# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:00:43 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2R,3R,4S,5R)-2-[6-azanyl-8-(quinolin-6-ylmethylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c(NCc4ccc5ncccc5c4)nc12
#
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
 GB8  GB8  (2R,3R,4S,5R)-2-[6-azanyl-8-(quinolin-6-ylmethylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol  ligand  52  31  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GB8
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
 GB8  C     C  CH1   0   0.169   1.3681   1.2217   0.3458
 GB8  N     N  NR5   0  -0.607   1.5111  -0.2128   0.2417
 GB8  O     O  O2    0  -0.491   2.0037   1.8296  -0.7455
 GB8  C1    C  CH1   0  -0.045   1.9590   1.8334   1.6250
 GB8  N1    N  N     0  -0.522   0.9118  -2.3552  -0.0682
 GB8  C2    C  CH1   0  -0.041   3.2516   2.4917   1.1206
 GB8  N2    N  N     0  -0.453   3.9283  -0.4847   0.1021
 GB8  O2    O  OH1   0  -0.662   3.5981   3.6451   1.8415
 GB8  C3    C  CH1   0   0.023   2.8840   2.8579  -0.3148
 GB8  N3    N  N     0  -0.469   4.5673  -2.7448  -0.3035
 GB8  O3    O  OH1   0  -0.670   1.0564   2.8029   2.0881
 GB8  C4    C  CH2   0  -0.164   4.0818   2.9357  -1.2269
 GB8  C5    C  CR5   0   0.716   0.4895  -1.1397   0.1468
 GB8  N5    N  NH1   0  -0.694  -0.8159  -0.7772   0.2283
 GB8  C6    C  CR56  0   0.026   2.2787  -2.2349  -0.1242
 GB8  N6    N  N     0  -0.430  -6.9383   0.5821   0.5620
 GB8  C7    C  CR56  0   0.497   2.6767  -0.9246   0.0740
 GB8  C8    C  CR16  0   0.034   4.8064  -1.4561  -0.0959
 GB8  C9    C  CR6   0   0.426   3.2990  -3.1734  -0.3210
 GB8  C10   C  CH2   0  -0.332  -1.8200  -1.8295   0.1733
 GB8  C11   C  CR6   0   0.069  -3.1895  -1.2154   0.2396
 GB8  C12   C  CR16  0  -0.358  -3.8638  -0.8642  -0.9006
 GB8  C13   C  CR66  0   0.090  -5.1365  -0.2575  -0.8328
 GB8  C14   C  CR66  0   0.198  -5.7215   0.0007   0.4314
 GB8  C15   C  CR16  0  -0.280  -5.0106  -0.3652   1.5961
 GB8  C16   C  CR16  0  -0.286  -3.7812  -0.9562   1.4979
 GB8  C17   C  CR16  0  -0.080  -7.5846   0.9103  -0.5246
 GB8  C18   C  CR16  0  -0.327  -7.0944   0.6961  -1.8307
 GB8  C19   C  CR16  0  -0.183  -5.8694   0.1124  -1.9823
 GB8  H     H  HCH1  0   0.258   0.2945   1.4299   0.3171
 GB8  H1    H  HCH1  0   0.250   2.1442   1.0650   2.3852
 GB8  HO1   H  HOH1  0   0.457   4.4493   3.4425  -3.0589
 GB8  H2    H  HCH1  0   0.258   4.0573   1.7521   1.1187
 GB8  HO2   H  HOH1  0   0.468   4.1521   3.3895   2.5858
 GB8  H3    H  HCH1  0   0.231   2.3589   3.8245  -0.3173
 GB8  HO3   H  HOH1  0   0.449   1.5780   3.5151   2.4811
 GB8  H4    H  HCH2  0   0.206   4.5655   1.9514  -1.2587
 GB8  H4A   H  HCH2  0   0.204   4.7949   3.6356  -0.7721
 GB8  HN4   H  HNH2  0   0.397   3.8022  -5.0822  -0.7979
 GB8  HN4A  H  HNH2  0   0.403   2.1166  -4.7919  -0.6862
