# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 13:00:25 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 1-[4-(pyridin-4-yloxy)phenyl]-3-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(NC(=O)Nc2ccc(Oc3ccncc3)cc2)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
 KIN  KIN  1-[4-(pyridin-4-yloxy)phenyl]-3-[3-(trifluoromethyl)phenyl]urea  ligand  41  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KIN
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
 KIN  C11   C  CR16  0  -0.231   2.5794  -3.7062   0.9962
 KIN  C13   C  CR16  0  -0.308   1.4469  -3.4220   0.2483
 KIN  C21   C  CR6   0   0.383   3.3803  -0.9983   7.2840
 KIN  C22   C  CR16  0  -0.352   2.9251  -0.0915   8.2461
 KIN  C24   C  CR16  0  -0.289   3.5934   0.0771   9.4447
 KIN  C27   C  CR16  0  -0.288   5.1979  -1.5703   8.7615
 KIN  C32   C  CR6   0   0.457   6.3884   0.3481  11.0242
 KIN  C33   C  CR16  0  -0.409   6.8276   1.1767   9.9983
 KIN  C35   C  CR16  0  -0.064   7.8780   2.0411  10.2697
 KIN  F01   F  F     0  -0.301  -0.7748  -2.7314  -1.1915
 KIN  C02   C  CT    0   1.051  -0.7564  -2.2270   0.0445
 KIN  F03   F  F     0  -0.315  -1.8450  -2.6942   0.6742
 KIN  F04   F  F     0  -0.314  -0.9252  -0.9018  -0.0710
 KIN  C05   C  CR6   0  -0.174   0.4982  -2.5655   0.7881
 KIN  C06   C  CR16  0  -0.386   0.6793  -2.0117   2.0464
 KIN  C08   C  CR6   0   0.410   1.8207  -2.3005   2.7959
 KIN  C09   C  CR16  0  -0.307   2.7801  -3.1608   2.2538
 KIN  N15   N  NH1   0  -0.801   1.9102  -1.6897   4.0432
 KIN  C17   C  C     0   0.758   2.8786  -1.8451   5.0005
 KIN  O18   O  O     0  -0.491   3.8493  -2.5682   4.8720
 KIN  N19   N  NH1   0  -0.797   2.6256  -1.0936   6.1153
 KIN  C26   C  CR6   0   0.280   4.7323  -0.6684   9.7003
 KIN  C29   C  CR16  0  -0.315   4.5295  -1.7431   7.5575
 KIN  O31   O  O2    0  -0.501   5.3796  -0.5387  10.9107
 KIN  N37   N  N     0  -0.419   8.4935   2.1311  11.4411
 KIN  C38   C  CR16  0  -0.063   8.0587   1.3283  12.4095
 KIN  C40   C  CR16  0  -0.399   7.0221   0.4268  12.2615
 KIN  H11   H  HCR6  0   0.270   3.3310  -4.3698   0.5902
 KIN  H13   H  HCR6  0   0.270   1.3220  -3.8642  -0.7295
 KIN  H22   H  HCR6  0   0.279   2.0319   0.4919   8.0570
 KIN  H24   H  HCR6  0   0.279   3.2192   0.7819  10.1760
 KIN  H27   H  HCR6  0   0.278   6.0867  -2.1553   8.9617
 KIN  H33   H  HCR6  0   0.290   6.3836   1.1681   9.0128
 KIN  H35   H  HCR6  0   0.268   8.2340   2.6961   9.4822
 KIN  H06   H  HCR6  0   0.287  -0.0677  -1.3466   2.4647
 KIN  H09   H  HCR6  0   0.291   3.6757  -3.4080   2.7982
 KIN  HN15  H  HNH1  0   0.419   1.1407  -1.0754   4.2618
 KIN  HN19  H  HNH1  0   0.418   1.8017  -0.5108   6.1046
 KIN  H29   H  HCR6  0   0.289   4.9149  -2.4558   6.8488
 KIN  H38   H  HCR6  0   0.268   8.5646   1.4039  13.3656
 KIN  H40   H  HCR6  0   0.282   6.7139  -0.2013  13.0867

