# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:41:11 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-[[2-methyl-3-(trifluoromethyl)phenyl]amino]pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Nc2ncccc2C(O)=O)cccc1C(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
 JBO  JBO  "2-[[2-methyl-3-(trifluoromethyl)phenyl]amino]pyridine-3-carboxylic acid"  ligand  31  21  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JBO
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
 JBO  C02  C  CT     0   1.048  -21.4170   5.2262   8.5670
 JBO  C04  C  CR6    0  -0.242  -20.5980   3.9763   8.4166
 JBO  C05  C  CR6    0   0.021  -19.2825   3.9242   8.8909
 JBO  C06  C  CH3    0  -0.777  -18.5806   5.0927   9.5285
 JBO  C07  C  CR6    0   0.330  -18.5738   2.7054   8.7738
 JBO  C09  C  CR6    0   0.510  -16.2638   1.7989   9.0878
 JBO  C10  C  CR6    0  -0.309  -15.0770   1.9564   9.8586
 JBO  C11  C  C      0   0.456  -14.8870   3.0199  10.9309
 JBO  C14  C  CR16   0  -0.161  -14.0429   1.0797   9.5887
 JBO  C15  C  CR16   0  -0.361  -14.1662   0.0989   8.6109
 JBO  C16  C  CR16   0  -0.051  -15.3595   0.0463   7.9197
 JBO  C18  C  CR16   0  -0.296  -19.1861   1.6080   8.1605
 JBO  C19  C  CR16   0  -0.249  -20.4758   1.7044   7.6739
 JBO  C20  C  CR16   0  -0.317  -21.1933   2.8793   7.8016
 JBO  F01  F  F      0  -0.303  -22.6698   5.0738   8.1236
 JBO  F03  F  F      0  -0.317  -21.5180   5.6155   9.8478
 JBO  F21  F  F      0  -0.318  -20.9071   6.2673   7.8874
 JBO  N08  N  NH1    0  -0.813  -17.3027   2.6567   9.3187
 JBO  N17  N  N      0  -0.472  -16.3777   0.8672   8.1455
 JBO  O12  O  OC    -1  -0.558  -13.7897   3.0550  11.5028
 JBO  O13  O  O      0  -0.595  -15.8612   3.7857  11.1546
 JBO  H1   H  HCH3   0   0.257  -18.4806   4.9559  10.6075
 JBO  H2   H  HCH3   0   0.250  -17.5719   5.1954   9.1268
 JBO  H3   H  HCH3   0   0.262  -19.0714   6.0458   9.3724
 JBO  H4   H  HCR6   0   0.257  -13.1262   1.1676  10.1562
 JBO  H5   H  HCR6   0   0.254  -13.3660  -0.5949   8.3947
 JBO  H6   H  HCR6   0   0.252  -15.5128  -0.6940   7.1411
 JBO  H7   H  HCR6   0   0.276  -18.6471   0.6802   8.0660
 JBO  H8   H  HCR6   0   0.257  -20.9320   0.8449   7.2007
 JBO  H9   H  HCR6   0   0.260  -22.2050   2.9257   7.4270
 JBO  H10  H  HNH1   0   0.451  -17.0361   3.3313  10.0539

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
 JBO  C19  C20  aromatic  1.383  0.020  1.383
 JBO  C19  C18  aromatic  1.382  0.020  1.382
 JBO  C20  C04  aromatic  1.391  0.020  1.391
 JBO  C16  N17  aromatic  1.327  0.020  1.327
 JBO  C16  C15  aromatic  1.380  0.020  1.380
 JBO  F21  C02  single    1.344  0.020  1.344
 JBO  F01  C02  single    1.338  0.020  1.338
 JBO  C18  C07  aromatic  1.398  0.020  1.398
 JBO  N17  C09  aromatic  1.330  0.020  1.330
 JBO  C04  C02  single    1.502  0.020  1.502
 JBO  C04  C05  aromatic  1.399  0.020  1.399
 JBO  C02  F03  single    1.342  0.020  1.342
 JBO  C15  C14  aromatic  1.390  0.020  1.390
 JBO  C07  C05  aromatic  1.415  0.020  1.415
 JBO  C07  N08  single    1.384  0.020  1.384
 JBO  C05  C06  single    1.505  0.020  1.505
 JBO  C09  N08  single    1.367  0.020  1.367
