# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 03:54:49 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: ~{N}-[3-[[5-fluoranyl-2-[[4-(2-methoxyethoxy)phenyl]amino]pyrimidin-4-yl]amino]phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(Nc2nc(Nc3ccc(OCCOC)cc3)ncc2F)c1
#
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
 7G9  7G9  ~{N}-[3-[[5-fluoranyl-2-[[4-(2-methoxyethoxy)phenyl]amino]pyrimidin-4-yl]amino]phenyl]propanamide  ligand  55  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7G9
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
 7G9  C1   C  CR6   0   0.312  -1.5599   3.8744  -0.0923
 7G9  C2   C  CR16  0  -0.118  -0.2047   3.9740  -0.1333
 7G9  C8   C  CR6   0   0.357   2.0639   0.3351  -0.0957
 7G9  C9   C  CR16  0  -0.312   2.4678  -1.0033  -0.0188
 7G9  C10  C  CR16  0  -0.314   3.8006  -1.3522   0.0077
 7G9  C11  C  CR6   0   0.375   4.7911  -0.3707  -0.0402
 7G9  C12  C  CR16  0  -0.355   4.4001   0.9584  -0.1278
 7G9  C13  C  CR16  0  -0.289   3.0534   1.3107  -0.1550
 7G9  C15  C  CH2   0  -0.198   7.1068   0.1545  -0.0057
 7G9  C16  C  CH2   0  -0.142   8.4224  -0.5554   0.1737
 7G9  O17  O  O2    0  -0.470   8.6826  -1.3694  -0.9371
 7G9  C20  C  CR6   0   0.407  -4.3336   1.3777   0.0064
 7G9  C21  C  CR16  0  -0.428  -3.8984   0.0586  -0.0114
 7G9  C22  C  CR6   0   0.430  -4.8187  -0.9937   0.0166
 7G9  C24  C  CR16  0  -0.209  -6.6025   0.5953   0.0814
 7G9  N26  N  NH1   0  -0.746  -4.2742  -2.2779  -0.0043
 7G9  C27  C  C     0   0.558  -4.9004  -3.4926   0.0166
 7G9  N3   N  N     0  -0.480   0.5862   2.8972  -0.1426
 7G9  C4   C  CR6   0   0.639  -0.0291   1.7282  -0.1081
 7G9  N5   N  N     0  -0.536  -1.3550   1.5315  -0.0699
 7G9  C6   C  CR6   0   0.464  -2.1396   2.5895  -0.0612
 7G9  N7   N  NH1   0  -0.766   0.6904   0.5734  -0.1101
 7G9  O14  O  O2    0  -0.469   6.0697  -0.8023   0.0070
 7G9  C18  C  CH3   0  -0.373   9.8848  -2.0767  -0.8144
 7G9  N19  N  NH1   0  -0.784  -3.4898   2.4868  -0.0225
 7G9  C23  C  CR16  0  -0.332  -6.1859  -0.7284   0.0630
 7G9  C25  C  CR16  0  -0.359  -5.7056   1.6434   0.0543
 7G9  C28  C  CH2   0  -0.582  -3.9299  -4.6594  -0.0366
 7G9  C29  C  CH3   0  -0.638  -4.6054  -6.0048   0.1541
 7G9  O30  O  O     0  -0.417  -6.1010  -3.6367   0.0638
 7G9  F31  F  F     0  -0.304  -2.3571   4.9568  -0.0820
 7G9  H1   H  HCR6  0   0.269   0.2736   4.9467  -0.1612
 7G9  H2   H  HCR6  0   0.229   1.7268  -1.7926   0.0235
 7G9  H3   H  HCR6  0   0.244   4.0808  -2.3957   0.0708
 7G9  H4   H  HCR6  0   0.256   5.1243   1.7594  -0.1762
 7G9  H5   H  HCR6  0   0.282   2.7881   2.3526  -0.2198
 7G9  H6   H  HCH2  0   0.218   6.9934   0.8723   0.8147
 7G9  H7   H  HCH2  0   0.218   7.1088   0.7219  -0.9440
