# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 12:33:17 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: [[(2R,3S,4R,5R)-5-(6-azanyl-8-oxidanylidene-7H-purin-9-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: Nc1ncnc2N([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)C(=O)Nc12
#
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
 H6Y  H6Y  '[[(2R,3S,4R,5R)-5-(6-azanyl-8-oxidanylidene-7H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  48  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 PERFECT
;

data_comp_H6Y
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
 H6Y  PG    P  P     0   1.458   7.8286  20.3738   4.3229
 H6Y  O1G   O  O     0  -0.679   8.2131  20.7957   5.6775
 H6Y  O2G   O  OH1   0  -0.728   6.5474  19.4595   4.1377
 H6Y  O3G   O  OH1   0  -0.759   8.8476  19.5491   3.4622
 H6Y  PB    P  P     0   1.499   6.7194  22.0854   2.1136
 H6Y  O1B   O  O     0  -0.665   6.9301  23.4689   1.6734
 H6Y  O2B   O  OH1   0  -0.710   5.2558  21.6115   2.4709
 H6Y  O3B   O  O2    0  -0.691   7.5144  21.7297   3.4488
 H6Y  PA    P  P     0   1.488   8.0322  21.1022  -0.3463
 H6Y  O1A   O  O     0  -0.667   8.4597  19.7608  -0.7681
 H6Y  O2A   O  OH1   0  -0.714   7.0804  21.9366  -1.2921
 H6Y  O3A   O  O2    0  -0.704   7.2441  20.9645   1.0751
 H6Y  O5'   O  O2    0  -0.577   9.1479  22.1995  -0.1025
 H6Y  C5'   C  CH2   0  -0.225  10.1412  22.0211   0.9177
 H6Y  C4'   C  CH1   0  -0.018  11.5206  22.1844   0.2957
 H6Y  O4'   O  O2    0  -0.489  12.4758  22.3208   1.3464
 H6Y  C3'   C  CH1   0  -0.029  11.9755  20.9855  -0.5266
 H6Y  O3'   O  OH1   0  -0.669  12.9258  21.4255  -1.4602
 H6Y  C2'   C  CH1   0  -0.064  12.6304  20.1151   0.5509
 H6Y  O2'   O  OH1   0  -0.654  13.6130  19.2426   0.0754
 H6Y  C1'   C  CH1   0   0.222  13.2834  21.1789   1.4361
 H6Y  N9    N  NR5   0  -0.618  13.4549  20.7935   2.8155
 H6Y  C8    C  CR5   0   0.752  12.4425  20.4599   3.6924
 H6Y  O8    O  O     0  -0.546  11.2466  20.4367   3.4223
 H6Y  N7    N  NR15  0  -0.741  13.0307  20.1846   4.8803
 H6Y  C5    C  CR56  0   0.169  14.4014  20.3436   4.7730
 H6Y  C6    C  CR6   0   0.490  15.4894  20.2080   5.6365
 H6Y  N6    N  NH2   0  -0.826  15.3863  19.8644   6.9263
 H6Y  N1    N  N     0  -0.464  16.7066  20.4646   5.1348
 H6Y  C2    C  CR16  0   0.053  16.8243  20.8331   3.8707
 H6Y  C4    C  CR56  0   0.504  14.6619  20.7323   3.4763
 H6Y  N3    N  N     0  -0.454  15.8570  20.9902   2.9760
 H6Y  H2G   H  HOH1  0   0.509   5.7951  19.6929   4.6990
 H6Y  H3G   H  HOH1  0   0.515   9.8041  19.8155   3.5544
 H6Y  H2B   H  HOH1  0   0.515   4.5602  21.9400   1.8831
 H6Y  H2A   H  HOH1  0   0.514   6.5028  21.4015  -1.8549
 H6Y  H5'1  H  HCH2  0   0.277   9.9840  22.7906   1.6739
 H6Y  H5'2  H  HCH2  0   0.235  10.0448  21.0483   1.3990
