# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 15:50:19 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-[3-(2,3,4,5,6-pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1c(F)c(F)c(Oc2cccc(NC(=O)c3ccccc3C(F)(F)F)c2)c(F)c1F
#
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
 FD8  FD8  N-[3-(2,3,4,5,6-pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide  ligand  40  31  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FD8
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
 FD8  N    N  NH1   0  -0.732  -2.3775  -1.1232   0.5297
 FD8  F1   F  F     0  -0.302  -6.0308   2.3998   0.8275
 FD8  O1   O  O     0  -0.439  -2.6223   0.2966  -1.2414
 FD8  C2   C  CR6   0  -0.219  -5.5058   0.3045  -0.1046
 FD8  F2   F  F     0  -0.310  -4.7895   2.3986  -0.9220
 FD8  O2   O  O2    0  -0.489   2.1022   0.0426  -0.6744
 FD8  C3   C  CR6   0  -0.036  -4.5667  -0.7072  -0.3225
 FD8  F3   F  F     0  -0.313  -3.9894   1.7511   0.9716
 FD8  C4   C  CR16  0  -0.255  -5.0041  -2.0038  -0.5643
 FD8  C5   C  CR16  0  -0.232  -6.3598  -2.2958  -0.6114
 FD8  C6   C  CR16  0  -0.237  -7.2877  -1.2894  -0.4043
 FD8  C7   C  CR16  0  -0.280  -6.8611   0.0053  -0.1438
 FD8  C8   C  C     0   0.470  -3.0911  -0.4382  -0.3955
 FD8  C9   C  CR6   0   0.395  -0.9962  -1.1548   0.7340
 FD8  C10  C  CR16  0  -0.354  -0.5445  -1.8796   1.8415
 FD8  C11  C  CR16  0  -0.234   0.8069  -1.9562   2.1096
 FD8  C12  C  CR16  0  -0.358   1.7419  -1.3248   1.2975
 FD8  C13  C  CR6   0   0.396   1.2763  -0.6162   0.2040
 FD8  C14  C  CR16  0  -0.408  -0.0770  -0.5188  -0.0939
 FD8  C15  C  CR6   0  -0.017   3.4312   0.0645  -0.4281
 FD8  C16  C  CR6   0   0.397   4.2655  -0.8988  -0.9740
 FD8  C17  C  CR6   0   0.271   5.6325  -0.8402  -0.7786
 FD8  C18  C  CR6   0   0.285   6.1749   0.1860  -0.0267
 FD8  C19  C  CR6   0   0.272   5.3532   1.1491   0.5299
 FD8  C20  C  CR6   0   0.399   3.9875   1.0834   0.3303
 FD8  HN   H  HNH1  0   0.429  -2.9168  -1.6453   1.2049
 FD8  H4   H  HCR6  0   0.281  -4.2809  -2.7912  -0.7345
 FD8  H5   H  HCR6  0   0.277  -6.6849  -3.3077  -0.8113
 FD8  H6   H  HCR6  0   0.277  -8.3467  -1.5054  -0.4370
 FD8  H7   H  HCR6  0   0.280  -7.6008   0.7738   0.0318
 FD8  H10  H  HCR6  0   0.276  -1.2538  -2.3815   2.4879
 FD8  H11  H  HCR6  0   0.273   1.1474  -2.5170   2.9694
 FD8  H12  H  HCR6  0   0.280   2.7946  -1.3997   1.5344
 FD8  H14  H  HCR6  0   0.300  -0.3867   0.0435  -0.9600
 FD8  C1   C  CT    0   1.067  -5.0771   1.7130   0.1902
 FD8  F4   F  F     0  -0.277   3.7436  -1.8879  -1.6856
 FD8  F5   F  F     0  -0.286   6.4254  -1.7639  -1.3058
 FD8  F6   F  F     0  -0.283   7.4852   0.2475   0.1602
 FD8  F7   F  F     0  -0.286   5.8790   2.1309   1.2503
 FD8  F8   F  F     0  -0.278   3.1980   2.0023   0.8682