 7G9  H8   H  HCH2  0   0.202   9.2006   0.2111   0.2990
 7G9  H9   H  HCH2  0   0.201   8.4041  -1.1418   1.1039
 7G9  H10  H  HCR6  0   0.272  -2.8400  -0.1469  -0.0481
 7G9  H11  H  HCR6  0   0.242  -7.6622   0.8094   0.1182
 7G9  H12  H  HNH1  0   0.377  -3.2684  -2.3063  -0.0373
 7G9  H13  H  HNH1  0   0.375   0.1109  -0.2474  -0.0665
 7G9  H14  H  HCH3  0   0.193   9.8875  -2.7386   0.0604
 7G9  H15  H  HCH3  0   0.223  10.0086  -2.6883  -1.7075
 7G9  H16  H  HCH3  0   0.192  10.7538  -1.4117  -0.7304
 7G9  H17  H  HNH1  0   0.392  -3.9745   3.3690  -0.0090
 7G9  H18  H  HCR6  0   0.288  -6.9102  -1.5240   0.0851
 7G9  H19  H  HCR6  0   0.226  -6.0668   2.6650   0.0703
 7G9  H20  H  HCH2  0   0.253  -3.4119  -4.6282  -1.0010
 7G9  H21  H  HCH3  0   0.233  -5.0961  -6.0697   1.1238
 7G9  H22  H  HCH3  0   0.237  -5.3601  -6.1853  -0.6089
 7G9  H23  H  HCH2  0   0.240  -3.1559  -4.5132   0.7230
 7G9  H24  H  HCH3  0   0.220  -3.8699  -6.8061   0.0951

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
 7G9  F31  C1   single    1.344  0.020  1.344
 7G9  N19  C20  single    1.394  0.020  1.394
 7G9  N19  C6   single    1.355  0.020  1.355
 7G9  C21  C20  aromatic  1.389  0.020  1.389
 7G9  C21  C22  aromatic  1.398  0.020  1.398
 7G9  C20  C25  aromatic  1.398  0.020  1.398
 7G9  C1   C6   aromatic  1.410  0.020  1.410
 7G9  C1   C2   aromatic  1.359  0.020  1.359
 7G9  N26  C22  single    1.395  0.020  1.395
 7G9  N26  C27  single    1.367  0.020  1.367
 7G9  C22  C23  aromatic  1.394  0.020  1.394
 7G9  C6   N5   aromatic  1.317  0.020  1.317
 7G9  C25  C24  aromatic  1.380  0.020  1.380
 7G9  C2   N3   aromatic  1.336  0.020  1.336
 7G9  C28  C27  single    1.519  0.020  1.519
 7G9  C28  C29  single    1.518  0.020  1.518
 7G9  C23  C24  aromatic  1.388  0.020  1.388
 7G9  C27  O30  double    1.210  0.020  1.210
 7G9  N5   C4   aromatic  1.341  0.020  1.341
 7G9  N3   C4   aromatic  1.321  0.020  1.321
 7G9  C4   N7   single    1.361  0.020  1.361
 7G9  N7   C8   single    1.394  0.020  1.394
 7G9  C13  C8   aromatic  1.391  0.020  1.391
 7G9  C13  C12  aromatic  1.392  0.020  1.392
 7G9  C8   C9   aromatic  1.400  0.020  1.400
 7G9  C12  C11  aromatic  1.388  0.020  1.388
 7G9  C9   C10  aromatic  1.378  0.020  1.378
 7G9  C16  C15  single    1.506  0.020  1.506
 7G9  C16  O17  single    1.402  0.020  1.402
 7G9  C11  C10  aromatic  1.395  0.020  1.395
 7G9  C11  O14  single    1.350  0.020  1.350
 7G9  C15  O14  single    1.411  0.020  1.411
 7G9  O17  C18  single    1.400  0.020  1.400
 7G9  C2   H1   single    0.930  0.020  1.080
 7G9  C9   H2   single    0.930  0.020  1.080
 7G9  C10  H3   single    0.930  0.020  1.080
 7G9  C12  H4   single    0.930  0.020  1.080
 7G9  C13  H5   single    0.930  0.020  1.080
