# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:16:40 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-[[5-[3-(dimethylamino)phenoxy]pyrimidin-2-yl]amino]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc(Oc2cnc(Nc3cccc(O)c3)nc2)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
 S1W  S1W  3-[[5-[3-(dimethylamino)phenoxy]pyrimidin-2-yl]amino]phenol  ligand  42  24  .  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_S1W
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
 S1W  N1   N  NT    0  -0.507  37.2222   0.7746  45.1295
 S1W  N3   N  N     0  -0.448  42.3564   1.4119  41.7049
 S1W  C4   C  CR16  0  -0.374  38.0088   2.2741  46.8760
 S1W  C5   C  CR16  0  -0.381  40.2886   3.0993  46.8227
 S1W  C6   C  CR16  0  -0.231  39.0354   3.0295  47.4130
 S1W  C7   C  CH3   0  -0.531  35.8166   0.9850  45.3966
 S1W  C8   C  CH3   0  -0.548  37.4998  -0.0225  43.9601
 S1W  C10  C  CR6   0   0.140  42.0638   1.6902  44.0365
 S1W  C13  C  CR16  0  -0.382  43.8902  -2.2576  39.4165
 S1W  C15  C  CR16  0  -0.026  42.5484   0.4077  44.2102
 S1W  C17  C  CR16  0  -0.234  44.3912  -3.5255  39.1842
 S1W  C1   C  CR6   0   0.424  38.2057   1.5483  45.6856
 S1W  C11  C  CR6   0   0.610  42.8072   0.1809  41.9739
 S1W  C12  C  CR16  0  -0.477  43.9564  -2.6847  41.7896
 S1W  C14  C  CR16  0  -0.056  41.9874   2.1533  42.7299
 S1W  C16  C  CR6   0   0.401  44.4606  -3.9575  41.5307
 S1W  C18  C  CR16  0  -0.368  44.6825  -4.3910  40.2279
 S1W  C2   C  CR16  0  -0.479  39.4771   1.6192  45.0828
 S1W  C3   C  CR6   0   0.404  40.4874   2.3787  45.6538
 S1W  C9   C  CR6   0   0.382  43.6672  -1.8249  40.7296
 S1W  N2   N  NH1   0  -0.770  43.1654  -0.5372  40.8748
 S1W  N4   N  N     0  -0.455  42.9200  -0.3471  43.1880
 S1W  O1   O  O2    0  -0.511  41.7332   2.4848  45.0932
 S1W  H4   H  HCR6  0   0.257  37.0660   2.2415  47.4022
 S1W  H5   H  HCR6  0   0.257  41.0857   3.6893  47.2542
 S1W  H6   H  HCR6  0   0.255  38.8548   3.5725  48.3321
 S1W  H8   H  HCH3  0   0.252  35.6563   1.7593  46.1393
 S1W  H9   H  HCH3  0   0.237  35.2933   1.2981  44.4887
 S1W  H7   H  HCH3  0   0.237  35.3421   0.0707  45.7592
 S1W  H10  H  HCH3  0   0.262  36.6633  -0.6974  43.7878
 S1W  H11  H  HCH3  0   0.228  37.6371   0.5780  43.0531
 S1W  H12  H  HCH3  0   0.243  38.3876  -0.6413  44.0971
 S1W  H14  H  HCR6  0   0.264  43.6710  -1.5999  38.5845
 S1W  H16  H  HCR6  0   0.291  42.6461  -0.0224  45.2020
 S1W  H17  H  HCR6  0   0.259  44.5579  -3.8480  38.1647
 S1W  H13  H  HCR6  0   0.299  43.7915  -2.3668  42.8082
 S1W  H15  H  HCR6  0   0.294  41.6236   3.1533  42.5159
 S1W  H18  H  HCR6  0   0.259  45.0746  -5.3816  40.0382
 S1W  H3   H  HCR6  0   0.273  39.6643   1.0994  44.1547
 S1W  H2   H  HNH1  0   0.411  43.0254  -0.0329  40.0120
