# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 17:09:54 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@@H](O[C@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)n2cnc3C(=O)NC(=O)Nc23
#
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
 L8S  L8S  9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione  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 PERFECT
;

data_comp_L8S
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
 L8S  N1   N  NR16  0  -0.736  225.5184  207.2292  202.4573
 L8S  N3   N  NR16  0  -0.748  224.7858  206.7931  204.6161
 L8S  C4   C  CR56  0   0.639  224.8835  205.4745  204.3051
 L8S  C5   C  CR56  0  -0.074  225.2843  204.9876  203.0877
 L8S  C6   C  CR6   0   0.527  225.6432  205.9014  202.0425
 L8S  C8   C  CR15  0   0.097  224.8745  203.2978  204.2964
 L8S  C1'  C  CH1   0   0.208  224.2173  204.4311  206.4868
 L8S  C2   C  CR6   0   0.666  225.0969  207.7360  203.6684
 L8S  C2'  C  CH1   0  -0.045  222.8359  205.0696  206.6825
 L8S  C3'  C  CH1   0   0.014  222.1971  204.1413  207.7117
 L8S  C4'  C  CH1   0  -0.063  222.7946  202.8040  207.2619
 L8S  C5'  C  CH2   0  -0.193  222.7808  201.7354  208.3262
 L8S  N7   N  N     0  -0.437  225.2688  203.6198  203.1036
 L8S  N9   N  NR5   0  -0.537  224.6235  204.4028  205.0813
 L8S  O1A  O  OH1   0  -0.709  222.0070  198.8726  207.2146
 L8S  O1B  O  OH1   0  -0.720  226.4797  199.6885  205.9668
 L8S  O1G  O  OH1   0  -0.701  227.1681  195.1781  206.1283
 L8S  O2   O  O     0  -0.472  225.0085  208.9271  203.8805
 L8S  O2'  O  OH1   0  -0.658  222.9960  206.4069  207.0665
 L8S  O2A  O  O     0  -0.676  223.3270  200.1949  205.3921
 L8S  O2B  O  O     0  -0.661  225.4482  197.5953  204.7903
 L8S  O2G  O  OH1   0  -0.714  228.5920  197.0283  205.5887
 L8S  O3'  O  OH1   0  -0.653  220.8059  204.2155  207.6511
 L8S  O3A  O  O2    0  -0.666  224.5043  198.5783  207.0291
 L8S  O3B  O  O2    0  -0.666  226.6123  197.4611  207.1276
 L8S  O4'  O  O2    0  -0.485  224.1474  203.1304  206.9628
 L8S  O5'  O  O2    0  -0.567  223.5920  200.6041  207.9850
 L8S  O6   O  O     0  -0.451  226.0178  205.6297  200.9194
 L8S  PA   P  P     0   1.486  223.3105  199.6465  206.7587
 L8S  PB   P  P     0   1.479  225.7467  198.2872  206.0474
 L8S  PG   P  P     0   1.224  227.8425  196.4183  206.8515
 L8S  S3G  S  S1    0  -0.468  228.8258  196.1311  208.4632
 L8S  H1   H  HNR6  0   0.428  225.7521  207.9320  201.7668
 L8S  H2   H  HNR6  0   0.436  224.3941  207.1100  205.4967
 L8S  H3   H  HCR5  0   0.297  224.7309  202.2951  204.6671
 L8S  H4   H  HCH1  0   0.294  224.9826  204.9869  207.0382
 L8S  H5   H  HCH1  0   0.267  222.2565  204.9903  205.7524
 L8S  H6   H  HCH1  0   0.249  222.5832  204.3917  208.7101
 L8S  H7   H  HCH1  0   0.264  222.2701  202.4608  206.3608
 L8S  H8   H  HCH2  0   0.270  223.2070  202.1169  209.2535
 L8S  H9   H  HCH2  0   0.265  221.7525  201.4246  208.5242
 L8S  H10  H  HOH1  0   0.512  221.5282  198.4306  206.4986
 L8S  H11  H  HOH1  0   0.513  226.7614  199.9461  205.0779
 L8S  H12  H  HOH1  0   0.474  222.1625  206.8712  206.9378
 L8S  H13  H  HOH1  0   0.512  229.3561  197.5805  205.8055
 L8S  H14  H  HOH1  0   0.467  220.4349  203.8969  208.4792
 L8S  H16  H  HOH1  0   0.511  226.6997  194.5716  206.7188

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
 L8S  O6   C6   double    1.215  0.020  1.215
 L8S  N7   C5   aromatic  1.368  0.020  1.368
