# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Sep 30 23:11:23 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: [(2~{R},3~{R},4~{S},5~{S})-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl bis(oxidanyl)phosphinothioyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c2ncn([C@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=S)[C@H](O)[C@@H]3O)c2n1
#
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
 GZF  GZF  "[(2R,3R,4S,5S)-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl bis(oxidanyl)phosphinothioyl hydrogen phosphate"  ligand  43  28  .  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_GZF
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
 GZF  O01  O  OH1   0  -0.653  -34.2106   -3.2929  22.1574
 GZF  C02  C  CH1   0   0.021  -34.3716   -4.6733  22.2491
 GZF  C03  C  CH1   0  -0.035  -33.0136   -5.3691  22.4130
 GZF  C04  C  CH2   0  -0.191  -31.9352   -4.5800  23.1228
 GZF  O05  O  O2    0  -0.567  -32.3314   -4.3628  24.4795
 GZF  P06  P  P     0   1.490  -32.0070   -3.0408  25.2724
 GZF  O07  O  OH1   0  -0.725  -32.3859   -3.5462  26.7275
 GZF  O08  O  O     0  -0.662  -32.5486   -1.7572  24.8093
 GZF  O09  O  O2    0  -0.677  -30.3794   -2.9453  25.2516
 GZF  P10  P  P     0   1.190  -29.2456   -3.8469  25.9694
 GZF  O11  O  OH1   0  -0.696  -28.0103   -3.1423  25.2588
 GZF  O12  O  OH1   0  -0.707  -29.1865   -3.2744  27.4563
 GZF  S13  S  S1    0  -0.497  -29.4405   -5.7481  25.8033
 GZF  O14  O  O2    0  -0.487  -33.2945   -6.5683  23.1061
 GZF  C15  C  CH1   0   0.178  -34.4779   -6.4754  23.8529
 GZF  N16  N  NR5   0  -0.541  -35.2425   -7.6790  23.6316
 GZF  C17  C  CR15  0   0.104  -35.5791   -8.6149  24.5796
 GZF  N18  N  N     0  -0.445  -36.2572   -9.6132  24.1093
 GZF  C19  C  CR56  0  -0.038  -36.3762   -9.3354  22.7678
 GZF  C20  C  CR6   0   0.456  -36.9762   -9.9828  21.6852
 GZF  O21  O  OH1   0  -0.587  -37.6051  -11.1298  21.8672
 GZF  N22  N  N     0  -0.516  -36.9199   -9.4561  20.4824
 GZF  C23  C  CR6   0   0.545  -36.2788   -8.2837  20.3083
 GZF  N24  N  NH2   0  -0.821  -36.2927   -7.7776  19.0571
 GZF  N25  N  N     0  -0.496  -35.6684   -7.5733  21.2537
 GZF  C26  C  CR56  0   0.511  -35.7476   -8.1361  22.4499
 GZF  C27  C  CH1   0  -0.053  -35.2141   -5.1779  23.4375
 GZF  O28  O  OH1   0  -0.649  -35.2507   -4.2231  24.4578
 GZF  H1   H  HOH1  0   0.459  -35.0456   -2.8999  21.8852
 GZF  H2   H  HCH1  0   0.250  -34.8323   -5.0824  21.3442
 GZF  H3   H  HCH1  0   0.270  -32.6017   -5.6354  21.4346
 GZF  H4   H  HCH2  0   0.257  -31.0077   -5.1563  23.1343
 GZF  H5   H  HCH2  0   0.252  -31.7426   -3.6450  22.5930
 GZF  H6   H  HOH1  0   0.508  -32.6021   -2.8414  27.3548
 GZF  H7   H  HOH1  0   0.505  -29.5543   -3.8655  28.1280
