# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  4 06:08:13 2021
#   Inital geometry file: a 134 line input string
#   Ligand name: 7-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-7-oxidanylidene-heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)CCCCCC(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
 WAQ  WAQ  '7-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-7-oxidanylidene-heptanoic acid'  ligand  57  33  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WAQ
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
 WAQ  N1    N  N     0  -0.474   0.2906   -1.7321   3.2674
 WAQ  C2    C  CR16  0   0.039   0.5789   -0.8263   4.1985
 WAQ  N3    N  N     0  -0.459   0.1757   -0.7840   5.4566
 WAQ  C4    C  CR56  0   0.485  -0.6153   -1.8143   5.7522
 WAQ  C5    C  CR56  0  -0.002  -1.0015   -2.8329   4.8961
 WAQ  C6    C  CR6   0   0.457  -0.5040   -2.7616   3.5816
 WAQ  N6    N  NH2   0  -0.817  -0.7902   -3.6739   2.6521
 WAQ  N7    N  N     0  -0.453  -1.8125   -3.7277   5.5419
 WAQ  C8    C  CR15  0   0.099  -1.9136   -3.2605   6.7528
 WAQ  N9    N  NR5   0  -0.538  -1.2149   -2.0992   6.9439
 WAQ  C1'   C  CH1   0   0.183  -1.0633   -1.3046   8.1562
 WAQ  C2'   C  CH1   0  -0.051  -1.8642   -0.0025   8.0874
 WAQ  O2'   O  OH1   0  -0.663  -1.2044    0.9416   8.8842
 WAQ  C3'   C  CH1   0  -0.033  -3.1859   -0.4387   8.7274
 WAQ  O3'   O  OH1   0  -0.657  -3.9191    0.6063   9.2978
 WAQ  C4'   C  CH1   0   0.018  -2.6840   -1.3788   9.8189
 WAQ  O4'   O  O2    0  -0.497  -1.5575   -2.0305   9.2436
 WAQ  C5'   C  CH2   0  -0.205  -3.6735   -2.3847  10.3445
 WAQ  O5'   O  O2    0  -0.575  -4.1815   -3.1649   9.2570
 WAQ  OAB   O  OH1   0  -0.592  -8.1664  -10.8295  15.9021
 WAQ  OAC   O  O     0  -0.416  -6.7617   -6.1921  10.8555
 WAQ  OAD   O  O     0  -0.664  -5.6259   -4.9191   8.1025
 WAQ  OAE   O  O     0  -0.449  -7.2974  -12.6946  15.0492
 WAQ  OAH   O  OH1   0  -0.735  -6.5364   -3.3486  10.0010
 WAQ  CAK   C  CH2   0  -0.430  -4.9418   -8.6518  13.9691
 WAQ  CAL   C  CH2   0  -0.441  -5.7950   -9.5039  14.9041
 WAQ  CAM   C  CH2   0  -0.434  -5.7566   -7.8239  12.9823
 WAQ  CAN   C  CH2   0  -0.558  -6.6068  -10.5668  14.1585
 WAQ  CAO   C  CH2   0  -0.582  -4.8618   -6.9088  12.1609
 WAQ  OAU   O  O2    0  -0.592  -4.8044   -5.1664  10.5674
 WAQ  CAW   C  C     0   0.536  -7.3715  -11.4899  15.0652
 WAQ  CAX   C  C     0   0.611  -5.6053   -6.0898  11.1553
 WAQ  PBG   P  P     0   1.499  -5.3658   -4.2047   9.3575
 WAQ  H2    H  HCR6  0   0.252   1.2296   -0.0196   3.8777
 WAQ  HN6   H  HNH2  0   0.403  -0.4265   -3.5812   1.7196
 WAQ  HN6A  H  HNH2  0   0.412  -1.3920   -4.4522   2.8553
 WAQ  H8    H  HCR5  0   0.296  -2.4785   -3.7239   7.5440