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
 FD8  N    C8   single    1.354  0.020  1.354
 FD8  N    C9   single    1.397  0.020  1.397
 FD8  C1   F1   single    1.337  0.020  1.337
 FD8  C1   C2   single    1.502  0.020  1.502
 FD8  C1   F2   single    1.338  0.020  1.338
 FD8  C1   F3   single    1.340  0.020  1.340
 FD8  O1   C8   double    1.215  0.020  1.215
 FD8  C2   C3   aromatic  1.397  0.020  1.397
 FD8  C2   C7   aromatic  1.388  0.020  1.388
 FD8  O2   C13  single    1.374  0.020  1.374
 FD8  O2   C15  single    1.352  0.020  1.352
 FD8  C3   C4   aromatic  1.390  0.020  1.390
 FD8  C3   C8   single    1.502  0.020  1.502
 FD8  C4   C5   aromatic  1.388  0.020  1.388
 FD8  F4   C16  single    1.326  0.020  1.326
 FD8  C5   C6   aromatic  1.384  0.020  1.384
 FD8  F5   C17  single    1.326  0.020  1.326
 FD8  C6   C7   aromatic  1.388  0.020  1.388
 FD8  F6   C18  single    1.325  0.020  1.325
 FD8  F7   C19  single    1.326  0.020  1.326
 FD8  F8   C20  single    1.326  0.020  1.326
 FD8  C9   C10  aromatic  1.399  0.020  1.399
 FD8  C9   C14  aromatic  1.391  0.020  1.391
 FD8  C10  C11  aromatic  1.380  0.020  1.380
 FD8  C11  C12  aromatic  1.390  0.020  1.390
 FD8  C12  C13  aromatic  1.384  0.020  1.384
 FD8  C13  C14  aromatic  1.389  0.020  1.389
 FD8  C15  C16  aromatic  1.386  0.020  1.386
 FD8  C15  C20  aromatic  1.387  0.020  1.387
 FD8  C16  C17  aromatic  1.382  0.020  1.382
 FD8  C17  C18  aromatic  1.383  0.020  1.383
 FD8  C18  C19  aromatic  1.383  0.020  1.383
 FD8  C19  C20  aromatic  1.382  0.020  1.382
 FD8  N    HN   single    0.860  0.020  1.020
 FD8  C4   H4   single    0.930  0.020  1.080
 FD8  C5   H5   single    0.930  0.020  1.080
 FD8  C6   H6   single    0.930  0.020  1.080
 FD8  C7   H7   single    0.930  0.020  1.080
 FD8  C10  H10  single    0.930  0.020  1.080
 FD8  C11  H11  single    0.930  0.020  1.080
 FD8  C12  H12  single    0.930  0.020  1.080
 FD8  C14  H14  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
 FD8  HN   N    C9   114.75  3.000
 FD8  HN   N    C8   115.91  3.000
 FD8  C9   N    C8   129.23  3.000
 FD8  C7   C2   C3   119.70  3.000
 FD8  C7   C2   C1   119.10  3.000
 FD8  C3   C2   C1   121.19  3.000
 FD8  C15  O2   C13  118.83  3.000
 FD8  C8   C3   C4   117.90  3.000
 FD8  C8   C3   C2   122.56  3.000
 FD8  C4   C3   C2   119.41  3.000
 FD8  H4   C4   C5   119.62  3.000
 FD8  H4   C4   C3   119.72  3.000
 FD8  C5   C4   C3   120.65  3.000
 FD8  H5   C5   C6   120.43  3.000
 FD8  H5   C5   C4   119.79  3.000
 FD8  C6   C5   C4   119.78  3.000
 FD8  H6   C6   C7   119.55  3.000
 FD8  H6   C6   C5   120.44  3.000
 FD8  C7   C6   C5   120.01  3.000
 FD8  H7   C7   C6   118.90  3.000
 FD8  H7   C7   C2   120.67  3.000
 FD8  C6   C7   C2   120.42  3.000
 FD8  C3   C8   O1   121.43  3.000
