  N3  C       0.00   0.0  0
 QBQ  CONST_12  N    C    N3  C10   180.00   0.0  0
 QBQ  CONST_13  C1   N1   C   N     180.00   0.0  0
 QBQ  CONST_14  O13  C10  N3  C     180.00   0.0  0
 QBQ  CONST_15  H7   C4   N2  C5      0.00   0.0  0
 QBQ  CONST_16  H6   C3   C4  N2    180.00   0.0  0
 QBQ  CONST_17  H16  N3   C   N1    180.00   0.0  0
 QBQ  CONST_18  H5   N    C   N1      0.00   0.0  0
 QBQ  Var_01    O2   P    O1  C7   -177.87  30.0  3
 QBQ  Var_02    H9   C7   O1  P      57.60  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
 QBQ  chir_01  C5  N2   O   C9  positiv
 QBQ  chir_02  C6  O    C8  C7  negativ
 QBQ  chir_03  C8  O11  C6  C9  positiv
 QBQ  chir_04  C9  O12  C8  C5  positiv
 QBQ  chir_05  P   O3   O4  O2  both
 QBQ  chir_06  P1  O5   O7  O6  both

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
 QBQ  plan-1  C4   0.020
 QBQ  plan-1  C5   0.020
 QBQ  plan-1  N1   0.020
 QBQ  plan-1  N2   0.020
 QBQ  plan-1  C10  0.020
 QBQ  plan-1  N3   0.020
 QBQ  plan-1  C    0.020
 QBQ  plan-1  C1   0.020
 QBQ  plan-1  C2   0.020
 QBQ  plan-1  C3   0.020
 QBQ  plan-1  O13  0.020
 QBQ  plan-1  H7   0.020
 QBQ  plan-1  H16  0.020
 QBQ  plan-1  H5   0.020
 QBQ  plan-1  H4   0.020
 QBQ  plan-1  H6   0.020
 QBQ  plan-1  N    0.020