 WAQ  H1'   H  HCH1  0   0.284   0.0048   -1.1053   8.2809
 WAQ  H2'   H  HCH1  0   0.264  -1.9902    0.3486   7.0565
 WAQ  HO2'  H  HOH1  0   0.453  -1.8652    1.5642   9.2112
 WAQ  H3'   H  HCH1  0   0.255  -3.7752   -0.9924   7.9869
 WAQ  HO3'  H  HOH1  0   0.470  -4.4723    1.0067   8.6195
 WAQ  H4'   H  HCH1  0   0.260  -2.3688   -0.7881  10.6889
 WAQ  H5'   H  HCH2  0   0.273  -3.1931   -3.0372  11.0764
 WAQ  H5'A  H  HCH2  0   0.263  -4.4784   -1.8418  10.8442
 WAQ  HOAB  H  HOH1  0   0.480  -8.6450  -11.4544  16.4675
 WAQ  HOAH  H  HOH1  0   0.507  -7.4088   -3.7677   9.9942
 WAQ  HAK   H  HCH2  0   0.224  -4.2418   -9.2926  13.4228
 WAQ  HAKA  H  HCH2  0   0.235  -4.3297   -7.9821  14.5798
 WAQ  HAL   H  HCH2  0   0.243  -5.1403   -9.9935  15.6295
 WAQ  HALA  H  HCH2  0   0.234  -6.4623   -8.8535  15.4737
 WAQ  HAM   H  HCH2  0   0.240  -6.3198   -8.4789  12.3144
 WAQ  HAMA  H  HCH2  0   0.234  -6.4916   -7.2262  13.5293
 WAQ  HAN   H  HCH2  0   0.274  -7.3274  -10.0856  13.4900
 WAQ  HANA  H  HCH2  0   0.258  -5.9505  -11.1749  13.5349
 WAQ  HAO   H  HCH2  0   0.286  -4.2946   -6.2328  12.8071
 WAQ  HAOA  H  HCH2  0   0.292  -4.1106   -7.4910  11.6151

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
 WAQ  N1   C6    aromatic  1.338  0.020  1.338
 WAQ  N1   C2    aromatic  1.331  0.020  1.331
 WAQ  C2   N3    aromatic  1.322  0.020  1.322
 WAQ  C2   H2    single    0.930  0.020  1.080
 WAQ  N3   C4    aromatic  1.332  0.020  1.332
 WAQ  C5   C4    aromatic  1.385  0.020  1.385
 WAQ  C4   N9    aromatic  1.364  0.020  1.364
 WAQ  C6   C5    aromatic  1.407  0.020  1.407
 WAQ  C5   N7    aromatic  1.369  0.020  1.369
 WAQ  N6   C6    single    1.333  0.020  1.333
 WAQ  N6   HN6   single    0.860  0.020  1.020
 WAQ  N6   HN6A  single    0.860  0.020  1.020
 WAQ  N7   C8    aromatic  1.302  0.020  1.302
 WAQ  C8   N9    aromatic  1.369  0.020  1.369
 WAQ  C8   H8    single    0.930  0.020  1.080
 WAQ  N9   C1'   single    1.457  0.020  1.457
 WAQ  C2'  C1'   single    1.530  0.020  1.530
 WAQ  C1'  O4'   single    1.398  0.020  1.398
 WAQ  C1'  H1'   single    0.970  0.020  1.090
 WAQ  C2'  O2'   single    1.401  0.020  1.401
 WAQ  C2'  C3'   single    1.532  0.020  1.532
 WAQ  C2'  H2'   single    0.970  0.020  1.090
 WAQ  O2'  HO2'  single    0.850  0.020  0.980
 WAQ  C3'  O3'   single    1.398  0.020  1.398
 WAQ  C3'  C4'   single    1.525  0.020  1.525
 WAQ  C3'  H3'   single    0.970  0.020  1.090
 WAQ  O3'  HO3'  single    0.850  0.020  0.980
 WAQ  O4'  C4'   single    1.423  0.020  1.423
 WAQ  C4'  C5'   single    1.506  0.020  1.506
 WAQ  C4'  H4'   single    0.970  0.020  1.090
 WAQ  O5'  C5'   single    1.432  0.020  1.432
