# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 05:55:30 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: [[(1S,2S,4S,5R)-2-(6-aminopurin-9-yl)-4-oxidanyl-5-bicyclo[3.1.0]hexanyl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@]4(CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C[C@H]34
#
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
 0OH  0OH  '[[(1S,2S,4S,5R)-2-(6-aminopurin-9-yl)-4-oxidanyl-5-bicyclo[3.1.0]hexanyl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  49  31  .  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_0OH
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
 0OH  OAF  O  OH1   0  -0.732   97.3612  -19.0595  217.3256
 0OH  PBC  P  P     0   1.470   96.3701  -17.9002  217.7570
 0OH  OAG  O  O     0  -0.677   95.1295  -17.7168  216.9913
 0OH  OAB  O  OH1   0  -0.714   97.3292  -16.6454  217.8964
 0OH  OAS  O  O2    0  -0.676   96.1307  -18.2837  219.3200
 0OH  PBE  P  P     0   1.476   95.9077  -19.7129  220.0164
 0OH  OAI  O  OH1   0  -0.751   94.9292  -19.3150  221.1695
 0OH  OAD  O  O     0  -0.669   97.1224  -20.4682  220.3509
 0OH  OAT  O  O2    0  -0.707   94.9708  -20.4217  218.8935
 0OH  PBD  P  P     0   1.507   94.6658  -21.9925  218.6433
 0OH  OAH  O  OH1   0  -0.714   96.0405  -22.4891  218.0435
 0OH  OAC  O  O     0  -0.673   93.4393  -22.1683  217.8536
 0OH  OAR  O  O2    0  -0.594   94.6679  -22.6321  220.1019
 0OH  CAL  C  CH2   0  -0.210   93.5519  -22.4578  220.9941
 0OH  CBB  C  CR5   0  -0.082   94.0014  -22.8028  222.3779
 0OH  CAZ  C  CR15  0  -0.283   93.9614  -24.2122  222.9094
 0OH  CAN  C  CH2   0  -0.478   92.9509  -23.2092  223.3636
 0OH  CAX  C  CR15  0   0.076   95.2389  -22.1514  222.9568
 0OH  OAE  O  OH1   0  -0.691   94.9945  -20.7797  223.2681
 0OH  CAM  C  CH2   0  -0.549   95.5957  -22.9947  224.1838
 0OH  CAY  C  CR15  0  -0.064   95.1445  -24.4187  223.8282
 0OH  N9   N  NR5   0  -0.509   96.1950  -25.1741  223.1601
 0OH  C8   C  CR15  0   0.107   96.5322  -25.1830  221.8351
 0OH  N7   N  N     0  -0.454   97.5697  -25.9225  221.5664
 0OH  C5   C  CR56  0  -0.009   97.9467  -26.4286  222.7819
 0OH  C4   C  CR56  0   0.488   97.1070  -25.9715  223.7858
 0OH  N3   N  N     0  -0.460   97.1910  -26.2638  225.0827
 0OH  C2   C  CR16  0   0.041   98.2019  -27.0762  225.3354
 0OH  N1   N  N     0  -0.475   99.0838  -27.5909  224.4814
 0OH  C6   C  CR6   0   0.454   98.9871  -27.2871  223.1826
 0OH  N6   N  NH2   0  -0.817   99.8622  -27.8102  222.3213
 0OH  H1   H  HOH1  0   0.512   97.2938  -19.3228  216.3973
 0OH  H2   H  HOH1  0   0.510   96.8763  -15.7908  217.8857
 0OH  H3   H  HOH1  0   0.515   94.9787  -19.8661  222.0208
 0OH  H4   H  HOH1  0   0.512   95.9830  -23.3027  217.5227
 0OH  H5   H  HCH2  0   0.259   93.1850  -21.4284  220.9540
 0OH  H6   H  HCH2  0   0.269   92.7315  -23.1083  220.6853
 0OH  H7   H  HCR5  0   0.291   93.6271  -25.0400  222.2943
 0OH  H8   H  HCH2  0   0.274   92.9830  -22.8217  224.3735
