# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 28 05:29:32 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CO)[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
 JNT  JNT  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate'  ligand  59  36  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JNT
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
 JNT  O5'  O  O2     0  -0.617  -0.9126   2.6921  -0.2820
 JNT  C5'  C  CH2    0  -0.150  -2.2162   3.1753  -0.0596
 JNT  C4'  C  CR15   0  -0.046  -3.0979   2.7822  -1.2298
 JNT  O4'  O  O      0  -0.491  -3.0692   1.3666  -1.4384
 JNT  C3'  C  CR15   0  -0.030  -4.5564   3.1328  -0.9751
 JNT  O3'  O  OH1    0  -0.668  -5.2053   3.3179  -2.2056
 JNT  C2'  C  CR15   0  -0.050  -5.0430   1.8554  -0.2844
 JNT  O2'  O  OH1    0  -0.652  -6.4172   1.6261  -0.3664
 JNT  C1'  C  CR15   0   0.226  -4.2847   0.7857  -1.0720
 JNT  N9   N  NR5    0  -0.542  -4.0257  -0.4200  -0.3193
 JNT  C8   C  CR15   0   0.071  -3.0636  -0.6173   0.6370
 JNT  N7   N  N      0  -0.458  -3.1014  -1.8101   1.1576
 JNT  C5   C  CR56   0  -0.011  -4.1414  -2.4335   0.5190
 JNT  C4   C  CR56   0   0.488  -4.7292  -1.5859  -0.4073
 JNT  N3   N  N      0  -0.455  -5.7546  -1.8768  -1.2056
 JNT  C2   C  CR16   0   0.041  -6.1824  -3.1132  -1.0217
 JNT  N1   N  N      0  -0.475  -5.7228  -4.0307  -0.1741
 JNT  C6   C  CR6    0   0.450  -4.6911  -3.7240   0.6198
 JNT  N6   N  NH2    0  -0.817  -4.2346  -4.6371   1.4815
 JNT  C1A  C  CH2    0  -0.163   8.1753  -3.3202  -0.2067
 JNT  C2A  C  CH1    0  -0.028   6.6855  -3.0190  -0.2017
 JNT  O2C  O  OH1    0  -0.666   6.0270  -3.6730  -1.2754
 JNT  C3A  C  CH1    0  -0.031   6.4179  -1.4998  -0.2039
 JNT  O3C  O  OH1    0  -0.658   7.0703  -0.8947   0.8908
 JNT  C4A  C  CH1    0  -0.005   4.9130  -1.1585  -0.2068
 JNT  O4C  O  OH1    0  -0.688   4.2706  -1.5995  -1.3774
 JNT  C5A  C  CH2    0  -0.141   4.7024   0.3424  -0.1060
 JNT  O5A  O  O2     0  -0.620   3.3132   0.6083  -0.0755
 JNT  PB   P  P      0   1.338   2.8408   1.9669   0.7203
 JNT  O2B  O  OP    -1  -0.795   3.5035   3.1584   0.1032
 JNT  O1B  O  O      0  -0.796   2.9102   1.7382   2.1970
 JNT  O3A  O  O2     0  -0.734   1.2854   1.8639   0.1961
 JNT  PA   P  P      0   1.354  -0.0051   2.3839   1.0590
 JNT  O1A  O  O      0  -0.794   0.2959   3.6671   1.7645
 JNT  O2A  O  OP    -1  -0.775  -0.6168   1.2367   1.8074
 JNT  H1   H  HCH2   0   0.204  -2.6378   2.7844   0.8755
 JNT  H2   H  HCH2   0   0.230  -2.2235   4.2683   0.0216
 JNT  H3   H  HCR5   0   0.264  -2.7289   3.2656  -2.1394