 S1W  H1   H  HOH1  0   0.473  44.5601  -4.4060  43.3860
 S1W  O2   O  OH1   0  -0.637  44.7511  -4.8115  42.5329

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
 S1W  C17  C13  aromatic  1.383  0.020  1.383
 S1W  C17  C18  aromatic  1.387  0.020  1.387
 S1W  C13  C9   aromatic  1.400  0.020  1.400
 S1W  C18  C16  aromatic  1.391  0.020  1.391
 S1W  C9   N2   single    1.390  0.020  1.390
 S1W  C9   C12  aromatic  1.395  0.020  1.395
 S1W  N2   C11  single    1.361  0.020  1.361
 S1W  N3   C11  aromatic  1.338  0.020  1.338
 S1W  N3   C14  aromatic  1.318  0.020  1.318
 S1W  C11  N4   aromatic  1.329  0.020  1.329
 S1W  C16  C12  aromatic  1.393  0.020  1.393
 S1W  C16  O2   single    1.348  0.020  1.348
 S1W  C14  C10  aromatic  1.388  0.020  1.388
 S1W  N4   C15  aromatic  1.324  0.020  1.324
 S1W  C10  C15  aromatic  1.382  0.020  1.382
 S1W  C10  O1   single    1.363  0.020  1.363
 S1W  C8   N1   single    1.442  0.020  1.442
 S1W  O1   C3   single    1.370  0.020  1.370
 S1W  C2   C3   aromatic  1.387  0.020  1.387
 S1W  C2   C1   aromatic  1.409  0.020  1.409
 S1W  C3   C5   aromatic  1.387  0.020  1.387
 S1W  N1   C1   single    1.369  0.020  1.369
 S1W  N1   C7   single    1.446  0.020  1.446
 S1W  C1   C4   aromatic  1.408  0.020  1.408
 S1W  C5   C6   aromatic  1.387  0.020  1.387
 S1W  C4   C6   aromatic  1.383  0.020  1.383
 S1W  C4   H4   single    0.930  0.020  1.080
 S1W  C5   H5   single    0.930  0.020  1.080
 S1W  C6   H6   single    0.930  0.020  1.080
 S1W  C7   H8   single    0.970  0.020  1.090
 S1W  C7   H9   single    0.970  0.020  1.090
 S1W  C7   H7   single    0.970  0.020  1.090
 S1W  C8   H10  single    0.970  0.020  1.090
 S1W  C8   H11  single    0.970  0.020  1.090
 S1W  C8   H12  single    0.970  0.020  1.090
 S1W  C13  H14  single    0.930  0.020  1.080
 S1W  C15  H16  single    0.930  0.020  1.080
 S1W  C17  H17  single    0.930  0.020  1.080
 S1W  C12  H13  single    0.930  0.020  1.080
 S1W  C14  H15  single    0.930  0.020  1.080
 S1W  C18  H18  single    0.930  0.020  1.080
 S1W  C2   H3   single    0.930  0.020  1.080
 S1W  N2   H2   single    0.860  0.020  1.020
 S1W  O2   H1   single    0.850  0.020  0.980

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
 S1W  C1   N1   C8   120.22  3.000
 S1W  C1   N1   C7   122.75  3.000
 S1W  C8   N1   C7   114.66  3.000
 S1W  C14  N3   C11  117.10  3.000
 S1W  H4   C4   C1   121.22  3.000
 S1W  H4   C4   C6   118.37  3.000
 S1W  C1   C4   C6   120.40  3.000
 S1W  H5   C5   C3   120.92  3.000
 S1W  H5   C5   C6   121.58  3.000
 S1W  C3   C5   C6   117.51  3.000
 S1W  H6   C6   C5   119.12  3.000
 S1W  H6   C6   C4   118.67  3.000
 S1W  C5   C6   C4   122.20  3.000
 S1W  H7   C7   H9   107.90  3.000