 GB8  HN5   H  HNH1  0   0.404  -1.0316  -0.0340   0.8761
 GB8  H8    H  HCR6  0   0.247   5.8510  -1.1646  -0.0887
 GB8  H10   H  HCH2  0   0.262  -1.6962  -2.3779  -0.7608
 GB8  H10A  H  HCH2  0   0.248  -1.6887  -2.5498   0.9877
 GB8  H12   H  HCR6  0   0.261  -3.4273  -1.0551  -1.8745
 GB8  H15   H  HCR6  0   0.263  -5.4603  -0.1717   2.5614
 GB8  H16   H  HCR6  0   0.261  -3.2502  -1.2374   2.3996
 GB8  H17   H  HCR6  0   0.265  -8.5560   1.3753  -0.3919
 GB8  H18   H  HCR6  0   0.273  -7.6888   0.9930  -2.6836
 GB8  H19   H  HCR6  0   0.274  -5.4537  -0.0709  -2.9654
 GB8  O1    O  OH1   0  -0.672   3.6690   3.3660  -2.5026
 GB8  N4    N  NH2   0  -0.822   3.0536  -4.4828  -0.4944

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
 GB8  C    N     single    1.445  0.020  1.445
 GB8  C    O     single    1.402  0.020  1.402
 GB8  C    C1    single    1.536  0.020  1.536
 GB8  N    C5    aromatic  1.383  0.020  1.383
 GB8  N    C7    aromatic  1.376  0.020  1.376
 GB8  O    C3    single    1.421  0.020  1.421
 GB8  C1   C2    single    1.536  0.020  1.536
 GB8  C1   O3    single    1.403  0.020  1.403
 GB8  N1   C5    aromatic  1.305  0.020  1.305
 GB8  N1   C6    aromatic  1.373  0.020  1.373
 GB8  O1   C4    single    1.408  0.020  1.408
 GB8  C2   O2    single    1.404  0.020  1.404
 GB8  C2   C3    single    1.526  0.020  1.526
 GB8  N2   C7    aromatic  1.327  0.020  1.327
 GB8  N2   C8    aromatic  1.324  0.020  1.324
 GB8  C3   C4    single    1.508  0.020  1.508
 GB8  N3   C8    aromatic  1.327  0.020  1.327
 GB8  N3   C9    aromatic  1.339  0.020  1.339
 GB8  N4   C9    single    1.343  0.020  1.343
 GB8  C5   N5    single    1.357  0.020  1.357
 GB8  N5   C10   single    1.456  0.020  1.456
 GB8  C6   C7    aromatic  1.384  0.020  1.384
 GB8  C6   C9    aromatic  1.400  0.020  1.400
 GB8  N6   C14   aromatic  1.355  0.020  1.355
 GB8  N6   C17   aromatic  1.306  0.020  1.306
 GB8  C10  C11   single    1.502  0.020  1.502
 GB8  C11  C12   aromatic  1.370  0.020  1.370
 GB8  C11  C16   aromatic  1.414  0.020  1.414
 GB8  C12  C13   aromatic  1.412  0.020  1.412
 GB8  C13  C14   aromatic  1.417  0.020  1.417
 GB8  C13  C19   aromatic  1.413  0.020  1.413
 GB8  C14  C15   aromatic  1.413  0.020  1.413
 GB8  C15  C16   aromatic  1.368  0.020  1.368
 GB8  C17  C18   aromatic  1.411  0.020  1.411
 GB8  C18  C19   aromatic  1.365  0.020  1.365
 GB8  C    H     single    0.970  0.020  1.090
 GB8  C1   H1    single    0.970  0.020  1.090
 GB8  O1   HO1   single    0.850  0.020  0.980
 GB8  C2   H2    single    0.970  0.020  1.090
 GB8  O2   HO2   single    0.850  0.020  0.980
 GB8  C3   H3    single    0.970  0.020  1.090
 GB8  O3   HO3   single    0.850  0.020  0.980
 GB8  C4   H4    single    0.970  0.020  1.090
 GB8  C4   H4A   single    0.970  0.020  1.090