 JNT  H4   H  HCR5   0   0.252  -4.6556   4.0121  -0.3242
 JNT  H5   H  HOH1   0   0.449  -6.1503   3.1840  -2.0666
 JNT  H6   H  HCR5   0   0.249  -4.6962   1.8562   0.7567
 JNT  H7   H  HOH1   0   0.469  -6.8553   2.1026   0.3460
 JNT  H8   H  HCR5   0   0.258  -4.8681   0.4786  -1.9476
 JNT  H9   H  HCR5   0   0.324  -2.3398   0.1450   0.9009
 JNT  H10  H  HCR6   0   0.250  -7.0170  -3.4277  -1.6398
 JNT  H11  H  HNH2   0   0.401  -4.5906  -5.5769   1.4501
 JNT  H12  H  HNH2   0   0.409  -3.3919  -4.4713   2.0032
 JNT  H13  H  HOH1   0   0.457   9.2978  -4.8893  -0.0816
 JNT  H16  H  HCH1   0   0.237   6.2432  -3.4416   0.7094
 JNT  H17  H  HOH1   0   0.457   6.5120  -3.4963  -2.0906
 JNT  H19  H  HOH1   0   0.449   6.6909  -1.2396   1.7075
 JNT  H20  H  HCH1   0   0.192   4.4633  -1.6238   0.6892
 JNT  H21  H  HOH1   0   0.447   4.5509  -2.5139  -1.5246
 JNT  H22  H  HCH2   0   0.211   5.2038   0.7117   0.7922
 JNT  H23  H  HCH2   0   0.206   5.1662   0.8375  -0.9684
 JNT  H14  H  HCH2   0   0.214   8.6489  -2.7979   0.6298
 JNT  O1C  O  OH1    0  -0.670   8.3535  -4.7144  -0.1197
 JNT  H18  H  HCH1   0   0.235   6.8717  -1.0623  -1.1026
 JNT  H15  H  HCH2   0   0.194   8.6178  -2.9127  -1.1294

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
 JNT  N1   C2   aromatic  1.331  0.020  1.331
 JNT  N1   C6   aromatic  1.337  0.020  1.337
 JNT  N6   C6   single    1.336  0.020  1.336
 JNT  C2   N3   aromatic  1.321  0.020  1.321
 JNT  C6   C5   aromatic  1.406  0.020  1.406
 JNT  N3   C4   aromatic  1.332  0.020  1.332
 JNT  C5   C4   aromatic  1.386  0.020  1.386
 JNT  C5   N7   aromatic  1.370  0.020  1.370
 JNT  C4   N9   aromatic  1.365  0.020  1.365
 JNT  N7   C8   aromatic  1.302  0.020  1.302
 JNT  O2'  C2'  single    1.396  0.020  1.396
 JNT  N9   C8   aromatic  1.371  0.020  1.371
 JNT  N9   C1'  single    1.445  0.020  1.445
 JNT  C1'  C2'  single    1.530  0.020  1.530
 JNT  C1'  O4'  single    1.396  0.020  1.396
 JNT  C2'  C3'  single    1.532  0.020  1.532
 JNT  O4'  C4'  single    1.431  0.020  1.431
 JNT  C3'  O3'  single    1.403  0.020  1.403
 JNT  C3'  C4'  single    1.522  0.020  1.522
 JNT  C4'  C5'  single    1.517  0.020  1.517
 JNT  O5'  C5'  single    1.408  0.020  1.408
 JNT  O5'  PA   single    1.648  0.020  1.648
 JNT  O1A  PA   deloc     1.495  0.020  1.495
 JNT  O2A  PA   deloc     1.500  0.020  1.500
 JNT  PA   O3A  single    1.637  0.020  1.637
 JNT  O2C  C2A  single    1.419  0.020  1.419
 JNT  O3A  PB   single    1.645  0.020  1.645
 JNT  O4C  C4A  single    1.406  0.020  1.406
 JNT  C2A  C1A  single    1.520  0.020  1.520