 S1W  H7   C7   H8   107.82  3.000
 S1W  H9   C7   H8   107.05  3.000
 S1W  H7   C7   N1   111.21  3.000
 S1W  H9   C7   N1   110.69  3.000
 S1W  H8   C7   N1   111.96  3.000
 S1W  H12  C8   H11  108.21  3.000
 S1W  H12  C8   H10  107.08  3.000
 S1W  H11  C8   H10  107.75  3.000
 S1W  H12  C8   N1   111.61  3.000
 S1W  H11  C8   N1   113.09  3.000
 S1W  H10  C8   N1   108.86  3.000
 S1W  O1   C10  C14  121.46  3.000
 S1W  O1   C10  C15  121.91  3.000
 S1W  C14  C10  C15  116.56  3.000
 S1W  H14  C13  C9   120.03  3.000
 S1W  H14  C13  C17  120.07  3.000
 S1W  C9   C13  C17  119.90  3.000
 S1W  H16  C15  N4   117.03  3.000
 S1W  H16  C15  C10  120.94  3.000
 S1W  N4   C15  C10  122.03  3.000
 S1W  H17  C17  C18  119.38  3.000
 S1W  H17  C17  C13  119.16  3.000
 S1W  C18  C17  C13  121.46  3.000
 S1W  C2   C1   C4   117.52  3.000
 S1W  C4   C1   N1   122.28  3.000
 S1W  C2   C1   N1   120.19  3.000
 S1W  N4   C11  N2   120.40  3.000
 S1W  N4   C11  N3   125.29  3.000
 S1W  N2   C11  N3   114.31  3.000
 S1W  H13  C12  C9   120.24  3.000
 S1W  H13  C12  C16  119.97  3.000
 S1W  C9   C12  C16  119.79  3.000
 S1W  H15  C14  C10  120.75  3.000
 S1W  H15  C14  N3   117.31  3.000
 S1W  C10  C14  N3   121.93  3.000
 S1W  O2   C16  C18  117.67  3.000
 S1W  O2   C16  C12  121.23  3.000
 S1W  C18  C16  C12  121.10  3.000
 S1W  H18  C18  C16  120.48  3.000
 S1W  H18  C18  C17  121.03  3.000
 S1W  C16  C18  C17  118.49  3.000
 S1W  H3   C2   C3   119.41  3.000
 S1W  H3   C2   C1   119.99  3.000
 S1W  C3   C2   C1   120.58  3.000
 S1W  O1   C3   C2   122.43  3.000
 S1W  C2   C3   C5   121.79  3.000
 S1W  O1   C3   C5   115.77  3.000
 S1W  N2   C9   C12  124.51  3.000
 S1W  C12  C9   C13  119.27  3.000
 S1W  N2   C9   C13  116.22  3.000
 S1W  H2   N2   C9   115.08  3.000
 S1W  H2   N2   C11  112.97  3.000
 S1W  C9   N2   C11  131.94  3.000
 S1W  C11  N4   C15  117.08  3.000
 S1W  C3   O1   C10  119.51  3.000
 S1W  H1   O2   C16  110.41  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
 S1W  CONST_01  C15  N4   C11  N3      0.00   0.0  0
 S1W  CONST_02  C15  C10  C14  N3      0.00   0.0  0
 S1W  CONST_03  C3   C2   C1   C4      0.00   0.0  0
 S1W  CONST_04  C3   C5   C6   C4      0.00   0.0  0
 S1W  CONST_05  C1   C2   C3   C5      0.00   0.0  0
 S1W  CONST_06  C1   C4   C6   C5      0.00   0.0  0
 S1W  CONST_07  C2   C3   C5   C6      0.00   0.0  0
 S1W  CONST_08  C2   C1   C4   C6      0.00   0.0  0
 S1W  CONST_09  C11  N3   C14  C10     0.00   0.0  0
 S1W  CONST_10  C11  N4   C15  C10     0.00   0.0  0
 S1W  CONST_11  C16  C18  C17  C13     0.00   0.0  0
 S1W  CONST_12  C16  C12  C9   C13     0.00   0.0  0
 S1W  CONST_13  C12  C9   C13  C17     0.00   0.0  0
 S1W  CONST_14  C12  C16  C18  C17     0.00   0.0  0
