# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:34:11 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-[(4-{[2-(trifluoromethyl)phenyl]amino}pyrimidin-2-yl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2nccc(Nc3ccccc3C(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
 0C3  0C3  '4-[(4-{[2-(trifluoromethyl)phenyl]amino}pyrimidin-2-yl)amino]benzoic acid'  ligand  40  27  .  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_0C3
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
 0C3  N01  N  N     0  -0.492  -1.1129  -1.9699   0.6852
 0C3  N02  N  N     0  -0.509   0.5639  -0.3070   0.4529
 0C3  N03  N  NH1   0  -0.792   2.7856  -0.7601   0.8590
 0C3  N04  N  NH1   0  -0.769  -1.5894   0.2193   0.0332
 0C3  C05  C  CR16  0   0.005  -0.1563  -2.8350   1.0346
 0C3  C06  C  CR6   0   0.610  -0.6943  -0.7457   0.4110
 0C3  C07  C  CR6   0   0.548   1.4960  -1.1743   0.8087
 0C3  C08  C  CR16  0  -0.445   1.1712  -2.5098   1.1193
 0C3  C09  C  CR6   0   0.341   3.2208   0.5593   0.6417
 0C3  C10  C  CR16  0  -0.252   2.7218   1.5955   1.4225
 0C3  C11  C  CR16  0  -0.254   3.1733   2.8922   1.2408
 0C3  C12  C  CR16  0  -0.242   4.1407   3.1671   0.2856
 0C3  C13  C  CR16  0  -0.309   4.6438   2.1420  -0.4988
 0C3  C14  C  CR6   0  -0.243   4.1808   0.8409  -0.3363
 0C3  C15  C  CT    0   1.072   4.6833  -0.2519  -1.2308
 0C3  C16  C  CR6   0   0.379  -2.9589   0.1925  -0.1245
 0C3  C17  C  CR16  0  -0.346  -3.5588   1.3831  -0.5656
 0C3  C18  C  CR16  0  -0.247  -4.9200   1.4639  -0.7498
 0C3  C19  C  CR6   0  -0.103  -5.7418   0.3624  -0.5028
 0C3  C20  C  CR16  0  -0.249  -5.1463  -0.8187  -0.0643
 0C3  C21  C  CR16  0  -0.302  -3.7790  -0.9142   0.1250
 0C3  C22  C  C     0   0.523  -7.1942   0.4957  -0.7186
 0C3  O23  O  OH1   0  -0.598  -7.8655  -0.6233  -0.4696
 0C3  O24  O  O     0  -0.449  -7.7333   1.5144  -1.0875
 0C3  F25  F  F     0  -0.298   5.5752   0.1892  -2.1203
 0C3  F26  F  F     0  -0.318   5.2855  -1.2373  -0.5433
 0C3  F27  F  F     0  -0.309   3.6903  -0.8216  -1.9267
 0C3  H1   H  HNH1  0   0.412   3.4783  -1.4590   1.0772
 0C3  H2   H  HNH1  0   0.411  -1.1475   1.1040  -0.1692
 0C3  H3   H  HCR6  0   0.272  -0.4845  -3.8431   1.2604
 0C3  H4   H  HCR6  0   0.280   1.9198  -3.2345   1.4057
 0C3  H5   H  HCR6  0   0.275   1.9861   1.3805   2.1848
 0C3  H6   H  HCR6  0   0.272   2.7785   3.6860   1.8607
 0C3  H7   H  HCR6  0   0.270   4.5057   4.1758   0.1495
 0C3  H8   H  HCR6  0   0.276   5.3916   2.3696  -1.2455
 0C3  H9   H  HCR6  0   0.274  -2.9413   2.2506  -0.7658
 0C3  H10  H  HCR6  0   0.265  -5.3487   2.3954  -1.0937
 0C3  H11  H  HCR6  0   0.266  -5.7472  -1.6940   0.1418
