# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:20:30 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: 7-(2-methoxyethoxymethyl)-1,3-dimethyl-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOCn1cnc2N(C)C(=O)N(C)C(=O)c12
#
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
 QOK  QOK  7-(2-methoxyethoxymethyl)-1,3-dimethyl-purine-2,6-dione  ligand  35  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QOK
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
 QOK  N3   N  NR5   0  -0.499  -23.8537  -1.5632  -40.0212
 QOK  C4   C  CR6   0   0.561  -25.3183   0.3847  -39.2393
 QOK  C7   C  CR15  0   0.132  -24.1931  -2.7470  -40.5536
 QOK  C8   C  CH2   0  -0.058  -22.5039  -1.0614  -39.8347
 QOK  C17  C  CH2   0  -0.163  -21.4791   0.6191  -42.8955
 QOK  C1   C  CR56  0   0.134  -25.0377  -0.8939  -39.7993
 QOK  N9   N  NR6   0  -0.607  -26.6940   0.6393  -39.2060
 QOK  C14  C  CH3   0  -0.528  -27.1512   1.9159  -38.6691
 QOK  O10  O  O     0  -0.461  -24.4975   1.1841  -38.8263
 QOK  O13  O  O2    0  -0.467  -22.1740  -0.0790  -40.7492
 QOK  C16  C  CH2   0  -0.191  -22.0373  -0.5321  -42.0817
 QOK  O18  O  O2    0  -0.488  -21.3658   0.1822  -44.2239
 QOK  C19  C  CH3   0  -0.396  -20.8753   1.1798  -45.0828
 QOK  N6   N  N     0  -0.467  -25.4942  -2.9084  -40.6837
 QOK  C2   C  CR56  0   0.442  -26.0148  -1.7574  -40.2171
 QOK  N5   N  NR6   0  -0.592  -27.3375  -1.4367  -40.1397
 QOK  C11  C  CR6   0   0.760  -27.7031  -0.2095  -39.6500
 QOK  O15  O  O     0  -0.492  -28.8704   0.1265  -39.5986
 QOK  C12  C  CH3   0  -0.532  -28.3739  -2.3449  -40.6015
 QOK  H1   H  HCR5  0   0.309  -23.4513  -3.4805  -40.8320
 QOK  H27  H  HCH2  0   0.255  -21.8412  -1.9312  -39.8949
 QOK  H28  H  HCH2  0   0.276  -22.4255  -0.6263  -38.8419
 QOK  H37  H  HCH2  0   0.208  -20.5033   0.9253  -42.4927
 QOK  H38  H  HCH2  0   0.208  -22.1499   1.4867  -42.8187
 QOK  H33  H  HCH3  0   0.256  -27.8556   1.7568  -37.8563
 QOK  H32  H  HCH3  0   0.267  -26.2962   2.4618  -38.2895
 QOK  H34  H  HCH3  0   0.256  -27.6319   2.5100  -39.4439
 QOK  H35  H  HCH2  0   0.224  -23.0036  -0.8418  -42.4988
 QOK  H36  H  HCH2  0   0.220  -21.3600  -1.3946  -42.1303
 QOK  H40  H  HCH3  0   0.235  -20.7936   0.7529  -46.0815
 QOK  H39  H  HCH3  0   0.206  -21.5445   2.0470  -45.1303
 QOK  H41  H  HCH3  0   0.206  -19.8848   1.5359  -44.7759
 QOK  H30  H  HCH3  0   0.260  -29.1236  -2.4913  -39.8279
 QOK  H29  H  HCH3  0   0.258  -28.8571  -1.9611  -41.4985
 QOK  H31  H  HCH3  0   0.268  -27.9155  -3.3008  -40.8308

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
 QOK  C19  O18  single    1.405  0.020  1.405
 QOK  O18  C17  single    1.403  0.020  1.403
 QOK  C17  C16  single    1.516  0.020  1.516
 QOK  C16  O13  single    1.414  0.020  1.414