 GB8  N4   HN4   single    0.890  0.020  1.040
 GB8  N4   HN4A  single    0.890  0.020  1.040
 GB8  N5   HN5   single    0.890  0.020  1.040
 GB8  C8   H8    single    0.930  0.020  1.080
 GB8  C10  H10   single    0.970  0.020  1.090
 GB8  C10  H10A  single    0.970  0.020  1.090
 GB8  C12  H12   single    0.930  0.020  1.080
 GB8  C15  H15   single    0.930  0.020  1.080
 GB8  C16  H16   single    0.930  0.020  1.080
 GB8  C17  H17   single    0.930  0.020  1.080
 GB8  C18  H18   single    0.930  0.020  1.080
 GB8  C19  H19   single    0.930  0.020  1.080

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
 GB8  H     C    C1   108.88  3.000
 GB8  H     C    O    110.00  3.000
 GB8  C1    C    O    107.53  3.000
 GB8  H     C    N    106.51  3.000
 GB8  C1    C    N    114.65  3.000
 GB8  O     C    N    109.24  3.000
 GB8  C7    N    C5   105.71  3.000
 GB8  C7    N    C    127.30  3.000
 GB8  C5    N    C    126.67  3.000
 GB8  C3    O    C    111.03  3.000
 GB8  H1    C1   O3   111.34  3.000
 GB8  H1    C1   C2   112.70  3.000
 GB8  O3    C1   C2   110.71  3.000
 GB8  H1    C1   C    111.30  3.000
 GB8  O3    C1   C    107.61  3.000
 GB8  C2    C1   C    102.77  3.000
 GB8  C6    N1   C5   104.32  3.000
 GB8  H2    C2   C3   109.76  3.000
 GB8  H2    C2   O2   112.00  3.000
 GB8  C3    C2   O2   110.20  3.000
 GB8  H2    C2   C1   109.32  3.000
 GB8  C3    C2   C1   102.07  3.000
 GB8  O2    C2   C1   113.04  3.000
 GB8  C8    N2   C7   112.28  3.000
 GB8  HO2   O2   C2   108.73  3.000
 GB8  H3    C3   C4   109.42  3.000
 GB8  H3    C3   C2   109.15  3.000
 GB8  C4    C3   C2   112.96  3.000
 GB8  H3    C3   O    109.85  3.000
 GB8  C4    C3   O    110.26  3.000
 GB8  C2    C3   O    105.11  3.000
 GB8  C9    N3   C8   118.92  3.000
 GB8  HO3   O3   C1   107.24  3.000
 GB8  H4A   C4   H4   107.32  3.000
 GB8  H4A   C4   C3   107.35  3.000
 GB8  H4    C4   C3   108.75  3.000
 GB8  H4A   C4   O1   111.78  3.000
 GB8  H4    C4   O1   112.16  3.000
 GB8  C3    C4   O1   109.33  3.000
 GB8  N5    C5   N1   124.75  3.000
 GB8  N5    C5   N    121.83  3.000
 GB8  N1    C5   N    113.38  3.000
 GB8  HN5   N5   C10  114.15  3.000
 GB8  HN5   N5   C5   116.16  3.000
 GB8  C10   N5   C5   117.91  3.000
 GB8  C9    C6   C7   116.44  3.000
 GB8  C9    C6   N1   132.25  3.000
 GB8  C7    C6   N1   111.31  3.000
 GB8  C17   N6   C14  118.16  3.000
 GB8  C6    C7   N2   126.03  3.000
 GB8  C6    C7   N    105.29  3.000
 GB8  N2    C7   N    128.68  3.000
 GB8  H8    C8   N3   115.82  3.000
 GB8  H8    C8   N2   116.14  3.000
 GB8  N3    C8   N2   128.04  3.000
 GB8  C6    C9   N4   122.57  3.000
 GB8  C6    C9   N3   118.29  3.000
 GB8  N4    C9   N3   119.12  3.000
 GB8  H10A  C10  H10  107.02  3.000
 GB8  H10A  C10  C11  110.20  3.000
 GB8  H10   C10  C11  110.30  3.000
 GB8  H10A  C10  N5   111.39  3.000
