# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 22:08:23 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 2-{[3-(trifluoromethyl)phenyl]amino}pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccnc1Nc2cccc(c2)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
 NFL  NFL  '2-{[3-(trifluoromethyl)phenyl]amino}pyridine-3-carboxylic acid'  ligand  28  20  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NFL
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
 NFL  F3   F  F      0  -0.303   0.3130   0.3452  -5.0771
 NFL  C15  C  CT     0   1.048   0.8621   0.2217  -3.8654
 NFL  F1   F  F      0  -0.316   1.7688   1.2043  -3.7468
 NFL  F2   F  F      0  -0.316   1.5530  -0.9287  -3.8670
 NFL  C9   C  CR6    0  -0.169  -0.1493   0.2623  -2.7630
 NFL  C10  C  CR16   0  -0.411   0.2984   0.0778  -1.4649
 NFL  C11  C  CR6    0   0.408  -0.5893   0.1089  -0.3807
 NFL  C12  C  CR16   0  -0.319  -1.9477   0.3303  -0.6508
 NFL  C13  C  CR16   0  -0.229  -2.3749   0.5145  -1.9558
 NFL  C14  C  CR16   0  -0.324  -1.4946   0.4859  -3.0271
 NFL  N2   N  NH1    0  -0.807  -0.0324  -0.0810   0.8640
 NFL  C1   C  C      0   0.513  -0.5830  -0.1092   2.1127
 NFL  N1   N  N      0  -0.477  -1.8971   0.0346   2.2539
 NFL  C2   C  C      0  -0.311   0.2867  -0.2964   3.2237
 NFL  C6   C  C      0   0.458   1.7939  -0.4646   3.1114
 NFL  O8   O  OC    -1  -0.565   2.4239  -0.6317   4.1642
 NFL  O7   O  O      0  -0.602   2.2956  -0.4211   1.9571
 NFL  C3   C  C1     0  -0.158  -0.3043  -0.3197   4.4734
 NFL  C4   C  C1     0  -0.367  -1.6782  -0.1658   4.6224
 NFL  C5   C  C1     0  -0.042  -2.4221   0.0070   3.4731
 NFL  H10  H  HCR6   0   0.274   1.3513  -0.0942  -1.2714
 NFL  H12  H  HCR6   0   0.288  -2.6596   0.3561   0.1565
 NFL  H13  H  HCR6   0   0.262  -3.4278   0.6842  -2.1399
 NFL  H14  H  HCR6   0   0.263  -1.8607   0.6359  -4.0324
 NFL  HN2  H  HNH1   0   0.427   0.9910  -0.2046   0.9283
 NFL  H3   H  H      0   0.261   0.3242  -0.4605   5.3426
 NFL  H4   H  H      0   0.258  -2.1505  -0.1800   5.5946
 NFL  H5   H  H      0   0.256  -3.4988   0.1290   3.5276

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
 NFL  F3   C15  single    1.336  0.020  1.336
 NFL  C15  F1   single    1.342  0.020  1.342
 NFL  C15  F2   single    1.342  0.020  1.342
 NFL  C15  C9   single    1.497  0.020  1.497
 NFL  C9   C10  aromatic  1.385  0.020  1.385
 NFL  C9   C14  aromatic  1.389  0.020  1.389
 NFL  C10  C11  aromatic  1.402  0.020  1.402
 NFL  C10  H10  single    0.930  0.020  1.080
 NFL  C11  C12  aromatic  1.403  0.020  1.403
 NFL  C11  N2   single    1.377  0.020  1.377
 NFL  C12  C13  aromatic  1.385  0.020  1.385
 NFL  C12  H12  single    0.930  0.020  1.080
 NFL  C13  C14  aromatic  1.387  0.020  1.387
 NFL  C13  H13  single    0.930  0.020  1.080
 NFL  C14  H14  single    0.930  0.020  1.080
 NFL  N2   C1   single    1.365  0.020  1.365
 NFL  N2   HN2  single    0.860  0.020  1.020
 NFL  C1   N1   aromatic  1.329  0.020  1.329
 NFL  C1   C2   aromatic  1.423  0.020  1.423
 NFL  N1   C5   aromatic  1.328  0.020  1.328
 NFL  C2   C6   single    1.521  0.020  1.521
 NFL  C2   C3   aromatic  1.383  0.020  1.383
 NFL  C6   O8   deloc     1.238  0.020  1.238
 NFL  C6   O7   deloc     1.259  0.020  1.259
 NFL  C3   C4   aromatic  1.391  0.020  1.391
 NFL  C3   H3   single    0.930  0.020  1.080
 NFL  C4   C5   aromatic  1.380  0.020  1.380
 NFL  C4   H4   single    0.930  0.020  1.080
 NFL  C5   H5   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
 NFL  C9   C15  F2   111.85  3.000
 NFL  C9   C15  F1   111.81  3.000
 NFL  F2   C15  F1   106.25  3.000
 NFL  C9   C15  F3   112.82  3.000
 NFL  F2   C15  F3   106.84  3.000
 NFL  F1   C15  F3   106.86  3.000
 NFL  C14  C9   C10  120.84  3.000
 NFL  C14  C9   C15  121.25  3.000