 QOK  O13  C8   single    1.382  0.020  1.382
 QOK  C7   N6   aromatic  1.318  0.020  1.318
 QOK  C7   N3   aromatic  1.342  0.020  1.342
 QOK  N6   C2   aromatic  1.347  0.020  1.347
 QOK  C8   N3   single    1.452  0.020  1.452
 QOK  N3   C1   aromatic  1.378  0.020  1.378
 QOK  C2   C1   aromatic  1.369  0.020  1.369
 QOK  C2   N5   single    1.363  0.020  1.363
 QOK  C12  N5   single    1.453  0.020  1.453
 QOK  C1   C4   single    1.424  0.020  1.424
 QOK  N5   C11  single    1.371  0.020  1.371
 QOK  C4   O10  double    1.218  0.020  1.218
 QOK  C4   N9   single    1.399  0.020  1.399
 QOK  C11  N9   single    1.391  0.020  1.391
 QOK  C11  O15  double    1.216  0.020  1.216
 QOK  N9   C14  single    1.458  0.020  1.458
 QOK  C7   H1   single    0.930  0.020  1.080
 QOK  C8   H27  single    0.970  0.020  1.090
 QOK  C8   H28  single    0.970  0.020  1.090
 QOK  C17  H37  single    0.970  0.020  1.090
 QOK  C17  H38  single    0.970  0.020  1.090
 QOK  C14  H33  single    0.970  0.020  1.090
 QOK  C14  H32  single    0.970  0.020  1.090
 QOK  C14  H34  single    0.970  0.020  1.090
 QOK  C16  H35  single    0.970  0.020  1.090
 QOK  C16  H36  single    0.970  0.020  1.090
 QOK  C19  H40  single    0.970  0.020  1.090
 QOK  C19  H39  single    0.970  0.020  1.090
 QOK  C19  H41  single    0.970  0.020  1.090
 QOK  C12  H30  single    0.970  0.020  1.090
 QOK  C12  H29  single    0.970  0.020  1.090
 QOK  C12  H31  single    0.970  0.020  1.090

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
 QOK  C1   N3   C8   127.60  3.000
 QOK  C1   N3   C7   105.97  3.000
 QOK  C8   N3   C7   126.23  3.000
 QOK  O10  C4   N9   122.34  3.000
 QOK  N9   C4   C1   111.50  3.000
 QOK  O10  C4   C1   126.16  3.000
 QOK  H1   C7   N6   124.74  3.000
 QOK  H1   C7   N3   121.86  3.000
 QOK  N6   C7   N3   113.40  3.000
 QOK  H28  C8   H27  108.94  3.000
 QOK  H28  C8   O13  107.62  3.000
 QOK  H27  C8   O13  112.57  3.000
 QOK  H28  C8   N3   108.83  3.000
 QOK  H27  C8   N3   106.32  3.000
 QOK  O13  C8   N3   112.49  3.000
 QOK  H38  C17  H37  107.23  3.000
 QOK  H38  C17  O18  111.17  3.000
 QOK  H37  C17  O18  111.22  3.000
 QOK  H38  C17  C16  109.70  3.000
 QOK  H37  C17  C16  109.98  3.000
 QOK  O18  C17  C16  107.55  3.000
 QOK  C2   C1   C4   123.07  3.000
 QOK  C4   C1   N3   131.98  3.000
 QOK  C2   C1   N3   104.93  3.000
 QOK  C11  N9   C14  115.09  3.000
 QOK  C14  N9   C4   118.44  3.000
 QOK  C11  N9   C4   126.47  3.000
 QOK  H34  C14  H32  108.85  3.000
 QOK  H34  C14  H33  109.03  3.000
 QOK  H32  C14  H33  108.86  3.000
 QOK  H34  C14  N9   110.75  3.000
 QOK  H32  C14  N9   108.82  3.000
 QOK  H33  C14  N9   110.50  3.000
 QOK  C16  O13  C8   114.76  3.000
 QOK  H36  C16  H35  107.75  3.000
 QOK  H36  C16  O13  110.68  3.000
 QOK  H35  C16  O13  111.32  3.000
