# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 05:18:24 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-fluoranyl-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: Nc1nc(F)nc2n(cnc12)[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
 JSQ  JSQ  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-fluoranyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  47  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_JSQ
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
 JSQ  N3    N  N     0  -0.491  24.2307   3.3539  36.2419
 JSQ  C2    C  CR6   0   0.570  23.7803   3.5630  37.4477
 JSQ  C5    C  CR56  0  -0.004  24.7879   5.7166  36.3591
 JSQ  C4    C  CR56  0   0.494  24.7330   4.4832  35.7330
 JSQ  C6    C  CR6   0   0.476  24.2570   5.7765  37.6626
 JSQ  F2    F  F     0  -0.287  23.2553   2.4934  38.0410
 JSQ  C1'   C  CH1   0   0.167  25.4537   3.6267  33.5029
 JSQ  C2'   C  CH1   0  -0.065  24.1252   3.2913  32.8018
 JSQ  C3'   C  CH1   0   0.004  24.1902   4.2551  31.6155
 JSQ  C4'   C  CH1   0   0.020  25.6722   4.1815  31.2619
 JSQ  C5'   C  CH2   0  -0.216  26.2257   5.3275  30.4568
 JSQ  C8    C  CR15  0   0.098  25.6570   5.9919  34.4544
 JSQ  N1    N  N     0  -0.504  23.7500   4.6497  38.1825
 JSQ  N6    N  NH2   0  -0.807  24.2389   6.8884  38.3878
 JSQ  N7    N  N     0  -0.447  25.3709   6.6469  35.5410
 JSQ  N9    N  NR5   0  -0.533  25.2918   4.6710  34.5089
 JSQ  O1A   O  OH1   0  -0.711  25.3650   8.8520  31.5172
 JSQ  O1B   O  O     0  -0.661  23.0682   7.5869  27.7431
 JSQ  O1G   O  O     0  -0.671  21.8649  10.7709  27.7847
 JSQ  O2'   O  OH1   0  -0.656  24.1372   1.9837  32.3071
 JSQ  O2A   O  O     0  -0.670  25.9007   8.1575  29.0309
 JSQ  O2B   O  OH1   0  -0.703  21.6170   6.4753  29.6388
 JSQ  O2G   O  OH1   0  -0.712  21.5883  11.2879  30.3318
 JSQ  O3'   O  OH1   0  -0.659  23.4151   3.9237  30.5083
 JSQ  O3A   O  O2    0  -0.695  23.7713   7.3396  30.2563
 JSQ  O3B   O  O2    0  -0.685  21.9405   8.9391  29.6495
 JSQ  O3G   O  OH1   0  -0.751  23.8086  10.5256  29.5281
 JSQ  O4'   O  O2    0  -0.497  26.3342   4.0779  32.5178
 JSQ  O5'   O  O2    0  -0.570  25.9771   6.5780  31.1157
 JSQ  PA    P  P     0   1.483  25.3392   7.8001  30.3393
 JSQ  PB    P  P     0   1.494  22.6399   7.5718  29.1442
 JSQ  PG    P  P     0   1.477  22.2587  10.4565  29.1634
 JSQ  H1'   H  HCH1  0   0.286  25.8674   2.7532  34.0158
 JSQ  H2'   H  HCH1  0   0.269  23.2670   3.4764  33.4575
 JSQ  H3'   H  HCH1  0   0.244  23.9535   5.2566  31.9939
 JSQ  H4'   H  HCH1  0   0.260  25.8606   3.2784  30.6664
 JSQ  H5'2  H  HCH2  0   0.285  27.3041   5.2243  30.3324
 JSQ  H5'1  H  HCH2  0   0.260  25.7759   5.2918  29.4619
 JSQ  H8    H  HCR5  0   0.299  26.1359   6.4153  33.5873
