# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:41:19 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(NC(=O)c2ccccc2NCc3ccncc3)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
 5T2  5T2  2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide  ligand  43  27  .  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_5T2
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
 5T2  C1   C  CR16  0  -0.284  -1.3722   4.4168  -0.1991
 5T2  C2   C  CR16  0  -0.236  -2.6821   4.2513   0.2373
 5T2  C3   C  CR16  0  -0.360  -3.2308   2.9928   0.3753
 5T2  C11  C  CR6   0   0.415   2.0779   0.0803  -0.6452
 5T2  C12  C  CR16  0  -0.385   3.2632   0.2735   0.0625
 5T2  C13  C  CR6   0  -0.179   4.3424  -0.5765  -0.1277
 5T2  C14  C  CR16  0  -0.298   4.2540  -1.6417  -1.0139
 5T2  C15  C  CR16  0  -0.235   3.0741  -1.8267  -1.7175
 5T2  C16  C  CR16  0  -0.294   1.9908  -0.9793  -1.5498
 5T2  C17  C  CH2   0  -0.332  -4.4477   0.4098   0.5305
 5T2  C18  C  CR6   0   0.162  -4.7883  -1.0502   0.4338
 5T2  C19  C  CR16  0  -0.359  -4.8049  -1.6969  -0.7979
 5T2  C20  C  CR16  0  -0.056  -5.1208  -3.0452  -0.8443
 5T2  C22  C  CR16  0  -0.056  -5.3952  -3.1499   1.4059
 5T2  C23  C  CR16  0  -0.370  -5.0889  -1.8047   1.5589
 5T2  C24  C  CT    0   1.053   5.5858  -0.3635   0.6788
 5T2  C4   C  CR6   0   0.391  -2.4888   1.8329   0.0790
 5T2  C5   C  CR6   0  -0.151  -1.1331   1.9985  -0.3175
 5T2  C6   C  CR16  0  -0.296  -0.6192   3.2899  -0.4647
 5T2  C7   C  C     0   0.564  -0.2846   0.8170  -0.6031
 5T2  N8   N  NH1   0  -0.704  -3.0543   0.6074   0.2085
 5T2  N9   N  NH1   0  -0.763   1.0535   1.0043  -0.4285
 5T2  O10  O  O     0  -0.482  -0.7478  -0.2607  -0.9566
 5T2  N21  N  N     0  -0.407  -5.4136  -3.7679   0.2319
 5T2  F25  F  F     0  -0.309   5.8468   0.9351   0.8722
 5T2  F26  F  F     0  -0.314   5.4855  -0.9189   1.8965
 5T2  F27  F  F     0  -0.305   6.6644  -0.8990   0.0991
 5T2  H1   H  HCR6  0   0.255  -0.9496   5.4025  -0.3337
 5T2  H2   H  HCR6  0   0.262  -3.2914   5.1171   0.4640
 5T2  H3   H  HCR6  0   0.279  -4.2549   2.9055   0.7106
 5T2  H4   H  HCR6  0   0.287   3.3289   1.0980   0.7625
 5T2  H5   H  HCR6  0   0.273   5.0833  -2.3169  -1.1714
 5T2  H6   H  HCR6  0   0.272   2.9968  -2.6438  -2.4218
 5T2  H7   H  HCR6  0   0.284   1.0980  -1.1438  -2.1310
 5T2  H8   H  HCH2  0   0.253  -5.0944   0.9700  -0.1562
 5T2  H9   H  HCH2  0   0.255  -4.6684   0.7739   1.5382
 5T2  H10  H  HCR6  0   0.274  -4.5852  -1.1637  -1.7146
 5T2  H11  H  HCR6  0   0.266  -5.1433  -3.5628  -1.7969
 5T2  H12  H  HCR6  0   0.267  -5.6348  -3.7513   2.2759
 5T2  H13  H  HCR6  0   0.270  -5.0877  -1.3591   2.5453
 5T2  H14  H  HCR6  0   0.262   0.3933   3.4267  -0.8245
 5T2  H15  H  HNH1  0   0.407  -2.5382  -0.1695  -0.1734
 5T2  H16  H  HNH1  0   0.423   1.3357   1.8415   0.0568

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
