# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 03:11:45 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-fluoranyl-2-(iminomethyl)-~{N}-(2-phenoxyethyl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cnc(C=N)nc1N(CCOc2ccccc2)Cc3ccc4OCOc4c3
#
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
 GH4  GH4  ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-fluoranyl-2-(iminomethyl)-~{N}-(2-phenoxyethyl)pyrimidin-4-amine  ligand  48  29  .  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_GH4
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
 GH4  C2   C  CR16  0  -0.332   1.4482  -2.9922  -2.0411
 GH4  C3   C  CR56  0   0.282   0.5392  -3.3074  -1.0629
 GH4  C5   C  CH2   0   0.067  -0.6083  -4.2628   0.5738
 GH4  C9   C  CR6   0   0.114   0.8266  -0.6517  -1.7466
 GH4  C10  C  CH2   0  -0.364   0.9827   0.7796  -2.2012
 GH4  C11  C  CR16  0  -0.377  -4.1951   1.0634  -0.6689
 GH4  C12  C  CR16  0  -0.241  -5.3741   0.4684  -0.2300
 GH4  C13  C  CR16  0  -0.282  -5.5480   0.1233   1.1003
 GH4  C14  C  CR16  0  -0.241  -4.5219   0.3796   2.0049
 GH4  C21  C  CR6   0   0.435   1.4822   1.8143  -0.0900
 GH4  C28  C  CR6   0   0.386   1.2720   2.5729   1.0831
 GH4  C1   C  CR16  0  -0.326   1.5805  -1.6373  -2.3667
 GH4  O4   O  O     0  -0.488   0.2010  -4.5248  -0.5639
 GH4  O6   O  O     0  -0.486  -1.0303  -2.9090   0.4793
 GH4  C7   C  CR56  0   0.312  -0.2098  -2.3285  -0.4325
 GH4  C8   C  CR16  0  -0.388  -0.0976  -0.9985  -0.7509
 GH4  C15  C  CR16  0  -0.341  -3.3427   0.9683   1.5849
 GH4  C16  C  CR6   0   0.399  -3.1730   1.3142   0.2429
 GH4  O17  O  O2    0  -0.476  -1.9906   1.8801  -0.0766
 GH4  C19  C  CH2   0  -0.371  -0.3241   2.7622  -1.5146
 GH4  N20  N  NT    0  -0.491   0.6914   1.7769  -1.1823
 GH4  N22  N  N     0  -0.459   2.5639   1.0324  -0.1077
 GH4  N23  N  N     0  -0.532   5.4385  -0.0713   1.6864
 GH4  C25  C  CR6   0   0.320   3.3747   1.0026   0.9326
 GH4  N26  N  N     0  -0.433   3.2494   1.6964   2.0495
 GH4  C27  C  CR16  0  -0.177   2.1782   2.4852   2.1062
 GH4  F29  F  F     0  -0.295   0.2066   3.3653   1.2475
 GH4  H1   H  HCR6  0   0.270   2.0446  -3.7473  -2.5349
 GH4  H2   H  HCH2  0   0.245  -1.4763  -4.9212   0.5701
 GH4  H3   H  HCH2  0   0.230  -0.0219  -4.4056   1.4888
 GH4  H4   H  HCH2  0   0.272   1.9870   0.9261  -2.6049
 GH4  H5   H  HCH2  0   0.279   0.2898   0.9688  -3.0231
 GH4  H7   H  HCR6  0   0.258  -6.1610   0.2767  -0.9481
 GH4  H8   H  HCR6  0   0.252  -6.4683  -0.3382   1.4323
 GH4  H9   H  HCR6  0   0.257  -4.6401   0.1172   3.0484
 GH4  H10  H  HCR6  0   0.247   2.3028  -1.3559  -3.1230
 GH4  H11  H  HCR6  0   0.273  -0.6857  -0.2535  -0.2325
 GH4  H12  H  HCR6  0   0.261  -2.5435   1.1661   2.2887
 GH4  H15  H  HCH2  0   0.281  -0.1618   3.0878  -2.5446
 GH4  H16  H  HCH2  0   0.283  -0.2156   3.6513  -0.9031
 GH4  H17  H  H     0   0.345   5.2463   0.5188   2.4970
 GH4  H19  H  HCR6  0   0.295   2.0204   3.0657   3.0089
 GH4  C24  C  C1    0  -0.085   4.5421   0.0916   0.8132
 GH4  C18  C  CH2   0  -0.197  -1.7349   2.2221  -1.4216