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
 KIN  C11  C13   aromatic  1.387  0.020  1.387
 KIN  C11  C09   aromatic  1.385  0.020  1.385
 KIN  C11  H11   single    0.930  0.020  1.080
 KIN  C13  C05   aromatic  1.387  0.020  1.387
 KIN  C13  H13   single    0.930  0.020  1.080
 KIN  C21  C22   aromatic  1.398  0.020  1.398
 KIN  C21  C29   aromatic  1.396  0.020  1.396
 KIN  C21  N19   single    1.394  0.020  1.394
 KIN  C22  C24   aromatic  1.383  0.020  1.383
 KIN  C22  H22   single    0.930  0.020  1.080
 KIN  C24  C26   aromatic  1.385  0.020  1.385
 KIN  C24  H24   single    0.930  0.020  1.080
 KIN  C27  C26   aromatic  1.383  0.020  1.383
 KIN  C27  C29   aromatic  1.388  0.020  1.388
 KIN  C27  H27   single    0.930  0.020  1.080
 KIN  C32  C33   aromatic  1.390  0.020  1.390
 KIN  C32  C40   aromatic  1.392  0.020  1.392
 KIN  C32  O31   single    1.348  0.020  1.348
 KIN  C33  C35   aromatic  1.387  0.020  1.387
 KIN  C33  H33   single    0.930  0.020  1.080
 KIN  C35  N37   aromatic  1.326  0.020  1.326
 KIN  C35  H35   single    0.930  0.020  1.080
 KIN  F01  C02   single    1.335  0.020  1.335
 KIN  C02  F04   single    1.341  0.020  1.341
 KIN  C02  F03   single    1.342  0.020  1.342
 KIN  C02  C05   single    1.497  0.020  1.497
 KIN  C05  C06   aromatic  1.387  0.020  1.387
 KIN  C06  C08   aromatic  1.396  0.020  1.396
 KIN  C06  H06   single    0.930  0.020  1.080
 KIN  C08  N15   single    1.392  0.020  1.392
 KIN  C08  C09   aromatic  1.398  0.020  1.398
 KIN  C09  H09   single    0.930  0.020  1.080
 KIN  N15  C17   single    1.371  0.020  1.371
 KIN  N15  HN15  single    0.860  0.020  1.020
 KIN  C17  O18   double    1.217  0.020  1.217
 KIN  C17  N19   single    1.368  0.020  1.368
 KIN  N19  HN19  single    0.860  0.020  1.020
 KIN  C26  O31   single    1.379  0.020  1.379
 KIN  C29  H29   single    0.930  0.020  1.080
 KIN  N37  C38   aromatic  1.331  0.020  1.331
 KIN  C38  C40   aromatic  1.382  0.020  1.382
 KIN  C38  H38   single    0.930  0.020  1.080
 KIN  C40  H40   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
 KIN  H11   C11  C09  118.79  3.000
 KIN  H11   C11  C13  119.39  3.000
 KIN  C09   C11  C13  121.82  3.000
 KIN  H13   C13  C05  121.72  3.000
 KIN  H13   C13  C11  119.91  3.000
 KIN  C05   C13  C11  118.37  3.000
 KIN  C29   C21  N19  124.97  3.000
 KIN  N19   C21  C22  116.41  3.000
 KIN  C29   C21  C22  118.62  3.000
 KIN  H22   C22  C24  118.95  3.000
 KIN  H22   C22  C21  119.83  3.000
 KIN  C24   C22  C21  121.21  3.000
 KIN  H24   C24  C26  120.67  3.000
 KIN  H24   C24  C22  119.87  3.000
 KIN  C26   C24  C22  119.46  3.000
 KIN  H27   C27  C29  119.24  3.000
 KIN  H27   C27  C26  120.22  3.000
 KIN  C29   C27  C26  120.54  3.000
 KIN  C40   C32  O31  116.91  3.000
 KIN  O31   C32  C33  124.51  3.000
 KIN  C40   C32  C33  118.58  3.000
