# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 20:02:45 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(c(c1NC(=O)Nc2ccc(F)cc2)c3ccc(F)cc3)C(F)(F)F
#
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
 3O6  3O6  1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea  ligand  41  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3O6
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
 3O6  C13  C  CR5   0   0.614  -0.5837   1.0433  -0.7979
 3O6  C15  C  C     0   0.716   1.6497   0.2890  -0.3606
 3O6  C20  C  CR16  0  -0.402   6.2587  -1.1166  -0.6418
 3O6  C21  C  CR6   0   0.511   6.4642  -1.0634   0.7222
 3O6  C24  C  CR16  0  -0.279   4.1411  -0.6519   1.1065
 3O6  C01  C  CH3   0  -0.525   0.3978   3.2985  -1.2946
 3O6  N02  N  NR5   0  -0.288  -0.6478   2.3909  -0.8810
 3O6  N03  N  N     0  -0.287  -1.8079   2.8576  -0.4704
 3O6  C04  C  CR5   0  -0.032  -2.5169   1.7975  -0.1324
 3O6  C05  C  CR5   0  -0.158  -1.7991   0.6032  -0.3082
 3O6  C06  C  CR6   0   0.053  -2.1794  -0.7877  -0.0423
 3O6  C07  C  CR16  0  -0.292  -2.6384  -1.1786   1.2152
 3O6  C08  C  CR16  0  -0.395  -2.9730  -2.4981   1.4759
 3O6  C09  C  CR6   0   0.519  -2.8370  -3.4279   0.4632
 3O6  F10  F  F     0  -0.313  -3.1549  -4.7078   0.7102
 3O6  C11  C  CR16  0  -0.395  -2.3831  -3.0813  -0.7941
 3O6  C12  C  CR16  0  -0.302  -2.0591  -1.7555  -1.0389
 3O6  N14  N  NH1   0  -0.797   0.5401   0.3270  -1.1732
 3O6  O16  O  O     0  -0.487   1.7128   0.9361   0.6670
 3O6  N17  N  NH1   0  -0.782   2.6356  -0.5228  -0.8326
 3O6  C18  C  CR6   0   0.354   3.9089  -0.6790  -0.2680
 3O6  C19  C  CR16  0  -0.315   4.9781  -0.9159  -1.1307
 3O6  C23  C  CR16  0  -0.407   5.4245  -0.8356   1.6008
 3O6  C25  C  CT    0   1.073  -3.9072   1.9712   0.3623
 3O6  F26  F  F     0  -0.317  -3.9871   1.8648   1.6991
 3O6  F27  F  F     0  -0.305  -4.4004   3.1669   0.0394
 3O6  F28  F  F     0  -0.309  -4.7253   1.0415  -0.1432
 3O6  H1   H  HCR6  0   0.283   7.0819  -1.3006  -1.3193
 3O6  H2   H  HCR6  0   0.280   3.3327  -0.5007   1.8044
 3O6  H3   H  HCH3  0   0.268   0.9318   3.6873  -0.4301
 3O6  H4   H  HCH3  0   0.266   1.0957   2.7745  -1.9406
 3O6  H5   H  HCH3  0   0.276  -0.0489   4.1198  -1.8468
 3O6  H6   H  HCR6  0   0.261  -2.7174  -0.4532   2.0133
 3O6  H7   H  HCR6  0   0.284  -3.3242  -2.7980   2.4542
 3O6  H8   H  HCR6  0   0.284  -2.2907  -3.8279  -1.5715
 3O6  H9   H  HCR6  0   0.264  -1.7270  -1.4730  -2.0295
 3O6  H10  H  HNH1  0   0.420   0.4727  -0.2788  -1.9767
 3O6  H11  H  HNH1  0   0.415   2.5233  -0.9036  -1.7604
 3O6  H12  H  HCR6  0   0.280   4.8134  -0.9429  -2.2008
 3O6  H13  H  HCR6  0   0.282   5.6031  -0.8127   2.6680
 3O6  F22  F  F     0  -0.318   7.7052  -1.2428   1.2063