 7G9  C15  H6   single    0.970  0.020  1.090
 7G9  C15  H7   single    0.970  0.020  1.090
 7G9  C16  H8   single    0.970  0.020  1.090
 7G9  C16  H9   single    0.970  0.020  1.090
 7G9  C21  H10  single    0.930  0.020  1.080
 7G9  C24  H11  single    0.930  0.020  1.080
 7G9  N26  H12  single    0.860  0.020  1.020
 7G9  N7   H13  single    0.860  0.020  1.020
 7G9  C18  H14  single    0.970  0.020  1.090
 7G9  C18  H15  single    0.970  0.020  1.090
 7G9  C18  H16  single    0.970  0.020  1.090
 7G9  N19  H17  single    0.860  0.020  1.020
 7G9  C23  H18  single    0.930  0.020  1.080
 7G9  C25  H19  single    0.930  0.020  1.080
 7G9  C28  H20  single    0.970  0.020  1.090
 7G9  C29  H21  single    0.970  0.020  1.090
 7G9  C29  H22  single    0.970  0.020  1.090
 7G9  C28  H23  single    0.970  0.020  1.090
 7G9  C29  H24  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
 7G9  F31  C1   C6   119.33  3.000
 7G9  C6   C1   C2   118.51  3.000
 7G9  F31  C1   C2   122.16  3.000
 7G9  H1   C2   N3   117.49  3.000
 7G9  H1   C2   C1   120.42  3.000
 7G9  N3   C2   C1   122.09  3.000
 7G9  N7   C8   C13  125.49  3.000
 7G9  C13  C8   C9   117.88  3.000
 7G9  N7   C8   C9   116.63  3.000
 7G9  H2   C9   C10  118.45  3.000
 7G9  H2   C9   C8   120.08  3.000
 7G9  C10  C9   C8   121.48  3.000
 7G9  H3   C10  C11  119.77  3.000
 7G9  H3   C10  C9   119.71  3.000
 7G9  C11  C10  C9   120.52  3.000
 7G9  O14  C11  C12  125.10  3.000
 7G9  O14  C11  C10  116.50  3.000
 7G9  C12  C11  C10  118.41  3.000
 7G9  H4   C12  C13  117.37  3.000
 7G9  H4   C12  C11  121.57  3.000
 7G9  C13  C12  C11  121.06  3.000
 7G9  H5   C13  C12  118.96  3.000
 7G9  H5   C13  C8   120.38  3.000
 7G9  C12  C13  C8   120.65  3.000
 7G9  H7   C15  H6   107.57  3.000
 7G9  H7   C15  O14  111.09  3.000
 7G9  H6   C15  O14  111.18  3.000
 7G9  H7   C15  C16  110.14  3.000
 7G9  H6   C15  C16  108.06  3.000
 7G9  O14  C15  C16  108.75  3.000
 7G9  H9   C16  H8   106.69  3.000
 7G9  H9   C16  O17  111.33  3.000
 7G9  H8   C16  O17  111.34  3.000
 7G9  H9   C16  C15  109.73  3.000
 7G9  H8   C16  C15  107.66  3.000
 7G9  O17  C16  C15  109.97  3.000
 7G9  C18  O17  C16  112.54  3.000
 7G9  C25  C20  N19  116.33  3.000
 7G9  C25  C20  C21  119.23  3.000
 7G9  N19  C20  C21  124.45  3.000
 7G9  H10  C21  C22  120.20  3.000
 7G9  H10  C21  C20  119.26  3.000
 7G9  C22  C21  C20  120.54  3.000
 7G9  C23  C22  N26  123.97  3.000
 7G9  C23  C22  C21  120.20  3.000
 7G9  N26  C22  C21  115.83  3.000
 7G9  H11  C24  C25  119.15  3.000
 7G9  H11  C24  C23  118.91  3.000
 7G9  C25  C24  C23  121.95  3.000
 7G9  H12  N26  C27  115.67  3.000
 7G9  H12  N26  C22  114.61  3.000
 7G9  C27  N26  C22  129.72  3.000
