# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:27:13 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-({4-[(2-chlorophenyl)amino]-5-fluoropyrimidin-2-yl}amino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2ncc(F)c(Nc3ccccc3Cl)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
 0C6  0C6  '4-({4-[(2-chlorophenyl)amino]-5-fluoropyrimidin-2-yl}amino)benzoic acid'  ligand  37  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0C6
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
 0C6  CL1  CL  CL    0  -0.111   5.6265  -0.3097   1.3292
 0C6  C02  C   CR6   0  -0.127   4.8282   0.9316   0.4187
 0C6  C03  C   CR16  0  -0.213   5.3784   2.2027   0.3950
 0C6  C04  C   CR16  0  -0.271   4.7460   3.2096  -0.3160
 0C6  C05  C   CR16  0  -0.248   3.5777   2.9286  -1.0103
 0C6  C06  C   CR16  0  -0.284   3.0400   1.6525  -0.9989
 0C6  C07  C   CR6   0   0.425   3.6520   0.6300  -0.2737
 0C6  N08  N   NH1   0  -0.772   3.1681  -0.6791  -0.2617
 0C6  C09  C   CR6   0   0.436   1.8732  -1.0717  -0.2116
 0C6  C10  C   CR6   0   0.322   1.5538  -2.4429  -0.2208
 0C6  C12  C   CR16  0  -0.136   0.2425  -2.8030  -0.1619
 0C6  N13  N   N     0  -0.477  -0.7396  -1.8984  -0.0988
 0C6  C14  C   CR6   0   0.622  -0.3581  -0.6345  -0.0904
 0C6  N15  N   NH1   0  -0.771  -1.2865   0.3692  -0.0203
 0C6  C16  C   CR6   0   0.381  -2.6629   0.3413   0.0646
 0C6  C17  C   CR16  0  -0.346  -3.3054   1.5843   0.1841
 0C6  C18  C   CR16  0  -0.246  -4.6760   1.6669   0.2731
 0C6  C19  C   CR6   0  -0.103  -5.4645   0.5150   0.2440
 0C6  C20  C   C     0   0.524  -6.9295   0.6518   0.3403
 0C6  O21  O   OH1   0  -0.598  -7.5685  -0.5113   0.2784
 0C6  O22  O   O     0  -0.449  -7.5052   1.7094   0.4622
 0C6  C23  C   CR16  0  -0.250  -4.8267  -0.7179   0.1233
 0C6  C24  C   CR16  0  -0.301  -3.4493  -0.8162   0.0354
 0C6  N25  N   N     0  -0.507   0.8985  -0.1874  -0.1414
 0C6  F11  F   F     0  -0.302   2.5380  -3.3545  -0.2814
 0C6  H1   H   HCR6  0   0.283   6.2930   2.4024   0.9363
 0C6  H2   H   HCR6  0   0.269   5.1689   4.2047  -0.3281
 0C6  H3   H   HCR6  0   0.268   3.0840   3.7035  -1.5809
 0C6  H4   H   HCR6  0   0.280   2.1419   1.4469  -1.5605
 0C6  H5   H   HNH1  0   0.410   3.8606  -1.4083  -0.1852
 0C6  H6   H   HCR6  0   0.295  -0.0412  -3.8497  -0.1664
 0C6  H7   H   HNH1  0   0.413  -0.8706   1.2886  -0.0118
 0C6  H8   H   HCR6  0   0.275  -2.7135   2.4916   0.2075
 0C6  H9   H   HCR6  0   0.265  -5.1386   2.6403   0.3670
 0C6  H10  H   HOH1  0   0.485  -8.5233  -0.3632   0.3415
 0C6  H11  H   HCR6  0   0.266  -5.4021  -1.6333   0.0950
 0C6  H12  H   HCR6  0   0.292  -2.9888  -1.7855  -0.0571

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
 0C6  C05  C06  aromatic  1.385  0.020  1.385
 0C6  C05  C04  aromatic  1.388  0.020  1.388
 0C6  C06  C07  aromatic  1.395  0.020  1.395
 0C6  C04  C03  aromatic  1.385  0.020  1.385
 0C6  C07  N08  single    1.396  0.020  1.396
 0C6  C07  C02  aromatic  1.398  0.020  1.398
 0C6  C03  C02  aromatic  1.385  0.020  1.385
 0C6  N08  C09  single    1.354  0.020  1.354
 0C6  C02  CL1  single    1.734  0.020  1.734
 0C6  F11  C10  single    1.343  0.020  1.343
 0C6  C09  C10  aromatic  1.408  0.020  1.408
 0C6  C09  N25  aromatic  1.318  0.020  1.318
 0C6  C10  C12  aromatic  1.361  0.020  1.361
 0C6  O22  C20  double    1.210  0.020  1.210
 0C6  N25  C14  aromatic  1.335  0.020  1.335