 GH4  H6   H  HCR6  0   0.278  -4.0963   1.3212  -1.7148
 GH4  H13  H  HCH2  0   0.230  -1.8519   1.3501  -2.0768
 GH4  H14  H  HCH2  0   0.251  -2.4288   2.9930  -1.7753
 GH4  H18  H  H     0   0.259   4.5942  -0.4670  -0.1202

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
 GH4  N23  C24  double    1.262  0.020  1.262
 GH4  C24  C25  single    1.486  0.020  1.486
 GH4  N26  C25  aromatic  1.321  0.020  1.321
 GH4  N26  C27  aromatic  1.332  0.020  1.332
 GH4  C25  N22  aromatic  1.319  0.020  1.319
 GH4  C27  C28  aromatic  1.370  0.020  1.370
 GH4  N22  C21  aromatic  1.335  0.020  1.335
 GH4  C28  C21  aromatic  1.413  0.020  1.413
 GH4  C28  F29  single    1.338  0.020  1.338
 GH4  C21  N20  single    1.349  0.020  1.349
 GH4  C18  C19  single    1.513  0.020  1.513
 GH4  C18  O17  single    1.411  0.020  1.411
 GH4  C19  N20  single    1.453  0.020  1.453
 GH4  N20  C10  single    1.455  0.020  1.455
 GH4  O17  C16  single    1.349  0.020  1.349
 GH4  C15  C16  aromatic  1.396  0.020  1.396
 GH4  C15  C14  aromatic  1.383  0.020  1.383
 GH4  C16  C11  aromatic  1.392  0.020  1.392
 GH4  C10  C9   single    1.510  0.020  1.510
 GH4  C1   C9   aromatic  1.387  0.020  1.387
 GH4  C1   C2   aromatic  1.400  0.020  1.400
 GH4  C14  C13  aromatic  1.392  0.020  1.392
 GH4  C9   C8   aromatic  1.402  0.020  1.402
 GH4  C2   C3   aromatic  1.372  0.020  1.372
 GH4  C11  C12  aromatic  1.392  0.020  1.392
 GH4  C8   C7   aromatic  1.372  0.020  1.372
 GH4  C3   C7   aromatic  1.385  0.020  1.385
 GH4  C3   O4   single    1.358  0.020  1.358
 GH4  C13  C12  aromatic  1.385  0.020  1.385
 GH4  C7   O6   single    1.357  0.020  1.357
 GH4  O4   C5   single    1.421  0.020  1.421
 GH4  O6   C5   single    1.421  0.020  1.421
 GH4  C2   H1   single    0.930  0.020  1.080
 GH4  C5   H2   single    0.970  0.020  1.090
 GH4  C5   H3   single    0.970  0.020  1.090
 GH4  C10  H4   single    0.970  0.020  1.090
 GH4  C10  H5   single    0.970  0.020  1.090
 GH4  C11  H6   single    0.930  0.020  1.080
 GH4  C12  H7   single    0.930  0.020  1.080
 GH4  C13  H8   single    0.930  0.020  1.080
 GH4  C14  H9   single    0.930  0.020  1.080
 GH4  C1   H10  single    0.930  0.020  1.080
 GH4  C8   H11  single    0.930  0.020  1.080
 GH4  C15  H12  single    0.930  0.020  1.080
 GH4  C18  H13  single    0.970  0.020  1.090
 GH4  C18  H14  single    0.970  0.020  1.090
 GH4  C19  H15  single    0.970  0.020  1.090
 GH4  C19  H16  single    0.970  0.020  1.090
 GH4  N23  H17  single    0.890  0.020  1.040
 GH4  C24  H18  single    0.930  0.020  1.080
 GH4  C27  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
 GH4  H1   C2   C1   121.17  3.000
 GH4  H1   C2   C3   122.03  3.000
 GH4  C1   C2   C3   116.80  3.000
 GH4  C7   C3   O4   109.37  3.000
 GH4  O4   C3   C2   129.26  3.000
 GH4  C7   C3   C2   121.37  3.000
 GH4  H3   C5   H2   110.51  3.000
 GH4  H3   C5   O6   109.78  3.000
 GH4  H2   C5   O6   109.81  3.000
 GH4  H3   C5   O4   109.86  3.000
 GH4  H2   C5   O4   109.86  3.000
 GH4  O6   C5   O4   106.95  3.000
 GH4  C8   C9   C1   119.99  3.000