 7G9  O30  C27  C28  122.95  3.000
 7G9  O30  C27  N26  124.12  3.000
 7G9  C28  C27  N26  112.92  3.000
 7G9  C4   N3   C2   115.92  3.000
 7G9  N7   C4   N5   113.48  3.000
 7G9  N7   C4   N3   120.30  3.000
 7G9  N5   C4   N3   126.22  3.000
 7G9  C6   N5   C4   118.12  3.000
 7G9  N19  C6   N5   122.21  3.000
 7G9  N5   C6   C1   119.14  3.000
 7G9  N19  C6   C1   118.66  3.000
 7G9  H13  N7   C4   112.83  3.000
 7G9  H13  N7   C8   115.32  3.000
 7G9  C4   N7   C8   131.76  3.000
 7G9  C15  O14  C11  118.61  3.000
 7G9  H16  C18  H15  108.23  3.000
 7G9  H16  C18  H14  107.62  3.000
 7G9  H15  C18  H14  108.35  3.000
 7G9  H16  C18  O17  112.36  3.000
 7G9  H15  C18  O17  108.02  3.000
 7G9  H14  C18  O17  112.13  3.000
 7G9  H17  N19  C6   114.44  3.000
 7G9  H17  N19  C20  113.93  3.000
 7G9  C6   N19  C20  131.63  3.000
 7G9  H18  C23  C24  120.19  3.000
 7G9  H18  C23  C22  121.35  3.000
 7G9  C24  C23  C22  118.46  3.000
 7G9  H19  C25  C24  119.94  3.000
 7G9  H19  C25  C20  120.45  3.000
 7G9  C24  C25  C20  119.61  3.000
 7G9  H23  C28  H20  105.84  3.000
 7G9  H23  C28  C29  110.25  3.000
 7G9  H20  C28  C29  110.27  3.000
 7G9  H23  C28  C27  108.96  3.000
 7G9  H20  C28  C27  108.14  3.000
 7G9  C29  C28  C27  113.10  3.000
 7G9  H24  C29  H22  107.96  3.000
 7G9  H24  C29  H21  107.98  3.000
 7G9  H22  C29  H21  107.58  3.000
 7G9  H24  C29  C28  110.17  3.000
 7G9  H22  C29  C28  111.57  3.000
 7G9  H21  C29  C28  111.43  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
 7G9  CONST_01  C4   N5   C6   C1      0.00   0.0  0
 7G9  CONST_02  C4   N3   C2   C1      0.00   0.0  0
 7G9  CONST_03  N5   C6   C1   C2      0.00   0.0  0
 7G9  CONST_04  N5   C4   N3   C2      0.00   0.0  0
 7G9  CONST_05  C11  C12  C13  C8      0.00   0.0  0
 7G9  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 7G9  CONST_07  C12  C13  C8   C9      0.00   0.0  0
 7G9  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 7G9  CONST_09  C13  C8   C9   C10     0.00   0.0  0
 7G9  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 7G9  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 7G9  CONST_12  C23  C24  C25  C20     0.00   0.0  0
 7G9  CONST_13  C24  C25  C20  C21     0.00   0.0  0
 7G9  CONST_14  C24  C23  C22  C21     0.00   0.0  0
 7G9  CONST_15  C25  C20  C21  C22     0.00   0.0  0
 7G9  CONST_16  C25  C24  C23  C22     0.00   0.0  0
 7G9  CONST_17  C6   C1   C2   N3      0.00   0.0  0
 7G9  CONST_18  C6   N5   C4   N3      0.00   0.0  0
 7G9  CONST_19  N19  C6   C1   C2    180.00   0.0  0
 7G9  CONST_20  N7   C4   N3   C2    180.00   0.0  0
 7G9  CONST_21  O14  C11  C10  C9    180.00   0.0  0
 7G9  CONST_22  N7   C8   C9   C10   180.00   0.0  0
 7G9  CONST_23  N7   C8   C13  C12   180.00   0.0  0