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
 3O6  C01  N02  single    1.445  0.020  1.445
 3O6  N02  N03  aromatic  1.316  0.020  1.316
 3O6  N02  C13  aromatic  1.352  0.020  1.352
 3O6  N03  C04  aromatic  1.319  0.020  1.319
 3O6  F28  C25  single    1.338  0.020  1.338
 3O6  N14  C13  single    1.385  0.020  1.385
 3O6  N14  C15  single    1.376  0.020  1.376
 3O6  C13  C05  aromatic  1.382  0.020  1.382
 3O6  C04  C05  aromatic  1.405  0.020  1.405
 3O6  C04  C25  single    1.486  0.020  1.486
 3O6  F26  C25  single    1.343  0.020  1.343
 3O6  C05  C06  single    1.466  0.020  1.466
 3O6  C12  C06  aromatic  1.394  0.020  1.394
 3O6  C12  C11  aromatic  1.387  0.020  1.387
 3O6  C25  F27  single    1.333  0.020  1.333
 3O6  N17  C15  single    1.362  0.020  1.362
 3O6  N17  C18  single    1.401  0.020  1.401
 3O6  C24  C18  aromatic  1.394  0.020  1.394
 3O6  C24  C23  aromatic  1.388  0.020  1.388
 3O6  C15  O16  double    1.216  0.020  1.216
 3O6  C06  C07  aromatic  1.395  0.020  1.395
 3O6  C11  C09  aromatic  1.381  0.020  1.381
 3O6  C18  C19  aromatic  1.394  0.020  1.394
 3O6  C23  C21  aromatic  1.380  0.020  1.380
 3O6  C07  C08  aromatic  1.386  0.020  1.386
 3O6  C09  C08  aromatic  1.381  0.020  1.381
 3O6  C09  F10  single    1.342  0.020  1.342
 3O6  C19  C20  aromatic  1.385  0.020  1.385
 3O6  C21  C20  aromatic  1.380  0.020  1.380
 3O6  C21  F22  single    1.344  0.020  1.344
 3O6  C20  H1   single    0.930  0.020  1.080
 3O6  C24  H2   single    0.930  0.020  1.080
 3O6  C01  H3   single    0.970  0.020  1.090
 3O6  C01  H4   single    0.970  0.020  1.090
 3O6  C01  H5   single    0.970  0.020  1.090
 3O6  C07  H6   single    0.930  0.020  1.080
 3O6  C08  H7   single    0.930  0.020  1.080
 3O6  C11  H8   single    0.930  0.020  1.080
 3O6  C12  H9   single    0.930  0.020  1.080
 3O6  N14  H10  single    0.860  0.020  1.020
 3O6  N17  H11  single    0.860  0.020  1.020
 3O6  C19  H12  single    0.930  0.020  1.080
 3O6  C23  H13  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
 3O6  N14  C13  C05  130.17  3.000
 3O6  C05  C13  N02  107.31  3.000
 3O6  N14  C13  N02  122.52  3.000
 3O6  N17  C15  O16  124.94  3.000
 3O6  O16  C15  N14  121.75  3.000
 3O6  N17  C15  N14  113.31  3.000
 3O6  H1   C20  C19  120.46  3.000
 3O6  H1   C20  C21  120.80  3.000
 3O6  C19  C20  C21  118.73  3.000
 3O6  C23  C21  F22  119.23  3.000
 3O6  F22  C21  C20  119.22  3.000
 3O6  C23  C21  C20  121.55  3.000
 3O6  H2   C24  C23  118.77  3.000
 3O6  H2   C24  C18  121.05  3.000
 3O6  C23  C24  C18  120.18  3.000
 3O6  H5   C01  H4   109.08  3.000
 3O6  H5   C01  H3   109.62  3.000
 3O6  H4   C01  H3   109.25  3.000
 3O6  H5   C01  N02  108.84  3.000