 5T2  F27  C24  single    1.337  0.020  1.337
 5T2  F25  C24  single    1.339  0.020  1.339
 5T2  C24  F26  single    1.342  0.020  1.342
 5T2  C24  C13  single    1.497  0.020  1.497
 5T2  C13  C12  aromatic  1.387  0.020  1.387
 5T2  C13  C14  aromatic  1.388  0.020  1.388
 5T2  C20  N21  aromatic  1.329  0.020  1.329
 5T2  C20  C19  aromatic  1.386  0.020  1.386
 5T2  C12  C11  aromatic  1.394  0.020  1.394
 5T2  N21  C22  aromatic  1.327  0.020  1.327
 5T2  C14  C15  aromatic  1.386  0.020  1.386
 5T2  C19  C18  aromatic  1.391  0.020  1.391
 5T2  C11  N9   single    1.396  0.020  1.396
 5T2  C11  C16  aromatic  1.396  0.020  1.396
 5T2  N9   C7   single    1.362  0.020  1.362
 5T2  C6   C1   aromatic  1.381  0.020  1.381
 5T2  C6   C5   aromatic  1.398  0.020  1.398
 5T2  O10  C7   double    1.225  0.020  1.225
 5T2  C15  C16  aromatic  1.386  0.020  1.386
 5T2  C7   C5   single    1.482  0.020  1.482
 5T2  C1   C2   aromatic  1.391  0.020  1.391
 5T2  C5   C4   aromatic  1.422  0.020  1.422
 5T2  C22  C23  aromatic  1.388  0.020  1.388
 5T2  C2   C3   aromatic  1.380  0.020  1.380
 5T2  C18  C23  aromatic  1.388  0.020  1.388
 5T2  C18  C17  single    1.502  0.020  1.502
 5T2  C4   C3   aromatic  1.408  0.020  1.408
 5T2  C4   N8   single    1.356  0.020  1.356
 5T2  N8   C17  single    1.444  0.020  1.444
 5T2  C1   H1   single    0.930  0.020  1.080
 5T2  C2   H2   single    0.930  0.020  1.080
 5T2  C3   H3   single    0.930  0.020  1.080
 5T2  C12  H4   single    0.930  0.020  1.080
 5T2  C14  H5   single    0.930  0.020  1.080
 5T2  C15  H6   single    0.930  0.020  1.080
 5T2  C16  H7   single    0.930  0.020  1.080
 5T2  C17  H8   single    0.970  0.020  1.090
 5T2  C17  H9   single    0.970  0.020  1.090
 5T2  C19  H10  single    0.930  0.020  1.080
 5T2  C20  H11  single    0.930  0.020  1.080
 5T2  C22  H12  single    0.930  0.020  1.080
 5T2  C23  H13  single    0.930  0.020  1.080
 5T2  C6   H14  single    0.930  0.020  1.080
 5T2  N8   H15  single    0.860  0.020  1.020
 5T2  N9   H16  single    0.860  0.020  1.020

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
 5T2  H1   C1   C6   120.47  3.000
 5T2  H1   C1   C2   121.05  3.000
 5T2  C6   C1   C2   118.48  3.000
 5T2  H2   C2   C3   118.99  3.000
 5T2  H2   C2   C1   120.04  3.000
 5T2  C3   C2   C1   120.96  3.000
 5T2  H3   C3   C4   119.86  3.000
 5T2  H3   C3   C2   118.77  3.000
 5T2  C4   C3   C2   121.37  3.000
 5T2  N9   C11  C16  123.85  3.000
 5T2  C16  C11  C12  119.16  3.000
 5T2  N9   C11  C12  116.95  3.000
 5T2  H4   C12  C13  120.52  3.000
 5T2  H4   C12  C11  119.01  3.000
 5T2  C13  C12  C11  120.47  3.000
 5T2  C24  C13  C14  120.38  3.000
 5T2  C14  C13  C12  120.55  3.000
 5T2  C24  C13  C12  119.02  3.000
 5T2  H5   C14  C15  119.72  3.000
 5T2  H5   C14  C13  121.56  3.000
 5T2  C15  C14  C13  118.72  3.000