 NFL  C10  C9   C15  117.91  3.000
 NFL  H10  C10  C11  118.72  3.000
 NFL  H10  C10  C9   120.14  3.000
 NFL  C11  C10  C9   121.14  3.000
 NFL  N2   C11  C12  125.99  3.000
 NFL  N2   C11  C10  116.10  3.000
 NFL  C12  C11  C10  117.90  3.000
 NFL  H12  C12  C13  119.95  3.000
 NFL  H12  C12  C11  119.99  3.000
 NFL  C13  C12  C11  120.07  3.000
 NFL  H13  C13  C14  119.30  3.000
 NFL  H13  C13  C12  118.75  3.000
 NFL  C14  C13  C12  121.95  3.000
 NFL  H14  C14  C13  120.06  3.000
 NFL  H14  C14  C9   121.83  3.000
 NFL  C13  C14  C9   118.11  3.000
 NFL  HN2  N2   C1   109.90  3.000
 NFL  HN2  N2   C11  118.27  3.000
 NFL  C1   N2   C11  131.81  3.000
 NFL  C2   C1   N1   122.36  3.000
 NFL  C2   C1   N2   118.05  3.000
 NFL  N1   C1   N2   119.59  3.000
 NFL  C5   N1   C1   119.09  3.000
 NFL  C3   C2   C6   119.25  3.000
 NFL  C3   C2   C1   116.52  3.000
 NFL  C6   C2   C1   124.23  3.000
 NFL  O7   C6   O8   125.54  3.000
 NFL  O7   C6   C2   117.31  3.000
 NFL  O8   C6   C2   117.15  3.000
 NFL  H3   C3   C4   120.15  3.000
 NFL  H3   C3   C2   118.69  3.000
 NFL  C4   C3   C2   121.16  3.000
 NFL  H4   C4   C5   121.01  3.000
 NFL  H4   C4   C3   121.78  3.000
 NFL  C5   C4   C3   117.21  3.000
 NFL  H5   C5   C4   120.48  3.000
 NFL  H5   C5   N1   115.86  3.000
 NFL  C4   C5   N1   123.66  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
 NFL  CONST_01  C12  C11  C10  C9      0.00   0.0  0
 NFL  CONST_02  C12  C13  C14  C9      0.00   0.0  0
 NFL  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 NFL  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 NFL  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 NFL  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 NFL  CONST_07  C4   C5   N1   C1      0.00   0.0  0
 NFL  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 NFL  CONST_09  C3   C2   C1   N1      0.00   0.0  0
 NFL  CONST_10  C3   C4   C5   N1      0.00   0.0  0
 NFL  CONST_11  C5   N1   C1   C2      0.00   0.0  0
 NFL  CONST_12  C5   C4   C3   C2      0.00   0.0  0
 NFL  CONST_13  C11  C10  C9   C15   180.00   0.0  0
 NFL  CONST_14  C13  C14  C9   C15   180.00   0.0  0
 NFL  CONST_15  N2   C11  C10  C9    180.00   0.0  0
 NFL  CONST_16  N2   C11  C12  C13   180.00   0.0  0
 NFL  CONST_17  C5   N1   C1   N2    180.00   0.0  0
 NFL  CONST_18  C3   C2   C1   N2    180.00   0.0  0
 NFL  CONST_19  C6   C2   C1   N1    180.00   0.0  0
 NFL  CONST_20  C4   C3   C2   C6    180.00   0.0  0
 NFL  CONST_21  H13  C13  C14  C9    180.00   0.0  0
 NFL  CONST_22  H14  C14  C9   C10   180.00   0.0  0
 NFL  CONST_23  H12  C12  C11  C10   180.00   0.0  0
 NFL  CONST_24  H10  C10  C11  C12   180.00   0.0  0
 NFL  CONST_25  H5   C5   N1   C1    180.00   0.0  0
 NFL  CONST_26  H3   C3   C2   C1    180.00   0.0  0
 NFL  CONST_27  H4   C4   C5   N1    180.00   0.0  0
 NFL  Var_01    C1   N2   C11  C10   179.80  30.0  2
 NFL  Var_02    N1   C1   N2   C11     1.77  30.0  2
 NFL  Var_03    C10  C9   C15  F3    176.91  30.0  2
 NFL  Var_04    O8   C6   C2   C1   -179.35  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
 NFL  plan-1  C15  0.020
 NFL  plan-1  C9   0.020
 NFL  plan-1  C10  0.020
 NFL  plan-1  C11  0.020
 NFL  plan-1  C12  0.020
 NFL  plan-1  C13  0.020
 NFL  plan-1  C14  0.020
 NFL  plan-1  N2   0.020
 NFL  plan-1  H10  0.020
 NFL  plan-1  H12  0.020
 NFL  plan-1  H13  0.020
 NFL  plan-1  H14  0.020
 NFL  plan-2  N2   0.020
 NFL  plan-2  C1   0.020
 NFL  plan-2  N1   0.020
 NFL  plan-2  C2   0.020
 NFL  plan-2  C6   0.020
 NFL  plan-2  C3   0.020
 NFL  plan-2  C4   0.020
 NFL  plan-2  C5   0.020
 NFL  plan-2  H3   0.020
 NFL  plan-2  H4   0.020
 NFL  plan-2  H5   0.020
 NFL  plan-3  C2   0.020
 NFL  plan-3  C6   0.020
 NFL  plan-3  O8   0.020
 NFL  plan-3  O7   0.020