 0C3  H12  H  HCR6  0   0.292  -3.3500  -1.8414   0.4655
 0C3  H13  H  HOH1  0   0.485  -8.8107  -0.4794  -0.6227

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
 0C3  O24  C22  double    1.210  0.020  1.210
 0C3  O23  C22  single    1.329  0.020  1.329
 0C3  C22  C19  single    1.474  0.020  1.474
 0C3  C12  C11  aromatic  1.387  0.020  1.387
 0C3  C12  C13  aromatic  1.385  0.020  1.385
 0C3  C19  C18  aromatic  1.396  0.020  1.396
 0C3  C19  C20  aromatic  1.393  0.020  1.393
 0C3  C11  C10  aromatic  1.385  0.020  1.385
 0C3  C18  C17  aromatic  1.376  0.020  1.376
 0C3  C13  C14  aromatic  1.391  0.020  1.391
 0C3  C20  C21  aromatic  1.384  0.020  1.384
 0C3  C10  C09  aromatic  1.390  0.020  1.390
 0C3  C17  C16  aromatic  1.404  0.020  1.404
 0C3  C14  C09  aromatic  1.399  0.020  1.399
 0C3  C14  C15  single    1.499  0.020  1.499
 0C3  C09  N03  single    1.406  0.020  1.406
 0C3  C21  C16  aromatic  1.400  0.020  1.400
 0C3  C16  N04  single    1.379  0.020  1.379
 0C3  F27  C15  single    1.340  0.020  1.340
 0C3  F26  C15  single    1.344  0.020  1.344
 0C3  C15  F25  single    1.335  0.020  1.335
 0C3  N03  C07  single    1.355  0.020  1.355
 0C3  N02  C07  aromatic  1.322  0.020  1.322
 0C3  N02  C06  aromatic  1.333  0.020  1.333
 0C3  N04  C06  single    1.369  0.020  1.369
 0C3  C07  C08  aromatic  1.409  0.020  1.409
 0C3  C06  N01  aromatic  1.323  0.020  1.323
 0C3  C08  C05  aromatic  1.369  0.020  1.369
 0C3  N01  C05  aromatic  1.336  0.020  1.336
 0C3  N03  H1   single    0.860  0.020  1.020
 0C3  N04  H2   single    0.860  0.020  1.020
 0C3  C05  H3   single    0.930  0.020  1.080
 0C3  C08  H4   single    0.930  0.020  1.080
 0C3  C10  H5   single    0.930  0.020  1.080
 0C3  C11  H6   single    0.930  0.020  1.080
 0C3  C12  H7   single    0.930  0.020  1.080
 0C3  C13  H8   single    0.930  0.020  1.080
 0C3  C17  H9   single    0.930  0.020  1.080
 0C3  C18  H10  single    0.930  0.020  1.080
 0C3  C20  H11  single    0.930  0.020  1.080
 0C3  C21  H12  single    0.930  0.020  1.080
 0C3  O23  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
 0C3  C06  N01  C05  115.27  3.000
 0C3  C07  N02  C06  117.26  3.000
 0C3  H1   N03  C09  118.12  3.000
 0C3  H1   N03  C07  116.75  3.000
 0C3  C09  N03  C07  125.13  3.000
 0C3  H2   N04  C16  115.40  3.000
 0C3  H2   N04  C06  112.76  3.000
 0C3  C16  N04  C06  131.84  3.000
 0C3  H3   C05  C08  120.10  3.000
 0C3  H3   C05  N01  116.09  3.000
 0C3  C08  C05  N01  123.81  3.000
 0C3  N04  C06  N02  113.19  3.000
 0C3  N04  C06  N01  120.17  3.000
 0C3  N02  C06  N01  126.64  3.000
 0C3  C08  C07  N03  120.05  3.000
 0C3  C08  C07  N02  121.24  3.000
