# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:30:08 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-[(4-{[2-(trifluoromethoxy)phenyl]amino}pyrimidin-2-yl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2nccc(Nc3ccccc3OC(F)(F)F)n2)cc1
#
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
 0C8  0C8  '4-[(4-{[2-(trifluoromethoxy)phenyl]amino}pyrimidin-2-yl)amino]benzoic acid'  ligand  41  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0C8
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
 0C8  N01  N  N     0  -0.491  -1.4622  -2.0299   0.6638
 0C8  N02  N  N     0  -0.513   0.1596  -0.2986   0.6456
 0C8  N03  N  NH1   0  -0.767   2.3821  -0.7155   1.1261
 0C8  N04  N  NH1   0  -0.769  -1.9903   0.1900   0.1725
 0C8  C05  C  CR16  0   0.007  -0.4897  -2.8873   0.9880
 0C8  C06  C  CR6   0   0.614  -1.0786  -0.7739   0.5090
 0C8  C07  C  CR6   0   0.561   1.1071  -1.1576   0.9746
 0C8  C08  C  CR16  0  -0.453   0.8193  -2.5241   1.1623
 0C8  C09  C  CR6   0   0.305   2.8449   0.5938   0.9892
 0C8  C10  C  CR16  0  -0.284   2.1585   1.6976   1.4952
 0C8  C11  C  CR16  0  -0.252   2.6906   2.9709   1.3750
 0C8  C12  C  CR16  0  -0.267   3.9282   3.1701   0.7786
 0C8  C13  C  CR16  0  -0.298   4.6317   2.0835   0.2837
 0C8  C14  C  CR6   0   0.252   4.0790   0.8191   0.3764
 0C8  C15  C  CT    0   1.079   4.6815  -0.5840  -1.3929
 0C8  C16  C  CR6   0   0.382  -3.3493   0.1331  -0.0545
 0C8  C17  C  CR16  0  -0.346  -3.9721   1.3410  -0.4055
 0C8  C18  C  CR16  0  -0.249  -5.3263   1.3998  -0.6496
 0C8  C19  C  CR6   0  -0.104  -6.1149   0.2509  -0.5528
 0C8  C20  C  CR16  0  -0.246  -5.4952  -0.9468  -0.2044
 0C8  C21  C  CR16  0  -0.302  -4.1370  -1.0205   0.0428
 0C8  C22  C  C     0   0.524  -7.5686   0.2564  -0.8002
 0C8  O23  O  O     0  -0.449  -8.2742  -0.7233  -0.7186
 0C8  O24  O  OH1   0  -0.599  -8.0389   1.4561  -1.1248
 0C8  O25  O  O2    0  -0.521   4.7948  -0.2781  -0.0907
 0C8  F26  F  F     0  -0.296   5.1806   0.3629  -2.1883
 0C8  F27  F  F     0  -0.274   5.3583  -1.7009  -1.6009
 0C8  F28  F  F     0  -0.296   3.4174  -0.7769  -1.7694
 0C8  H1   H  HNH1  0   0.412   3.0781  -1.4297   1.2740
 0C8  H2   H  HNH1  0   0.411  -1.5737   1.1046   0.0785
 0C8  H3   H  HCR6  0   0.273  -0.7882  -3.9215   1.1153
 0C8  H4   H  HCR6  0   0.281   1.5809  -3.2444   1.4252
 0C8  H5   H  HCR6  0   0.278   1.2091   1.5568   1.9883
 0C8  H6   H  HCR6  0   0.268   2.1394   3.8128   1.7722
 0C8  H7   H  HCR6  0   0.269   4.3484   4.1633   0.7016
 0C8  H8   H  HCR6  0   0.281   5.6064   2.2183  -0.1658
 0C8  H9   H  HCR6  0   0.274  -3.3782   2.2438  -0.4863
 0C8  H10  H  HCR6  0   0.267  -5.7605   2.3528  -0.9175