 JBO  C09  C10  aromatic  1.424  0.020  1.424
 JBO  C14  C10  aromatic  1.382  0.020  1.382
 JBO  C10  C11  single    1.522  0.020  1.522
 JBO  O13  C11  deloc     1.259  0.020  1.259
 JBO  C11  O12  deloc     1.238  0.020  1.238
 JBO  C06  H1   single    0.970  0.020  1.090
 JBO  C06  H2   single    0.970  0.020  1.090
 JBO  C06  H3   single    0.970  0.020  1.090
 JBO  C14  H4   single    0.930  0.020  1.080
 JBO  C15  H5   single    0.930  0.020  1.080
 JBO  C16  H6   single    0.930  0.020  1.080
 JBO  C18  H7   single    0.930  0.020  1.080
 JBO  C19  H8   single    0.930  0.020  1.080
 JBO  C20  H9   single    0.930  0.020  1.080
 JBO  N08  H10  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
 JBO  F21  C02  F03  106.64  3.000
 JBO  F03  C02  F01  106.19  3.000
 JBO  F21  C02  F01  106.03  3.000
 JBO  F03  C02  C04  112.20  3.000
 JBO  F01  C02  C04  112.50  3.000
 JBO  F21  C02  C04  112.78  3.000
 JBO  C20  C04  C05  121.51  3.000
 JBO  C05  C04  C02  120.64  3.000
 JBO  C20  C04  C02  117.85  3.000
 JBO  C07  C05  C06  118.06  3.000
 JBO  C06  C05  C04  123.59  3.000
 JBO  C07  C05  C04  118.35  3.000
 JBO  H3   C06  H2   106.44  3.000
 JBO  H3   C06  H1   107.10  3.000
 JBO  H2   C06  H1   106.92  3.000
 JBO  H3   C06  C05  114.25  3.000
 JBO  H2   C06  C05  110.39  3.000
 JBO  H1   C06  C05  111.35  3.000
 JBO  N08  C07  C18  123.18  3.000
 JBO  N08  C07  C05  117.25  3.000
 JBO  C18  C07  C05  119.54  3.000
 JBO  N17  C09  N08  119.61  3.000
 JBO  N08  C09  C10  118.21  3.000
 JBO  N17  C09  C10  122.17  3.000
 JBO  C14  C10  C11  119.17  3.000
 JBO  C11  C10  C09  124.24  3.000
 JBO  C14  C10  C09  116.59  3.000
 JBO  O13  C11  O12  125.91  3.000
 JBO  O12  C11  C10  117.12  3.000
 JBO  O13  C11  C10  116.97  3.000
 JBO  H4   C14  C15  120.09  3.000
 JBO  H4   C14  C10  118.68  3.000
 JBO  C15  C14  C10  121.22  3.000
 JBO  H5   C15  C16  121.03  3.000
 JBO  H5   C15  C14  121.85  3.000
 JBO  C16  C15  C14  117.11  3.000
 JBO  H6   C16  N17  115.83  3.000
 JBO  H6   C16  C15  120.49  3.000
 JBO  N17  C16  C15  123.68  3.000
 JBO  H7   C18  C19  119.75  3.000
 JBO  H7   C18  C07  119.69  3.000
 JBO  C19  C18  C07  120.56  3.000
 JBO  H8   C19  C20  119.78  3.000
 JBO  H8   C19  C18  119.48  3.000
 JBO  C20  C19  C18  120.74  3.000
 JBO  H9   C20  C19  119.39  3.000
 JBO  H9   C20  C04  121.35  3.000
 JBO  C19  C20  C04  119.26  3.000
 JBO  H10  N08  C09  109.51  3.000
 JBO  H10  N08  C07  119.63  3.000
 JBO  C09  N08  C07  130.82  3.000
 JBO  C16  N17  C09  119.22  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
 JBO  CONST_01  C18  C19  C20  C04     0.00   0.0  0
 JBO  CONST_02  C18  C07  C05  C04     0.00   0.0  0
 JBO  CONST_03  C19  C20  C04  C05     0.00   0.0  0
 JBO  CONST_04  C19  C18  C07  C05     0.00   0.0  0
 JBO  CONST_05  C20  C19  C18  C07     0.00   0.0  0
 JBO  CONST_06  C20  C04  C05  C07     0.00   0.0  0
 JBO  CONST_07  C15  C16  N17  C09     0.00   0.0  0
 JBO  CONST_08  C15  C14  C10  C09     0.00   0.0  0
 JBO  CONST_09  C16  N17  C09  C10     0.00   0.0  0
 JBO  CONST_10  C16  C15  C14  C10     0.00   0.0  0
 JBO  CONST_11  N17  C16  C15  C14     0.00   0.0  0
 JBO  CONST_12  N17  C09  C10  C14     0.00   0.0  0