 GH4  C8   C9   C10  121.09  3.000
 GH4  C1   C9   C10  118.87  3.000
 GH4  H5   C10  H4   106.39  3.000
 GH4  H5   C10  N20  106.35  3.000
 GH4  H4   C10  N20  110.54  3.000
 GH4  H5   C10  C9   108.99  3.000
 GH4  H4   C10  C9   109.48  3.000
 GH4  N20  C10  C9   114.72  3.000
 GH4  H6   C11  C16  121.55  3.000
 GH4  H6   C11  C12  118.96  3.000
 GH4  C16  C11  C12  119.49  3.000
 GH4  H7   C12  C13  120.11  3.000
 GH4  H7   C12  C11  118.84  3.000
 GH4  C13  C12  C11  121.05  3.000
 GH4  H8   C13  C14  120.43  3.000
 GH4  H8   C13  C12  120.52  3.000
 GH4  C14  C13  C12  119.06  3.000
 GH4  H9   C14  C15  119.27  3.000
 GH4  H9   C14  C13  120.09  3.000
 GH4  C15  C14  C13  120.64  3.000
 GH4  N22  C21  N20  116.62  3.000
 GH4  N20  C21  C28  126.87  3.000
 GH4  N22  C21  C28  116.50  3.000
 GH4  F29  C28  C27  118.23  3.000
 GH4  F29  C28  C21  122.59  3.000
 GH4  C27  C28  C21  119.17  3.000
 GH4  H10  C1   C9   119.34  3.000
 GH4  H10  C1   C2   118.49  3.000
 GH4  C9   C1   C2   122.17  3.000
 GH4  C5   O4   C3   105.71  3.000
 GH4  C7   O6   C5   105.82  3.000
 GH4  C8   C7   O6   128.32  3.000
 GH4  O6   C7   C3   109.30  3.000
 GH4  C8   C7   C3   122.37  3.000
 GH4  H11  C8   C7   120.80  3.000
 GH4  H11  C8   C9   121.90  3.000
 GH4  C7   C8   C9   117.29  3.000
 GH4  H12  C15  C16  119.32  3.000
 GH4  H12  C15  C14  120.62  3.000
 GH4  C16  C15  C14  120.06  3.000
 GH4  O17  C16  C15  115.98  3.000
 GH4  C15  C16  C11  119.71  3.000
 GH4  O17  C16  C11  124.31  3.000
 GH4  C18  O17  C16  119.09  3.000
 GH4  H16  C19  H15  105.81  3.000
 GH4  H16  C19  N20  110.91  3.000
 GH4  H15  C19  N20  108.29  3.000
 GH4  H16  C19  C18  110.55  3.000
 GH4  H15  C19  C18  107.62  3.000
 GH4  N20  C19  C18  113.29  3.000
 GH4  C19  N20  C21  125.16  3.000
 GH4  C19  N20  C10  116.38  3.000
 GH4  C21  N20  C10  117.94  3.000
 GH4  C25  N22  C21  120.05  3.000
 GH4  H17  N23  C24  109.94  3.000
 GH4  N26  C25  C24  117.68  3.000
 GH4  N26  C25  N22  126.63  3.000
 GH4  C24  C25  N22  115.68  3.000
 GH4  C27  N26  C25  115.05  3.000
 GH4  H19  C27  N26  118.00  3.000
 GH4  H19  C27  C28  119.42  3.000
 GH4  N26  C27  C28  122.58  3.000
 GH4  H18  C24  C25  114.90  3.000
 GH4  H18  C24  N23  119.53  3.000
 GH4  C25  C24  N23  125.57  3.000
 GH4  H14  C18  H13  107.39  3.000
 GH4  H14  C18  C19  108.63  3.000
 GH4  H13  C18  C19  110.27  3.000
 GH4  H14  C18  O17  111.31  3.000
 GH4  H13  C18  O17  110.93  3.000
 GH4  C19  C18  O17  108.30  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
 GH4  CONST_01  C8   C9   C1   C2      0.00   0.0  0
 GH4  CONST_02  C8   C7   C3   C2      0.00   0.0  0
 GH4  CONST_03  C9   C1   C2   C3      0.00   0.0  0
 GH4  CONST_04  C9   C8   C7   C3      0.00   0.0  0
 GH4  CONST_05  C14  C15  C16  C11     0.00   0.0  0
 GH4  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 GH4  CONST_07  C15  C16  C11  C12     0.00   0.0  0
 GH4  CONST_08  C15  C14  C13  C12     0.00   0.0  0
 GH4  CONST_09  C16  C15  C14  C13     0.00   0.0  0
 GH4  CONST_10  C16  C11  C12  C13     0.00   0.0  0
 GH4  CONST_11  N26  C25  N22  C21     0.00   0.0  0
