# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:54:39 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1NC(=O)N2CCC(CC2)c3ccccc3C(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
 2T1  2T1  '2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid'  ligand  46  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_2T1
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
 2T1  N1    N  NR6    0  -0.493   0.6351   0.1844   1.0701
 2T1  N3    N  NH1    0  -0.821   2.8137   0.1475   0.3230
 2T1  C4    C  CR6    0  -0.301  -4.6320   0.0204  -0.4323
 2T1  C5    C  CR16   0  -0.281  -5.6770   0.5579  -1.1813
 2T1  C6    C  CR16   0  -0.260  -5.4835   1.6880  -1.9566
 2T1  C7    C  CR16   0  -0.397  -2.1579   0.1046   0.3136
 2T1  C8    C  C      0  -0.398  -1.0426  -0.3354  -0.6397
 2T1  C10   C  C      0  -0.304  -0.3864   0.6016   2.0116
 2T1  C13   C  CR6    0   0.356   4.1128   0.5672   0.0785
 2T1  C15   C  CR6    0  -0.234   5.0313  -0.3948  -0.4052
 2T1  C17   C  CR16   0  -0.317   4.5363   1.8936   0.2358
 2T1  C21   C  C      0   0.463   4.6685  -1.8538  -0.6507
 2T1  O3    O  OC    -1  -0.562   5.5741  -2.6171  -1.0108
 2T1  O2    O  O      0  -0.605   3.4651  -2.1931  -0.4770
 2T1  C16   C  CR16   0  -0.283   6.3354   0.0088  -0.6828
 2T1  C19   C  CR16   0  -0.271   6.7547   1.3168  -0.5120
 2T1  C18   C  CR16   0  -0.253   5.8400   2.2564  -0.0562
 2T1  C14   C  C      0   0.707   1.8704   0.7635   1.1000
 2T1  O1    O  O      0  -0.535   2.1043   1.7516   1.7890
 2T1  C11   C  C      0  -0.405  -1.6152   1.1458   1.2970
 2T1  C9    C  C      0  -0.320   0.1838  -0.8212   0.1260
 2T1  C3    C  CR6    0   0.238  -3.3621   0.6150  -0.4488
 2T1  C2    C  CR16   0  -0.320  -3.1979   1.7538  -1.2371
 2T1  C1    C  CR16   0  -0.226  -4.2354   2.2893  -1.9819
 2T1  F1    F  F      0  -0.318  -4.1299  -2.2435   0.0238
 2T1  F3    F  F      0  -0.318  -4.6935  -1.0054   1.6967
 2T1  F2    F  F      0  -0.301  -6.1685  -1.6299   0.2738
 2T1  HN3   H  HNH1   0   0.442   2.7282  -0.8542   0.0690
 2T1  H5    H  HCR6   0   0.270  -6.6554   0.0995  -1.1692
 2T1  H6    H  HCR6   0   0.266  -6.3031   2.0913  -2.5355
 2T1  H7    H  HCR6   0   0.245  -2.4194  -0.7705   0.9084
 2T1  H8    H  H      0   0.248  -1.3962  -1.1430  -1.2841
 2T1  H8A   H  H      0   0.233  -0.7518   0.4936  -1.2902
 2T1  H10   H  H      0   0.232  -0.6759  -0.2649   2.6190
 2T1  H10A  H  H      0   0.265   0.0261   1.3467   2.6851
 2T1  H17   H  HCR6   0   0.265   3.8461   2.6455   0.5829
 2T1  H16   H  HCR6   0   0.246   7.0329  -0.7341  -1.0462
 2T1  H19   H  HCR6   0   0.244   7.7747   1.6001  -0.7365
 2T1  H18   H  HCR6   0   0.251   6.1376   3.2898   0.0724
 2T1  H11   H  H      0   0.232  -1.3482   2.0687   0.7757
 2T1  H11A  H  H      0   0.245  -2.3780   1.3970   2.0371
 2T1  H9    H  H      0   0.257   0.9623  -1.0648  -0.5908
 2T1  H9A   H  H      0   0.236  -0.0591  -1.7448   0.6640