 GB8  H10   C10  N5   108.53  3.000
 GB8  C11   C10  N5   109.37  3.000
 GB8  C16   C11  C12  119.17  3.000
 GB8  C16   C11  C10  119.70  3.000
 GB8  C12   C11  C10  121.10  3.000
 GB8  H12   C12  C13  118.80  3.000
 GB8  H12   C12  C11  120.27  3.000
 GB8  C13   C12  C11  120.92  3.000
 GB8  C19   C13  C14  117.66  3.000
 GB8  C19   C13  C12  122.78  3.000
 GB8  C14   C13  C12  119.57  3.000
 GB8  C15   C14  C13  118.73  3.000
 GB8  C15   C14  N6   118.92  3.000
 GB8  C13   C14  N6   122.35  3.000
 GB8  H15   C15  C16  120.98  3.000
 GB8  H15   C15  C14  118.68  3.000
 GB8  C16   C15  C14  120.34  3.000
 GB8  H16   C16  C15  119.53  3.000
 GB8  H16   C16  C11  119.20  3.000
 GB8  C15   C16  C11  121.27  3.000
 GB8  H17   C17  C18  119.28  3.000
 GB8  H17   C17  N6   116.67  3.000
 GB8  C18   C17  N6   124.04  3.000
 GB8  H18   C18  C19  121.54  3.000
 GB8  H18   C18  C17  119.82  3.000
 GB8  C19   C18  C17  118.63  3.000
 GB8  H19   C19  C18  121.16  3.000
 GB8  H19   C19  C13  119.68  3.000
 GB8  C18   C19  C13  119.15  3.000
 GB8  HO1   O1   C4   108.09  3.000
 GB8  HN4A  N4   HN4  116.94  3.000
 GB8  HN4A  N4   C9   119.64  3.000
 GB8  HN4   N4   C9   118.93  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
 GB8  CONST_01  C6    N1   C5   N       0.00   0.0  0
 GB8  CONST_02  C8    N2   C7   N     180.00   0.0  0
 GB8  CONST_03  N1    C6   C7   N       0.00   0.0  0
 GB8  CONST_04  C9    C6   C7   N     180.00   0.0  0
 GB8  CONST_05  C7    N    C5   N1      0.00   0.0  0
 GB8  CONST_06  N2    C7   C6   N1    180.00   0.0  0
 GB8  CONST_07  N3    C9   C6   N1    180.00   0.0  0
 GB8  CONST_08  C5    N    C7   N2    180.00   0.0  0
 GB8  CONST_09  C9    C6   C7   N2      0.00   0.0  0
 GB8  CONST_10  C9    N3   C8   N2      0.00   0.0  0
 GB8  CONST_11  C7    N2   C8   N3      0.00   0.0  0
 GB8  CONST_12  C7    C6   C9   N3      0.00   0.0  0
 GB8  CONST_13  C6    C7   N    C5      0.00   0.0  0
 GB8  CONST_14  C7    C6   N1   C5      0.00   0.0  0
 GB8  CONST_15  C9    C6   N1   C5    180.00   0.0  0
 GB8  CONST_16  C8    N2   C7   C6      0.00   0.0  0
 GB8  CONST_17  C8    N3   C9   C6      0.00   0.0  0
 GB8  CONST_18  C12   C13  C14  N6    180.00   0.0  0
 GB8  CONST_19  C19   C13  C14  N6      0.00   0.0  0
 GB8  CONST_20  C16   C15  C14  N6    180.00   0.0  0
 GB8  CONST_21  C19   C18  C17  N6      0.00   0.0  0
 GB8  CONST_22  C14   C13  C12  C11     0.00   0.0  0
 GB8  CONST_23  C19   C13  C12  C11   180.00   0.0  0
 GB8  CONST_24  C14   C15  C16  C11     0.00   0.0  0
 GB8  CONST_25  C15   C16  C11  C12     0.00   0.0  0
 GB8  CONST_26  C15   C14  C13  C12     0.00   0.0  0
 GB8  CONST_27  C18   C19  C13  C12   180.00   0.0  0
 GB8  CONST_28  C16   C11  C12  C13     0.00   0.0  0
 GB8  CONST_29  C17   N6   C14  C13     0.00   0.0  0