 WAQ  C5'  H5'   single    0.970  0.020  1.090
 WAQ  C5'  H5'A  single    0.970  0.020  1.090
 WAQ  O5'  PBG   single    1.579  0.020  1.579
 WAQ  CAW  OAB   single    1.330  0.020  1.330
 WAQ  OAB  HOAB  single    0.850  0.020  0.980
 WAQ  OAC  CAX   double    1.199  0.020  1.199
 WAQ  OAD  PBG   double    1.467  0.020  1.467
 WAQ  OAE  CAW   double    1.207  0.020  1.207
 WAQ  PBG  OAH   single    1.587  0.020  1.587
 WAQ  OAH  HOAH  single    0.850  0.020  0.980
 WAQ  CAM  CAK   single    1.524  0.020  1.524
 WAQ  CAK  CAL   single    1.526  0.020  1.526
 WAQ  CAK  HAK   single    0.970  0.020  1.090
 WAQ  CAK  HAKA  single    0.970  0.020  1.090
 WAQ  CAN  CAL   single    1.531  0.020  1.531
 WAQ  CAL  HAL   single    0.970  0.020  1.090
 WAQ  CAL  HALA  single    0.970  0.020  1.090
 WAQ  CAO  CAM   single    1.521  0.020  1.521
 WAQ  CAM  HAM   single    0.970  0.020  1.090
 WAQ  CAM  HAMA  single    0.970  0.020  1.090
 WAQ  CAN  CAW   single    1.503  0.020  1.503
 WAQ  CAN  HAN   single    0.970  0.020  1.090
 WAQ  CAN  HANA  single    0.970  0.020  1.090
 WAQ  CAX  CAO   single    1.495  0.020  1.495
 WAQ  CAO  HAO   single    0.970  0.020  1.090
 WAQ  CAO  HAOA  single    0.970  0.020  1.090
 WAQ  PBG  OAU   single    1.644  0.020  1.644
 WAQ  OAU  CAX   single    1.356  0.020  1.356

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
 WAQ  C6    N1   C2   119.22  3.000
 WAQ  H2    C2   N3   116.14  3.000
 WAQ  H2    C2   N1   115.41  3.000
 WAQ  N3    C2   N1   128.44  3.000
 WAQ  C4    N3   C2   111.56  3.000
 WAQ  N9    C4   C5   105.29  3.000
 WAQ  N9    C4   N3   128.05  3.000
 WAQ  C5    C4   N3   126.66  3.000
 WAQ  N7    C5   C6   133.07  3.000
 WAQ  N7    C5   C4   110.74  3.000
 WAQ  C6    C5   C4   116.19  3.000
 WAQ  N6    C6   C5   122.72  3.000
 WAQ  N6    C6   N1   119.35  3.000
 WAQ  C5    C6   N1   117.92  3.000
 WAQ  HN6A  N6   HN6  118.41  3.000
 WAQ  HN6A  N6   C6   121.17  3.000
 WAQ  HN6   N6   C6   120.39  3.000
 WAQ  C8    N7   C5   104.49  3.000
 WAQ  H8    C8   N9   122.03  3.000
 WAQ  H8    C8   N7   124.72  3.000
 WAQ  N9    C8   N7   113.25  3.000
 WAQ  C1'   N9   C8   129.19  3.000
 WAQ  C1'   N9   C4   124.55  3.000
 WAQ  C8    N9   C4   106.23  3.000
 WAQ  H1'   C1'  O4'  110.56  3.000
 WAQ  H1'   C1'  C2'  111.17  3.000
 WAQ  O4'   C1'  C2'  106.97  3.000
 WAQ  H1'   C1'  N9   107.20  3.000
 WAQ  O4'   C1'  N9   109.10  3.000
 WAQ  C2'   C1'  N9   111.85  3.000
 WAQ  H2'   C2'  C3'  112.64  3.000
 WAQ  H2'   C2'  O2'  111.92  3.000
 WAQ  C3'   C2'  O2'  111.14  3.000
 WAQ  H2'   C2'  C1'  112.02  3.000
 WAQ  C3'   C2'  C1'  100.98  3.000
 WAQ  O2'   C2'  C1'  107.55  3.000
 WAQ  HO2'  O2'  C2'  107.76  3.000
 WAQ  H3'   C3'  C4'  110.42  3.000
