# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 03:08:20 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-fluoranyl-~{N}-[2-(4-fluorophenyl)-6-methyl-pyridin-3-yl]-4-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(NC(=O)c2ccc(cc2F)C(F)(F)F)c(n1)c3ccc(F)cc3
#
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
 6UG  6UG  2-fluoranyl-~{N}-[2-(4-fluorophenyl)-6-methyl-pyridin-3-yl]-4-(trifluoromethyl)benzamide  ligand  41  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6UG
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
 6UG  C2   C  CR16  0  -0.334  -3.9368  -3.0987  -0.6456
 6UG  C3   C  CR16  0  -0.164  -2.6029  -2.7429  -0.6323
 6UG  C5   C  C     0   0.525   0.1138  -1.6242   0.2169
 6UG  C7   C  CR16  0  -0.233   1.8578  -0.5650  -1.2549
 6UG  C9   C  CR6   0  -0.175   3.9181   0.2556  -0.3480
 6UG  C10  C  CR16  0  -0.430   3.5069  -0.0985   0.9303
 6UG  C11  C  CR6   0   0.578   2.2747  -0.6971   1.0851
 6UG  C12  C  CT    0   1.059   5.2352   0.9501  -0.5257
 6UG  C13  C  CR6   0   0.169  -3.2833  -0.5201  -0.0697
 6UG  C15  C  CR16  0  -0.265  -3.7108   1.9061  -0.4059
 6UG  C18  C  CR16  0  -0.393  -1.8885   2.5881   1.5786
 6UG  C17  C  CR6   0   0.523  -2.5853   3.5582   0.8850
 6UG  C16  C  CR16  0  -0.398  -3.4975   3.2416  -0.1037
 6UG  C19  C  CR16  0  -0.275  -2.1068   1.2572   1.2563
 6UG  C14  C  CR6   0   0.019  -3.0126   0.8989   0.2582
 6UG  N1   N  N     0  -0.434  -4.5638  -0.8721  -0.1269
 6UG  C1   C  CR6   0   0.226  -4.9031  -2.1265  -0.3987
 6UG  C    C  CH3   0  -0.723  -6.3632  -2.4593  -0.4037
 6UG  C4   C  CR6   0   0.256  -2.2565  -1.4283  -0.3440
 6UG  N    N  NH1   0  -0.743  -0.9209  -0.9952  -0.3901
 6UG  O    O  O     0  -0.438   0.0068  -2.6475   0.8617
 6UG  C6   C  CR6   0  -0.281   1.4273  -0.9391   0.0137
 6UG  F3   F  F     0  -0.303   6.1429   0.5391   0.3645
 6UG  F2   F  F     0  -0.301   5.7505   0.7491  -1.7408
 6UG  F1   F  F     0  -0.309   5.1065   2.2745  -0.3685
 6UG  C8   C  CR16  0  -0.275   3.0975   0.0239  -1.4430
 6UG  H1   H  HCR6  0   0.270  -4.2277  -4.1158  -0.8714
 6UG  H2   H  HCR6  0   0.284  -1.8438  -3.4733  -0.8747
 6UG  H3   H  HCR6  0   0.295   1.2290  -0.7554  -2.1148
 6UG  H4   H  HCR6  0   0.303   4.1203   0.0801   1.8037
 6UG  H5   H  HCR6  0   0.266  -4.4257   1.6476  -1.1760
 6UG  H6   H  HCR6  0   0.285  -1.1946   2.8608   2.3627
 6UG  H7   H  HCR6  0   0.284  -4.0331   4.0213  -0.6290
 6UG  H8   H  HCR6  0   0.271  -1.5818   0.4964   1.8194
 6UG  H9   H  HCH3  0   0.256  -6.7024  -2.7019   0.6057
 6UG  H10  H  HCH3  0   0.250  -6.9545  -1.6142  -0.7528
 6UG  H11  H  HCH3  0   0.247  -6.5763  -3.3205  -1.0349
 6UG  H12  H  HNH1  0   0.420  -0.7516  -0.0783  -0.7769
 6UG  H13  H  HCR6  0   0.287   3.4074   0.2896  -2.4435