 0C3  N03  C07  N02  118.71  3.000
 0C3  H4   C08  C07  122.30  3.000
 0C3  H4   C08  C05  121.92  3.000
 0C3  C07  C08  C05  115.78  3.000
 0C3  C14  C09  C10  119.27  3.000
 0C3  C14  C09  N03  120.61  3.000
 0C3  C10  C09  N03  120.10  3.000
 0C3  H5   C10  C11  120.03  3.000
 0C3  H5   C10  C09  119.48  3.000
 0C3  C11  C10  C09  120.48  3.000
 0C3  H6   C11  C12  120.24  3.000
 0C3  H6   C11  C10  119.53  3.000
 0C3  C12  C11  C10  120.22  3.000
 0C3  H7   C12  C13  119.76  3.000
 0C3  H7   C12  C11  120.47  3.000
 0C3  C13  C12  C11  119.77  3.000
 0C3  H8   C13  C14  120.54  3.000
 0C3  H8   C13  C12  119.11  3.000
 0C3  C14  C13  C12  120.35  3.000
 0C3  C15  C14  C13  120.05  3.000
 0C3  C15  C14  C09  120.03  3.000
 0C3  C13  C14  C09  119.90  3.000
 0C3  F27  C15  F26  106.62  3.000
 0C3  F26  C15  F25  106.49  3.000
 0C3  F27  C15  F25  106.84  3.000
 0C3  F25  C15  C14  112.39  3.000
 0C3  F26  C15  C14  112.30  3.000
 0C3  F27  C15  C14  111.81  3.000
 0C3  C21  C16  C17  118.42  3.000
 0C3  C21  C16  N04  125.23  3.000
 0C3  C17  C16  N04  116.35  3.000
 0C3  H9   C17  C18  119.48  3.000
 0C3  H9   C17  C16  119.56  3.000
 0C3  C18  C17  C16  120.96  3.000
 0C3  H10  C18  C19  120.16  3.000
 0C3  H10  C18  C17  119.03  3.000
 0C3  C19  C18  C17  120.81  3.000
 0C3  C22  C19  C20  122.93  3.000
 0C3  C20  C19  C18  118.21  3.000
 0C3  C22  C19  C18  118.86  3.000
 0C3  H11  C20  C21  117.84  3.000
 0C3  H11  C20  C19  120.57  3.000
 0C3  C21  C20  C19  121.59  3.000
 0C3  H12  C21  C20  119.76  3.000
 0C3  H12  C21  C16  120.24  3.000
 0C3  C20  C21  C16  119.99  3.000
 0C3  O24  C22  O23  122.76  3.000
 0C3  O23  C22  C19  113.22  3.000
 0C3  O24  C22  C19  124.03  3.000
 0C3  H13  O23  C22  109.78  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
 0C3  CONST_01  C07  N02  C06  N01     0.00   0.0  0
 0C3  CONST_02  C07  C08  C05  N01     0.00   0.0  0
 0C3  CONST_03  C05  C08  C07  N02     0.00   0.0  0
 0C3  CONST_04  C05  N01  C06  N02     0.00   0.0  0
 0C3  CONST_05  C08  C07  N02  C06     0.00   0.0  0
 0C3  CONST_06  C08  C05  N01  C06     0.00   0.0  0
 0C3  CONST_07  C12  C11  C10  C09     0.00   0.0  0
 0C3  CONST_08  C12  C13  C14  C09     0.00   0.0  0
 0C3  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 0C3  CONST_10  C13  C14  C09  C10     0.00   0.0  0
 0C3  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 0C3  CONST_12  C14  C09  C10  C11     0.00   0.0  0
 0C3  CONST_13  C19  C18  C17  C16     0.00   0.0  0
 0C3  CONST_14  C19  C20  C21  C16     0.00   0.0  0
 0C3  CONST_15  C20  C19  C18  C17     0.00   0.0  0
 0C3  CONST_16  C20  C21  C16  C17     0.00   0.0  0