 0C8  H11  H  HCR6  0   0.264  -6.0850  -1.8503  -0.1209
 0C8  H12  H  HCR6  0   0.291  -3.6902  -1.9627   0.3116
 0C8  H13  H  HOH1  0   0.485  -8.9949   1.4040  -1.2704

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
 0C8  O23  C22  double    1.210  0.020  1.210
 0C8  O24  C22  single    1.329  0.020  1.329
 0C8  C22  C19  single    1.475  0.020  1.475
 0C8  C12  C11  aromatic  1.388  0.020  1.388
 0C8  C12  C13  aromatic  1.386  0.020  1.386
 0C8  C19  C20  aromatic  1.393  0.020  1.393
 0C8  C19  C18  aromatic  1.397  0.020  1.397
 0C8  C11  C10  aromatic  1.385  0.020  1.385
 0C8  C20  C21  aromatic  1.382  0.020  1.382
 0C8  C13  C14  aromatic  1.383  0.020  1.383
 0C8  C18  C17  aromatic  1.377  0.020  1.377
 0C8  C10  C09  aromatic  1.395  0.020  1.395
 0C8  C21  C16  aromatic  1.400  0.020  1.400
 0C8  C14  C09  aromatic  1.396  0.020  1.396
 0C8  C14  O25  single    1.391  0.020  1.391
 0C8  F27  C15  single    1.322  0.020  1.322
 0C8  C09  N03  single    1.395  0.020  1.395
 0C8  C17  C16  aromatic  1.404  0.020  1.404
 0C8  O25  C15  single    1.342  0.020  1.342
 0C8  C16  N04  single    1.379  0.020  1.379
 0C8  C15  F26  single    1.333  0.020  1.333
 0C8  C15  F28  single    1.333  0.020  1.333
 0C8  N03  C07  single    1.358  0.020  1.358
 0C8  N02  C07  aromatic  1.321  0.020  1.321
 0C8  N02  C06  aromatic  1.333  0.020  1.333
 0C8  N04  C06  single    1.369  0.020  1.369
 0C8  C07  C08  aromatic  1.409  0.020  1.409
 0C8  C06  N01  aromatic  1.322  0.020  1.322
 0C8  C08  C05  aromatic  1.370  0.020  1.370
 0C8  N01  C05  aromatic  1.336  0.020  1.336
 0C8  N03  H1   single    0.860  0.020  1.020
 0C8  N04  H2   single    0.860  0.020  1.020
 0C8  C05  H3   single    0.930  0.020  1.080
 0C8  C08  H4   single    0.930  0.020  1.080
 0C8  C10  H5   single    0.930  0.020  1.080
 0C8  C11  H6   single    0.930  0.020  1.080
 0C8  C12  H7   single    0.930  0.020  1.080
 0C8  C13  H8   single    0.930  0.020  1.080
 0C8  C17  H9   single    0.930  0.020  1.080
 0C8  C18  H10  single    0.930  0.020  1.080
 0C8  C20  H11  single    0.930  0.020  1.080
 0C8  C21  H12  single    0.930  0.020  1.080
 0C8  O24  H13  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
 0C8  C06  N01  C05  115.26  3.000
 0C8  C07  N02  C06  117.38  3.000
 0C8  H1   N03  C09  116.76  3.000
 0C8  H1   N03  C07  115.71  3.000
 0C8  C09  N03  C07  127.29  3.000
 0C8  H2   N04  C16  115.39  3.000
 0C8  H2   N04  C06  112.71  3.000
 0C8  C16  N04  C06  131.90  3.000
 0C8  H3   C05  C08  120.08  3.000
 0C8  H3   C05  N01  116.12  3.000
 0C8  C08  C05  N01  123.80  3.000
 0C8  N04  C06  N02  113.12  3.000
 0C8  N04  C06  N01  120.30  3.000
 0C8  N02  C06  N01  126.58  3.000
