# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 15 01:53:05 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O)N4CC[NH2+]CC4
#
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
 O05  O05  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  56  33  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O05
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
 O05  C2   C  CR6    0   0.619  -12.2483  24.5531  -36.8133
 O05  C3   C  CH2    0  -1.039  -16.0597  18.9960  -29.8098
 O05  C4   C  CR56   0   0.512  -13.7413  22.9747  -36.4431
 O05  C5   C  CR56   0  -0.052  -14.2425  23.0441  -37.7323
 O05  C6   C  CR6    0   0.466  -13.6281  23.9898  -38.5747
 O05  C8   C  CR15   0   0.093  -15.3971  21.5751  -36.7482
 O05  C9   C  CH2    0  -0.350  -10.8963  25.4064  -34.9734
 O05  C10  C  CH2    0  -0.325  -11.7302  26.4842  -34.3050
 O05  C11  C  CH2    0  -0.325  -11.7296  27.7085  -36.4807
 O05  C12  C  CH2    0  -0.350  -10.8999  26.5783  -37.0642
 O05  O2A  O  O      0  -0.804  -18.2657  20.0107  -31.2111
 O05  PA   P  P      0   1.288  -17.5112  18.7448  -30.8925
 O05  O1A  O  OP    -1  -0.816  -18.2791  17.5407  -30.4112
 O05  PB   P  P      0   1.216  -16.1300  20.3578  -28.5477
 O05  O3B  O  OP    -1  -0.878  -17.5300  20.3512  -27.9461
 O05  O1B  O  O      0  -0.880  -15.8305  21.6698  -29.3450
 O05  O2B  O  OP    -1  -0.892  -15.0056  20.0367  -27.5624
 O05  O5'  O  O2     0  -0.634  -16.7871  18.2186  -32.3137
 O05  C4'  C  CH1    0  -0.008  -15.2070  19.9401  -33.0762
 O05  O4'  O  O2     0  -0.511  -14.5864  20.2689  -34.3311
 O05  C3'  C  CH1    0  -0.101  -15.5192  21.2740  -32.3749
 O05  O7   O  OH1    0  -0.752  -14.5584  21.6623  -31.4432
 O05  C2'  C  CH1    0  -0.012  -15.4932  22.2617  -33.5489
 O05  O8   O  OH1    0  -0.666  -15.2386  23.5728  -33.1605
 O05  C1'  C  CH1    0   0.211  -14.4034  21.6484  -34.4306
 O05  N9   N  NR5    0  -0.545  -14.4892  22.0211  -35.8209
 O05  N7   N  N      0  -0.452  -15.2763  22.1576  -37.9036
 O05  N6   N  NH2    0  -0.821  -14.0000  24.1674  -39.8440
 O05  N3   N  N      0  -0.513  -12.7525  23.6989  -35.9320
 O05  N1   N  N      0  -0.531  -12.6379  24.7310  -38.0810
 O05  N2   N  NT     0  -0.491  -11.1933  25.3318  -36.3887
 O05  N4   N  NT2    1  -0.644  -11.5123  27.7846  -35.0058
 O05  H19  H  HCH2   0   0.230  -15.9098  18.0485  -29.2849
 O05  H18  H  HCH2   0   0.237  -15.1555  19.1435  -30.4056
 O05  H15  H  HCR5   0   0.288  -16.1167  20.8052  -36.5159
 O05  H13  H  HCH2   0   0.300  -11.0936  24.4551  -34.4894
 O05  H14  H  HCH2   0   0.278   -9.8323  25.6272  -34.8536
 O05  H11  H  HCH2   0   0.309  -11.4549  26.6255  -33.2625
 O05  H12  H  HCH2   0   0.297  -12.7938  26.2579  -34.3666
 O05  H9   H  HCH2   0   0.309  -11.4551  28.6737  -36.9001
 O05  H8   H  HCH2   0   0.297  -12.7941  27.5421  -36.6378
 O05  H7   H  HCH2   0   0.299  -11.1088  26.4978  -38.1263
 O05  H6   H  HCH2   0   0.276   -9.8346  26.7965  -36.9530
 O05  H16  H  HCH2   0   0.194  -17.2782  19.7186  -33.6628
 O05  H17  H  HCH2   0   0.220  -16.2089  18.4382  -34.2294
 O05  H1   H  HCH1   0   0.231  -14.4954  19.3563  -32.4828
 O05  H2   H  HCH1   0   0.264  -16.5118  21.2300  -31.9177
 O05  H23  H  HOH1   0   0.460  -15.0468  21.6544  -30.5120