 2T1  H2    H  HCR6   0   0.261  -2.2298   2.2377  -1.2738
 2T1  H1    H  HCR6   0   0.265  -4.0669   3.1742  -2.5814
 2T1  C12   C  CT     0   1.057  -4.9048  -1.2082   0.3858

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
 2T1  C9   N1    single    1.451  0.020  1.451
 2T1  C14  N1    single    1.365  0.020  1.365
 2T1  N1   C10   single    1.451  0.020  1.451
 2T1  C13  N3    single    1.387  0.020  1.387
 2T1  N3   C14   single    1.369  0.020  1.369
 2T1  N3   HN3   single    0.860  0.020  1.020
 2T1  C3   C4    aromatic  1.402  0.020  1.402
 2T1  C5   C4    aromatic  1.394  0.020  1.394
 2T1  C4   C12   single    1.501  0.020  1.501
 2T1  C6   C5    aromatic  1.384  0.020  1.384
 2T1  C5   H5    single    0.930  0.020  1.080
 2T1  C1   C6    aromatic  1.386  0.020  1.386
 2T1  C6   H6    single    0.930  0.020  1.080
 2T1  C8   C7    single    1.532  0.020  1.532
 2T1  C3   C7    single    1.514  0.020  1.514
 2T1  C7   C11   single    1.532  0.020  1.532
 2T1  C7   H7    single    0.970  0.020  1.090
 2T1  C8   C9    single    1.525  0.020  1.525
 2T1  C8   H8    single    0.970  0.020  1.090
 2T1  C8   H8A   single    0.970  0.020  1.090
 2T1  C11  C10   single    1.522  0.020  1.522
 2T1  C10  H10   single    0.970  0.020  1.090
 2T1  C10  H10A  single    0.970  0.020  1.090
 2T1  C15  C13   aromatic  1.415  0.020  1.415
 2T1  C13  C17   aromatic  1.401  0.020  1.401
 2T1  C21  C15   single    1.523  0.020  1.523
 2T1  C16  C15   aromatic  1.393  0.020  1.393
 2T1  C18  C17   aromatic  1.384  0.020  1.384
 2T1  C17  H17   single    0.930  0.020  1.080
 2T1  O2   C21   deloc     1.262  0.020  1.262
 2T1  C21  O3    deloc     1.238  0.020  1.238
 2T1  C16  C19   aromatic  1.384  0.020  1.384
 2T1  C16  H16   single    0.930  0.020  1.080
 2T1  C19  C18   aromatic  1.388  0.020  1.388
 2T1  C19  H19   single    0.930  0.020  1.080
 2T1  C18  H18   single    0.930  0.020  1.080
 2T1  C14  O1    double    1.227  0.020  1.227
 2T1  C11  H11   single    0.970  0.020  1.090
 2T1  C11  H11A  single    0.970  0.020  1.090
 2T1  C9   H9    single    0.970  0.020  1.090
 2T1  C9   H9A   single    0.970  0.020  1.090
 2T1  C2   C3    aromatic  1.395  0.020  1.395
 2T1  C1   C2    aromatic  1.385  0.020  1.385
 2T1  C2   H2    single    0.930  0.020  1.080
 2T1  C1   H1    single    0.930  0.020  1.080
 2T1  F1   C12   single    1.343  0.020  1.343
 2T1  C12  F2    single    1.337  0.020  1.337
 2T1  C12  F3    single    1.343  0.020  1.343

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
 2T1  C9    N1   C14  126.14  3.000
 2T1  C14   N1   C10  120.08  3.000
 2T1  C9    N1   C10  113.74  3.000
 2T1  HN3   N3   C14  121.13  3.000
 2T1  HN3   N3   C13  109.05  3.000
 2T1  C14   N3   C13  127.56  3.000
 2T1  C12   C4   C3   121.20  3.000
 2T1  C12   C4   C5   118.19  3.000
 2T1  C3    C4   C5   120.61  3.000
 2T1  H5    C5   C6   118.64  3.000
 2T1  H5    C5   C4   120.62  3.000
 2T1  C6    C5   C4   120.74  3.000