 0OH  H9   H  HCH2  0   0.284   91.9465  -23.3356  222.9795
 0OH  H10  H  HCR5  0   0.248   96.0528  -22.2104  222.2253
 0OH  H11  H  HOH1  0   0.488   95.7057  -20.4514  223.8334
 0OH  H12  H  HCH2  0   0.289   96.6555  -22.9456  224.4324
 0OH  H13  H  HCH2  0   0.277   95.0414  -22.6447  225.0565
 0OH  H14  H  HCR5  0   0.291   94.8825  -24.9845  224.7226
 0OH  H15  H  HCR5  0   0.291   95.9700  -24.6246  221.1019
 0OH  H16  H  HCR6  0   0.251   98.3368  -27.3634  226.3729
 0OH  H17  H  HNH2  0   0.403  100.6391  -28.3522  222.6580
 0OH  H18  H  HNH2  0   0.410   99.8618  -27.5348  221.3549

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
 0OH  OAG  PBC  double    1.469  0.020  1.469
 0OH  OAB  PBC  single    1.586  0.020  1.586
 0OH  OAF  PBC  single    1.585  0.020  1.585
 0OH  PBC  OAS  single    1.627  0.020  1.627
 0OH  OAC  PBD  double    1.469  0.020  1.469
 0OH  OAH  PBD  single    1.580  0.020  1.580
 0OH  OAT  PBD  single    1.620  0.020  1.620
 0OH  OAT  PBE  single    1.625  0.020  1.625
 0OH  PBD  OAR  single    1.593  0.020  1.593
 0OH  OAS  PBE  single    1.605  0.020  1.605
 0OH  PBE  OAD  double    1.469  0.020  1.469
 0OH  PBE  OAI  single    1.564  0.020  1.564
 0OH  OAR  CAL  single    1.439  0.020  1.439
 0OH  CAL  CBB  single    1.495  0.020  1.495
 0OH  N7   C8   aromatic  1.302  0.020  1.302
 0OH  N7   C5   aromatic  1.370  0.020  1.370
 0OH  C8   N9   aromatic  1.367  0.020  1.367
 0OH  N6   C6   single    1.335  0.020  1.335
 0OH  CBB  CAZ  single    1.507  0.020  1.507
 0OH  CBB  CAX  single    1.514  0.020  1.514
 0OH  CBB  CAN  single    1.497  0.020  1.497
 0OH  C5   C6   aromatic  1.407  0.020  1.407
 0OH  C5   C4   aromatic  1.386  0.020  1.386
 0OH  CAZ  CAN  single    1.494  0.020  1.494
 0OH  CAZ  CAY  single    1.512  0.020  1.512
 0OH  C6   N1   aromatic  1.337  0.020  1.337
 0OH  CAX  OAE  single    1.428  0.020  1.428
 0OH  CAX  CAM  single    1.531  0.020  1.531
 0OH  N9   C4   aromatic  1.363  0.020  1.363
 0OH  N9   CAY  single    1.456  0.020  1.456
 0OH  C4   N3   aromatic  1.332  0.020  1.332
 0OH  CAY  CAM  single    1.536  0.020  1.536
 0OH  N1   C2   aromatic  1.331  0.020  1.331
 0OH  N3   C2   aromatic  1.321  0.020  1.321
 0OH  OAF  H1   single    0.850  0.020  0.980
 0OH  OAB  H2   single    0.850  0.020  0.980
 0OH  OAI  H3   single    0.850  0.020  0.980
 0OH  OAH  H4   single    0.850  0.020  0.980
 0OH  CAL  H5   single    0.970  0.020  1.090
 0OH  CAL  H6   single    0.970  0.020  1.090
 0OH  CAZ  H7   single    0.970  0.020  1.090
 0OH  CAN  H8   single    0.970  0.020  1.090
 0OH  CAN  H9   single    0.970  0.020  1.090
 0OH  CAX  H10  single    0.970  0.020  1.090
 0OH  OAE  H11  single    0.850  0.020  0.980
 0OH  CAM  H12  single    0.970  0.020  1.090
 0OH  CAM  H13  single    0.970  0.020  1.090
 0OH  CAY  H14  single    0.970  0.020  1.090
 0OH  C8   H15  single    0.930  0.020  1.080
 0OH  C2   H16  single    0.930  0.020  1.080
 0OH  N6   H17  single    0.860  0.020  1.020