 WAQ  H3'   C3'  O3'  111.78  3.000
 WAQ  C4'   C3'  O3'  109.96  3.000
 WAQ  H3'   C3'  C2'  108.99  3.000
 WAQ  C4'   C3'  C2'  100.99  3.000
 WAQ  O3'   C3'  C2'  114.21  3.000
 WAQ  HO3'  O3'  C3'  108.96  3.000
 WAQ  H4'   C4'  C5'  105.76  3.000
 WAQ  H4'   C4'  O4'  109.85  3.000
 WAQ  C5'   C4'  O4'  110.82  3.000
 WAQ  H4'   C4'  C3'  109.26  3.000
 WAQ  C5'   C4'  C3'  116.44  3.000
 WAQ  O4'   C4'  C3'  104.68  3.000
 WAQ  C4'   O4'  C1'  110.90  3.000
 WAQ  H5'A  C5'  H5'  108.34  3.000
 WAQ  H5'A  C5'  O5'  110.92  3.000
 WAQ  H5'   C5'  O5'  109.86  3.000
 WAQ  H5'A  C5'  C4'  108.18  3.000
 WAQ  H5'   C5'  C4'  110.12  3.000
 WAQ  O5'   C5'  C4'  109.40  3.000
 WAQ  PBG   O5'  C5'  125.21  3.000
 WAQ  HOAB  OAB  CAW  110.01  3.000
 WAQ  HOAH  OAH  PBG  115.37  3.000
 WAQ  HAKA  CAK  HAK  106.20  3.000
 WAQ  HAKA  CAK  CAM  109.15  3.000
 WAQ  HAK   CAK  CAM  109.67  3.000
 WAQ  HAKA  CAK  CAL  108.23  3.000
 WAQ  HAK   CAK  CAL  109.66  3.000
 WAQ  CAM   CAK  CAL  113.65  3.000
 WAQ  HALA  CAL  HAL  106.66  3.000
 WAQ  HALA  CAL  CAN  110.08  3.000
 WAQ  HAL   CAL  CAN  109.26  3.000
 WAQ  HALA  CAL  CAK  109.19  3.000
 WAQ  HAL   CAL  CAK  108.78  3.000
 WAQ  CAN   CAL  CAK  112.68  3.000
 WAQ  HAMA  CAM  HAM  106.68  3.000
 WAQ  HAMA  CAM  CAO  109.67  3.000
 WAQ  HAM   CAM  CAO  109.51  3.000
 WAQ  HAMA  CAM  CAK  109.40  3.000
 WAQ  HAM   CAM  CAK  110.24  3.000
 WAQ  CAO   CAM  CAK  111.22  3.000
 WAQ  HANA  CAN  HAN  106.99  3.000
 WAQ  HANA  CAN  CAW  107.98  3.000
 WAQ  HAN   CAN  CAW  107.67  3.000
 WAQ  HANA  CAN  CAL  110.27  3.000
 WAQ  HAN   CAN  CAL  109.96  3.000
 WAQ  CAW   CAN  CAL  113.72  3.000
 WAQ  HAOA  CAO  HAO  105.49  3.000
 WAQ  HAOA  CAO  CAX  107.27  3.000
 WAQ  HAO   CAO  CAX  108.47  3.000
 WAQ  HAOA  CAO  CAM  110.65  3.000
 WAQ  HAO   CAO  CAM  110.98  3.000
 WAQ  CAX   CAO  CAM  113.60  3.000
 WAQ  PBG   OAU  CAX  121.03  3.000
 WAQ  CAN   CAW  OAE  125.01  3.000
 WAQ  CAN   CAW  OAB  112.25  3.000
 WAQ  OAE   CAW  OAB  122.73  3.000
 WAQ  OAU   CAX  CAO  111.76  3.000
 WAQ  OAU   CAX  OAC  121.28  3.000
 WAQ  CAO   CAX  OAC  126.95  3.000
 WAQ  OAU   PBG  OAH  105.61  3.000
 WAQ  OAU   PBG  OAD  113.90  3.000
 WAQ  OAH   PBG  OAD  118.61  3.000
 WAQ  OAU   PBG  O5'  100.13  3.000
 WAQ  OAH   PBG  O5'  102.94  3.000
 WAQ  OAD   PBG  O5'  113.52  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
 WAQ  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 WAQ  CONST_02  N7    C5   C6   N1    180.00   0.0  0
 WAQ  CONST_03  C4    N3   C2   N1      0.00   0.0  0