 JSQ  HN62  H  HNH2  0   0.411  23.8434   6.8893  39.3124
 JSQ  HN61  H  HNH2  0   0.418  24.6124   7.7492  38.0274
 JSQ  H1    H  HOH1  0   0.509  25.1196   9.7517  31.2540
 JSQ  HO2'  H  HOH1  0   0.462  24.0460   1.3733  33.0457
 JSQ  H2    H  HOH1  0   0.520  20.9343   6.2439  28.9913
 JSQ  H3    H  HOH1  0   0.512  20.6957  11.6073  30.1390
 JSQ  HO3'  H  HOH1  0   0.460  22.5515   4.3371  30.5931
 JSQ  H4    H  HOH1  0   0.518  24.3334  11.1179  28.9701

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
 JSQ  O1G  PG    double    1.468  0.020  1.468
 JSQ  PG   O3G   single    1.594  0.020  1.594
 JSQ  PG   O3B   single    1.625  0.020  1.625
 JSQ  PG   O2G   single    1.583  0.020  1.583
 JSQ  O1B  PB    double    1.465  0.020  1.465
 JSQ  O3B  PB    single    1.617  0.020  1.617
 JSQ  O2B  PB    single    1.579  0.020  1.579
 JSQ  PB   O3A   single    1.603  0.020  1.603
 JSQ  O2A  PA    double    1.468  0.020  1.468
 JSQ  O3A  PA    single    1.636  0.020  1.636
 JSQ  O3'  C3'   single    1.392  0.020  1.392
 JSQ  C5'  C4'   single    1.506  0.020  1.506
 JSQ  C5'  O5'   single    1.435  0.020  1.435
 JSQ  PA   O5'   single    1.582  0.020  1.582
 JSQ  PA   O1A   single    1.579  0.020  1.579
 JSQ  C4'  C3'   single    1.525  0.020  1.525
 JSQ  C4'  O4'   single    1.423  0.020  1.423
 JSQ  C3'  C2'   single    1.530  0.020  1.530
 JSQ  O2'  C2'   single    1.398  0.020  1.398
 JSQ  O4'  C1'   single    1.396  0.020  1.396
 JSQ  C2'  C1'   single    1.539  0.020  1.539
 JSQ  C1'  N9    single    1.459  0.020  1.459
 JSQ  N9   C8    aromatic  1.372  0.020  1.372
 JSQ  N9   C4    aromatic  1.359  0.020  1.359
 JSQ  C8   N7    aromatic  1.301  0.020  1.301
 JSQ  N7   C5    aromatic  1.369  0.020  1.369
 JSQ  C4   N3    aromatic  1.337  0.020  1.337
 JSQ  C4   C5    aromatic  1.384  0.020  1.384
 JSQ  N3   C2    aromatic  1.304  0.020  1.304
 JSQ  C5   C6    aromatic  1.409  0.020  1.409
 JSQ  C2   F2    single    1.331  0.020  1.331
 JSQ  C2   N1    aromatic  1.312  0.020  1.312
 JSQ  C6   N1    aromatic  1.341  0.020  1.341
 JSQ  C6   N6    single    1.328  0.020  1.328
 JSQ  C1'  H1'   single    0.970  0.020  1.090
 JSQ  C2'  H2'   single    0.970  0.020  1.090
 JSQ  C3'  H3'   single    0.970  0.020  1.090
 JSQ  C4'  H4'   single    0.970  0.020  1.090
 JSQ  C5'  H5'2  single    0.970  0.020  1.090
 JSQ  C5'  H5'1  single    0.970  0.020  1.090
 JSQ  C8   H8    single    0.930  0.020  1.080
 JSQ  N6   HN62  single    0.860  0.020  1.020
 JSQ  N6   HN61  single    0.860  0.020  1.020
 JSQ  O1A  H1    single    0.850  0.020  0.980
 JSQ  O2'  HO2'  single    0.850  0.020  0.980
 JSQ  O2B  H2    single    0.850  0.020  0.980
 JSQ  O2G  H3    single    0.850  0.020  0.980
 JSQ  O3'  HO3'  single    0.850  0.020  0.980