 6UG  F4   F  F     0  -0.311  -2.3738   4.8479   1.1838
 6UG  F    F  F     0  -0.289   1.8781  -1.0235   2.3161

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
 6UG  F    C11  single    1.334  0.020  1.334
 6UG  O    C5   double    1.214  0.020  1.214
 6UG  C11  C10  aromatic  1.379  0.020  1.379
 6UG  C11  C6   aromatic  1.387  0.020  1.387
 6UG  C2   C1   aromatic  1.393  0.020  1.393
 6UG  C2   C3   aromatic  1.381  0.020  1.381
 6UG  C5   C6   single    1.495  0.020  1.495
 6UG  C5   N    single    1.355  0.020  1.355
 6UG  C    C1   single    1.497  0.020  1.497
 6UG  C10  C9   aromatic  1.389  0.020  1.389
 6UG  C1   N1   aromatic  1.328  0.020  1.328
 6UG  C3   C4   aromatic  1.390  0.020  1.390
 6UG  C6   C7   aromatic  1.391  0.020  1.391
 6UG  N1   C13  aromatic  1.329  0.020  1.329
 6UG  C4   C13  aromatic  1.398  0.020  1.398
 6UG  C4   N    single    1.405  0.020  1.405
 6UG  C15  C16  aromatic  1.386  0.020  1.386
 6UG  C15  C14  aromatic  1.394  0.020  1.394
 6UG  C13  C14  single    1.481  0.020  1.481
 6UG  C16  C17  aromatic  1.382  0.020  1.382
 6UG  F2   C12  single    1.335  0.020  1.335
 6UG  F3   C12  single    1.336  0.020  1.336
 6UG  C9   C12  single    1.500  0.020  1.500
 6UG  C9   C8   aromatic  1.388  0.020  1.388
 6UG  C14  C19  aromatic  1.395  0.020  1.395
 6UG  C7   C8   aromatic  1.385  0.020  1.385
 6UG  C12  F1   single    1.340  0.020  1.340
 6UG  C17  F4   single    1.341  0.020  1.341
 6UG  C17  C18  aromatic  1.381  0.020  1.381
 6UG  C19  C18  aromatic  1.387  0.020  1.387
 6UG  C2   H1   single    0.930  0.020  1.080
 6UG  C3   H2   single    0.930  0.020  1.080
 6UG  C7   H3   single    0.930  0.020  1.080
 6UG  C10  H4   single    0.930  0.020  1.080
 6UG  C15  H5   single    0.930  0.020  1.080
 6UG  C18  H6   single    0.930  0.020  1.080
 6UG  C16  H7   single    0.930  0.020  1.080
 6UG  C19  H8   single    0.930  0.020  1.080
 6UG  C    H9   single    0.970  0.020  1.090
 6UG  C    H10  single    0.970  0.020  1.090
 6UG  C    H11  single    0.970  0.020  1.090
 6UG  N    H12  single    0.860  0.020  1.020
 6UG  C8   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
 6UG  H1   C2   C1   120.44  3.000
 6UG  H1   C2   C3   120.28  3.000
 6UG  C1   C2   C3   119.26  3.000
 6UG  H2   C3   C4   120.71  3.000
 6UG  H2   C3   C2   120.15  3.000
 6UG  C4   C3   C2   119.12  3.000
 6UG  C6   C5   O    122.40  3.000
 6UG  C6   C5   N    113.42  3.000
 6UG  O    C5   N    124.19  3.000
 6UG  H3   C7   C8   119.13  3.000
 6UG  H3   C7   C6   119.84  3.000
 6UG  C8   C7   C6   121.01  3.000
 6UG  C8   C9   C12  120.21  3.000
 6UG  C8   C9   C10  120.57  3.000
 6UG  C12  C9   C10  119.16  3.000
 6UG  H4   C10  C11  119.19  3.000
 6UG  H4   C10  C9   122.21  3.000