 H6Y  H4'   H  HCH1  0   0.275  11.5296  23.0977  -0.3067
 H6Y  H3'   H  HCH1  0   0.254  11.1370  20.4698  -1.0114
 H6Y  H1'   H  HCH1  0   0.271  14.2936  21.3897   1.0698
 H6Y  HO3'  H  HOH1  0   0.450  13.4901  20.6761  -1.6861
 H6Y  H2'   H  HCH1  0   0.258  11.8534  19.5765   1.1033
 H6Y  HO2'  H  HOH1  0   0.471  13.1909  18.4282  -0.2162
 H6Y  H7    H  HNR5  0   0.434  12.5099  19.9081   5.6983
 H6Y  H61N  H  HNH2  0   0.407  16.2263  19.6727   7.4456
 H6Y  H62N  H  HNH2  0   0.411  14.5225  19.5351   7.3196
 H6Y  H2    H  HCR6  0   0.261  17.8330  21.0275   3.5248

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
 H6Y  PG   O1G   double    1.470  0.020  1.470
 H6Y  PG   O2G   single    1.585  0.020  1.585
 H6Y  PG   O3G   single    1.568  0.020  1.568
 H6Y  PG   O3B   single    1.644  0.020  1.644
 H6Y  PB   O1B   double    1.467  0.020  1.467
 H6Y  PB   O2B   single    1.579  0.020  1.579
 H6Y  PB   O3B   single    1.594  0.020  1.594
 H6Y  PB   O3A   single    1.616  0.020  1.616
 H6Y  PA   O1A   double    1.470  0.020  1.470
 H6Y  PA   O2A   single    1.580  0.020  1.580
 H6Y  PA   O3A   single    1.631  0.020  1.631
 H6Y  PA   O5'   single    1.584  0.020  1.584
 H6Y  O5'  C5'   single    1.435  0.020  1.435
 H6Y  C5'  C4'   single    1.522  0.020  1.522
 H6Y  C4'  O4'   single    1.427  0.020  1.427
 H6Y  C4'  C3'   single    1.523  0.020  1.523
 H6Y  O4'  C1'   single    1.401  0.020  1.401
 H6Y  C3'  O3'   single    1.403  0.020  1.403
 H6Y  C3'  C2'   single    1.532  0.020  1.532
 H6Y  C2'  O2'   single    1.397  0.020  1.397
 H6Y  C2'  C1'   single    1.530  0.020  1.530
 H6Y  C1'  N9    single    1.442  0.020  1.442
 H6Y  N9   C8    single    1.380  0.020  1.380
 H6Y  N9   C4    single    1.377  0.020  1.377
 H6Y  C8   O8    double    1.226  0.020  1.226
 H6Y  C8   N7    single    1.354  0.020  1.354
 H6Y  N7   C5    single    1.384  0.020  1.384
 H6Y  C5   C6    aromatic  1.396  0.020  1.396
 H6Y  C5   C4    aromatic  1.378  0.020  1.378
 H6Y  N3   C4    aromatic  1.321  0.020  1.321
 H6Y  C6   N6    single    1.339  0.020  1.339
 H6Y  C6   N1    aromatic  1.341  0.020  1.341
 H6Y  N1   C2    aromatic  1.322  0.020  1.322
 H6Y  C2   N3    aromatic  1.327  0.020  1.327
 H6Y  O2G  H2G   single    0.850  0.020  0.980
 H6Y  O3G  H3G   single    0.850  0.020  0.980
 H6Y  O2B  H2B   single    0.850  0.020  0.980
 H6Y  O2A  H2A   single    0.850  0.020  0.980
 H6Y  C5'  H5'1  single    0.970  0.020  1.090
 H6Y  C5'  H5'2  single    0.970  0.020  1.090
 H6Y  C4'  H4'   single    0.970  0.020  1.090
 H6Y  C3'  H3'   single    0.970  0.020  1.090
 H6Y  C1'  H1'   single    0.970  0.020  1.090
 H6Y  O3'  HO3'  single    0.850  0.020  0.980
 H6Y  C2'  H2'   single    0.970  0.020  1.090
 H6Y  O2'  HO2'  single    0.850  0.020  0.980