 0C8  C08  C07  N03  119.52  3.000
 0C8  C08  C07  N02  121.16  3.000
 0C8  N03  C07  N02  119.32  3.000
 0C8  H4   C08  C07  122.33  3.000
 0C8  H4   C08  C05  121.86  3.000
 0C8  C07  C08  C05  115.81  3.000
 0C8  C14  C09  C10  117.81  3.000
 0C8  C14  C09  N03  119.18  3.000
 0C8  C10  C09  N03  122.94  3.000
 0C8  H5   C10  C11  119.84  3.000
 0C8  H5   C10  C09  119.70  3.000
 0C8  C11  C10  C09  120.46  3.000
 0C8  H6   C11  C12  120.02  3.000
 0C8  H6   C11  C10  119.19  3.000
 0C8  C12  C11  C10  120.77  3.000
 0C8  H7   C12  C13  119.83  3.000
 0C8  H7   C12  C11  120.59  3.000
 0C8  C13  C12  C11  119.57  3.000
 0C8  H8   C13  C14  120.12  3.000
 0C8  H8   C13  C12  120.54  3.000
 0C8  C14  C13  C12  119.34  3.000
 0C8  O25  C14  C13  119.54  3.000
 0C8  O25  C14  C09  118.36  3.000
 0C8  C13  C14  C09  122.02  3.000
 0C8  F28  C15  F27  108.58  3.000
 0C8  F28  C15  F26  106.81  3.000
 0C8  F27  C15  F26  108.32  3.000
 0C8  F28  C15  O25  112.77  3.000
 0C8  F26  C15  O25  112.66  3.000
 0C8  F27  C15  O25  107.57  3.000
 0C8  C21  C16  C17  118.48  3.000
 0C8  C17  C16  N04  116.29  3.000
 0C8  C21  C16  N04  125.23  3.000
 0C8  H9   C17  C18  119.35  3.000
 0C8  H9   C17  C16  119.50  3.000
 0C8  C18  C17  C16  121.15  3.000
 0C8  H10  C18  C19  121.03  3.000
 0C8  H10  C18  C17  118.46  3.000
 0C8  C19  C18  C17  120.52  3.000
 0C8  C22  C19  C20  118.93  3.000
 0C8  C20  C19  C18  118.25  3.000
 0C8  C22  C19  C18  122.81  3.000
 0C8  H11  C20  C21  118.50  3.000
 0C8  H11  C20  C19  119.65  3.000
 0C8  C21  C20  C19  121.85  3.000
 0C8  H12  C21  C20  119.93  3.000
 0C8  H12  C21  C16  120.32  3.000
 0C8  C20  C21  C16  119.76  3.000
 0C8  O24  C22  O23  122.75  3.000
 0C8  O24  C22  C19  113.16  3.000
 0C8  O23  C22  C19  124.09  3.000
 0C8  H13  O24  C22  109.73  3.000
 0C8  C15  O25  C14  117.53  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
 0C8  CONST_01  C07  N02  C06  N01     0.00   0.0  0
 0C8  CONST_02  C07  C08  C05  N01     0.00   0.0  0
 0C8  CONST_03  C05  C08  C07  N02     0.00   0.0  0
 0C8  CONST_04  C05  N01  C06  N02     0.00   0.0  0
 0C8  CONST_05  C08  C07  N02  C06     0.00   0.0  0
 0C8  CONST_06  C08  C05  N01  C06     0.00   0.0  0
 0C8  CONST_07  C12  C11  C10  C09     0.00   0.0  0
 0C8  CONST_08  C12  C13  C14  C09     0.00   0.0  0
 0C8  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 0C8  CONST_10  C13  C14  C09  C10     0.00   0.0  0
 0C8  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 0C8  CONST_12  C14  C09  C10  C11     0.00   0.0  0
 0C8  CONST_13  C19  C20  C21  C16     0.00   0.0  0
 0C8  CONST_14  C19  C18  C17  C16     0.00   0.0  0
 0C8  CONST_15  C20  C19  C18  C17     0.00   0.0  0