 6UG  C11  C10  C9   118.61  3.000
 6UG  F    C11  C6   119.24  3.000
 6UG  C6   C11  C10  122.34  3.000
 6UG  F    C11  C10  118.40  3.000
 6UG  F1   C12  F2   107.02  3.000
 6UG  F1   C12  F3   106.93  3.000
 6UG  F2   C12  F3   107.33  3.000
 6UG  F1   C12  C9   111.07  3.000
 6UG  F3   C12  C9   112.04  3.000
 6UG  F2   C12  C9   112.16  3.000
 6UG  C4   C13  N1   121.81  3.000
 6UG  C4   C13  C14  122.11  3.000
 6UG  N1   C13  C14  116.06  3.000
 6UG  H5   C15  C14  119.83  3.000
 6UG  H5   C15  C16  119.15  3.000
 6UG  C14  C15  C16  121.02  3.000
 6UG  H6   C18  C19  120.75  3.000
 6UG  H6   C18  C17  120.69  3.000
 6UG  C19  C18  C17  118.56  3.000
 6UG  C16  C17  F4   118.95  3.000
 6UG  F4   C17  C18  118.96  3.000
 6UG  C16  C17  C18  122.09  3.000
 6UG  H7   C16  C17  120.60  3.000
 6UG  H7   C16  C15  120.82  3.000
 6UG  C17  C16  C15  118.59  3.000
 6UG  H8   C19  C14  120.45  3.000
 6UG  H8   C19  C18  118.52  3.000
 6UG  C14  C19  C18  121.01  3.000
 6UG  C19  C14  C15  118.73  3.000
 6UG  C19  C14  C13  121.54  3.000
 6UG  C15  C14  C13  119.68  3.000
 6UG  C1   N1   C13  120.35  3.000
 6UG  C    C1   N1   117.38  3.000
 6UG  N1   C1   C2   121.23  3.000
 6UG  C    C1   C2   121.39  3.000
 6UG  H11  C    H10  108.77  3.000
 6UG  H11  C    H9   107.41  3.000
 6UG  H10  C    H9   107.46  3.000
 6UG  H11  C    C1   111.63  3.000
 6UG  H10  C    C1   110.98  3.000
 6UG  H9   C    C1   110.43  3.000
 6UG  N    C4   C13  120.29  3.000
 6UG  N    C4   C3   121.45  3.000
 6UG  C13  C4   C3   118.17  3.000
 6UG  H12  N    C4   116.88  3.000
 6UG  H12  N    C5   117.73  3.000
 6UG  C4   N    C5   124.64  3.000
 6UG  C11  C6   C7   117.93  3.000
 6UG  C7   C6   C5   121.27  3.000
 6UG  C11  C6   C5   120.76  3.000
 6UG  H13  C8   C9   121.33  3.000
 6UG  H13  C8   C7   119.14  3.000
 6UG  C9   C8   C7   119.53  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
 6UG  CONST_01  C13  N1   C1   C2     0.00   0.0  0
 6UG  CONST_02  C13  C4   C3   C2     0.00   0.0  0
 6UG  CONST_03  N1   C1   C2   C3     0.00   0.0  0
 6UG  CONST_04  N1   C13  C4   C3     0.00   0.0  0
 6UG  CONST_05  C14  C13  C4   C3   180.00   0.0  0
 6UG  CONST_06  C10  C11  C6   C7     0.00   0.0  0
 6UG  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 6UG  CONST_08  C6   C11  C10  C9     0.00   0.0  0
 6UG  CONST_09  C6   C7   C8   C9     0.00   0.0  0
 6UG  CONST_10  C8   C9   C10  C11    0.00   0.0  0
 6UG  CONST_11  C8   C7   C6   C11    0.00   0.0  0
 6UG  CONST_12  C16  C15  C14  C13  180.00   0.0  0
 6UG  CONST_13  C18  C19  C14  C13  180.00   0.0  0
 6UG  CONST_14  C18  C17  C16  C15    0.00   0.0  0
 6UG  CONST_17  C18  C19  C14  C15    0.00   0.0  0
 6UG  CONST_18  C14  C15  C16  C17    0.00   0.0  0