 O05  H3   H  HCH1   0   0.241  -16.4437  22.2371  -34.0961
 O05  H24  H  HOH1   0   0.435  -14.6929  23.4892  -32.3622
 O05  H    H  HCH1   0   0.244  -13.4109  21.9669  -34.0855
 O05  H5   H  HNH2   0   0.401  -13.5689  24.8812  -40.4051
 O05  H4   H  HNH2   0   0.410  -14.7691  23.6527  -40.2348
 O05  H10  H  HNT2   0   0.466  -10.5633  28.1147  -34.8204
 O05  H25  H  HNT2   0   0.481  -12.1259  28.4955  -34.6076
 O05  C5'  C  CH2    0  -0.182  -16.4363  19.0777  -33.3711

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
 O05  N6   C6   single    1.335  0.020  1.335
 O05  C6   N1   aromatic  1.332  0.020  1.332
 O05  C6   C5   aromatic  1.408  0.020  1.408
 O05  N1   C2   aromatic  1.338  0.020  1.338
 O05  N7   C5   aromatic  1.373  0.020  1.373
 O05  N7   C8   aromatic  1.300  0.020  1.300
 O05  C12  C11  single    1.519  0.020  1.519
 O05  C12  N2   single    1.448  0.020  1.448
 O05  C5   C4   aromatic  1.385  0.020  1.385
 O05  C11  N4   single    1.493  0.020  1.493
 O05  C2   N2   single    1.378  0.020  1.378
 O05  C2   N3   aromatic  1.327  0.020  1.327
 O05  C8   N9   aromatic  1.372  0.020  1.372
 O05  N2   C9   single    1.448  0.020  1.448
 O05  C4   N3   aromatic  1.328  0.020  1.328
 O05  C4   N9   aromatic  1.362  0.020  1.362
 O05  N4   C10  single    1.493  0.020  1.493
 O05  N9   C1'  single    1.442  0.020  1.442
 O05  C9   C10  single    1.518  0.020  1.518
 O05  C1'  O4'  single    1.395  0.020  1.395
 O05  C1'  C2'  single    1.530  0.020  1.530
 O05  O4'  C4'  single    1.438  0.020  1.438
 O05  C2'  O8   single    1.391  0.020  1.391
 O05  C2'  C3'  single    1.534  0.020  1.534
 O05  C5'  C4'  single    1.530  0.020  1.530
 O05  C5'  O5'  single    1.407  0.020  1.407
 O05  C4'  C3'  single    1.539  0.020  1.539
 O05  O5'  PA   single    1.680  0.020  1.680
 O05  C3'  O7   single    1.393  0.020  1.393
 O05  O2A  PA   deloc     1.508  0.020  1.508
 O05  PA   O1A  deloc     1.507  0.020  1.507
 O05  PA   C3   single    1.828  0.020  1.828
 O05  C3   PB   single    1.858  0.020  1.858
 O05  O1B  PB   deloc     1.564  0.020  1.564
 O05  PB   O3B  deloc     1.524  0.020  1.524
 O05  PB   O2B  deloc     1.529  0.020  1.529
 O05  C3   H19  single    0.970  0.020  1.090
 O05  C3   H18  single    0.970  0.020  1.090
 O05  C8   H15  single    0.930  0.020  1.080
 O05  C9   H13  single    0.970  0.020  1.090
 O05  C9   H14  single    0.970  0.020  1.090
 O05  C10  H11  single    0.970  0.020  1.090
 O05  C10  H12  single    0.970  0.020  1.090
 O05  C11  H9   single    0.970  0.020  1.090
 O05  C11  H8   single    0.970  0.020  1.090
 O05  C12  H7   single    0.970  0.020  1.090
 O05  C12  H6   single    0.970  0.020  1.090
 O05  C5'  H16  single    0.970  0.020  1.090
 O05  C5'  H17  single    0.970  0.020  1.090
 O05  C4'  H1   single    0.970  0.020  1.090
 O05  C3'  H2   single    0.970  0.020  1.090
 O05  O7   H23  single    0.850  0.020  0.980
 O05  C2'  H3   single    0.970  0.020  1.090
 O05  O8   H24  single    0.850  0.020  0.980
 O05  C1'  H    single    0.970  0.020  1.090
 O05  N6   H5   single    0.860  0.020  1.020
 O05  N6   H4   single    0.860  0.020  1.020
 O05  N4   H10  single    0.890  0.020  1.040
 O05  N4   H25  single    0.890  0.020  1.040

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