 GH4  CONST_12  N26  C27  C28  C21     0.00   0.0  0
 GH4  CONST_13  C25  N26  C27  C28     0.00   0.0  0
 GH4  CONST_14  C25  N22  C21  C28     0.00   0.0  0
 GH4  CONST_15  C7   C8   C9   C1      0.00   0.0  0
 GH4  CONST_16  C7   C3   C2   C1      0.00   0.0  0
 GH4  CONST_17  C27  N26  C25  N22     0.00   0.0  0
 GH4  CONST_18  C27  C28  C21  N22     0.00   0.0  0
 GH4  CONST_19  C10  C9   C1   C2    180.00   0.0  0
 GH4  CONST_20  C7   C8   C9   C10   180.00   0.0  0
 GH4  CONST_21  O17  C16  C11  C12   180.00   0.0  0
 GH4  CONST_22  O17  C16  C15  C14   180.00   0.0  0
 GH4  CONST_23  C24  C25  N22  C21   180.00   0.0  0
 GH4  CONST_24  C25  N22  C21  N20   180.00   0.0  0
 GH4  CONST_25  C27  C28  C21  N20   180.00   0.0  0
 GH4  CONST_26  F29  C28  C21  N22   180.00   0.0  0
 GH4  CONST_27  C27  N26  C25  C24   180.00   0.0  0
 GH4  CONST_28  F29  C28  C27  N26   180.00   0.0  0
 GH4  CONST_29  H10  C1   C2   C3    180.00   0.0  0
 GH4  CONST_30  H11  C8   C7   C3    180.00   0.0  0
 GH4  CONST_31  H1   C2   C1   C9    180.00   0.0  0
 GH4  CONST_32  H12  C15  C16  C11   180.00   0.0  0
 GH4  CONST_33  H8   C13  C12  C11   180.00   0.0  0
 GH4  CONST_34  H9   C14  C13  C12   180.00   0.0  0
 GH4  CONST_35  H6   C11  C12  C13   180.00   0.0  0
 GH4  CONST_36  H7   C12  C13  C14   180.00   0.0  0
 GH4  CONST_37  H19  C27  C28  C21   180.00   0.0  0
 GH4  CONST_38  N22  C21  N20  C10     0.00   0.0  0
 GH4  CONST_39  C28  C21  N20  C10   180.00   0.0  0
 GH4  Var_01    O6   C5   O4   C3     16.45  30.0  1
 GH4  Var_02    C7   C3   O4   C5    -10.44  30.0  1
 GH4  Var_03    C8   C7   O6   C5   -170.91  30.0  1
 GH4  Var_04    C21  N20  C10  C9     63.91  30.0  2
 GH4  Var_05    N20  C10  C9   C1   -152.69  30.0  3
 GH4  Var_06    N23  C24  C25  N22   179.22  30.0  1
 GH4  Var_07    C18  C19  N20  C21  -111.80  30.0  3
 GH4  Var_08    C19  C18  O17  C16  -176.90  30.0  3
 GH4  Var_09    N20  C19  C18  O17    64.19  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
 GH4  plan-1  C11  0.020
 GH4  plan-1  C12  0.020
 GH4  plan-1  C13  0.020
 GH4  plan-1  C14  0.020
 GH4  plan-1  C15  0.020
 GH4  plan-1  C16  0.020
 GH4  plan-1  O17  0.020
 GH4  plan-1  H7   0.020
 GH4  plan-1  H8   0.020
 GH4  plan-1  H9   0.020
 GH4  plan-1  H12  0.020
 GH4  plan-1  H6   0.020
 GH4  plan-2  C21  0.020
 GH4  plan-2  C28  0.020
 GH4  plan-2  N20  0.020
 GH4  plan-2  N22  0.020
 GH4  plan-2  C25  0.020
 GH4  plan-2  N26  0.020
 GH4  plan-2  C27  0.020
 GH4  plan-2  F29  0.020
 GH4  plan-2  H19  0.020
 GH4  plan-2  C24  0.020
 GH4  plan-3  C2   0.020
 GH4  plan-3  C3   0.020
 GH4  plan-3  C9   0.020
 GH4  plan-3  C10  0.020
 GH4  plan-3  C1   0.020
 GH4  plan-3  O4   0.020
 GH4  plan-3  O6   0.020
 GH4  plan-3  C7   0.020
 GH4  plan-3  C8   0.020
 GH4  plan-3  H1   0.020
 GH4  plan-3  H10  0.020
 GH4  plan-3  H11  0.020
 GH4  plan-4  C10  0.020
 GH4  plan-4  C21  0.020
 GH4  plan-4  C19  0.020
 GH4  plan-4  N20  0.020
 GH4  plan-5  N23  0.020
 GH4  plan-5  C25  0.020
 GH4  plan-5  H17  0.020
 GH4  plan-5  C24  0.020
 GH4  plan-5  H18  0.020