 JNT  C2A  C3A  single    1.543  0.020  1.543
 JNT  C1A  O1C  single    1.408  0.020  1.408
 JNT  O1B  PB   deloc     1.496  0.020  1.496
 JNT  PB   O5A  single    1.644  0.020  1.644
 JNT  PB   O2B  deloc     1.497  0.020  1.497
 JNT  C4A  C3A  single    1.543  0.020  1.543
 JNT  C4A  C5A  single    1.519  0.020  1.519
 JNT  O5A  C5A  single    1.415  0.020  1.415
 JNT  C5'  H1   single    0.970  0.020  1.090
 JNT  C5'  H2   single    0.970  0.020  1.090
 JNT  C4'  H3   single    0.970  0.020  1.090
 JNT  C3'  H4   single    0.970  0.020  1.090
 JNT  O3'  H5   single    0.850  0.020  0.980
 JNT  C2'  H6   single    0.970  0.020  1.090
 JNT  O2'  H7   single    0.850  0.020  0.980
 JNT  C1'  H8   single    0.970  0.020  1.090
 JNT  C8   H9   single    0.930  0.020  1.080
 JNT  C2   H10  single    0.930  0.020  1.080
 JNT  N6   H11  single    0.860  0.020  1.020
 JNT  N6   H12  single    0.860  0.020  1.020
 JNT  O1C  H13  single    0.850  0.020  0.980
 JNT  C1A  H14  single    0.970  0.020  1.090
 JNT  C1A  H15  single    0.970  0.020  1.090
 JNT  C2A  H16  single    0.970  0.020  1.090
 JNT  O2C  H17  single    0.850  0.020  0.980
 JNT  C3A  H18  single    0.970  0.020  1.090
 JNT  O3C  H19  single    0.850  0.020  0.980
 JNT  C4A  H20  single    0.970  0.020  1.090
 JNT  O4C  H21  single    0.850  0.020  0.980
 JNT  C5A  H22  single    0.970  0.020  1.090
 JNT  C5A  H23  single    0.970  0.020  1.090
 JNT  C3A  O3C  single    1.411  0.020  1.411

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
 JNT  PA   O5'  C5'  116.46  3.000
 JNT  H2   C5'  H1   106.83  3.000
 JNT  H2   C5'  C4'  108.17  3.000
 JNT  H1   C5'  C4'  109.98  3.000
 JNT  H2   C5'  O5'  111.10  3.000
 JNT  H1   C5'  O5'  111.59  3.000
 JNT  C4'  C5'  O5'  109.11  3.000
 JNT  H3   C4'  C3'  111.14  3.000
 JNT  H3   C4'  O4'  108.00  3.000
 JNT  C3'  C4'  O4'  105.76  3.000
 JNT  H3   C4'  C5'  109.32  3.000
 JNT  C3'  C4'  C5'  111.61  3.000
 JNT  O4'  C4'  C5'  110.92  3.000
 JNT  C1'  O4'  C4'  110.84  3.000
 JNT  H4   C3'  C2'  111.82  3.000
 JNT  H4   C3'  O3'  111.86  3.000
 JNT  C2'  C3'  O3'  111.01  3.000
 JNT  H4   C3'  C4'  111.72  3.000
 JNT  O3'  C3'  C4'  109.08  3.000
 JNT  C2'  C3'  C4'  100.82  3.000
 JNT  H5   O3'  C3'  107.96  3.000
 JNT  H6   C2'  C1'  109.41  3.000
 JNT  H6   C2'  O2'  111.54  3.000
 JNT  C1'  C2'  O2'  110.06  3.000
 JNT  H6   C2'  C3'  109.08  3.000
 JNT  C1'  C2'  C3'  101.16  3.000
 JNT  O2'  C2'  C3'  115.05  3.000
 JNT  H7   O2'  C2'  108.86  3.000
 JNT  H8   C1'  N9   106.12  3.000
 JNT  H8   C1'  C2'  110.09  3.000