 GB8  CONST_30  C16   C15  C14  C13     0.00   0.0  0
 GB8  CONST_31  C17   C18  C19  C13     0.00   0.0  0
 GB8  CONST_32  C18   C17  N6   C14     0.00   0.0  0
 GB8  CONST_33  C18   C19  C13  C14     0.00   0.0  0
 GB8  CONST_34  C17   N6   C14  C15   180.00   0.0  0
 GB8  CONST_35  C19   C13  C14  C15   180.00   0.0  0
 GB8  CONST_36  N1    C5   N    C     180.00   0.0  0
 GB8  CONST_37  N2    C7   N    C       0.00   0.0  0
 GB8  CONST_38  C6    C7   N    C     180.00   0.0  0
 GB8  CONST_39  N5    C5   N    C       0.00   0.0  0
 GB8  CONST_40  N4    C9   C6   N1      0.00   0.0  0
 GB8  CONST_41  C8    N3   C9   N4    180.00   0.0  0
 GB8  CONST_42  C7    C6   C9   N4    180.00   0.0  0
 GB8  CONST_43  C7    N    C5   N5    180.00   0.0  0
 GB8  CONST_44  C6    N1   C5   N5    180.00   0.0  0
 GB8  CONST_45  C13   C12  C11  C10   180.00   0.0  0
 GB8  CONST_46  C15   C16  C11  C10   180.00   0.0  0
 GB8  CONST_47  H15   C15  C14  N6      0.00   0.0  0
 GB8  CONST_48  H18   C18  C17  N6    180.00   0.0  0
 GB8  CONST_49  H8    C8   N2   C7    180.00   0.0  0
 GB8  CONST_50  H16   C16  C11  C12   180.00   0.0  0
 GB8  CONST_51  H19   C19  C13  C12     0.00   0.0  0
 GB8  CONST_52  H17   C17  N6   C14   180.00   0.0  0
 GB8  CONST_53  H12   C12  C13  C14   180.00   0.0  0
 GB8  CONST_54  C10   N5   C5   N     180.00   0.0  0
 GB8  CONST_55  C10   N5   C5   N1      0.00   0.0  0
 GB8  CONST_57  HN4   N4   C9   N3      0.00   0.0  0
 GB8  CONST_58  HN4A  N4   C9   N3    180.00   0.0  0
 GB8  Var_01    C11   C10  N5   C5   -178.40  30.0  3
 GB8  Var_02    C12   C11  C10  N5     91.01  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
 GB8  chir_01  C   N   O   C1  positiv
 GB8  chir_02  C1  O3  C   C2  negativ
 GB8  chir_03  C2  O2  C3  C1  positiv
 GB8  chir_04  C3  O   C2  C4  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
 GB8  plan-1  C     0.020
 GB8  plan-1  N     0.020
 GB8  plan-1  N1    0.020
 GB8  plan-1  N2    0.020
 GB8  plan-1  N3    0.020
 GB8  plan-1  C5    0.020
 GB8  plan-1  N5    0.020
 GB8  plan-1  C6    0.020
 GB8  plan-1  C7    0.020
 GB8  plan-1  C8    0.020
 GB8  plan-1  C9    0.020
 GB8  plan-1  H8    0.020
 GB8  plan-1  N4    0.020
 GB8  plan-2  N6    0.020
 GB8  plan-2  C10   0.020
 GB8  plan-2  C11   0.020
 GB8  plan-2  C12   0.020
 GB8  plan-2  C13   0.020
 GB8  plan-2  C14   0.020
 GB8  plan-2  C15   0.020
 GB8  plan-2  C16   0.020
 GB8  plan-2  C17   0.020
 GB8  plan-2  C18   0.020
 GB8  plan-2  C19   0.020
 GB8  plan-2  H12   0.020
 GB8  plan-2  H15   0.020
 GB8  plan-2  H16   0.020
 GB8  plan-2  H17   0.020
 GB8  plan-2  H18   0.020
 GB8  plan-2  H19   0.020
 GB8  plan-3  C5    0.020
 GB8  plan-3  N5    0.020
 GB8  plan-3  C10   0.020
 GB8  plan-3  HN5   0.020
 GB8  plan-4  C9    0.020
 GB8  plan-4  HN4   0.020
 GB8  plan-4  HN4A  0.020
 GB8  plan-4  N4    0.020