 0C3  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 0C3  CONST_18  C21  C16  C17  C18     0.00   0.0  0
 0C3  CONST_19  C11  C10  C09  N03   180.00   0.0  0
 0C3  CONST_20  C13  C14  C09  N03   180.00   0.0  0
 0C3  CONST_21  C06  N02  C07  N03   180.00   0.0  0
 0C3  CONST_22  C05  C08  C07  N03   180.00   0.0  0
 0C3  CONST_23  C18  C17  C16  N04   180.00   0.0  0
 0C3  CONST_24  C20  C21  C16  N04   180.00   0.0  0
 0C3  CONST_25  C07  N02  C06  N04   180.00   0.0  0
 0C3  CONST_26  C05  N01  C06  N04   180.00   0.0  0
 0C3  CONST_27  C15  C14  C09  C10   180.00   0.0  0
 0C3  CONST_28  C15  C14  C13  C12   180.00   0.0  0
 0C3  CONST_29  C22  C19  C18  C17   180.00   0.0  0
 0C3  CONST_30  C22  C19  C20  C21   180.00   0.0  0
 0C3  CONST_31  H4   C08  C05  N01   180.00   0.0  0
 0C3  CONST_32  H3   C05  N01  C06   180.00   0.0  0
 0C3  CONST_33  H6   C11  C10  C09   180.00   0.0  0
 0C3  CONST_34  H8   C13  C14  C09   180.00   0.0  0
 0C3  CONST_35  H7   C12  C11  C10   180.00   0.0  0
 0C3  CONST_36  H5   C10  C11  C12   180.00   0.0  0
 0C3  CONST_37  H10  C18  C17  C16   180.00   0.0  0
 0C3  CONST_38  H11  C20  C21  C16   180.00   0.0  0
 0C3  CONST_39  H12  C21  C16  C17   180.00   0.0  0
 0C3  CONST_40  H9   C17  C18  C19   180.00   0.0  0
 0C3  CONST_41  H13  O23  C22  C19   180.00   0.0  0
 0C3  Var_01    C16  N04  C06  N01     0.84  30.0  1
 0C3  Var_02    C09  N03  C07  N02     4.24  30.0  1
 0C3  Var_03    C17  C16  N04  C06  -178.44  30.0  3
 0C3  Var_04    C10  C09  N03  C07    57.37  30.0  3
 0C3  Var_05    F27  C15  C14  C09    58.75  30.0  2
 0C3  Var_06    O24  C22  C19  C18    -0.81  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
 0C3  plan-1  N01  0.020
 0C3  plan-1  N02  0.020
 0C3  plan-1  N03  0.020
 0C3  plan-1  N04  0.020
 0C3  plan-1  C05  0.020
 0C3  plan-1  C06  0.020
 0C3  plan-1  C07  0.020
 0C3  plan-1  C08  0.020
 0C3  plan-1  H3   0.020
 0C3  plan-1  H4   0.020
 0C3  plan-2  N03  0.020
 0C3  plan-2  C09  0.020
 0C3  plan-2  C10  0.020
 0C3  plan-2  C11  0.020
 0C3  plan-2  C12  0.020
 0C3  plan-2  C13  0.020
 0C3  plan-2  C14  0.020
 0C3  plan-2  C15  0.020
 0C3  plan-2  H5   0.020
 0C3  plan-2  H6   0.020
 0C3  plan-2  H7   0.020
 0C3  plan-2  H8   0.020
 0C3  plan-3  N04  0.020
 0C3  plan-3  C16  0.020
 0C3  plan-3  C17  0.020
 0C3  plan-3  C18  0.020
 0C3  plan-3  C19  0.020
 0C3  plan-3  C20  0.020
 0C3  plan-3  C21  0.020
 0C3  plan-3  C22  0.020
 0C3  plan-3  H9   0.020
 0C3  plan-3  H10  0.020
 0C3  plan-3  H11  0.020
 0C3  plan-3  H12  0.020
 0C3  plan-4  C19  0.020
 0C3  plan-4  C22  0.020
 0C3  plan-4  O23  0.020
 0C3  plan-4  O24  0.020
 0C3  plan-4  H13  0.020