 JSQ  O3G  H4    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
 JSQ  C4    N3   C2    110.27  3.000
 JSQ  N1    C2   F2    114.00  3.000
 JSQ  N1    C2   N3    131.19  3.000
 JSQ  F2    C2   N3    114.81  3.000
 JSQ  N7    C5   C6    133.19  3.000
 JSQ  C6    C5   C4    116.19  3.000
 JSQ  N7    C5   C4    110.61  3.000
 JSQ  N9    C4   C5    105.54  3.000
 JSQ  C5    C4   N3    126.55  3.000
 JSQ  N9    C4   N3    127.91  3.000
 JSQ  N6    C6   N1    119.14  3.000
 JSQ  N6    C6   C5    123.11  3.000
 JSQ  N1    C6   C5    117.75  3.000
 JSQ  H1'   C1'  O4'   110.50  3.000
 JSQ  H1'   C1'  N9    106.87  3.000
 JSQ  O4'   C1'  N9    108.98  3.000
 JSQ  H1'   C1'  C2'   111.46  3.000
 JSQ  N9    C1'  C2'   111.98  3.000
 JSQ  O4'   C1'  C2'   107.06  3.000
 JSQ  H2'   C2'  O2'   112.11  3.000
 JSQ  H2'   C2'  C3'   113.01  3.000
 JSQ  O2'   C2'  C3'   108.33  3.000
 JSQ  H2'   C2'  C1'   111.51  3.000
 JSQ  O2'   C2'  C1'   110.95  3.000
 JSQ  C3'   C2'  C1'   100.33  3.000
 JSQ  H3'   C3'  O3'   111.83  3.000
 JSQ  H3'   C3'  C4'   109.50  3.000
 JSQ  O3'   C3'  C4'   110.20  3.000
 JSQ  H3'   C3'  C2'   107.38  3.000
 JSQ  C4'   C3'  C2'   100.99  3.000
 JSQ  O3'   C3'  C2'   116.31  3.000
 JSQ  H4'   C4'  O4'   109.81  3.000
 JSQ  H4'   C4'  C5'   105.83  3.000
 JSQ  O4'   C4'  C5'   110.86  3.000
 JSQ  H4'   C4'  C3'   109.40  3.000
 JSQ  O4'   C4'  C3'   104.53  3.000
 JSQ  C5'   C4'  C3'   116.38  3.000
 JSQ  H5'1  C5'  H5'2  107.48  3.000
 JSQ  H5'1  C5'  O5'   112.04  3.000
 JSQ  H5'2  C5'  O5'   107.83  3.000
 JSQ  H5'1  C5'  C4'   108.10  3.000
 JSQ  H5'2  C5'  C4'   110.63  3.000
 JSQ  O5'   C5'  C4'   110.73  3.000
 JSQ  H8    C8   N9    121.93  3.000
 JSQ  H8    C8   N7    124.92  3.000
 JSQ  N9    C8   N7    113.15  3.000
 JSQ  C6    N1   C2    118.05  3.000
 JSQ  HN61  N6   HN62  118.36  3.000
 JSQ  HN61  N6   C6    121.08  3.000
 JSQ  HN62  N6   C6    120.55  3.000
 JSQ  C8    N7   C5    104.52  3.000
 JSQ  C8    N9   C1'   129.22  3.000
 JSQ  C8    N9   C4    106.17  3.000
 JSQ  C1'   N9   C4    124.60  3.000
 JSQ  H1    O1A  PA    114.31  3.000
 JSQ  HO2'  O2'  C2'   108.71  3.000
 JSQ  H2    O2B  PB    114.39  3.000
 JSQ  H3    O2G  PG    114.65  3.000
 JSQ  HO3'  O3'  C3'   109.14  3.000
 JSQ  PB    O3A  PA    132.12  3.000
 JSQ  PG    O3B  PB    127.70  3.000
 JSQ  H4    O3G  PG    114.94  3.000
 JSQ  C4'   O4'  C1'   110.66  3.000
 JSQ  PA    O5'  C5'   121.17  3.000
 JSQ  O5'   PA   O3A   101.18  3.000
 JSQ  O5'   PA   O2A   118.12  3.000
 JSQ  O3A   PA   O2A   112.94  3.000
 JSQ  O5'   PA   O1A    98.16  3.000
 JSQ  O3A   PA   O1A   103.94  3.000
 JSQ  O2A   PA   O1A   119.76  3.000
 JSQ  O3B   PB   O3A   102.17  3.000
 JSQ  O3A   PB   O2B    98.01  3.000
 JSQ  O3B   PB   O2B   102.07  3.000