 0C6  C18  C17  aromatic  1.376  0.020  1.376
 0C6  C18  C19  aromatic  1.396  0.020  1.396
 0C6  C17  C16  aromatic  1.404  0.020  1.404
 0C6  C20  C19  single    1.475  0.020  1.475
 0C6  C20  O21  single    1.329  0.020  1.329
 0C6  C12  N13  aromatic  1.337  0.020  1.337
 0C6  C19  C23  aromatic  1.393  0.020  1.393
 0C6  C14  N13  aromatic  1.320  0.020  1.320
 0C6  C14  N15  single    1.369  0.020  1.369
 0C6  C16  N15  single    1.379  0.020  1.379
 0C6  C16  C24  aromatic  1.400  0.020  1.400
 0C6  C23  C24  aromatic  1.384  0.020  1.384
 0C6  C03  H1   single    0.930  0.020  1.080
 0C6  C04  H2   single    0.930  0.020  1.080
 0C6  C05  H3   single    0.930  0.020  1.080
 0C6  C06  H4   single    0.930  0.020  1.080
 0C6  N08  H5   single    0.860  0.020  1.020
 0C6  C12  H6   single    0.930  0.020  1.080
 0C6  N15  H7   single    0.860  0.020  1.020
 0C6  C17  H8   single    0.930  0.020  1.080
 0C6  C18  H9   single    0.930  0.020  1.080
 0C6  O21  H10  single    0.850  0.020  0.980
 0C6  C23  H11  single    0.930  0.020  1.080
 0C6  C24  H12  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
 0C6  C07  C02  C03  121.58  3.000
 0C6  C03  C02  CL1  118.88  3.000
 0C6  C07  C02  CL1  119.54  3.000
 0C6  H1   C03  C04  120.58  3.000
 0C6  H1   C03  C02  119.79  3.000
 0C6  C04  C03  C02  119.63  3.000
 0C6  H2   C04  C05  120.66  3.000
 0C6  H2   C04  C03  119.75  3.000
 0C6  C05  C04  C03  119.59  3.000
 0C6  H3   C05  C06  119.17  3.000
 0C6  H3   C05  C04  120.21  3.000
 0C6  C06  C05  C04  120.62  3.000
 0C6  H4   C06  C07  119.74  3.000
 0C6  H4   C06  C05  119.64  3.000
 0C6  C07  C06  C05  120.62  3.000
 0C6  N08  C07  C06  122.67  3.000
 0C6  N08  C07  C02  119.33  3.000
 0C6  C06  C07  C02  117.94  3.000
 0C6  H5   N08  C09  116.38  3.000
 0C6  H5   N08  C07  116.14  3.000
 0C6  C09  N08  C07  127.14  3.000
 0C6  N25  C09  C10  119.08  3.000
 0C6  N25  C09  N08  120.98  3.000
 0C6  C10  C09  N08  119.94  3.000
 0C6  F11  C10  C12  121.90  3.000
 0C6  C12  C10  C09  118.42  3.000
 0C6  F11  C10  C09  119.68  3.000
 0C6  H6   C12  N13  117.46  3.000
 0C6  H6   C12  C10  120.48  3.000
 0C6  N13  C12  C10  122.07  3.000
 0C6  C14  N13  C12  115.84  3.000
 0C6  N25  C14  N15  113.26  3.000
 0C6  N15  C14  N13  120.41  3.000
 0C6  N25  C14  N13  126.33  3.000
 0C6  H7   N15  C16  115.42  3.000
 0C6  H7   N15  C14  112.89  3.000
 0C6  C16  N15  C14  131.68  3.000
 0C6  C24  C16  C17  118.47  3.000
 0C6  C24  C16  N15  125.18  3.000
 0C6  C17  C16  N15  116.35  3.000
 0C6  H8   C17  C18  119.50  3.000
 0C6  H8   C17  C16  119.54  3.000
 0C6  C18  C17  C16  120.95  3.000
 0C6  H9   C18  C19  120.18  3.000
 0C6  H9   C18  C17  119.05  3.000
 0C6  C19  C18  C17  120.77  3.000
 0C6  C23  C19  C20  122.86  3.000
 0C6  C23  C19  C18  118.25  3.000
 0C6  C20  C19  C18  118.89  3.000
 0C6  O22  C20  O21  122.74  3.000
 0C6  O21  C20  C19  113.18  3.000
 0C6  O22  C20  C19  124.08  3.000
 0C6  H10  O21  C20  109.72  3.000
 0C6  H11  C23  C24  117.89  3.000
 0C6  H11  C23  C19  120.51  3.000
 0C6  C24  C23  C19  121.60  3.000
 0C6  H12  C24  C23  119.67  3.000
 0C6  H12  C24  C16  120.38  3.000
 0C6  C23  C24  C16  119.95  3.000
 0C6  C14  N25  C09  118.26  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
 0C6  CONST_01  C05  C06  C07  C02    0.00   0.0  0