 O05  N2   C2   N1   116.08  3.000
 O05  N2   C2   N3   116.74  3.000
 O05  N1   C2   N3   127.17  3.000
 O05  H18  C3   H19  105.38  3.000
 O05  H18  C3   PB   107.62  3.000
 O05  H19  C3   PB   108.31  3.000
 O05  H18  C3   PA   110.64  3.000
 O05  H19  C3   PA   105.91  3.000
 O05  PB   C3   PA   118.23  3.000
 O05  N3   C4   N9   127.94  3.000
 O05  N9   C4   C5   105.16  3.000
 O05  N3   C4   C5   126.90  3.000
 O05  N7   C5   C6   133.47  3.000
 O05  N7   C5   C4   110.88  3.000
 O05  C6   C5   C4   115.65  3.000
 O05  N1   C6   N6   119.06  3.000
 O05  N1   C6   C5   118.46  3.000
 O05  N6   C6   C5   122.48  3.000
 O05  H15  C8   N7   124.97  3.000
 O05  H15  C8   N9   121.84  3.000
 O05  N7   C8   N9   113.18  3.000
 O05  H14  C9   H13  107.76  3.000
 O05  H14  C9   N2   108.49  3.000
 O05  H13  C9   N2   110.69  3.000
 O05  H14  C9   C10  110.06  3.000
 O05  H13  C9   C10  109.04  3.000
 O05  N2   C9   C10  110.75  3.000
 O05  H12  C10  H11  109.17  3.000
 O05  H12  C10  N4   107.27  3.000
 O05  H11  C10  N4   107.45  3.000
 O05  H12  C10  C9   111.35  3.000
 O05  H11  C10  C9   112.05  3.000
 O05  N4   C10  C9   109.36  3.000
 O05  H8   C11  H9   109.07  3.000
 O05  H8   C11  N4   107.01  3.000
 O05  H9   C11  N4   107.40  3.000
 O05  H8   C11  C12  111.40  3.000
 O05  H9   C11  C12  111.99  3.000
 O05  N4   C11  C12  109.76  3.000
 O05  H6   C12  H7   107.57  3.000
 O05  H6   C12  N2   108.77  3.000
 O05  H7   C12  N2   110.71  3.000
 O05  H6   C12  C11  110.17  3.000
 O05  H7   C12  C11  109.03  3.000
 O05  N2   C12  C11  110.54  3.000
 O05  O5'  PA   O1A  103.86  3.000
 O05  O1A  PA   O2A  118.90  3.000
 O05  O5'  PA   O2A  107.45  3.000
 O05  O1A  PA   C3   108.98  3.000
 O05  O2A  PA   C3   114.02  3.000
 O05  O5'  PA   C3   101.65  3.000
 O05  O2B  PB   O1B  111.34  3.000
 O05  O2B  PB   O3B  114.85  3.000
 O05  O1B  PB   O3B  112.38  3.000
 O05  O2B  PB   C3   104.83  3.000
 O05  O3B  PB   C3   107.44  3.000
 O05  O1B  PB   C3   105.15  3.000
 O05  C5'  O5'  PA   123.52  3.000
 O05  H1   C4'  C3'  110.30  3.000
 O05  H1   C4'  O4'  108.32  3.000
 O05  C3'  C4'  O4'  106.68  3.000
 O05  H1   C4'  C5'  109.02  3.000
 O05  C3'  C4'  C5'  114.41  3.000
 O05  O4'  C4'  C5'  107.90  3.000
 O05  C1'  O4'  C4'  110.18  3.000
 O05  H2   C3'  C2'  111.16  3.000
 O05  H2   C3'  O7   110.94  3.000
 O05  C2'  C3'  O7   108.69  3.000
 O05  H2   C3'  C4'  109.86  3.000
 O05  O7   C3'  C4'  113.98  3.000
 O05  C2'  C3'  C4'  101.88  3.000
 O05  H23  O7   C3'  105.65  3.000
 O05  H3   C2'  C1'  108.70  3.000
 O05  H3   C2'  O8   108.61  3.000
 O05  C1'  C2'  O8   114.10  3.000
 O05  H3   C2'  C3'  110.64  3.000
 O05  O8   C2'  C3'  113.34  3.000
 O05  C1'  C2'  C3'  101.24  3.000
 O05  H24  O8   C2'  104.56  3.000
 O05  H    C1'  N9   106.37  3.000
 O05  H    C1'  C2'  110.27  3.000
 O05  N9   C1'  C2'  114.18  3.000
 O05  H    C1'  O4'  112.51  3.000
 O05  C2'  C1'  O4'  105.18  3.000
 O05  N9   C1'  O4'  108.45  3.000
 O05  C1'  N9   C8   127.37  3.000
 O05  C1'  N9   C4   126.06  3.000
 O05  C8   N9   C4   106.39  3.000
 O05  C8   N7   C5   104.39  3.000
 O05  H4   N6   H5   118.36  3.000
 O05  H4   N6   C6   121.01  3.000
 O05  H5   N6   C6   120.40  3.000
 O05  C4   N3   C2   112.24  3.000
 O05  C6   N1   C2   119.58  3.000