 3O6  H4   C01  N02  109.41  3.000
 3O6  H3   C01  N02  110.62  3.000
 3O6  N03  N02  C01  120.29  3.000
 3O6  N03  N02  C13  112.09  3.000
 3O6  C01  N02  C13  127.55  3.000
 3O6  C04  N03  N02  105.59  3.000
 3O6  C25  C04  C05  128.26  3.000
 3O6  C25  C04  N03  119.62  3.000
 3O6  C05  C04  N03  112.12  3.000
 3O6  C06  C05  C04  130.65  3.000
 3O6  C06  C05  C13  126.46  3.000
 3O6  C04  C05  C13  102.88  3.000
 3O6  C12  C06  C07  118.57  3.000
 3O6  C07  C06  C05  120.98  3.000
 3O6  C12  C06  C05  120.43  3.000
 3O6  H6   C07  C08  118.83  3.000
 3O6  H6   C07  C06  120.10  3.000
 3O6  C08  C07  C06  121.06  3.000
 3O6  H7   C08  C09  120.55  3.000
 3O6  H7   C08  C07  120.82  3.000
 3O6  C09  C08  C07  118.63  3.000
 3O6  C11  C09  F10  119.00  3.000
 3O6  F10  C09  C08  118.93  3.000
 3O6  C11  C09  C08  122.06  3.000
 3O6  H8   C11  C12  120.87  3.000
 3O6  H8   C11  C09  120.61  3.000
 3O6  C12  C11  C09  118.52  3.000
 3O6  H9   C12  C11  118.87  3.000
 3O6  H9   C12  C06  119.96  3.000
 3O6  C11  C12  C06  121.15  3.000
 3O6  H10  N14  C15  120.53  3.000
 3O6  H10  N14  C13  118.19  3.000
 3O6  C15  N14  C13  120.58  3.000
 3O6  H11  N17  C18  115.43  3.000
 3O6  H11  N17  C15  117.58  3.000
 3O6  C18  N17  C15  125.77  3.000
 3O6  C19  C18  N17  117.80  3.000
 3O6  C19  C18  C24  119.05  3.000
 3O6  N17  C18  C24  123.11  3.000
 3O6  H12  C19  C18  119.93  3.000
 3O6  H12  C19  C20  119.06  3.000
 3O6  C18  C19  C20  121.01  3.000
 3O6  H13  C23  C24  120.07  3.000
 3O6  H13  C23  C21  120.46  3.000
 3O6  C24  C23  C21  119.46  3.000
 3O6  F28  C25  F27  107.79  3.000
 3O6  F27  C25  F26  106.86  3.000
 3O6  F28  C25  F26  106.54  3.000
 3O6  F27  C25  C04  111.74  3.000
 3O6  F26  C25  C04  112.19  3.000
 3O6  F28  C25  C04  111.42  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
 3O6  CONST_01  C04  N03  N02  C13    0.00   0.0  0
 3O6  CONST_02  N03  C04  C05  C13    0.00   0.0  0
 3O6  CONST_05  C24  C18  C19  C20    0.00   0.0  0
 3O6  CONST_06  C24  C23  C21  C20    0.00   0.0  0
 3O6  CONST_07  C18  C24  C23  C21    0.00   0.0  0
 3O6  CONST_08  C18  C19  C20  C21    0.00   0.0  0
 3O6  CONST_09  C05  C04  N03  N02    0.00   0.0  0
 3O6  CONST_10  C04  C05  C13  N02    0.00   0.0  0
 3O6  CONST_11  C06  C05  C13  N02  180.00   0.0  0
 3O6  CONST_12  C05  C13  N02  N03    0.00   0.0  0
 3O6  CONST_13  C06  C05  C04  N03  180.00   0.0  0
 3O6  CONST_16  C11  C12  C06  C05  180.00   0.0  0
 3O6  CONST_17  C08  C07  C06  C05  180.00   0.0  0
 3O6  CONST_18  C09  C11  C12  C06    0.00   0.0  0
 3O6  CONST_19  C09  C08  C07  C06    0.00   0.0  0
 3O6  CONST_20  C11  C12  C06  C07    0.00   0.0  0
 3O6  CONST_21  C11  C09  C08  C07    0.00   0.0  0