 FD8  C3   C8   N    113.20  3.000
 FD8  O1   C8   N    125.34  3.000
 FD8  C14  C9   C10  119.66  3.000
 FD8  C14  C9   N    123.79  3.000
 FD8  C10  C9   N    116.55  3.000
 FD8  H10  C10  C11  119.98  3.000
 FD8  H10  C10  C9   120.08  3.000
 FD8  C11  C10  C9   119.93  3.000
 FD8  H11  C11  C12  119.22  3.000
 FD8  H11  C11  C10  119.45  3.000
 FD8  C12  C11  C10  121.33  3.000
 FD8  H12  C12  C13  122.41  3.000
 FD8  H12  C12  C11  119.69  3.000
 FD8  C13  C12  C11  117.90  3.000
 FD8  C14  C13  C12  122.22  3.000
 FD8  C14  C13  O2   114.52  3.000
 FD8  C12  C13  O2   123.26  3.000
 FD8  H14  C14  C13  119.26  3.000
 FD8  H14  C14  C9   121.79  3.000
 FD8  C13  C14  C9   118.95  3.000
 FD8  C20  C15  C16  118.98  3.000
 FD8  C20  C15  O2   120.39  3.000
 FD8  C16  C15  O2   120.57  3.000
 FD8  C17  C16  C15  120.67  3.000
 FD8  C17  C16  F4   119.80  3.000
 FD8  C15  C16  F4   119.53  3.000
 FD8  C18  C17  C16  119.75  3.000
 FD8  C18  C17  F5   119.89  3.000
 FD8  C16  C17  F5   120.36  3.000
 FD8  C19  C18  C17  120.17  3.000
 FD8  C19  C18  F6   119.90  3.000
 FD8  C17  C18  F6   119.93  3.000
 FD8  C20  C19  C18  119.74  3.000
 FD8  C20  C19  F7   120.36  3.000
 FD8  C18  C19  F7   119.90  3.000
 FD8  C19  C20  C15  120.69  3.000
 FD8  C19  C20  F8   119.81  3.000
 FD8  C15  C20  F8   119.50  3.000
 FD8  F3   C1   F2   107.20  3.000
 FD8  F3   C1   C2   111.90  3.000
 FD8  F2   C1   C2   112.26  3.000
 FD8  F3   C1   F1   106.65  3.000
 FD8  F2   C1   F1   106.64  3.000
 FD8  C2   C1   F1   111.83  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
 FD8  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 FD8  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 FD8  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 FD8  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 FD8  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 FD8  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 FD8  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 FD8  CONST_08  C12  C13  C14  C9      0.00   0.0  0
 FD8  CONST_09  C13  C14  C9   C10     0.00   0.0  0
 FD8  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 FD8  CONST_11  C14  C9   C10  C11     0.00   0.0  0
 FD8  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 FD8  CONST_13  C18  C17  C16  C15     0.00   0.0  0
 FD8  CONST_14  C18  C19  C20  C15     0.00   0.0  0
 FD8  CONST_15  C19  C20  C15  C16     0.00   0.0  0
 FD8  CONST_16  C19  C18  C17  C16     0.00   0.0  0
 FD8  CONST_17  C20  C15  C16  C17     0.00   0.0  0
 FD8  CONST_18  C20  C19  C18  C17     0.00   0.0  0
 FD8  CONST_19  C11  C10  C9   N     180.00   0.0  0
 FD8  CONST_20  C13  C14  C9   N     180.00   0.0  0
 FD8  CONST_21  C4   C3   C2   C1    180.00   0.0  0
 FD8  CONST_22  C6   C7   C2   C1    180.00   0.0  0