 GZF  H9   H  HCH1  0   0.269  -34.2646   -6.4472  24.9267
 GZF  H10  H  HCR5  0   0.295  -35.2852   -8.4867  25.6118
 GZF  H12  H  HNH2  0   0.395  -35.6578   -7.0284  18.8409
 GZF  H13  H  HNH2  0   0.395  -36.5474   -8.3856  18.2982
 GZF  H14  H  HCH1  0   0.252  -36.2297   -5.4193  23.1042
 GZF  H15  H  HOH1  0   0.457  -35.9132   -4.4945  25.1011
 GZF  H8   H  HOH1  0   0.509  -27.1742   -3.6192  25.3629
 GZF  H16  H  HOH1  0   0.480  -37.9580  -11.4392  21.0203

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
 GZF  N24  C23  single    1.350  0.020  1.350
 GZF  C02  C03  single    1.535  0.020  1.535
 GZF  C02  C27  single    1.542  0.020  1.542
 GZF  C02  O01  single    1.393  0.020  1.393
 GZF  C23  N25  aromatic  1.331  0.020  1.331
 GZF  C23  N22  aromatic  1.347  0.020  1.347
 GZF  N25  C26  aromatic  1.324  0.020  1.324
 GZF  O14  C03  single    1.413  0.020  1.413
 GZF  O14  C15  single    1.402  0.020  1.402
 GZF  C03  C04  single    1.513  0.020  1.513
 GZF  C27  C15  single    1.549  0.020  1.549
 GZF  C27  O28  single    1.398  0.020  1.398
 GZF  C15  N16  single    1.443  0.020  1.443
 GZF  N22  C20  aromatic  1.314  0.020  1.314
 GZF  C26  N16  aromatic  1.364  0.020  1.364
 GZF  C26  C19  aromatic  1.391  0.020  1.391
 GZF  N16  C17  aromatic  1.374  0.020  1.374
 GZF  C20  C19  aromatic  1.397  0.020  1.397
 GZF  C20  O21  single    1.321  0.020  1.321
 GZF  C19  N18  aromatic  1.375  0.020  1.375
 GZF  C04  O05  single    1.430  0.020  1.430
 GZF  C17  N18  aromatic  1.295  0.020  1.295
 GZF  O05  P06  single    1.575  0.020  1.575
 GZF  O08  P06  double    1.468  0.020  1.468
 GZF  P06  O09  single    1.630  0.020  1.630
 GZF  P06  O07  single    1.586  0.020  1.586
 GZF  O09  P10  single    1.617  0.020  1.617
 GZF  O11  P10  single    1.590  0.020  1.590
 GZF  P10  S13  double    1.918  0.020  1.918
 GZF  P10  O12  single    1.594  0.020  1.594
 GZF  O01  H1   single    0.850  0.020  0.980
 GZF  C02  H2   single    0.970  0.020  1.090
 GZF  C03  H3   single    0.970  0.020  1.090
 GZF  C04  H4   single    0.970  0.020  1.090
 GZF  C04  H5   single    0.970  0.020  1.090
 GZF  O07  H6   single    0.850  0.020  0.980
 GZF  O12  H7   single    0.850  0.020  0.980
 GZF  C15  H9   single    0.970  0.020  1.090
 GZF  C17  H10  single    0.930  0.020  1.080
 GZF  N24  H12  single    0.890  0.020  1.040
 GZF  N24  H13  single    0.890  0.020  1.040
 GZF  C27  H14  single    0.970  0.020  1.090
 GZF  O28  H15  single    0.850  0.020  0.980
 GZF  O11  H8   single    0.850  0.020  0.980
 GZF  O21  H16  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
 GZF  H1   O01  C02  108.85  3.000
 GZF  H2   C02  C27  106.55  3.000
 GZF  H2   C02  C03  106.93  3.000
 GZF  C27  C02  C03  104.64  3.000