 6UG  CONST_19  C14  C19  C18  C17    0.00   0.0  0
 6UG  CONST_20  C19  C14  C15  C16    0.00   0.0  0
 6UG  CONST_21  C19  C18  C17  C16    0.00   0.0  0
 6UG  CONST_24  C1   N1   C13  C14  180.00   0.0  0
 6UG  CONST_25  C4   C3   C2   C1     0.00   0.0  0
 6UG  CONST_26  C4   C13  N1   C1     0.00   0.0  0
 6UG  CONST_27  N    C4   C3   C2   180.00   0.0  0
 6UG  CONST_28  C    C1   C2   C3   180.00   0.0  0
 6UG  CONST_29  C10  C11  C6   C5   180.00   0.0  0
 6UG  CONST_30  C8   C7   C6   C5   180.00   0.0  0
 6UG  CONST_31  F    C11  C6   C7   180.00   0.0  0
 6UG  CONST_32  C12  C9   C8   C7   180.00   0.0  0
 6UG  CONST_33  F    C11  C10  C9   180.00   0.0  0
 6UG  CONST_34  C12  C9   C10  C11  180.00   0.0  0
 6UG  CONST_35  C    C1   N1   C13  180.00   0.0  0
 6UG  CONST_36  F4   C17  C16  C15  180.00   0.0  0
 6UG  CONST_37  C19  C18  C17  F4   180.00   0.0  0
 6UG  CONST_38  N    C4   C13  C14    0.00   0.0  0
 6UG  CONST_39  N    C4   C13  N1   180.00   0.0  0
 6UG  CONST_40  H3   C7   C8   C9   180.00   0.0  0
 6UG  CONST_41  H13  C8   C9   C10  180.00   0.0  0
 6UG  CONST_42  H2   C3   C4   C13  180.00   0.0  0
 6UG  CONST_43  H5   C15  C14  C13    0.00   0.0  0
 6UG  CONST_44  H8   C19  C14  C13    0.00   0.0  0
 6UG  CONST_45  H7   C16  C17  C18  180.00   0.0  0
 6UG  CONST_46  H6   C18  C17  C16  180.00   0.0  0
 6UG  CONST_47  H1   C2   C1   N1   180.00   0.0  0
 6UG  CONST_48  H4   C10  C11  C6   180.00   0.0  0
 6UG  CONST_49  C6   C5   N    C4   180.00   0.0  0
 6UG  CONST_53  O    C5   N    C4     0.00   0.0  0
 6UG  Var_01    O    C5   C6   C7   129.62  30.0  2
 6UG  Var_02    F2   C12  C9   C10  154.49  30.0  2
 6UG  Var_03    H9   C    C1   C2    93.04  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
 6UG  plan-1  C2   0.020
 6UG  plan-1  C3   0.020
 6UG  plan-1  C13  0.020
 6UG  plan-1  C14  0.020
 6UG  plan-1  N1   0.020
 6UG  plan-1  C1   0.020
 6UG  plan-1  C    0.020
 6UG  plan-1  C4   0.020
 6UG  plan-1  N    0.020
 6UG  plan-1  H1   0.020
 6UG  plan-1  H2   0.020
 6UG  plan-2  C5   0.020
 6UG  plan-2  C7   0.020
 6UG  plan-2  C9   0.020
 6UG  plan-2  C10  0.020
 6UG  plan-2  C11  0.020
 6UG  plan-2  C12  0.020
 6UG  plan-2  C6   0.020
 6UG  plan-2  C8   0.020
 6UG  plan-2  H3   0.020
 6UG  plan-2  H4   0.020
 6UG  plan-2  H13  0.020
 6UG  plan-2  F    0.020
 6UG  plan-3  C13  0.020
 6UG  plan-3  C15  0.020
 6UG  plan-3  C18  0.020
 6UG  plan-3  C17  0.020
 6UG  plan-3  C16  0.020
 6UG  plan-3  C19  0.020
 6UG  plan-3  C14  0.020
 6UG  plan-3  H5   0.020
 6UG  plan-3  H6   0.020
 6UG  plan-3  H7   0.020
 6UG  plan-3  H8   0.020
 6UG  plan-3  F4   0.020
 6UG  plan-4  C5   0.020
 6UG  plan-4  C4   0.020
 6UG  plan-4  N    0.020
 6UG  plan-4  O    0.020
 6UG  plan-4  C6   0.020
 6UG  plan-4  H12  0.020