 H6Y  N7   H7    single    0.860  0.020  1.020
 H6Y  N6   H61N  single    0.860  0.020  1.020
 H6Y  N6   H62N  single    0.860  0.020  1.020
 H6Y  C2   H2    single    0.930  0.020  1.080

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
 H6Y  O3B   PG   O3G   105.44  3.000
 H6Y  O3B   PG   O2G   105.02  3.000
 H6Y  O3G   PG   O2G    99.08  3.000
 H6Y  O3B   PG   O1G   107.66  3.000
 H6Y  O3G   PG   O1G   119.13  3.000
 H6Y  O2G   PG   O1G   118.99  3.000
 H6Y  H2G   O2G  PG    114.95  3.000
 H6Y  H3G   O3G  PG    115.60  3.000
 H6Y  O3A   PB   O3B   102.81  3.000
 H6Y  O3A   PB   O2B   103.78  3.000
 H6Y  O3B   PB   O2B   101.87  3.000
 H6Y  O3A   PB   O1B   114.51  3.000
 H6Y  O3B   PB   O1B   112.96  3.000
 H6Y  O2B   PB   O1B   118.94  3.000
 H6Y  H2B   O2B  PB    115.26  3.000
 H6Y  PB    O3B  PG    136.46  3.000
 H6Y  O5'   PA   O3A   105.35  3.000
 H6Y  O5'   PA   O2A    98.66  3.000
 H6Y  O3A   PA   O2A   105.97  3.000
 H6Y  O5'   PA   O1A   118.14  3.000
 H6Y  O3A   PA   O1A   108.28  3.000
 H6Y  O2A   PA   O1A   119.04  3.000
 H6Y  H2A   O2A  PA    114.55  3.000
 H6Y  PA    O3A  PB    131.19  3.000
 H6Y  C5'   O5'  PA    120.72  3.000
 H6Y  H5'2  C5'  H5'1  108.11  3.000
 H6Y  H5'2  C5'  C4'   110.89  3.000
 H6Y  H5'1  C5'  C4'   109.78  3.000
 H6Y  H5'2  C5'  O5'   111.33  3.000
 H6Y  H5'1  C5'  O5'   107.79  3.000
 H6Y  C4'   C5'  O5'   108.88  3.000
 H6Y  H4'   C4'  C3'   110.94  3.000
 H6Y  H4'   C4'  O4'   108.67  3.000
 H6Y  C3'   C4'  O4'   105.84  3.000
 H6Y  H4'   C4'  C5'   108.78  3.000
 H6Y  C3'   C4'  C5'   114.00  3.000
 H6Y  O4'   C4'  C5'   108.43  3.000
 H6Y  C1'   O4'  C4'   110.79  3.000
 H6Y  H3'   C3'  C2'   111.74  3.000
 H6Y  H3'   C3'  O3'   111.77  3.000
 H6Y  C2'   C3'  O3'   110.89  3.000
 H6Y  H3'   C3'  C4'   112.35  3.000
 H6Y  C2'   C3'  C4'   101.25  3.000
 H6Y  O3'   C3'  C4'   108.34  3.000
 H6Y  HO3'  O3'  C3'   107.96  3.000
 H6Y  H2'   C2'  C1'   110.67  3.000
 H6Y  H2'   C2'  O2'   111.32  3.000
 H6Y  C1'   C2'  O2'   109.32  3.000
 H6Y  H2'   C2'  C3'   109.32  3.000
 H6Y  C1'   C2'  C3'   101.20  3.000
 H6Y  O2'   C2'  C3'   114.58  3.000
 H6Y  HO2'  O2'  C2'   108.84  3.000
 H6Y  H1'   C1'  N9    105.17  3.000
 H6Y  H1'   C1'  C2'   109.51  3.000
 H6Y  N9    C1'  C2'   114.72  3.000
 H6Y  H1'   C1'  O4'   110.69  3.000
 H6Y  N9    C1'  O4'   110.33  3.000
 H6Y  C2'   C1'  O4'   106.47  3.000
 H6Y  C4    N9   C8    109.10  3.000
 H6Y  C4    N9   C1'   125.09  3.000
 H6Y  C8    N9   C1'   125.79  3.000
 H6Y  N7    C8   O8    127.82  3.000
 H6Y  N7    C8   N9    106.73  3.000
 H6Y  O8    C8   N9    125.45  3.000
 H6Y  H7    N7   C5    127.30  3.000
 H6Y  H7    N7   C8    122.89  3.000
 H6Y  C5    N7   C8    109.81  3.000
 H6Y  C4    C5   C6    117.53  3.000
 H6Y  C4    C5   N7    107.01  3.000