 5T2  H6   C15  C16  119.02  3.000
 5T2  H6   C15  C14  119.48  3.000
 5T2  C16  C15  C14  121.49  3.000
 5T2  H7   C16  C15  119.27  3.000
 5T2  H7   C16  C11  121.13  3.000
 5T2  C15  C16  C11  119.60  3.000
 5T2  H9   C17  H8   106.72  3.000
 5T2  H9   C17  N8   110.77  3.000
 5T2  H8   C17  N8   111.07  3.000
 5T2  H9   C17  C18  109.70  3.000
 5T2  H8   C17  C18  108.80  3.000
 5T2  N8   C17  C18  109.73  3.000
 5T2  C23  C18  C19  117.55  3.000
 5T2  C23  C18  C17  121.69  3.000
 5T2  C19  C18  C17  120.76  3.000
 5T2  H10  C19  C20  119.80  3.000
 5T2  H10  C19  C18  121.20  3.000
 5T2  C20  C19  C18  118.99  3.000
 5T2  H11  C20  N21  116.56  3.000
 5T2  H11  C20  C19  119.91  3.000
 5T2  N21  C20  C19  123.53  3.000
 5T2  H12  C22  N21  116.64  3.000
 5T2  H12  C22  C23  119.86  3.000
 5T2  N21  C22  C23  123.50  3.000
 5T2  H13  C23  C22  119.98  3.000
 5T2  H13  C23  C18  120.98  3.000
 5T2  C22  C23  C18  119.04  3.000
 5T2  F27  C24  F26  106.75  3.000
 5T2  F26  C24  F25  106.55  3.000
 5T2  F27  C24  F25  107.10  3.000
 5T2  F26  C24  C13  111.58  3.000
 5T2  F25  C24  C13  112.19  3.000
 5T2  F27  C24  C13  112.31  3.000
 5T2  N8   C4   C5   121.97  3.000
 5T2  N8   C4   C3   120.30  3.000
 5T2  C5   C4   C3   117.71  3.000
 5T2  C7   C5   C6   120.37  3.000
 5T2  C7   C5   C4   120.43  3.000
 5T2  C6   C5   C4   119.18  3.000
 5T2  H14  C6   C5   119.70  3.000
 5T2  H14  C6   C1   118.06  3.000
 5T2  C5   C6   C1   122.22  3.000
 5T2  O10  C7   N9   121.95  3.000
 5T2  O10  C7   C5   122.71  3.000
 5T2  N9   C7   C5   115.33  3.000
 5T2  H15  N8   C4   116.54  3.000
 5T2  H15  N8   C17  118.25  3.000
 5T2  C4   N8   C17  123.20  3.000
 5T2  H16  N9   C7   116.80  3.000
 5T2  H16  N9   C11  114.77  3.000
 5T2  C7   N9   C11  127.56  3.000
 5T2  C22  N21  C20  117.39  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
 5T2  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 5T2  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 5T2  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 5T2  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5T2  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 5T2  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 5T2  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 5T2  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 5T2  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 5T2  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 5T2  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 5T2  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 5T2  CONST_13  N21  C20  C19  C18     0.00   0.0  0
 5T2  CONST_14  N21  C22  C23  C18     0.00   0.0  0
 5T2  CONST_15  C22  N21  C20  C19     0.00   0.0  0
 5T2  CONST_16  C22  C23  C18  C19     0.00   0.0  0
 5T2  CONST_17  C23  C22  N21  C20     0.00   0.0  0
 5T2  CONST_18  C23  C18  C19  C20     0.00   0.0  0