 0C6  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 0C6  CONST_03  C06  C05  C04  C03    0.00   0.0  0
 0C6  CONST_04  C06  C07  C02  C03    0.00   0.0  0
 0C6  CONST_05  C07  C06  C05  C04    0.00   0.0  0
 0C6  CONST_06  C07  C02  C03  C04    0.00   0.0  0
 0C6  CONST_07  N13  C12  C10  C09    0.00   0.0  0
 0C6  CONST_08  N13  C14  N25  C09    0.00   0.0  0
 0C6  CONST_09  C14  N25  C09  C10    0.00   0.0  0
 0C6  CONST_10  C14  N13  C12  C10    0.00   0.0  0
 0C6  CONST_11  N25  C09  C10  C12    0.00   0.0  0
 0C6  CONST_12  N25  C14  N13  C12    0.00   0.0  0
 0C6  CONST_13  C19  C18  C17  C16    0.00   0.0  0
 0C6  CONST_14  C19  C23  C24  C16    0.00   0.0  0
 0C6  CONST_15  C23  C19  C18  C17    0.00   0.0  0
 0C6  CONST_16  C23  C24  C16  C17    0.00   0.0  0
 0C6  CONST_17  C24  C16  C17  C18    0.00   0.0  0
 0C6  CONST_18  C24  C23  C19  C18    0.00   0.0  0
 0C6  CONST_19  C06  C07  C02  CL1  180.00   0.0  0
 0C6  CONST_20  C04  C03  C02  CL1  180.00   0.0  0
 0C6  CONST_21  N08  C07  C02  C03  180.00   0.0  0
 0C6  CONST_22  N08  C07  C06  C05  180.00   0.0  0
 0C6  CONST_23  C12  C10  C09  N08  180.00   0.0  0
 0C6  CONST_24  C14  N25  C09  N08  180.00   0.0  0
 0C6  CONST_25  N15  C14  N25  C09  180.00   0.0  0
 0C6  CONST_26  N15  C14  N13  C12  180.00   0.0  0
 0C6  CONST_27  F11  C10  C12  N13  180.00   0.0  0
 0C6  CONST_28  C18  C17  C16  N15  180.00   0.0  0
 0C6  CONST_29  C23  C24  C16  N15  180.00   0.0  0
 0C6  CONST_30  C20  C19  C18  C17  180.00   0.0  0
 0C6  CONST_31  C24  C23  C19  C20  180.00   0.0  0
 0C6  CONST_32  F11  C10  C09  N25  180.00   0.0  0
 0C6  CONST_33  H4   C06  C07  C02  180.00   0.0  0
 0C6  CONST_34  H2   C04  C03  C02  180.00   0.0  0
 0C6  CONST_35  H3   C05  C04  C03  180.00   0.0  0
 0C6  CONST_36  H1   C03  C04  C05  180.00   0.0  0
 0C6  CONST_37  H6   C12  C10  C09  180.00   0.0  0
 0C6  CONST_38  H9   C18  C17  C16  180.00   0.0  0
 0C6  CONST_39  H11  C23  C24  C16  180.00   0.0  0
 0C6  CONST_40  H12  C24  C16  C17  180.00   0.0  0
 0C6  CONST_41  H8   C17  C18  C19  180.00   0.0  0
 0C6  CONST_42  H10  O21  C20  C19  180.00   0.0  0
 0C6  Var_01    C09  N08  C07  C02  142.75  30.0  2
 0C6  Var_02    C10  C09  N08  C07  179.34  30.0  2
 0C6  Var_03    C16  N15  C14  N13    0.82  30.0  2
 0C6  Var_04    C17  C16  N15  C14  177.08  30.0  3
 0C6  Var_05    O22  C20  C19  C18   -1.02  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
 0C6  plan-1  CL1  0.020
 0C6  plan-1  C02  0.020
 0C6  plan-1  C03  0.020
 0C6  plan-1  C04  0.020
 0C6  plan-1  C05  0.020
 0C6  plan-1  C06  0.020
 0C6  plan-1  C07  0.020
 0C6  plan-1  N08  0.020
 0C6  plan-1  H1   0.020
 0C6  plan-1  H2   0.020
 0C6  plan-1  H3   0.020
 0C6  plan-1  H4   0.020
 0C6  plan-2  N08  0.020
 0C6  plan-2  C09  0.020
 0C6  plan-2  C10  0.020
 0C6  plan-2  C12  0.020
 0C6  plan-2  N13  0.020
 0C6  plan-2  C14  0.020
 0C6  plan-2  N15  0.020
 0C6  plan-2  N25  0.020
 0C6  plan-2  F11  0.020
 0C6  plan-2  H6   0.020
 0C6  plan-3  N15  0.020
 0C6  plan-3  C16  0.020
 0C6  plan-3  C17  0.020
 0C6  plan-3  C18  0.020
 0C6  plan-3  C19  0.020
 0C6  plan-3  C20  0.020
 0C6  plan-3  C23  0.020
 0C6  plan-3  C24  0.020
 0C6  plan-3  H8   0.020
 0C6  plan-3  H9   0.020
 0C6  plan-3  H11  0.020
 0C6  plan-3  H12  0.020
 0C6  plan-4  C19  0.020
 0C6  plan-4  C20  0.020
 0C6  plan-4  O21  0.020
 0C6  plan-4  O22  0.020
 0C6  plan-4  H10  0.020