 2T1  H6    C6   C1   120.73  3.000
 2T1  H6    C6   C5   119.90  3.000
 2T1  C1    C6   C5   119.37  3.000
 2T1  H7    C7   C3   110.78  3.000
 2T1  H7    C7   C11  106.28  3.000
 2T1  C3    C7   C11  112.09  3.000
 2T1  H7    C7   C8   106.48  3.000
 2T1  C11   C7   C8   109.69  3.000
 2T1  C3    C7   C8   111.26  3.000
 2T1  H8A   C8   H8   107.21  3.000
 2T1  H8A   C8   C9   109.05  3.000
 2T1  H8    C8   C9   108.72  3.000
 2T1  H8A   C8   C7   110.26  3.000
 2T1  H8    C8   C7   110.12  3.000
 2T1  C9    C8   C7   111.38  3.000
 2T1  H10A  C10  H10  107.39  3.000
 2T1  H10A  C10  C11  110.64  3.000
 2T1  H10   C10  C11  109.23  3.000
 2T1  H10A  C10  N1   109.42  3.000
 2T1  H10   C10  N1   108.54  3.000
 2T1  C11   C10  N1   111.50  3.000
 2T1  C17   C13  C15  119.05  3.000
 2T1  C17   C13  N3   123.35  3.000
 2T1  C15   C13  N3   117.55  3.000
 2T1  C16   C15  C21  117.92  3.000
 2T1  C16   C15  C13  118.60  3.000
 2T1  C21   C15  C13  123.47  3.000
 2T1  H17   C17  C18  119.21  3.000
 2T1  H17   C17  C13  120.19  3.000
 2T1  C18   C17  C13  120.60  3.000
 2T1  O2    C21  O3   124.87  3.000
 2T1  O3    C21  C15  117.60  3.000
 2T1  O2    C21  C15  117.54  3.000
 2T1  H16   C16  C19  119.67  3.000
 2T1  H16   C16  C15  118.14  3.000
 2T1  C19   C16  C15  122.19  3.000
 2T1  H19   C19  C18  120.80  3.000
 2T1  H19   C19  C16  120.49  3.000
 2T1  C18   C19  C16  118.72  3.000
 2T1  H18   C18  C19  120.25  3.000
 2T1  H18   C18  C17  118.93  3.000
 2T1  C19   C18  C17  120.82  3.000
 2T1  O1    C14  N3   123.35  3.000
 2T1  O1    C14  N1   121.78  3.000
 2T1  N3    C14  N1   114.87  3.000
 2T1  H11A  C11  H11  107.43  3.000
 2T1  H11A  C11  C10  109.14  3.000
 2T1  H11   C11  C10  109.19  3.000
 2T1  H11A  C11  C7   110.12  3.000
 2T1  H11   C11  C7   110.75  3.000
 2T1  C10   C11  C7   110.15  3.000
 2T1  H9A   C9   H9   107.09  3.000
 2T1  H9A   C9   C8   109.67  3.000
 2T1  H9    C9   C8   108.46  3.000
 2T1  H9A   C9   N1   109.48  3.000
 2T1  H9    C9   N1   111.22  3.000
 2T1  C8    C9   N1   110.85  3.000
 2T1  C2    C3   C7   117.79  3.000
 2T1  C2    C3   C4   117.35  3.000
 2T1  C7    C3   C4   124.85  3.000
 2T1  H2    C2   C1   118.60  3.000
 2T1  H2    C2   C3   119.29  3.000
 2T1  C1    C2   C3   122.11  3.000
 2T1  H1    C1   C2   119.84  3.000
 2T1  H1    C1   C6   120.34  3.000
 2T1  C2    C1   C6   119.82  3.000
 2T1  F2    C12  F3   106.14  3.000
 2T1  F3    C12  F1   106.78  3.000
 2T1  F2    C12  F1   106.24  3.000
 2T1  F3    C12  C4   112.32  3.000
 2T1  F2    C12  C4   112.60  3.000
 2T1  F1    C12  C4   112.29  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
 2T1  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 2T1  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 2T1  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 2T1  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 2T1  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 2T1  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 2T1  CONST_07  C19  C16  C15  C13    0.00   0.0  0