 7G9  CONST_24  O14  C11  C12  C13   180.00   0.0  0
 7G9  CONST_25  N26  C22  C21  C20   180.00   0.0  0
 7G9  CONST_26  N19  C20  C21  C22   180.00   0.0  0
 7G9  CONST_27  N19  C20  C25  C24   180.00   0.0  0
 7G9  CONST_28  N26  C22  C23  C24   180.00   0.0  0
 7G9  CONST_29  F31  C1   C2   N3    180.00   0.0  0
 7G9  CONST_30  N19  C6   N5   C4    180.00   0.0  0
 7G9  CONST_31  F31  C1   C6   N5    180.00   0.0  0
 7G9  CONST_32  N7   C4   N5   C6    180.00   0.0  0
 7G9  CONST_33  H4   C12  C13  C8    180.00   0.0  0
 7G9  CONST_34  H3   C10  C9   C8    180.00   0.0  0
 7G9  CONST_35  H5   C13  C8   C9    180.00   0.0  0
 7G9  CONST_36  H2   C9   C10  C11   180.00   0.0  0
 7G9  CONST_37  H11  C24  C25  C20   180.00   0.0  0
 7G9  CONST_38  H19  C25  C20  C21   180.00   0.0  0
 7G9  CONST_39  H18  C23  C22  C21   180.00   0.0  0
 7G9  CONST_40  H1   C2   N3   C4    180.00   0.0  0
 7G9  CONST_41  H10  C21  C22  C23   180.00   0.0  0
 7G9  CONST_42  C27  N26  C22  C21   180.00   0.0  0
 7G9  CONST_43  C23  C22  N26  C27     0.00   0.0  0
 7G9  CONST_44  H12  N26  C22  C21     0.00   0.0  0
 7G9  CONST_45  C28  C27  N26  C22   180.00   0.0  0
 7G9  CONST_46  O30  C27  N26  C22     0.00   0.0  0
 7G9  Var_01    C20  N19  C6   C1    179.59  30.0  2
 7G9  Var_02    N5   C4   N7   C8   -177.39  30.0  1
 7G9  Var_03    C4   N7   C8   C9    176.14  30.0  3
 7G9  Var_04    C6   N19  C20  C21    -0.57  30.0  3
 7G9  Var_05    C16  C15  O14  C11   175.16  30.0  2
 7G9  Var_06    O14  C15  C16  O17    66.13  30.0  3
 7G9  Var_07    C29  C28  C27  N26   173.08  30.0  2
 7G9  Var_08    H14  C18  O17  C16    60.17  30.0  3
 7G9  Var_09    H21  C29  C28  C27   -60.87  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
 7G9  plan-1  C1   0.020
 7G9  plan-1  C2   0.020
 7G9  plan-1  N3   0.020
 7G9  plan-1  C4   0.020
 7G9  plan-1  N5   0.020
 7G9  plan-1  C6   0.020
 7G9  plan-1  N7   0.020
 7G9  plan-1  N19  0.020
 7G9  plan-1  F31  0.020
 7G9  plan-1  H1   0.020
 7G9  plan-2  C8   0.020
 7G9  plan-2  C9   0.020
 7G9  plan-2  C10  0.020
 7G9  plan-2  C11  0.020
 7G9  plan-2  C12  0.020
 7G9  plan-2  C13  0.020
 7G9  plan-2  N7   0.020
 7G9  plan-2  O14  0.020
 7G9  plan-2  H2   0.020
 7G9  plan-2  H3   0.020
 7G9  plan-2  H4   0.020
 7G9  plan-2  H5   0.020
 7G9  plan-3  C20  0.020
 7G9  plan-3  C21  0.020
 7G9  plan-3  C22  0.020
 7G9  plan-3  C24  0.020
 7G9  plan-3  N26  0.020
 7G9  plan-3  N19  0.020
 7G9  plan-3  C23  0.020
 7G9  plan-3  C25  0.020
 7G9  plan-3  H10  0.020
 7G9  plan-3  H11  0.020
 7G9  plan-3  H18  0.020
 7G9  plan-3  H19  0.020
 7G9  plan-4  C22  0.020
 7G9  plan-4  N26  0.020
 7G9  plan-4  C27  0.020
 7G9  plan-4  C28  0.020
 7G9  plan-4  O30  0.020
 7G9  plan-4  H12  0.020