 KIN  H33   C33  C35  119.63  3.000
 KIN  H33   C33  C32  122.58  3.000
 KIN  C35   C33  C32  117.79  3.000
 KIN  H35   C35  N37  116.62  3.000
 KIN  H35   C35  C33  118.87  3.000
 KIN  N37   C35  C33  124.51  3.000
 KIN  C05   C02  F04  111.81  3.000
 KIN  C05   C02  F03  111.60  3.000
 KIN  F04   C02  F03  106.41  3.000
 KIN  C05   C02  F01  112.70  3.000
 KIN  F03   C02  F01  106.97  3.000
 KIN  F04   C02  F01  106.98  3.000
 KIN  C06   C05  C02  118.03  3.000
 KIN  C06   C05  C13  120.68  3.000
 KIN  C02   C05  C13  121.28  3.000
 KIN  H06   C06  C08  118.90  3.000
 KIN  H06   C06  C05  120.34  3.000
 KIN  C08   C06  C05  120.76  3.000
 KIN  N15   C08  C09  124.99  3.000
 KIN  C09   C08  C06  118.71  3.000
 KIN  N15   C08  C06  116.30  3.000
 KIN  H09   C09  C08  121.06  3.000
 KIN  H09   C09  C11  119.28  3.000
 KIN  C08   C09  C11  119.66  3.000
 KIN  HN15  N15  C17  117.17  3.000
 KIN  HN15  N15  C08  114.37  3.000
 KIN  C17   N15  C08  128.44  3.000
 KIN  N19   C17  O18  124.05  3.000
 KIN  N19   C17  N15  112.10  3.000
 KIN  O18   C17  N15  123.85  3.000
 KIN  HN19  N19  C17  117.36  3.000
 KIN  HN19  N19  C21  114.28  3.000
 KIN  C17   N19  C21  128.34  3.000
 KIN  O31   C26  C27  119.96  3.000
 KIN  O31   C26  C24  119.83  3.000
 KIN  C27   C26  C24  120.18  3.000
 KIN  H29   C29  C27  118.76  3.000
 KIN  H29   C29  C21  121.25  3.000
 KIN  C27   C29  C21  119.99  3.000
 KIN  C26   O31  C32  119.16  3.000
 KIN  C38   N37  C35  116.75  3.000
 KIN  H38   C38  C40  119.33  3.000
 KIN  H38   C38  N37  116.56  3.000
 KIN  C40   C38  N37  124.11  3.000
 KIN  H40   C40  C38  120.72  3.000
 KIN  H40   C40  C32  121.02  3.000
 KIN  C38   C40  C32  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
 KIN  CONST_01  C06   C05  C13  C11     0.00   0.0  0
 KIN  CONST_02  C06   C08  C09  C11     0.00   0.0  0
 KIN  CONST_03  C08   C09  C11  C13     0.00   0.0  0
 KIN  CONST_04  C08   C06  C05  C13     0.00   0.0  0
 KIN  CONST_05  C26   C24  C22  C21     0.00   0.0  0
 KIN  CONST_06  C26   C27  C29  C21     0.00   0.0  0
 KIN  CONST_07  C27   C29  C21  C22     0.00   0.0  0
 KIN  CONST_08  C27   C26  C24  C22     0.00   0.0  0
 KIN  CONST_09  C29   C21  C22  C24     0.00   0.0  0
 KIN  CONST_10  C29   C27  C26  C24     0.00   0.0  0
 KIN  CONST_11  N37   C35  C33  C32     0.00   0.0  0
 KIN  CONST_12  N37   C38  C40  C32     0.00   0.0  0
 KIN  CONST_13  C38   C40  C32  C33     0.00   0.0  0
 KIN  CONST_14  C38   N37  C35  C33     0.00   0.0  0
 KIN  CONST_15  C40   C32  C33  C35     0.00   0.0  0
 KIN  CONST_16  C40   C38  N37  C35     0.00   0.0  0
 KIN  CONST_17  C09   C11  C13  C05     0.00   0.0  0
 KIN  CONST_18  C09   C08  C06  C05     0.00   0.0  0
 KIN  CONST_19  C02   C05  C13  C11   180.00   0.0  0
 KIN  CONST_20  N15   C08  C09  C11   180.00   0.0  0
 KIN  CONST_21  O31   C26  C24  C22   180.00   0.0  0