 JNT  N9   C1'  C2'  113.84  3.000
 JNT  H8   C1'  O4'  111.74  3.000
 JNT  C2'  C1'  O4'  106.01  3.000
 JNT  N9   C1'  O4'  109.14  3.000
 JNT  C4   N9   C8   106.49  3.000
 JNT  C8   N9   C1'  127.55  3.000
 JNT  C4   N9   C1'  125.94  3.000
 JNT  H9   C8   N7   124.49  3.000
 JNT  H9   C8   N9   122.51  3.000
 JNT  N7   C8   N9   112.98  3.000
 JNT  C5   N7   C8   104.62  3.000
 JNT  C6   C5   C4   116.31  3.000
 JNT  C4   C5   N7   110.79  3.000
 JNT  C6   C5   N7   132.90  3.000
 JNT  N3   C4   C5   126.40  3.000
 JNT  C5   C4   N9   105.11  3.000
 JNT  N3   C4   N9   128.49  3.000
 JNT  C2   N3   C4   111.74  3.000
 JNT  H10  C2   N1   115.37  3.000
 JNT  H10  C2   N3   116.17  3.000
 JNT  N1   C2   N3   128.46  3.000
 JNT  C6   N1   C2   119.09  3.000
 JNT  N6   C6   N1   119.32  3.000
 JNT  N6   C6   C5   122.68  3.000
 JNT  N1   C6   C5   118.00  3.000
 JNT  H12  N6   H11  117.86  3.000
 JNT  H12  N6   C6   120.57  3.000
 JNT  H11  N6   C6   119.85  3.000
 JNT  H15  C1A  H14  106.86  3.000
 JNT  H15  C1A  C2A  108.86  3.000
 JNT  H14  C1A  C2A  109.09  3.000
 JNT  H15  C1A  O1C  111.54  3.000
 JNT  H14  C1A  O1C  111.76  3.000
 JNT  C2A  C1A  O1C  108.66  3.000
 JNT  H16  C2A  C3A  108.09  3.000
 JNT  H16  C2A  O2C  105.28  3.000
 JNT  C3A  C2A  O2C  111.85  3.000
 JNT  H16  C2A  C1A  108.75  3.000
 JNT  C3A  C2A  C1A  111.42  3.000
 JNT  O2C  C2A  C1A  111.16  3.000
 JNT  H17  O2C  C2A  108.76  3.000
 JNT  H18  C3A  C4A  108.27  3.000
 JNT  H18  C3A  O3C  105.85  3.000
 JNT  C4A  C3A  O3C  110.95  3.000
 JNT  O3C  C3A  C2A  109.94  3.000
 JNT  H18  C3A  C2A  108.78  3.000
 JNT  C4A  C3A  C2A  112.77  3.000
 JNT  H19  O3C  C3A  108.77  3.000
 JNT  H20  C4A  C5A  107.81  3.000
 JNT  H20  C4A  O4C  110.91  3.000
 JNT  C5A  C4A  O4C  107.56  3.000
 JNT  H20  C4A  C3A  107.59  3.000
 JNT  C5A  C4A  C3A  110.71  3.000
 JNT  O4C  C4A  C3A  112.19  3.000
 JNT  H21  O4C  C4A  106.90  3.000
 JNT  H23  C5A  H22  107.43  3.000
 JNT  H23  C5A  O5A  110.32  3.000
 JNT  H22  C5A  O5A  111.67  3.000
 JNT  H23  C5A  C4A  109.58  3.000
 JNT  H22  C5A  C4A  108.95  3.000
 JNT  O5A  C5A  C4A  108.86  3.000
 JNT  PB   O5A  C5A  116.61  3.000
 JNT  O3A  PB   O1B  110.42  3.000
 JNT  O1B  PB   O2B  120.55  3.000
 JNT  O3A  PB   O2B  109.71  3.000
 JNT  O2B  PB   O5A  109.34  3.000
 JNT  O1B  PB   O5A  109.77  3.000
 JNT  O3A  PB   O5A   93.76  3.000
 JNT  PA   O3A  PB   123.89  3.000
 JNT  O2A  PA   O1A  120.20  3.000
 JNT  O2A  PA   O3A  109.97  3.000
 JNT  O1A  PA   O3A  111.26  3.000
 JNT  O3A  PA   O5'   93.70  3.000
 JNT  O2A  PA   O5'  108.93  3.000