 0OH  N6   H18  single    0.860  0.020  1.020

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
 0OH  H1   OAF  PBC  114.63  3.000
 0OH  OAS  PBC  OAB  101.01  3.000
 0OH  OAS  PBC  OAG  113.94  3.000
 0OH  OAB  PBC  OAG  117.24  3.000
 0OH  OAS  PBC  OAF  100.43  3.000
 0OH  OAB  PBC  OAF  102.98  3.000
 0OH  OAG  PBC  OAF  118.52  3.000
 0OH  H2   OAB  PBC  114.52  3.000
 0OH  PBE  OAS  PBC  130.31  3.000
 0OH  OAT  PBE  OAD  114.19  3.000
 0OH  OAD  PBE  OAI  118.71  3.000
 0OH  OAT  PBE  OAI  105.05  3.000
 0OH  OAI  PBE  OAS  100.39  3.000
 0OH  OAD  PBE  OAS  116.21  3.000
 0OH  OAT  PBE  OAS   99.71  3.000
 0OH  H3   OAI  PBE  116.72  3.000
 0OH  PBD  OAT  PBE  129.67  3.000
 0OH  OAR  PBD  OAC  116.44  3.000
 0OH  OAR  PBD  OAH  102.73  3.000
 0OH  OAC  PBD  OAH  118.99  3.000
 0OH  OAR  PBD  OAT  104.35  3.000
 0OH  OAH  PBD  OAT  101.52  3.000
 0OH  OAC  PBD  OAT  110.87  3.000
 0OH  H4   OAH  PBD  114.64  3.000
 0OH  CAL  OAR  PBD  121.20  3.000
 0OH  H6   CAL  H5   107.37  3.000
 0OH  H6   CAL  CBB  110.51  3.000
 0OH  H5   CAL  CBB  110.61  3.000
 0OH  H6   CAL  OAR  109.58  3.000
 0OH  H5   CAL  OAR  110.57  3.000
 0OH  CBB  CAL  OAR  108.21  3.000
 0OH  CAX  CBB  CAN  116.03  3.000
 0OH  CAN  CBB  CAZ   59.68  3.000
 0OH  CAX  CBB  CAZ  106.82  3.000
 0OH  CAN  CBB  CAL  117.45  3.000
 0OH  CAX  CBB  CAL  120.03  3.000
 0OH  CAZ  CBB  CAL  122.29  3.000
 0OH  H7   CAZ  CAY  118.80  3.000
 0OH  H7   CAZ  CAN  118.45  3.000
 0OH  CAY  CAZ  CAN  115.85  3.000
 0OH  H7   CAZ  CBB  121.49  3.000
 0OH  CAY  CAZ  CBB  108.74  3.000
 0OH  CAN  CAZ  CBB   59.83  3.000
 0OH  H9   CAN  H8   113.61  3.000
 0OH  H9   CAN  CAZ  116.17  3.000
 0OH  H8   CAN  CAZ  120.25  3.000
 0OH  H9   CAN  CBB  116.69  3.000
 0OH  H8   CAN  CBB  119.77  3.000
 0OH  CAZ  CAN  CBB   60.49  3.000
 0OH  H10  CAX  CAM  109.40  3.000
 0OH  H10  CAX  OAE  108.93  3.000
 0OH  CAM  CAX  OAE  113.22  3.000
 0OH  H10  CAX  CBB  109.19  3.000
 0OH  CAM  CAX  CBB  105.07  3.000
 0OH  OAE  CAX  CBB  110.92  3.000
 0OH  H11  OAE  CAX  109.16  3.000
 0OH  H13  CAM  H12  107.29  3.000
 0OH  H13  CAM  CAY  109.47  3.000
 0OH  H12  CAM  CAY  112.36  3.000
 0OH  H13  CAM  CAX  110.23  3.000
 0OH  H12  CAM  CAX  112.62  3.000
 0OH  CAY  CAM  CAX  104.87  3.000
 0OH  H14  CAY  N9   106.29  3.000
 0OH  H14  CAY  CAM  111.21  3.000
 0OH  N9   CAY  CAM  112.05  3.000
 0OH  H14  CAY  CAZ  112.41  3.000
 0OH  CAM  CAY  CAZ  104.12  3.000
 0OH  N9   CAY  CAZ  110.89  3.000
 0OH  C4   N9   C8   106.02  3.000
 0OH  C4   N9   CAY  125.13  3.000
 0OH  C8   N9   CAY  128.75  3.000
 0OH  H15  C8   N7   124.66  3.000
 0OH  H15  C8   N9   121.76  3.000
 0OH  N7   C8   N9   113.58  3.000
 0OH  C5   N7   C8   104.25  3.000
 0OH  C6   C5   C4   116.28  3.000
 0OH  C4   C5   N7   110.74  3.000
 0OH  C6   C5   N7   132.98  3.000
 0OH  N3   C4   C5   126.47  3.000
 0OH  N3   C4   N9   128.12  3.000
 0OH  C5   C4   N9   105.40  3.000
 0OH  C2   N3   C4   111.68  3.000