 5T2  CONST_19  C7   C5   C6   C1    180.00   0.0  0
 5T2  CONST_20  N8   C4   C3   C2    180.00   0.0  0
 5T2  CONST_21  C7   C5   C4   C3    180.00   0.0  0
 5T2  CONST_22  C24  C13  C12  C11   180.00   0.0  0
 5T2  CONST_23  N9   C11  C12  C13   180.00   0.0  0
 5T2  CONST_24  C24  C13  C14  C15   180.00   0.0  0
 5T2  CONST_25  N9   C11  C16  C15   180.00   0.0  0
 5T2  CONST_26  C20  C19  C18  C17   180.00   0.0  0
 5T2  CONST_27  C22  C23  C18  C17   180.00   0.0  0
 5T2  CONST_28  N8   C4   C5   C6    180.00   0.0  0
 5T2  CONST_29  H3   C3   C2   C1    180.00   0.0  0
 5T2  CONST_30  H14  C6   C1   C2    180.00   0.0  0
 5T2  CONST_31  H1   C1   C2   C3    180.00   0.0  0
 5T2  CONST_32  H6   C15  C16  C11   180.00   0.0  0
 5T2  CONST_33  H5   C14  C13  C12   180.00   0.0  0
 5T2  CONST_34  H7   C16  C11  C12   180.00   0.0  0
 5T2  CONST_35  H4   C12  C13  C14   180.00   0.0  0
 5T2  CONST_36  H11  C20  C19  C18   180.00   0.0  0
 5T2  CONST_37  H12  C22  C23  C18   180.00   0.0  0
 5T2  CONST_38  H13  C23  C18  C19   180.00   0.0  0
 5T2  CONST_39  H10  C19  C18  C23   180.00   0.0  0
 5T2  CONST_40  H2   C2   C3   C4    180.00   0.0  0
 5T2  CONST_41  C5   C7   N9   C11   180.00   0.0  0
 5T2  CONST_42  C17  N8   C4   C3      0.00   0.0  0
 5T2  CONST_45  C5   C4   N8   C17   180.00   0.0  0
 5T2  CONST_46  H15  N8   C4   C3    180.00   0.0  0
 5T2  CONST_47  H16  N9   C11  C12     0.00   0.0  0
 5T2  CONST_48  O10  C7   N9   C11     0.00   0.0  0
 5T2  Var_01    F27  C24  C13  C12  -157.78  30.0  2
 5T2  Var_02    C4   N8   C17  C18   173.11  30.0  2
 5T2  Var_03    N8   C17  C18  C19   -68.62  30.0  2
 5T2  Var_04    N9   C7   C5   C4   -153.90  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
 5T2  plan-1  C11  0.020
 5T2  plan-1  C12  0.020
 5T2  plan-1  C13  0.020
 5T2  plan-1  C14  0.020
 5T2  plan-1  C15  0.020
 5T2  plan-1  C16  0.020
 5T2  plan-1  C24  0.020
 5T2  plan-1  N9   0.020
 5T2  plan-1  H4   0.020
 5T2  plan-1  H5   0.020
 5T2  plan-1  H6   0.020
 5T2  plan-1  H7   0.020
 5T2  plan-2  C17  0.020
 5T2  plan-2  C18  0.020
 5T2  plan-2  C19  0.020
 5T2  plan-2  C20  0.020
 5T2  plan-2  C22  0.020
 5T2  plan-2  C23  0.020
 5T2  plan-2  N21  0.020
 5T2  plan-2  H10  0.020
 5T2  plan-2  H11  0.020
 5T2  plan-2  H12  0.020
 5T2  plan-2  H13  0.020
 5T2  plan-3  C1   0.020
 5T2  plan-3  C2   0.020
 5T2  plan-3  C3   0.020
 5T2  plan-3  C4   0.020
 5T2  plan-3  C5   0.020
 5T2  plan-3  C6   0.020
 5T2  plan-3  C7   0.020
 5T2  plan-3  N8   0.020
 5T2  plan-3  H1   0.020
 5T2  plan-3  H2   0.020
 5T2  plan-3  H3   0.020
 5T2  plan-3  H14  0.020
 5T2  plan-4  C11  0.020
 5T2  plan-4  C5   0.020
 5T2  plan-4  C7   0.020
 5T2  plan-4  N9   0.020
 5T2  plan-4  O10  0.020
 5T2  plan-4  H16  0.020
 5T2  plan-5  C17  0.020
 5T2  plan-5  C4   0.020
 5T2  plan-5  N8   0.020
 5T2  plan-5  H15  0.020