 GZF  H2   C02  O01  111.38  3.000
 GZF  C27  C02  O01  116.00  3.000
 GZF  C03  C02  O01  110.74  3.000
 GZF  H3   C03  O14  107.87  3.000
 GZF  H3   C03  C04  106.14  3.000
 GZF  O14  C03  C04  110.74  3.000
 GZF  H3   C03  C02  110.35  3.000
 GZF  C04  C03  C02  116.38  3.000
 GZF  O14  C03  C02  105.14  3.000
 GZF  H5   C04  H4   107.90  3.000
 GZF  H5   C04  O05  112.28  3.000
 GZF  H4   C04  O05  107.79  3.000
 GZF  H5   C04  C03  110.16  3.000
 GZF  H4   C04  C03  109.57  3.000
 GZF  O05  C04  C03  109.07  3.000
 GZF  P06  O05  C04  123.22  3.000
 GZF  O09  P06  O08  108.24  3.000
 GZF  O09  P06  O07  105.59  3.000
 GZF  O08  P06  O07  118.67  3.000
 GZF  O07  P06  O05   98.34  3.000
 GZF  O09  P06  O05  104.38  3.000
 GZF  O08  P06  O05  119.93  3.000
 GZF  H6   O07  P06  114.57  3.000
 GZF  P10  O09  P06  131.43  3.000
 GZF  S13  P10  O12  116.13  3.000
 GZF  O12  P10  O11  103.23  3.000
 GZF  S13  P10  O11  118.65  3.000
 GZF  O12  P10  O09  103.88  3.000
 GZF  S13  P10  O09  116.29  3.000
 GZF  O11  P10  O09   95.70  3.000
 GZF  H8   O11  P10  113.87  3.000
 GZF  H7   O12  P10  114.46  3.000
 GZF  C15  O14  C03  111.88  3.000
 GZF  H9   C15  C27  109.51  3.000
 GZF  H9   C15  N16  105.97  3.000
 GZF  C27  C15  N16  113.94  3.000
 GZF  H9   C15  O14  111.06  3.000
 GZF  N16  C15  O14  108.07  3.000
 GZF  C27  C15  O14  108.29  3.000
 GZF  C26  N16  C17  106.19  3.000
 GZF  C17  N16  C15  126.30  3.000
 GZF  C26  N16  C15  127.49  3.000
 GZF  H10  C17  N18  125.49  3.000
 GZF  H10  C17  N16  120.77  3.000
 GZF  N18  C17  N16  113.74  3.000
 GZF  C19  N18  C17  104.11  3.000
 GZF  C26  C19  C20  114.62  3.000
 GZF  C20  C19  N18  134.39  3.000
 GZF  C26  C19  N18  110.99  3.000
 GZF  N22  C20  O21  119.64  3.000
 GZF  O21  C20  C19  120.02  3.000
 GZF  N22  C20  C19  120.34  3.000
 GZF  H16  O21  C20  109.30  3.000
 GZF  C23  N22  C20  119.16  3.000
 GZF  N25  C23  N24  117.59  3.000
 GZF  N25  C23  N22  126.22  3.000
 GZF  N24  C23  N22  116.17  3.000
 GZF  H13  N24  H12  116.64  3.000
 GZF  H13  N24  C23  118.40  3.000
 GZF  H12  N24  C23  118.17  3.000
 GZF  C26  N25  C23  112.79  3.000
 GZF  N25  C26  C19  126.86  3.000
 GZF  C19  C26  N16  104.97  3.000
 GZF  N25  C26  N16  128.17  3.000
 GZF  H14  C27  O28  110.38  3.000
 GZF  H14  C27  C15  109.73  3.000
 GZF  O28  C27  C15  112.89  3.000
 GZF  H14  C27  C02  110.12  3.000
 GZF  O28  C27  C02  110.69  3.000
 GZF  C15  C27  C02  102.78  3.000
 GZF  H15  O28  C27  108.25  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
 GZF  CONST_01  C23  N25  C26  N16   180.00   0.0  0
 GZF  CONST_02  C20  C19  C26  N16   180.00   0.0  0
 GZF  CONST_03  N18  C19  C26  N16     0.00   0.0  0
 GZF  CONST_04  C19  N18  C17  N16     0.00   0.0  0