 JNT  O1A  PA   O5'  109.53  3.000
 JNT  H13  O1C  C1A  107.87  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
 JNT  CONST_01  C2   N3   C4   N9   180.00   0.0  0
 JNT  CONST_02  C6   C5   C4   N9   180.00   0.0  0
 JNT  CONST_03  N7   C5   C4   N9     0.00   0.0  0
 JNT  CONST_04  C5   N7   C8   N9     0.00   0.0  0
 JNT  CONST_05  C6   C5   N7   C8   180.00   0.0  0
 JNT  CONST_06  C4   C5   N7   C8     0.00   0.0  0
 JNT  CONST_07  N3   C4   N9   C8   180.00   0.0  0
 JNT  CONST_08  C5   C4   N9   C8     0.00   0.0  0
 JNT  CONST_09  N1   C6   C5   N7   180.00   0.0  0
 JNT  CONST_10  N3   C4   C5   N7   180.00   0.0  0
 JNT  CONST_11  C4   N9   C8   N7     0.00   0.0  0
 JNT  CONST_12  C2   N1   C6   C5     0.00   0.0  0
 JNT  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 JNT  CONST_14  N1   C2   N3   C4     0.00   0.0  0
 JNT  CONST_15  N1   C6   C5   C4     0.00   0.0  0
 JNT  CONST_16  C6   N1   C2   N3     0.00   0.0  0
 JNT  CONST_17  C6   C5   C4   N3     0.00   0.0  0
 JNT  CONST_18  N3   C4   N9   C1'    0.00   0.0  0
 JNT  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 JNT  CONST_20  N7   C8   N9   C1'  180.00   0.0  0
 JNT  CONST_21  N6   C6   C5   N7     0.00   0.0  0
 JNT  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 JNT  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 JNT  CONST_24  H9   C8   N9   C1'    0.00   0.0  0
 JNT  CONST_25  H10  C2   N3   C4   180.00   0.0  0
 JNT  CONST_26  H11  N6   C6   C5   180.00   0.0  0
 JNT  CONST_27  H12  N6   C6   C5     0.00   0.0  0
 JNT  Var_01    O1A  PA   O5'  C5'  -66.86  30.0  3
 JNT  Var_02    O3A  PB   O5A  C5A  170.78  30.0  1
 JNT  Var_03    H22  C5A  O5A  PB    31.20  30.0  3
 JNT  Var_04    H1   C5'  O5'  PA   -31.20  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
 JNT  chir_01  C4'  O4'  C3'  C5'  negativ
 JNT  chir_02  C3'  O3'  C4'  C2'  positiv
 JNT  chir_03  C2'  O2'  C3'  C1'  positiv
 JNT  chir_04  C1'  O4'  N9   C2'  negativ
 JNT  chir_05  C2A  O2C  C1A  C3A  negativ
 JNT  chir_06  C3A  O3C  C2A  C4A  negativ
 JNT  chir_07  C4A  O4C  C3A  C5A  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
 JNT  plan-1  C1'  0.020
 JNT  plan-1  N9   0.020
 JNT  plan-1  C8   0.020
 JNT  plan-1  N7   0.020
 JNT  plan-1  C5   0.020
 JNT  plan-1  C4   0.020
 JNT  plan-1  N3   0.020
 JNT  plan-1  C2   0.020
 JNT  plan-1  N1   0.020
 JNT  plan-1  C6   0.020
 JNT  plan-1  N6   0.020
 JNT  plan-1  H9   0.020
 JNT  plan-1  H10  0.020
 JNT  plan-2  C6   0.020
 JNT  plan-2  N6   0.020
 JNT  plan-2  H11  0.020
 JNT  plan-2  H12  0.020