 JSQ  O3A   PB   O1B   117.29  3.000
 JSQ  O2B   PB   O1B   119.74  3.000
 JSQ  O3B   PB   O1B   114.62  3.000
 JSQ  O3G   PG   O3B    99.35  3.000
 JSQ  O3B   PG   O2G   100.76  3.000
 JSQ  O3G   PG   O2G   102.72  3.000
 JSQ  O2G   PG   O1G   117.85  3.000
 JSQ  O3B   PG   O1G   115.37  3.000
 JSQ  O3G   PG   O1G   117.81  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
 JSQ  CONST_01  C8    N9   C4   N3   180.00   0.0  0
 JSQ  CONST_02  N7    C5   C4   N3   180.00   0.0  0
 JSQ  CONST_03  C6    C5   C4   N3     0.00   0.0  0
 JSQ  CONST_04  C6    N1   C2   N3     0.00   0.0  0
 JSQ  CONST_05  N9    C4   N3   C2   180.00   0.0  0
 JSQ  CONST_06  C5    C4   N3   C2     0.00   0.0  0
 JSQ  CONST_07  C5    C6   N1   C2     0.00   0.0  0
 JSQ  CONST_08  N9    C8   N7   C5     0.00   0.0  0
 JSQ  CONST_09  C8    N9   C4   C5     0.00   0.0  0
 JSQ  CONST_10  N7    C8   N9   C4     0.00   0.0  0
 JSQ  CONST_11  N1    C2   N3   C4     0.00   0.0  0
 JSQ  CONST_12  C8    N7   C5   C4     0.00   0.0  0
 JSQ  CONST_13  N1    C6   C5   C4     0.00   0.0  0
 JSQ  CONST_14  C8    N7   C5   C6   180.00   0.0  0
 JSQ  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 JSQ  CONST_16  N7    C5   C6   N1   180.00   0.0  0
 JSQ  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 JSQ  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 JSQ  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 JSQ  CONST_20  N7    C8   N9   C1'  180.00   0.0  0
 JSQ  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 JSQ  CONST_22  F2    C2   N3   C4   180.00   0.0  0
 JSQ  CONST_23  N6    C6   C5   C4   180.00   0.0  0
 JSQ  CONST_24  F2    C2   N1   C6   180.00   0.0  0
 JSQ  CONST_25  N7    C5   C6   N6     0.00   0.0  0
 JSQ  CONST_26  H8    C8   N7   C5   180.00   0.0  0
 JSQ  CONST_27  HN62  N6   C6   C5   180.00   0.0  0
 JSQ  CONST_28  HN61  N6   C6   C5     0.00   0.0  0
 JSQ  Var_01    O2A   PA   O5'  C5'  -47.76  30.0  1
 JSQ  Var_02    H5'2  C5'  O5'  PA   108.42  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
 JSQ  chir_01  C1'  O4'  C2'  N9   positiv
 JSQ  chir_02  C2'  O2'  C1'  C3'  negativ
 JSQ  chir_03  C3'  O3'  C4'  C2'  positiv
 JSQ  chir_04  C4'  O4'  C3'  C5'  negativ
 JSQ  chir_05  PA   O3A  O5'  O1A  both
 JSQ  chir_06  PB   O2B  O3B  O1B  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
 JSQ  plan-1  N3    0.020
 JSQ  plan-1  C2    0.020
 JSQ  plan-1  C5    0.020
 JSQ  plan-1  C4    0.020
 JSQ  plan-1  C6    0.020
 JSQ  plan-1  F2    0.020
 JSQ  plan-1  C1'   0.020
 JSQ  plan-1  C8    0.020
 JSQ  plan-1  N1    0.020
 JSQ  plan-1  N6    0.020
 JSQ  plan-1  N7    0.020
 JSQ  plan-1  N9    0.020
 JSQ  plan-1  H8    0.020
 JSQ  plan-2  C6    0.020
 JSQ  plan-2  N6    0.020
 JSQ  plan-2  HN62  0.020
 JSQ  plan-2  HN61  0.020