 WAQ  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 WAQ  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 WAQ  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 WAQ  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 WAQ  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 WAQ  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 WAQ  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 WAQ  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 WAQ  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 WAQ  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 WAQ  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 WAQ  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 WAQ  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 WAQ  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 WAQ  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 WAQ  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 WAQ  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 WAQ  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 WAQ  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 WAQ  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 WAQ  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 WAQ  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 WAQ  CONST_26  HN6   N6   C6   N1      0.00   0.0  0
 WAQ  CONST_27  HN6A  N6   C6   N1    180.00   0.0  0
 WAQ  CONST_28  HOAB  OAB  CAW  OAE     0.00   0.0  0
 WAQ  Var_01    OAD   PBG  O5'  C5'  -176.65  30.0  3
 WAQ  Var_02    CAL   CAN  CAW  OAB    54.95  30.0  2
 WAQ  Var_03    CAM   CAO  CAX  OAC    -8.41  30.0  3
 WAQ  Var_04    CAX   CAO  CAM  CAK   178.88  30.0  1
 WAQ  Var_05    CAW   CAN  CAL  CAK   175.41  30.0  1
 WAQ  Var_06    CAO   CAM  CAK  CAL   175.11  30.0  1
 WAQ  Var_07    CAN   CAL  CAK  CAM    63.55  30.0  3
 WAQ  Var_08    H5'   C5'  O5'  PBG    66.86  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
 WAQ  chir_01  C1'  N9   C2'  O4'  negativ
 WAQ  chir_02  C2'  O2'  C3'  C1'  positiv
 WAQ  chir_03  C3'  O3'  C4'  C2'  positiv
 WAQ  chir_04  C4'  O4'  C3'  C5'  negativ
 WAQ  chir_05  PBG  OAD  OAH  OAU  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
 WAQ  plan-1  N1    0.020
 WAQ  plan-1  C2    0.020
 WAQ  plan-1  N3    0.020
 WAQ  plan-1  C4    0.020
 WAQ  plan-1  C5    0.020
 WAQ  plan-1  C6    0.020
 WAQ  plan-1  N6    0.020
 WAQ  plan-1  N7    0.020
 WAQ  plan-1  C8    0.020
 WAQ  plan-1  N9    0.020
 WAQ  plan-1  C1'   0.020
 WAQ  plan-1  H2    0.020
 WAQ  plan-1  H8    0.020
 WAQ  plan-2  C6    0.020
 WAQ  plan-2  N6    0.020
 WAQ  plan-2  HN6   0.020
 WAQ  plan-2  HN6A  0.020
 WAQ  plan-3  OAB   0.020
 WAQ  plan-3  OAE   0.020
 WAQ  plan-3  CAN   0.020
 WAQ  plan-3  CAW   0.020
 WAQ  plan-3  HOAB  0.020
 WAQ  plan-4  OAC   0.020
 WAQ  plan-4  CAO   0.020
 WAQ  plan-4  OAU   0.020
 WAQ  plan-4  CAX   0.020