 L8S  N7   C8   aromatic  1.297  0.020  1.297
 L8S  C6   C5   single    1.434  0.020  1.434
 L8S  C6   N1   single    1.397  0.020  1.397
 L8S  C5   C4   aromatic  1.371  0.020  1.371
 L8S  N1   C2   single    1.379  0.020  1.379
 L8S  C8   N9   aromatic  1.378  0.020  1.378
 L8S  C4   N9   aromatic  1.349  0.020  1.349
 L8S  C4   N3   single    1.358  0.020  1.358
 L8S  N9   C1'  single    1.463  0.020  1.463
 L8S  C2   N3   single    1.373  0.020  1.373
 L8S  C2   O2   double    1.213  0.020  1.213
 L8S  O2A  PA   double    1.473  0.020  1.473
 L8S  O4'  C1'  single    1.387  0.020  1.387
 L8S  O4'  C4'  single    1.423  0.020  1.423
 L8S  C1'  C2'  single    1.534  0.020  1.534
 L8S  O2B  PB   double    1.466  0.020  1.466
 L8S  O1B  PB   single    1.584  0.020  1.584
 L8S  C2'  O2'  single    1.401  0.020  1.401
 L8S  C2'  C3'  single    1.526  0.020  1.526
 L8S  C4'  C3'  single    1.532  0.020  1.532
 L8S  C4'  C5'  single    1.508  0.020  1.508
 L8S  PA   O5'  single    1.581  0.020  1.581
 L8S  PA   O3A  single    1.625  0.020  1.625
 L8S  PA   O1A  single    1.583  0.020  1.583
 L8S  PB   O3A  single    1.610  0.020  1.610
 L8S  PB   O3B  single    1.612  0.020  1.612
 L8S  O5'  C5'  single    1.433  0.020  1.433
 L8S  C3'  O3'  single    1.395  0.020  1.395
 L8S  O1G  PG   single    1.586  0.020  1.586
 L8S  O2G  PG   single    1.590  0.020  1.590
 L8S  O3B  PG   single    1.636  0.020  1.636
 L8S  PG   S3G  double    1.910  0.020  1.910
 L8S  N1   H1   single    0.860  0.020  1.020
 L8S  N3   H2   single    0.860  0.020  1.020
 L8S  C8   H3   single    0.930  0.020  1.080
 L8S  C1'  H4   single    0.970  0.020  1.090
 L8S  C2'  H5   single    0.970  0.020  1.090
 L8S  C3'  H6   single    0.970  0.020  1.090
 L8S  C4'  H7   single    0.970  0.020  1.090
 L8S  C5'  H8   single    0.970  0.020  1.090
 L8S  C5'  H9   single    0.970  0.020  1.090
 L8S  O1A  H10  single    0.850  0.020  0.980
 L8S  O1B  H11  single    0.850  0.020  0.980
 L8S  O2'  H12  single    0.850  0.020  0.980
 L8S  O2G  H13  single    0.850  0.020  0.980
 L8S  O3'  H14  single    0.850  0.020  0.980
 L8S  O1G  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
 L8S  H1   N1   C2   114.49  3.000
 L8S  H1   N1   C6   115.89  3.000
 L8S  C2   N1   C6   129.61  3.000
 L8S  H2   N3   C2   118.18  3.000
 L8S  H2   N3   C4   121.98  3.000
 L8S  C2   N3   C4   119.51  3.000
 L8S  N9   C4   C5   106.57  3.000
 L8S  N9   C4   N3   128.75  3.000
 L8S  C5   C4   N3   124.68  3.000
 L8S  N7   C5   C6   130.43  3.000
 L8S  C6   C5   C4   119.61  3.000
 L8S  N7   C5   C4   109.96  3.000
 L8S  O6   C6   C5   127.48  3.000
 L8S  C5   C6   N1   111.53  3.000
 L8S  O6   C6   N1   120.99  3.000
 L8S  H3   C8   N9   121.69  3.000
 L8S  H3   C8   N7   125.97  3.000
 L8S  N9   C8   N7   112.33  3.000
 L8S  H4   C1'  O4'  109.79  3.000
 L8S  H4   C1'  N9   107.43  3.000
 L8S  O4'  C1'  N9   108.99  3.000
 L8S  H4   C1'  C2'  110.72  3.000
 L8S  O4'  C1'  C2'  107.53  3.000
 L8S  N9   C1'  C2'  112.36  3.000
 L8S  O2   C2   N3   122.50  3.000
 L8S  O2   C2   N1   122.46  3.000
 L8S  N3   C2   N1   115.04  3.000
 L8S  H5   C2'  O2'  111.18  3.000
 L8S  H5   C2'  C3'  107.84  3.000
 L8S  O2'  C2'  C3'  116.34  3.000
 L8S  H5   C2'  C1'  109.68  3.000
 L8S  C3'  C2'  C1'  102.11  3.000
 L8S  O2'  C2'  C1'  109.23  3.000
 L8S  H6   C3'  O3'  112.20  3.000
 L8S  H6   C3'  C4'  109.18  3.000
 L8S  O3'  C3'  C4'  115.00  3.000
 L8S  H6   C3'  C2'  109.08  3.000