 2T1  CONST_08  C19  C18  C17  C13    0.00   0.0  0
 2T1  CONST_09  C18  C17  C13  C15    0.00   0.0  0
 2T1  CONST_10  C18  C19  C16  C15    0.00   0.0  0
 2T1  CONST_11  C16  C15  C13  C17    0.00   0.0  0
 2T1  CONST_12  C16  C19  C18  C17    0.00   0.0  0
 2T1  CONST_13  C7   C3   C4   C5   180.00   0.0  0
 2T1  CONST_14  C1   C2   C3   C7   180.00   0.0  0
 2T1  CONST_15  C16  C15  C13  N3   180.00   0.0  0
 2T1  CONST_16  C18  C17  C13  N3   180.00   0.0  0
 2T1  CONST_17  C12  C4   C5   C6   180.00   0.0  0
 2T1  CONST_18  C12  C4   C3   C7     0.00   0.0  0
 2T1  CONST_19  C21  C15  C13  C17  180.00   0.0  0
 2T1  CONST_20  C19  C16  C15  C21  180.00   0.0  0
 2T1  CONST_21  C12  C4   C3   C2   180.00   0.0  0
 2T1  CONST_22  H2   C2   C3   C4   180.00   0.0  0
 2T1  CONST_23  H6   C6   C5   C4   180.00   0.0  0
 2T1  CONST_24  H1   C1   C6   C5   180.00   0.0  0
 2T1  CONST_25  H16  C16  C15  C13  180.00   0.0  0
 2T1  CONST_26  H18  C18  C17  C13  180.00   0.0  0
 2T1  CONST_27  H17  C17  C13  C15  180.00   0.0  0
 2T1  CONST_28  H19  C19  C16  C15  180.00   0.0  0
 2T1  CONST_29  H5   C5   C4   C3   180.00   0.0  0
 2T1  CONST_30  O1   C14  N1   C10    0.00   0.0  0
 2T1  CONST_31  C9   N1   C14  O1   180.00   0.0  0
 2T1  CONST_32  C13  N3   C14  N1   180.00   0.0  0
 2T1  CONST_35  C9   N1   C14  N3     0.00   0.0  0
 2T1  CONST_36  C10  N1   C14  N3   180.00   0.0  0
 2T1  CONST_37  HN3  N3   C13  C15    0.00   0.0  0
 2T1  CONST_38  O1   C14  N3   C13    0.00   0.0  0
 2T1  Var_01    C7   C8   C9   N1   -54.35  30.0  1
 2T1  Var_02    C7   C11  C10  N1    55.95  30.0  1
 2T1  Var_03    C10  N1   C9   C8    56.25  30.0  1
 2T1  Var_04    C9   N1   C10  C11  -57.61  30.0  1
 2T1  Var_05    F1   C12  C4   C5   119.86  30.0  2
 2T1  Var_06    O2   C21  C15  C13    3.86  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2T1  chir_01  C7  C8  C3  C11  positiv

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
 2T1  plan-1  N3   0.020
 2T1  plan-1  C13  0.020
 2T1  plan-1  C15  0.020
 2T1  plan-1  C17  0.020
 2T1  plan-1  C21  0.020
 2T1  plan-1  C16  0.020
 2T1  plan-1  C19  0.020
 2T1  plan-1  C18  0.020
 2T1  plan-1  H17  0.020
 2T1  plan-1  H16  0.020
 2T1  plan-1  H19  0.020
 2T1  plan-1  H18  0.020
 2T1  plan-2  C4   0.020
 2T1  plan-2  C5   0.020
 2T1  plan-2  C6   0.020
 2T1  plan-2  C7   0.020
 2T1  plan-2  C3   0.020
 2T1  plan-2  C2   0.020
 2T1  plan-2  C1   0.020
 2T1  plan-2  H5   0.020
 2T1  plan-2  H6   0.020
 2T1  plan-2  H2   0.020
 2T1  plan-2  H1   0.020
 2T1  plan-2  C12  0.020
 2T1  plan-3  N1   0.020
 2T1  plan-3  N3   0.020
 2T1  plan-3  C10  0.020
 2T1  plan-3  C13  0.020
 2T1  plan-3  C14  0.020
 2T1  plan-3  O1   0.020
 2T1  plan-3  C9   0.020
 2T1  plan-3  HN3  0.020
 2T1  plan-4  C15  0.020
 2T1  plan-4  C21  0.020
 2T1  plan-4  O3   0.020
 2T1  plan-4  O2   0.020