 GZF  CONST_05  N25  C26  N16  C17   180.00   0.0  0
 GZF  CONST_06  C19  C26  N16  C17     0.00   0.0  0
 GZF  CONST_07  C26  C19  N18  C17     0.00   0.0  0
 GZF  CONST_08  C20  C19  N18  C17   180.00   0.0  0
 GZF  CONST_09  N25  C26  C19  N18   180.00   0.0  0
 GZF  CONST_10  N22  C20  C19  N18   180.00   0.0  0
 GZF  CONST_11  C26  N16  C17  N18     0.00   0.0  0
 GZF  CONST_12  C23  N25  C26  C19     0.00   0.0  0
 GZF  CONST_13  C23  N22  C20  C19     0.00   0.0  0
 GZF  CONST_14  N25  C23  N22  C20     0.00   0.0  0
 GZF  CONST_15  N25  C26  C19  C20     0.00   0.0  0
 GZF  CONST_16  C26  N25  C23  N22     0.00   0.0  0
 GZF  CONST_17  C26  C19  C20  N22     0.00   0.0  0
 GZF  CONST_18  N25  C26  N16  C15     0.00   0.0  0
 GZF  CONST_19  C19  C26  N16  C15   180.00   0.0  0
 GZF  CONST_20  N18  C17  N16  C15   180.00   0.0  0
 GZF  CONST_21  O21  C20  C19  N18     0.00   0.0  0
 GZF  CONST_22  N24  C23  N22  C20   180.00   0.0  0
 GZF  CONST_23  C23  N22  C20  O21   180.00   0.0  0
 GZF  CONST_24  C26  C19  C20  O21   180.00   0.0  0
 GZF  CONST_25  C26  N25  C23  N24   180.00   0.0  0
 GZF  CONST_26  H10  C17  N16  C15     0.00   0.0  0
 GZF  CONST_27  H10  C17  N18  C19   180.00   0.0  0
 GZF  CONST_28  H10  C17  N16  C26   180.00   0.0  0
 GZF  CONST_29  H12  N24  C23  N22   180.00   0.0  0
 GZF  CONST_32  H13  N24  C23  N25   180.00   0.0  0
 GZF  Var_01    P06  O05  C04  C03  -144.23  30.0  3
 GZF  Var_02    O08  P06  O05  C04    62.24  30.0  3
 GZF  Var_03    O09  P06  O05  C04   -59.12  30.0  3
 GZF  Var_04    O07  P06  O05  C04  -167.67  30.0  3
 GZF  Var_05    P10  O09  P06  O05   -68.65  30.0  3
 GZF  Var_06    O11  P10  O09  P06   173.73  30.0  3
 GZF  Var_07    S13  P10  O09  P06    47.80  30.0  3
 GZF  Var_08    O12  P10  O09  P06   -81.10  30.0  3
 GZF  Var_09    P10  O09  P06  O07    34.47  30.0  3
 GZF  Var_10    P10  O09  P06  O08   162.53  30.0  3
 GZF  Var_11    H4   C04  O05  P06    96.87  30.0  2
 GZF  Var_12    H5   C04  O05  P06   -21.83  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
 GZF  chir_01  C02  C03  C27  O01  negativ
 GZF  chir_02  C03  O14  C02  C04  negativ
 GZF  chir_04  C15  O14  C27  N16  negativ
 GZF  chir_05  C27  O28  C15  C02  positiv
 GZF  chir_06  P06  O08  O09  O07  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
 GZF  plan-1  C15  0.020
 GZF  plan-1  N16  0.020
 GZF  plan-1  C17  0.020
 GZF  plan-1  N18  0.020
 GZF  plan-1  C19  0.020
 GZF  plan-1  C20  0.020
 GZF  plan-1  O21  0.020
 GZF  plan-1  N22  0.020
 GZF  plan-1  C23  0.020
 GZF  plan-1  N24  0.020
 GZF  plan-1  N25  0.020
 GZF  plan-1  C26  0.020
 GZF  plan-1  H10  0.020
 GZF  plan-2  C23  0.020
 GZF  plan-2  N24  0.020
 GZF  plan-2  H12  0.020
 GZF  plan-2  H13  0.020