 L8S  O3'  C3'  C2'  110.85  3.000
 L8S  C4'  C3'  C2'   99.77  3.000
 L8S  H7   C4'  O4'  110.69  3.000
 L8S  H7   C4'  C5'  110.70  3.000
 L8S  O4'  C4'  C5'  108.63  3.000
 L8S  H7   C4'  C3'  109.12  3.000
 L8S  C5'  C4'  C3'  114.05  3.000
 L8S  O4'  C4'  C3'  103.42  3.000
 L8S  H9   C5'  H8   108.28  3.000
 L8S  H9   C5'  O5'  110.57  3.000
 L8S  H8   C5'  O5'  104.92  3.000
 L8S  H9   C5'  C4'  109.76  3.000
 L8S  H8   C5'  C4'  110.42  3.000
 L8S  O5'  C5'  C4'  112.71  3.000
 L8S  C8   N7   C5   105.22  3.000
 L8S  C1'  N9   C8   127.81  3.000
 L8S  C1'  N9   C4   126.23  3.000
 L8S  C8   N9   C4   105.92  3.000
 L8S  H10  O1A  PA   114.67  3.000
 L8S  H11  O1B  PB   114.66  3.000
 L8S  H16  O1G  PG   114.69  3.000
 L8S  H12  O2'  C2'  108.96  3.000
 L8S  H13  O2G  PG   114.41  3.000
 L8S  H14  O3'  C3'  109.26  3.000
 L8S  PB   O3A  PA   125.76  3.000
 L8S  PG   O3B  PB   128.12  3.000
 L8S  C4'  O4'  C1'  109.58  3.000
 L8S  PA   O5'  C5'  124.18  3.000
 L8S  O5'  PA   O3A   97.95  3.000
 L8S  O3A  PA   O2A  113.02  3.000
 L8S  O5'  PA   O2A  119.49  3.000
 L8S  O3A  PA   O1A  103.63  3.000
 L8S  O5'  PA   O1A  102.67  3.000
 L8S  O2A  PA   O1A  117.29  3.000
 L8S  O3B  PB   O3A   95.65  3.000
 L8S  O3B  PB   O2B  116.24  3.000
 L8S  O3A  PB   O2B  116.82  3.000
 L8S  O3B  PB   O1B  103.83  3.000
 L8S  O3A  PB   O1B  103.19  3.000
 L8S  O2B  PB   O1B  117.93  3.000
 L8S  S3G  PG   O3B  109.92  3.000
 L8S  S3G  PG   O2G  119.03  3.000
 L8S  O3B  PG   O2G  104.12  3.000
 L8S  S3G  PG   O1G  119.09  3.000
 L8S  O3B  PG   O1G  104.81  3.000
 L8S  O2G  PG   O1G   97.94  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
 L8S  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 L8S  CONST_02  N7   C8   N9   C4     0.00   0.0  0
 L8S  CONST_03  N9   C8   N7   C5     0.00   0.0  0
 L8S  CONST_04  C8   N9   C4   C5     0.00   0.0  0
 L8S  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 L8S  CONST_06  C1'  N9   C4   N3     0.00   0.0  0
 L8S  CONST_07  C1'  N9   C4   C5   180.00   0.0  0
 L8S  CONST_08  N7   C8   N9   C1'  180.00   0.0  0
 L8S  CONST_09  C4   N3   C2   N1     0.00   0.0  0
 L8S  CONST_10  C6   N1   C2   N3     0.00   0.0  0
 L8S  CONST_11  C2   N1   C6   C5     0.00   0.0  0
 L8S  CONST_12  O2   C2   N3   C4   180.00   0.0  0
 L8S  CONST_13  O2   C2   N1   C6   180.00   0.0  0
 L8S  CONST_14  O6   C6   N1   C2   180.00   0.0  0
 L8S  CONST_15  H3   C8   N9   C4   180.00   0.0  0
 L8S  CONST_16  H2   N3   C2   N1   180.00   0.0  0
 L8S  CONST_17  H1   N1   C2   N3   180.00   0.0  0
 L8S  Var_01    O2A  PA   O5'  C5'   61.53  30.0  1
 L8S  Var_02    S3G  PG   O3B  PB   163.39  30.0  3
 L8S  Var_03    H8   C5'  O5'  PA   175.72  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
 L8S  chir_01  C1'  N9   O4'  C2'  positiv
 L8S  chir_02  C2'  O2'  C1'  C3'  negativ
 L8S  chir_03  C3'  O3'  C4'  C2'  negativ
 L8S  chir_04  C4'  O4'  C3'  C5'  positiv
 L8S  chir_05  PA   O5'  O3A  O1A  both
 L8S  chir_06  PB   O1B  O3A  O3B  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
 L8S  plan-1  N1   0.020
 L8S  plan-1  N3   0.020
 L8S  plan-1  C4   0.020
 L8S  plan-1  C5   0.020
 L8S  plan-1  C6   0.020
 L8S  plan-1  C8   0.020
 L8S  plan-1  C1'  0.020
 L8S  plan-1  C2   0.020
 L8S  plan-1  N7   0.020
 L8S  plan-1  N9   0.020
 L8S  plan-1  O2   0.020
 L8S  plan-1  O6   0.020
 L8S  plan-1  H1   0.020
 L8S  plan-1  H2   0.020
 L8S  plan-1  H3   0.020