 KIN  CONST_22  N19   C21  C22  C24   180.00   0.0  0
 KIN  CONST_23  N19   C21  C29  C27   180.00   0.0  0
 KIN  CONST_24  O31   C32  C33  C35   180.00   0.0  0
 KIN  CONST_25  C08   C06  C05  C02   180.00   0.0  0
 KIN  CONST_26  N15   C08  C06  C05   180.00   0.0  0
 KIN  CONST_27  O31   C26  C27  C29   180.00   0.0  0
 KIN  CONST_28  C38   C40  C32  O31   180.00   0.0  0
 KIN  CONST_29  H09   C09  C11  C13   180.00   0.0  0
 KIN  CONST_30  H06   C06  C05  C13   180.00   0.0  0
 KIN  CONST_31  H24   C24  C22  C21   180.00   0.0  0
 KIN  CONST_32  H27   C27  C29  C21   180.00   0.0  0
 KIN  CONST_33  H29   C29  C21  C22   180.00   0.0  0
 KIN  CONST_34  H35   C35  C33  C32   180.00   0.0  0
 KIN  CONST_35  H38   C38  C40  C32   180.00   0.0  0
 KIN  CONST_36  H40   C40  C32  C33   180.00   0.0  0
 KIN  CONST_37  H11   C11  C13  C05   180.00   0.0  0
 KIN  CONST_38  H13   C13  C05  C06   180.00   0.0  0
 KIN  CONST_39  H22   C22  C24  C26   180.00   0.0  0
 KIN  CONST_40  H33   C33  C35  N37   180.00   0.0  0
 KIN  CONST_41  C17   N19  C21  C22   180.00   0.0  0
 KIN  CONST_42  C17   N15  C08  C06   180.00   0.0  0
 KIN  CONST_43  C17   N15  C08  C09     0.00   0.0  0
 KIN  CONST_44  C29   C21  N19  C17     0.00   0.0  0
 KIN  CONST_45  HN19  N19  C21  C22     0.00   0.0  0
 KIN  CONST_46  HN15  N15  C08  C06     0.00   0.0  0
 KIN  CONST_47  O18   C17  N19  C21     0.00   0.0  0
 KIN  CONST_48  O18   C17  N15  C08     0.00   0.0  0
 KIN  CONST_49  N15   C17  N19  C21   180.00   0.0  0
 KIN  CONST_50  N19   C17  N15  C08   180.00   0.0  0
 KIN  Var_01    C40   C32  O31  C26  -179.08  30.0  3
 KIN  Var_02    F01   C02  C05  C13    -5.75  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
 KIN  plan-1  C11   0.020
 KIN  plan-1  C13   0.020
 KIN  plan-1  C02   0.020
 KIN  plan-1  C05   0.020
 KIN  plan-1  C06   0.020
 KIN  plan-1  C08   0.020
 KIN  plan-1  C09   0.020
 KIN  plan-1  N15   0.020
 KIN  plan-1  H11   0.020
 KIN  plan-1  H13   0.020
 KIN  plan-1  H06   0.020
 KIN  plan-1  H09   0.020
 KIN  plan-2  C21   0.020
 KIN  plan-2  C22   0.020
 KIN  plan-2  C24   0.020
 KIN  plan-2  C27   0.020
 KIN  plan-2  N19   0.020
 KIN  plan-2  C26   0.020
 KIN  plan-2  C29   0.020
 KIN  plan-2  O31   0.020
 KIN  plan-2  H22   0.020
 KIN  plan-2  H24   0.020
 KIN  plan-2  H27   0.020
 KIN  plan-2  H29   0.020
 KIN  plan-3  C32   0.020
 KIN  plan-3  C33   0.020
 KIN  plan-3  C35   0.020
 KIN  plan-3  O31   0.020
 KIN  plan-3  N37   0.020
 KIN  plan-3  C38   0.020
 KIN  plan-3  C40   0.020
 KIN  plan-3  H33   0.020
 KIN  plan-3  H35   0.020
 KIN  plan-3  H38   0.020
 KIN  plan-3  H40   0.020
 KIN  plan-4  C21   0.020
 KIN  plan-4  C08   0.020
 KIN  plan-4  N15   0.020
 KIN  plan-4  C17   0.020
 KIN  plan-4  O18   0.020
 KIN  plan-4  N19   0.020
 KIN  plan-4  HN15  0.020
 KIN  plan-4  HN19  0.020