 O05  C12  N2   C9   111.72  3.000
 O05  C9   N2   C2   119.16  3.000
 O05  C12  N2   C2   119.85  3.000
 O05  H25  N4   H10  105.22  3.000
 O05  H25  N4   C11  109.50  3.000
 O05  H10  N4   C11  109.33  3.000
 O05  H25  N4   C10  109.63  3.000
 O05  H10  N4   C10  109.37  3.000
 O05  C11  N4   C10  113.46  3.000
 O05  H17  C5'  H16  106.99  3.000
 O05  H17  C5'  C4'  108.28  3.000
 O05  H16  C5'  C4'  109.78  3.000
 O05  H17  C5'  O5'  106.52  3.000
 O05  H16  C5'  O5'  111.41  3.000
 O05  C4'  C5'  O5'  113.56  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
 O05  CONST_01  C5   C6   N1   C2     0.00   0.0  0
 O05  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 O05  CONST_03  N9   C4   N3   C2   180.00   0.0  0
 O05  CONST_04  N1   C6   C5   C4     0.00   0.0  0
 O05  CONST_05  C8   N7   C5   C4     0.00   0.0  0
 O05  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 O05  CONST_07  N7   C8   N9   C4     0.00   0.0  0
 O05  CONST_08  N9   C8   N7   C5     0.00   0.0  0
 O05  CONST_09  C8   N9   C4   C5     0.00   0.0  0
 O05  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 O05  CONST_11  C8   N7   C5   C6   180.00   0.0  0
 O05  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 O05  CONST_13  N9   C4   C5   C6   180.00   0.0  0
 O05  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 O05  CONST_15  N7   C5   C4   N9     0.00   0.0  0
 O05  CONST_16  N1   C6   C5   N7   180.00   0.0  0
 O05  CONST_17  N3   C4   C5   N7   180.00   0.0  0
 O05  CONST_18  N2   C2   N3   C4   180.00   0.0  0
 O05  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 O05  CONST_20  N2   C2   N1   C6   180.00   0.0  0
 O05  CONST_21  N7   C8   N9   C1'  180.00   0.0  0
 O05  CONST_22  N3   C4   N9   C1'    0.00   0.0  0
 O05  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 O05  CONST_24  N6   C6   C5   C4   180.00   0.0  0
 O05  CONST_25  N6   C6   C5   N7     0.00   0.0  0
 O05  CONST_26  H15  C8   N9   C4   180.00   0.0  0
 O05  CONST_27  H5   N6   C6   C5   180.00   0.0  0
 O05  CONST_28  H4   N6   C6   C5     0.00   0.0  0
 O05  Var_01    C11  C12  N2   C2    86.19  30.0  1
 O05  Var_02    C10  C9   N2   C2   -86.05  30.0  1
 O05  Var_03    N1   C2   N2   C9   167.12  30.0  1
 O05  Var_04    C11  N4   C10  C9    52.79  30.0  1
 O05  Var_05    C12  C11  N4   C10  -52.74  30.0  1
 O05  Var_06    N4   C11  C12  N2    54.94  30.0  1
 O05  Var_07    N4   C10  C9   N2   -55.36  30.0  1
 O05  Var_08    C4'  C5'  O5'  PA    73.74  30.0  1
 O05  Var_09    PB   C3   PA   O2A   31.89  30.0  3
 O05  Var_10    O1B  PB   C3   PA   -79.28  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
 O05  chir_02  C4'  O4'  C5'  C3'  positiv
 O05  chir_03  C3'  O7   C4'  C2'  positiv
 O05  chir_04  C2'  O8   C3'  C1'  positiv
 O05  chir_05  C1'  O4'  N9   C2'  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
 O05  plan-1  C6   0.020
 O05  plan-1  N6   0.020
 O05  plan-1  H5   0.020
 O05  plan-1  H4   0.020
 O05  plan-2  C2   0.020
 O05  plan-2  C4   0.020
 O05  plan-2  C5   0.020
 O05  plan-2  C6   0.020
 O05  plan-2  C8   0.020
 O05  plan-2  C1'  0.020
 O05  plan-2  N9   0.020
 O05  plan-2  N7   0.020
 O05  plan-2  N6   0.020
 O05  plan-2  N3   0.020
 O05  plan-2  N1   0.020
 O05  plan-2  N2   0.020
 O05  plan-2  H15  0.020