 FD8  CONST_23  C11  C12  C13  O2    180.00   0.0  0
 FD8  CONST_24  C9   C14  C13  O2    180.00   0.0  0
 FD8  CONST_25  C17  C16  C15  O2    180.00   0.0  0
 FD8  CONST_26  C19  C20  C15  O2    180.00   0.0  0
 FD8  CONST_27  C20  C15  C16  F4    180.00   0.0  0
 FD8  CONST_28  C18  C17  C16  F4    180.00   0.0  0
 FD8  CONST_29  C8   C3   C4   C5    180.00   0.0  0
 FD8  CONST_30  C15  C16  C17  F5    180.00   0.0  0
 FD8  CONST_31  C19  C18  C17  F5    180.00   0.0  0
 FD8  CONST_32  C16  C17  C18  F6    180.00   0.0  0
 FD8  CONST_33  C20  C19  C18  F6    180.00   0.0  0
 FD8  CONST_34  C8   C3   C2   C7    180.00   0.0  0
 FD8  CONST_35  C17  C18  C19  F7    180.00   0.0  0
 FD8  CONST_36  C15  C20  C19  F7    180.00   0.0  0
 FD8  CONST_37  C16  C15  C20  F8    180.00   0.0  0
 FD8  CONST_38  C18  C19  C20  F8    180.00   0.0  0
 FD8  CONST_39  H4   C4   C3   C2    180.00   0.0  0
 FD8  CONST_40  H6   C6   C7   C2    180.00   0.0  0
 FD8  CONST_41  H7   C7   C2   C3    180.00   0.0  0
 FD8  CONST_42  H5   C5   C4   C3    180.00   0.0  0
 FD8  CONST_43  H11  C11  C10  C9    180.00   0.0  0
 FD8  CONST_44  H14  C14  C9   C10   180.00   0.0  0
 FD8  CONST_45  H12  C12  C11  C10   180.00   0.0  0
 FD8  CONST_46  H10  C10  C11  C12   180.00   0.0  0
 FD8  CONST_47  C9   N    C8   C3    180.00   0.0  0
 FD8  CONST_48  C10  C9   N    C8    180.00   0.0  0
 FD8  CONST_49  C14  C9   N    C8      0.00   0.0  0
 FD8  CONST_50  HN   N    C9   C10     0.00   0.0  0
 FD8  CONST_51  C9   N    C8   O1      0.00   0.0  0
 FD8  Var_01    C16  C15  O2   C13    92.66  30.0  2
 FD8  Var_02    C2   C3   C8   N     121.24  30.0  2
 FD8  Var_03    C3   C2   C1   F1   -157.38  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
 FD8  plan-1  C2   0.020
 FD8  plan-1  C3   0.020
 FD8  plan-1  C4   0.020
 FD8  plan-1  C5   0.020
 FD8  plan-1  C6   0.020
 FD8  plan-1  C7   0.020
 FD8  plan-1  C8   0.020
 FD8  plan-1  H4   0.020
 FD8  plan-1  H5   0.020
 FD8  plan-1  H6   0.020
 FD8  plan-1  H7   0.020
 FD8  plan-1  C1   0.020
 FD8  plan-2  N    0.020
 FD8  plan-2  O2   0.020
 FD8  plan-2  C9   0.020
 FD8  plan-2  C10  0.020
 FD8  plan-2  C11  0.020
 FD8  plan-2  C12  0.020
 FD8  plan-2  C13  0.020
 FD8  plan-2  C14  0.020
 FD8  plan-2  H10  0.020
 FD8  plan-2  H11  0.020
 FD8  plan-2  H12  0.020
 FD8  plan-2  H14  0.020
 FD8  plan-3  O2   0.020
 FD8  plan-3  C15  0.020
 FD8  plan-3  C16  0.020
 FD8  plan-3  C17  0.020
 FD8  plan-3  C18  0.020
 FD8  plan-3  C19  0.020
 FD8  plan-3  C20  0.020
 FD8  plan-3  F4   0.020
 FD8  plan-3  F5   0.020
 FD8  plan-3  F6   0.020
 FD8  plan-3  F7   0.020
 FD8  plan-3  F8   0.020
 FD8  plan-4  N    0.020
 FD8  plan-4  O1   0.020
 FD8  plan-4  C3   0.020
 FD8  plan-4  C8   0.020
 FD8  plan-4  C9   0.020
 FD8  plan-4  HN   0.020