 S1W  CONST_15  N4   C11  N3   C14     0.00   0.0  0
 S1W  CONST_16  N4   C15  C10  C14     0.00   0.0  0
 S1W  CONST_17  C9   C13  C17  C18     0.00   0.0  0
 S1W  CONST_18  C9   C12  C16  C18     0.00   0.0  0
 S1W  CONST_19  C3   C2   C1   N1    180.00   0.0  0
 S1W  CONST_20  C6   C4   C1   N1    180.00   0.0  0
 S1W  CONST_21  O1   C10  C14  N3    180.00   0.0  0
 S1W  CONST_22  O1   C3   C5   C6    180.00   0.0  0
 S1W  CONST_23  N2   C11  N4   C15   180.00   0.0  0
 S1W  CONST_24  N2   C9   C13  C17   180.00   0.0  0
 S1W  CONST_25  O2   C16  C18  C17   180.00   0.0  0
 S1W  CONST_26  O1   C3   C2   C1    180.00   0.0  0
 S1W  CONST_27  N2   C11  N3   C14   180.00   0.0  0
 S1W  CONST_28  N2   C9   C12  C16   180.00   0.0  0
 S1W  CONST_29  O2   C16  C12  C9    180.00   0.0  0
 S1W  CONST_30  O1   C10  C15  N4    180.00   0.0  0
 S1W  CONST_31  H3   C2   C1   C4    180.00   0.0  0
 S1W  CONST_32  H5   C5   C6   C4    180.00   0.0  0
 S1W  CONST_33  H4   C4   C6   C5    180.00   0.0  0
 S1W  CONST_34  H18  C18  C17  C13   180.00   0.0  0
 S1W  CONST_35  H13  C12  C9   C13   180.00   0.0  0
 S1W  CONST_36  H15  C14  C10  C15   180.00   0.0  0
 S1W  CONST_37  H6   C6   C4   C1    180.00   0.0  0
 S1W  CONST_38  H16  C15  N4   C11   180.00   0.0  0
 S1W  CONST_39  H14  C13  C9   C12   180.00   0.0  0
 S1W  CONST_40  H17  C17  C18  C16   180.00   0.0  0
 S1W  CONST_41  C8   N1   C1   C4    180.00   0.0  0
 S1W  CONST_44  C2   C1   N1   C8      0.00   0.0  0
 S1W  Var_01    C9   N2   C11  N3   -179.89  30.0  1
 S1W  Var_02    C2   C3   O1   C10    -8.75  30.0  2
 S1W  Var_03    C11  N2   C9   C13   178.18  30.0  2
 S1W  Var_04    H10  C8   N1   C1    169.43  30.0  3
 S1W  Var_05    H8   C7   N1   C1     -4.73  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
 S1W  plan-1  N3   0.020
 S1W  plan-1  C10  0.020
 S1W  plan-1  C15  0.020
 S1W  plan-1  C11  0.020
 S1W  plan-1  C14  0.020
 S1W  plan-1  N2   0.020
 S1W  plan-1  N4   0.020
 S1W  plan-1  O1   0.020
 S1W  plan-1  H16  0.020
 S1W  plan-1  H15  0.020
 S1W  plan-2  C13  0.020
 S1W  plan-2  C17  0.020
 S1W  plan-2  C12  0.020
 S1W  plan-2  C16  0.020
 S1W  plan-2  C18  0.020
 S1W  plan-2  C9   0.020
 S1W  plan-2  N2   0.020
 S1W  plan-2  H14  0.020
 S1W  plan-2  H17  0.020
 S1W  plan-2  H13  0.020
 S1W  plan-2  H18  0.020
 S1W  plan-2  O2   0.020
 S1W  plan-3  N1   0.020
 S1W  plan-3  C4   0.020
 S1W  plan-3  C5   0.020
 S1W  plan-3  C6   0.020
 S1W  plan-3  C1   0.020
 S1W  plan-3  C2   0.020
 S1W  plan-3  C3   0.020
 S1W  plan-3  O1   0.020
 S1W  plan-3  H4   0.020
 S1W  plan-3  H5   0.020
 S1W  plan-3  H6   0.020
 S1W  plan-3  H3   0.020
 S1W  plan-4  N1   0.020
 S1W  plan-4  C7   0.020
 S1W  plan-4  C8   0.020
 S1W  plan-4  C1   0.020