 H6Y  C6    C5   N7    135.47  3.000
 H6Y  N1    C6   N6    118.64  3.000
 H6Y  N1    C6   C5    117.22  3.000
 H6Y  N6    C6   C5    124.13  3.000
 H6Y  H62N  N6   H61N  116.97  3.000
 H6Y  H62N  N6   C6    121.83  3.000
 H6Y  H61N  N6   C6    118.81  3.000
 H6Y  C2    N1   C6    119.46  3.000
 H6Y  H2    C2   N3    116.23  3.000
 H6Y  H2    C2   N1    115.98  3.000
 H6Y  N3    C2   N1    127.79  3.000
 H6Y  N3    C4   C5    125.61  3.000
 H6Y  N3    C4   N9    127.04  3.000
 H6Y  C5    C4   N9    107.35  3.000
 H6Y  C4    N3   C2    112.40  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
 H6Y  CONST_01  C2    N1   C6   C5      0.00   0.0  0
 H6Y  CONST_02  C2    N3   C4   C5      0.00   0.0  0
 H6Y  CONST_03  N3    C4   C5   C6      0.00   0.0  0
 H6Y  CONST_04  N3    C2   N1   C6      0.00   0.0  0
 H6Y  CONST_05  C4    C5   C6   N1      0.00   0.0  0
 H6Y  CONST_06  C4    N3   C2   N1      0.00   0.0  0
 H6Y  CONST_07  N7    C8   N9   C1'   180.00   0.0  0
 H6Y  CONST_08  C5    C4   N9   C1'   180.00   0.0  0
 H6Y  CONST_09  C5    N7   C8   N9      0.00   0.0  0
 H6Y  CONST_10  N7    C5   C4   N9      0.00   0.0  0
 H6Y  CONST_11  C5    C4   N9   C8      0.00   0.0  0
 H6Y  CONST_12  C4    C5   N7   C8      0.00   0.0  0
 H6Y  CONST_13  C4    N9   C8   N7      0.00   0.0  0
 H6Y  CONST_14  N6    C6   C5   N7      0.00   0.0  0
 H6Y  CONST_15  C4    C5   C6   N6    180.00   0.0  0
 H6Y  CONST_16  C2    N1   C6   N6    180.00   0.0  0
 H6Y  CONST_17  O8    C8   N9   C1'     0.00   0.0  0
 H6Y  CONST_18  C4    N9   C8   O8    180.00   0.0  0
 H6Y  CONST_19  C5    N7   C8   O8    180.00   0.0  0
 H6Y  CONST_20  H2    C2   N1   C6    180.00   0.0  0
 H6Y  CONST_21  H7    N7   C8   N9    180.00   0.0  0
 H6Y  CONST_22  H61N  N6   C6   C5    180.00   0.0  0
 H6Y  CONST_23  H62N  N6   C6   C5      0.00   0.0  0
 H6Y  Var_01    C4'   C5'  O5'  PA    126.57  30.0  3
 H6Y  Var_02    O1B   PB   O3B  PG   -171.50  30.0  2
 H6Y  Var_03    O1A   PA   O3A  PB    170.92  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
 H6Y  chir_03  C4'  C5'  O4'  C3'  negativ
 H6Y  chir_04  C3'  O3'  C4'  C2'  positiv
 H6Y  chir_05  C2'  O2'  C3'  C1'  positiv
 H6Y  chir_06  C1'  O4'  N9   C2'  negativ
 H6Y  chir_07  PB   O2B  O3B  O3A  both
 H6Y  chir_08  PA   O2A  O3A  O5'  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
 H6Y  plan-1  C1'   0.020
 H6Y  plan-1  N9    0.020
 H6Y  plan-1  C8    0.020
 H6Y  plan-1  O8    0.020
 H6Y  plan-1  N7    0.020
 H6Y  plan-1  C5    0.020
 H6Y  plan-1  C6    0.020
 H6Y  plan-1  N6    0.020
 H6Y  plan-1  N1    0.020
 H6Y  plan-1  C2    0.020
 H6Y  plan-1  C4    0.020
 H6Y  plan-1  N3    0.020
 H6Y  plan-1  H7    0.020
 H6Y  plan-1  H2    0.020
 H6Y  plan-2  C6    0.020
 H6Y  plan-2  N6    0.020
 H6Y  plan-2  H61N  0.020
 H6Y  plan-2  H62N  0.020