 JBO  CONST_13  C19  C20  C04  C02   180.00   0.0  0
 JBO  CONST_14  C07  C05  C04  C02   180.00   0.0  0
 JBO  CONST_15  N08  C07  C05  C04   180.00   0.0  0
 JBO  CONST_16  C20  C04  C05  C06   180.00   0.0  0
 JBO  CONST_17  C18  C07  C05  C06   180.00   0.0  0
 JBO  CONST_18  N17  C09  C10  C11   180.00   0.0  0
 JBO  CONST_19  C15  C14  C10  C11   180.00   0.0  0
 JBO  CONST_20  N08  C09  C10  C14   180.00   0.0  0
 JBO  CONST_21  N08  C09  N17  C16   180.00   0.0  0
 JBO  CONST_22  N08  C07  C18  C19   180.00   0.0  0
 JBO  CONST_23  H8   C19  C20  C04   180.00   0.0  0
 JBO  CONST_24  H9   C20  C04  C05   180.00   0.0  0
 JBO  CONST_25  H7   C18  C07  C05   180.00   0.0  0
 JBO  CONST_26  H8   C19  C18  C07   180.00   0.0  0
 JBO  CONST_27  H6   C16  N17  C09   180.00   0.0  0
 JBO  CONST_28  H4   C14  C10  C09   180.00   0.0  0
 JBO  CONST_29  H5   C15  C14  C10   180.00   0.0  0
 JBO  CONST_30  H6   C16  C15  C14   180.00   0.0  0
 JBO  CONST_31  H4   C14  C15  C16   180.00   0.0  0
 JBO  CONST_32  H9   C20  C19  C18   180.00   0.0  0
 JBO  CONST_33  H7   C18  C19  C20   180.00   0.0  0
 JBO  CONST_34  H5   C15  C16  N17   180.00   0.0  0
 JBO  Var_01    C09  N08  C07  C05  -160.98  30.0  2
 JBO  Var_02    N17  C09  N08  C07     4.30  30.0  2
 JBO  Var_03    C10  C09  N08  C07  -176.88  30.0  2
 JBO  Var_04    C18  C07  N08  C09    20.95  30.0  2
 JBO  Var_05    F21  C02  C04  C05    63.51  30.0  2
 JBO  Var_06    F01  C02  C04  C05  -176.62  30.0  2
 JBO  Var_07    F03  C02  C04  C05   -56.95  30.0  2
 JBO  Var_08    O13  C11  C10  C09     1.35  30.0  2
 JBO  Var_09    O12  C11  C10  C09  -178.58  30.0  2
 JBO  Var_10    O13  C11  C10  C14  -179.13  30.0  2
 JBO  Var_11    O12  C11  C10  C14     0.94  30.0  2
 JBO  Var_12    F21  C02  C04  C20  -116.90  30.0  2
 JBO  Var_13    F01  C02  C04  C20     2.98  30.0  2
 JBO  Var_14    F03  C02  C04  C20   122.65  30.0  2
 JBO  Var_15    H1   C06  C05  C04   106.80  30.0  2
 JBO  Var_16    H2   C06  C05  C04  -134.60  30.0  2
 JBO  Var_17    H3   C06  C05  C04   -14.69  30.0  2
 JBO  Var_18    H10  N08  C07  C05    21.55  30.0  2
 JBO  Var_19    H1   C06  C05  C07   -72.79  30.0  2
 JBO  Var_20    H2   C06  C05  C07    45.81  30.0  2
 JBO  Var_21    H3   C06  C05  C07   165.72  30.0  2
 JBO  Var_22    H10  N08  C09  C10     0.79  30.0  2
 JBO  Var_23    H10  N08  C07  C18  -156.53  30.0  2
 JBO  Var_24    H10  N08  C09  N17  -178.03  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
 JBO  plan-1  C09  0.020
 JBO  plan-1  C10  0.020
 JBO  plan-1  C11  0.020
 JBO  plan-1  C14  0.020
 JBO  plan-1  C15  0.020
 JBO  plan-1  C16  0.020
 JBO  plan-1  N08  0.020
 JBO  plan-1  N17  0.020
 JBO  plan-1  H4   0.020
 JBO  plan-1  H5   0.020
 JBO  plan-1  H6   0.020
 JBO  plan-2  C02  0.020
 JBO  plan-2  C04  0.020
 JBO  plan-2  C05  0.020
 JBO  plan-2  C06  0.020
 JBO  plan-2  C07  0.020
 JBO  plan-2  C18  0.020
 JBO  plan-2  C19  0.020
 JBO  plan-2  C20  0.020
 JBO  plan-2  N08  0.020
 JBO  plan-2  H7   0.020
 JBO  plan-2  H8   0.020
 JBO  plan-2  H9   0.020
 JBO  plan-3  C10  0.020
 JBO  plan-3  C11  0.020
 JBO  plan-3  O12  0.020
 JBO  plan-3  O13  0.020