 0OH  H16  C2   N1   115.39  3.000
 0OH  H16  C2   N3   116.15  3.000
 0OH  N1   C2   N3   128.46  3.000
 0OH  C6   N1   C2   119.16  3.000
 0OH  N6   C6   N1   119.36  3.000
 0OH  N1   C6   C5   117.95  3.000
 0OH  N6   C6   C5   122.70  3.000
 0OH  H18  N6   H17  118.04  3.000
 0OH  H18  N6   C6   120.86  3.000
 0OH  H17  N6   C6   120.13  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
 0OH  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 0OH  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 0OH  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 0OH  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 0OH  CONST_05  C6   C5   N7   C8    180.00   0.0  0
 0OH  CONST_06  C4   C5   N7   C8      0.00   0.0  0
 0OH  CONST_07  C5   C4   N9   C8      0.00   0.0  0
 0OH  CONST_08  N3   C4   N9   C8    180.00   0.0  0
 0OH  CONST_09  C4   N9   C8   N7      0.00   0.0  0
 0OH  CONST_10  N1   C6   C5   N7    180.00   0.0  0
 0OH  CONST_11  N3   C4   C5   N7    180.00   0.0  0
 0OH  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 0OH  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 0OH  CONST_14  N1   C6   C5   C4      0.00   0.0  0
 0OH  CONST_15  N1   C2   N3   C4      0.00   0.0  0
 0OH  CONST_16  C6   C5   C4   N3      0.00   0.0  0
 0OH  CONST_17  C6   N1   C2   N3      0.00   0.0  0
 0OH  CONST_18  N7   C8   N9   CAY   180.00   0.0  0
 0OH  CONST_19  C5   C4   N9   CAY   180.00   0.0  0
 0OH  CONST_20  N3   C4   N9   CAY     0.00   0.0  0
 0OH  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 0OH  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 0OH  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 0OH  CONST_24  H15  C8   N9   CAY     0.00   0.0  0
 0OH  CONST_25  H16  C2   N3   C4    180.00   0.0  0
 0OH  CONST_26  H17  N6   C6   C5    180.00   0.0  0
 0OH  CONST_27  H18  N6   C6   C5      0.00   0.0  0
 0OH  Var_01    CAY  CAZ  CAN  CBB    97.54  30.0  1
 0OH  Var_02    CAX  CBB  CAN  CAZ   -95.02  30.0  1
 0OH  Var_03    CAZ  CBB  CAL  OAR   -87.07  30.0  3
 0OH  Var_04    CBB  CAL  OAR  PBD  -163.40  30.0  3
 0OH  Var_05    OAT  PBE  OAS  PBC   -38.86  30.0  3
 0OH  Var_06    OAC  PBD  OAT  PBE   160.35  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
 0OH  chir_05  CAX  CBB  OAE  CAM  negativ
 0OH  chir_06  CAY  N9   CAZ  CAM  positiv
 0OH  chir_07  PBE  OAS  OAD  OAI  both
 0OH  chir_08  PBD  OAH  OAT  OAR  both
 0OH  chir_09  CBB  CAZ  CAX  CAN  both
 0OH  chir_10  CAZ  CBB  CAN  CAY  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
 0OH  plan-1  CAY  0.020
 0OH  plan-1  N9   0.020
 0OH  plan-1  C8   0.020
 0OH  plan-1  N7   0.020
 0OH  plan-1  C5   0.020
 0OH  plan-1  C4   0.020
 0OH  plan-1  N3   0.020
 0OH  plan-1  C2   0.020
 0OH  plan-1  N1   0.020
 0OH  plan-1  C6   0.020
 0OH  plan-1  N6   0.020
 0OH  plan-1  H15  0.020
 0OH  plan-1  H16  0.020
 0OH  plan-2  C6   0.020
 0OH  plan-2  N6   0.020
 0OH  plan-2  H17  0.020
 0OH  plan-2  H18  0.020