 3O6  CONST_22  C12  C06  C07  C08    0.00   0.0  0
 3O6  CONST_23  C12  C11  C09  C08    0.00   0.0  0
 3O6  CONST_24  C23  C24  C18  C19    0.00   0.0  0
 3O6  CONST_25  C23  C21  C20  C19    0.00   0.0  0
 3O6  CONST_26  C25  C04  C05  C13  180.00   0.0  0
 3O6  CONST_27  N17  C18  C19  C20  180.00   0.0  0
 3O6  CONST_28  F22  C21  C23  C24  180.00   0.0  0
 3O6  CONST_29  C04  N03  N02  C01  180.00   0.0  0
 3O6  CONST_30  C05  C13  N02  C01  180.00   0.0  0
 3O6  CONST_31  C25  C04  N03  N02  180.00   0.0  0
 3O6  CONST_32  N14  C13  N02  N03  180.00   0.0  0
 3O6  CONST_33  N14  C13  C05  C04  180.00   0.0  0
 3O6  CONST_34  N14  C13  C05  C06    0.00   0.0  0
 3O6  CONST_35  C25  C04  C05  C06    0.00   0.0  0
 3O6  CONST_36  F10  C09  C08  C07  180.00   0.0  0
 3O6  CONST_37  C12  C11  C09  F10  180.00   0.0  0
 3O6  CONST_38  C23  C24  C18  N17  180.00   0.0  0
 3O6  CONST_39  F22  C21  C20  C19  180.00   0.0  0
 3O6  CONST_40  H13  C23  C21  C20  180.00   0.0  0
 3O6  CONST_41  H2   C24  C23  C21  180.00   0.0  0
 3O6  CONST_42  H12  C19  C20  C21  180.00   0.0  0
 3O6  CONST_43  H9   C12  C06  C05    0.00   0.0  0
 3O6  CONST_44  H6   C07  C06  C05    0.00   0.0  0
 3O6  CONST_45  H8   C11  C12  C06  180.00   0.0  0
 3O6  CONST_46  H7   C08  C07  C06  180.00   0.0  0
 3O6  CONST_47  H1   C20  C19  C18  180.00   0.0  0
 3O6  CONST_54  O16  C15  N14  C13    0.00   0.0  0
 3O6  CONST_55  C18  N17  C15  O16    0.00   0.0  0
 3O6  CONST_56  N17  C15  N14  C13  180.00   0.0  0
 3O6  CONST_57  C18  N17  C15  N14  180.00   0.0  0
 3O6  Var_01    F28  C25  C04  N03  138.89  30.0  2
 3O6  Var_02    H3   C01  N02  C13  -95.37  30.0  2

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
 3O6  plan-1  C13  0.020
 3O6  plan-1  C01  0.020
 3O6  plan-1  N02  0.020
 3O6  plan-1  N03  0.020
 3O6  plan-1  C04  0.020
 3O6  plan-1  C05  0.020
 3O6  plan-1  C06  0.020
 3O6  plan-1  N14  0.020
 3O6  plan-1  C25  0.020
 3O6  plan-2  C20  0.020
 3O6  plan-2  C21  0.020
 3O6  plan-2  C24  0.020
 3O6  plan-2  N17  0.020
 3O6  plan-2  C18  0.020
 3O6  plan-2  C19  0.020
 3O6  plan-2  C23  0.020
 3O6  plan-2  H1   0.020
 3O6  plan-2  H2   0.020
 3O6  plan-2  H12  0.020
 3O6  plan-2  H13  0.020
 3O6  plan-2  F22  0.020
 3O6  plan-3  C05  0.020
 3O6  plan-3  C06  0.020
 3O6  plan-3  C07  0.020
 3O6  plan-3  C08  0.020
 3O6  plan-3  C09  0.020
 3O6  plan-3  F10  0.020
 3O6  plan-3  C11  0.020
 3O6  plan-3  C12  0.020
 3O6  plan-3  H6   0.020
 3O6  plan-3  H7   0.020
 3O6  plan-3  H8   0.020
 3O6  plan-3  H9   0.020
 3O6  plan-4  C13  0.020
 3O6  plan-4  C15  0.020
 3O6  plan-4  N14  0.020
 3O6  plan-4  O16  0.020
 3O6  plan-4  N17  0.020
 3O6  plan-4  C18  0.020
 3O6  plan-4  H10  0.020
 3O6  plan-4  H11  0.020