 QOK  H36  C16  C17  110.22  3.000
 QOK  H35  C16  C17  109.55  3.000
 QOK  O13  C16  C17  107.34  3.000
 QOK  C19  O18  C17  112.70  3.000
 QOK  H41  C19  H39  107.86  3.000
 QOK  H41  C19  H40  108.43  3.000
 QOK  H39  C19  H40  108.42  3.000
 QOK  H41  C19  O18  112.02  3.000
 QOK  H39  C19  O18  112.03  3.000
 QOK  H40  C19  O18  107.97  3.000
 QOK  C2   N6   C7   104.06  3.000
 QOK  N5   C2   N6   126.58  3.000
 QOK  N5   C2   C1   121.78  3.000
 QOK  N6   C2   C1   111.64  3.000
 QOK  C12  N5   C11  118.86  3.000
 QOK  C11  N5   C2   119.32  3.000
 QOK  C12  N5   C2   121.79  3.000
 QOK  O15  C11  N5   121.23  3.000
 QOK  O15  C11  N9   120.95  3.000
 QOK  N5   C11  N9   117.82  3.000
 QOK  H31  C12  H29  108.90  3.000
 QOK  H31  C12  H30  108.86  3.000
 QOK  H29  C12  H30  109.13  3.000
 QOK  H31  C12  N5   108.45  3.000
 QOK  H29  C12  N5   110.97  3.000
 QOK  H30  C12  N5   110.48  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
 QOK  CONST_01  C2   N6   C7   N3      0.00   0.0  0
 QOK  CONST_02  N6   C2   C1   N3      0.00   0.0  0
 QOK  CONST_03  C1   C2   N6   C7      0.00   0.0  0
 QOK  CONST_04  C2   C1   N3   C7      0.00   0.0  0
 QOK  CONST_05  N6   C7   N3   C1      0.00   0.0  0
 QOK  CONST_06  N5   C11  N9   C4      0.00   0.0  0
 QOK  CONST_07  C11  N9   C4   C1      0.00   0.0  0
 QOK  CONST_08  C2   N5   C11  N9      0.00   0.0  0
 QOK  CONST_09  C8   N3   C1   C4      0.00   0.0  0
 QOK  CONST_10  N6   C7   N3   C8    180.00   0.0  0
 QOK  CONST_11  C2   C1   N3   C8    180.00   0.0  0
 QOK  CONST_12  O15  C11  N9   C4    180.00   0.0  0
 QOK  CONST_13  C14  N9   C4   C1    180.00   0.0  0
 QOK  CONST_14  C12  N5   C11  N9    180.00   0.0  0
 QOK  CONST_15  N5   C11  N9   C14   180.00   0.0  0
 QOK  CONST_16  C11  N9   C4   O10   180.00   0.0  0
 QOK  CONST_17  O15  C11  N5   C2    180.00   0.0  0
 QOK  CONST_18  H1   C7   N3   C1    180.00   0.0  0
 QOK  CONST_19  O10  C4   N9   C14     0.00   0.0  0
 QOK  CONST_20  O15  C11  N9   C14     0.00   0.0  0
 QOK  CONST_21  C12  N5   C11  O15     0.00   0.0  0
 QOK  Var_01    O13  C8   N3   C7    105.48  30.0  2
 QOK  Var_02    H33  C14  N9   C4   -124.06  30.0  3
 QOK  Var_03    H30  C12  N5   C2    128.30  30.0  3
 QOK  Var_04    C17  C16  O13  C8   -171.74  30.0  1
 QOK  Var_05    O18  C17  C16  O13  -178.89  30.0  1
 QOK  Var_06    H40  C19  O18  C17   178.52  30.0  3

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
 QOK  plan-1  N3   0.020
 QOK  plan-1  C4   0.020
 QOK  plan-1  C7   0.020
 QOK  plan-1  C8   0.020
 QOK  plan-1  C1   0.020
 QOK  plan-1  N9   0.020
 QOK  plan-1  C14  0.020
 QOK  plan-1  O10  0.020
 QOK  plan-1  N6   0.020
 QOK  plan-1  C2   0.020
 QOK  plan-1  N5   0.020
 QOK  plan-1  C11  0.020
 QOK  plan-1  O15  0.020
 QOK  plan-1  C12  0.020
 QOK  plan-1  H1   0.020