 0C8  CONST_16  C20  C21  C16  C17     0.00   0.0  0
 0C8  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 0C8  CONST_18  C21  C16  C17  C18     0.00   0.0  0
 0C8  CONST_19  C11  C10  C09  N03   180.00   0.0  0
 0C8  CONST_20  C13  C14  C09  N03   180.00   0.0  0
 0C8  CONST_21  C06  N02  C07  N03   180.00   0.0  0
 0C8  CONST_22  C05  C08  C07  N03   180.00   0.0  0
 0C8  CONST_23  C20  C21  C16  N04   180.00   0.0  0
 0C8  CONST_24  C18  C17  C16  N04   180.00   0.0  0
 0C8  CONST_25  C07  N02  C06  N04   180.00   0.0  0
 0C8  CONST_26  C05  N01  C06  N04   180.00   0.0  0
 0C8  CONST_27  O25  C14  C09  C10   180.00   0.0  0
 0C8  CONST_28  O25  C14  C13  C12   180.00   0.0  0
 0C8  CONST_29  C22  C19  C18  C17   180.00   0.0  0
 0C8  CONST_30  C22  C19  C20  C21   180.00   0.0  0
 0C8  CONST_31  H4   C08  C05  N01   180.00   0.0  0
 0C8  CONST_32  H3   C05  N01  C06   180.00   0.0  0
 0C8  CONST_33  H6   C11  C10  C09   180.00   0.0  0
 0C8  CONST_34  H8   C13  C14  C09   180.00   0.0  0
 0C8  CONST_35  H7   C12  C11  C10   180.00   0.0  0
 0C8  CONST_36  H5   C10  C11  C12   180.00   0.0  0
 0C8  CONST_37  H11  C20  C21  C16   180.00   0.0  0
 0C8  CONST_38  H10  C18  C17  C16   180.00   0.0  0
 0C8  CONST_39  H12  C21  C16  C17   180.00   0.0  0
 0C8  CONST_40  H9   C17  C18  C19   180.00   0.0  0
 0C8  CONST_41  H13  O24  C22  C19   180.00   0.0  0
 0C8  Var_01    C16  N04  C06  N01     0.45  30.0  1
 0C8  Var_02    C09  N03  C07  N02     0.87  30.0  2
 0C8  Var_03    C21  C16  N04  C06     1.11  30.0  2
 0C8  Var_04    C10  C09  N03  C07    42.36  30.0  2
 0C8  Var_05    O23  C22  C19  C18  -179.74  30.0  2
 0C8  Var_06    F27  C15  O25  C14  -175.64  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
 0C8  plan-1  N01  0.020
 0C8  plan-1  N02  0.020
 0C8  plan-1  N03  0.020
 0C8  plan-1  N04  0.020
 0C8  plan-1  C05  0.020
 0C8  plan-1  C06  0.020
 0C8  plan-1  C07  0.020
 0C8  plan-1  C08  0.020
 0C8  plan-1  H3   0.020
 0C8  plan-1  H4   0.020
 0C8  plan-2  N03  0.020
 0C8  plan-2  C09  0.020
 0C8  plan-2  C10  0.020
 0C8  plan-2  C11  0.020
 0C8  plan-2  C12  0.020
 0C8  plan-2  C13  0.020
 0C8  plan-2  C14  0.020
 0C8  plan-2  O25  0.020
 0C8  plan-2  H5   0.020
 0C8  plan-2  H6   0.020
 0C8  plan-2  H7   0.020
 0C8  plan-2  H8   0.020
 0C8  plan-3  N04  0.020
 0C8  plan-3  C16  0.020
 0C8  plan-3  C17  0.020
 0C8  plan-3  C18  0.020
 0C8  plan-3  C19  0.020
 0C8  plan-3  C20  0.020
 0C8  plan-3  C21  0.020
 0C8  plan-3  C22  0.020
 0C8  plan-3  H9   0.020
 0C8  plan-3  H10  0.020
 0C8  plan-3  H11  0.020
 0C8  plan-3  H12  0.020
 0C8  plan-4  C19  0.020
 0C8  plan-4  C22  0.020
 0C8  plan-4  O23  0.020
 0C8  plan-4  O24  0.020
 0C8  plan-4  H13  0.020

