# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 12:37:31 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-chloro-5-({1-[(4-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)methyl]-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl}oxy)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)NN=C1CN2C=CC(=C(Oc3cc(Cl)cc(c3)C#N)C2=O)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
 2KW  2KW  3-chloro-5-({1-[(4-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)methyl]-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl}oxy)benzonitrile  ligand  40  29  .  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_2KW
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
 2KW  C8   C   CR6   0  -0.153  -0.8289  -2.6645  -0.1764
 2KW  C7   C   CR6   0   0.133  -0.7382  -1.5668   0.6192
 2KW  C9   C   CR16  0  -0.450   0.3275  -3.4361  -0.4349
 2KW  C10  C   CR16  0   0.073   1.5105  -3.0137   0.0710
 2KW  C5   C   CR16  0  -0.222  -2.1013   3.1185  -0.3962
 2KW  C4   C   CR6   0   0.010  -2.9657   2.5908   0.5607
 2KW  C3   C   CR16  0  -0.315  -2.8612   1.2764   0.9994
 2KW  C2   C   CR6   0   0.402  -1.8702   0.4731   0.4573
 2KW  C1   C   CR16  0  -0.262  -1.0000   0.9639  -0.5073
 2KW  C13  C   CT    0   1.081  -2.1579  -3.0390  -0.7778
 2KW  C12  C   CR6   0   0.566   0.5092  -1.1462   1.2201
 2KW  C18  C   CR5   0   0.512   3.2235  -0.2129   0.3997
 2KW  C21  C   CR5   0   0.645   4.2457   1.6156  -0.3244
 2KW  C    C   CR6   0  -0.026  -1.1278   2.2835  -0.9110
 2KW  F    F   F     0  -0.304  -2.6606  -2.0397  -1.5088
 2KW  N    N   NS    0  -0.238  -4.8046   4.1048   1.5521
 2KW  O    O   O2    0  -0.487  -1.8310  -0.8119   0.9039
 2KW  CL   CL  CL    0  -0.095  -0.0362   2.8971  -2.1007
 2KW  N11  N   NR6   0  -0.517   1.6014  -1.9143   0.8583
 2KW  F14  F   F     0  -0.295  -2.0541  -4.0996  -1.5785
 2KW  F15  F   F     0  -0.301  -3.0547  -3.3401   0.1633
 2KW  O16  O   O     0  -0.461   0.6162  -0.1788   1.9558
 2KW  N19  N   N     0  -0.272   2.5597   0.1356  -0.6465
 2KW  N20  N   NR15  0  -0.514   3.1857   1.2529  -1.0884
 2KW  N22  N   NR5   0  -0.546   4.2576   0.6353   0.6522
 2KW  O23  O   O     0  -0.508   5.0074   2.5593  -0.4466
 2KW  H1   H   HCR6  0   0.299   0.3044  -4.3242  -1.0452
 2KW  H2   H   HCR6  0   0.330   2.4342  -3.5375  -0.1255
 2KW  H3   H   HCR6  0   0.306  -2.1931   4.1446  -0.7219
 2KW  H4   H   HCR6  0   0.304  -3.5358   0.8841   1.7481
 2KW  H5   H   HCR6  0   0.315  -0.2251   0.3466  -0.9435
 2KW  H6   H   HCH3  0   0.268   5.8247  -0.3424   1.6441
 2KW  H7   H   HCH3  0   0.277   5.8678   1.4236   1.6700
 2KW  H8   H   HCH3  0   0.267   4.7157   0.5650   2.6946
 2KW  H9   H   HCH2  0   0.325   3.6475  -2.1865   1.1021
 2KW  H10  H   HCH2  0   0.315   2.9053  -1.1413   2.2999
 2KW  H11  H   HNR5  0   0.421   2.8359   1.7453  -1.8938
 2KW  C17  C   CH2   0  -0.412   2.9025  -1.4025   1.2414
 2KW  C6   C   CSP   0   0.068  -3.9848   3.4278   1.1103
 2KW  C24  C   CH3   0  -0.537   5.2169   0.5567   1.7285

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
 2KW  N20  N19  single    1.355  0.020  1.355
 2KW  N20  C21  single    1.356  0.020  1.356
 2KW  N19  C18  double    1.287  0.020  1.287
 2KW  C10  C9   double    1.354  0.020  1.354
 2KW  C10  N11  single    1.355  0.020  1.355
 2KW  C9   C8   single    1.414  0.020  1.414
 2KW  C21  O23  double    1.219  0.020  1.219
 2KW  C21  N22  single    1.384  0.020  1.384
 2KW  F15  C13  single    1.334  0.020  1.334
 2KW  C18  C17  single    1.492  0.020  1.492
 2KW  C18  N22  single    1.361  0.020  1.361
 2KW  C17  N11  single    1.450  0.020  1.450
 2KW  N22  C24  single    1.444  0.020  1.444
 2KW  N11  C12  single    1.383  0.020  1.383
 2KW  C8   C13  single    1.506  0.020  1.506
 2KW  C8   C7   double    1.359  0.020  1.359
 2KW  C13  F    single    1.336  0.020  1.336
 2KW  C13  F14  single    1.333  0.020  1.333
 2KW  C12  C7   single    1.447  0.020  1.447
 2KW  C12  O16  double    1.220  0.020  1.220
 2KW  C7   O    single    1.358  0.020  1.358
 2KW  O    C2   single    1.361  0.020  1.361
 2KW  C2   C1   aromatic  1.389  0.020  1.389
 2KW  C2   C3   aromatic  1.386  0.020  1.386
 2KW  C1   C    aromatic  1.386  0.020  1.386
 2KW  C3   C4   aromatic  1.390  0.020  1.390
 2KW  C    CL   single    1.727  0.020  1.727
 2KW  C    C5   aromatic  1.382  0.020  1.382
 2KW  C4   C5   aromatic  1.393  0.020  1.393
 2KW  C4   C6   single    1.429  0.020  1.429
 2KW  C6   N    triple    1.151  0.020  1.151
 2KW  C9   H1   single    0.930  0.020  1.080
 2KW  C10  H2   single    0.930  0.020  1.080
 2KW  C5   H3   single    0.930  0.020  1.080
 2KW  C3   H4   single    0.930  0.020  1.080
 2KW  C1   H5   single    0.930  0.020  1.080
 2KW  C24  H6   single    0.970  0.020  1.090
 2KW  C24  H7   single    0.970  0.020  1.090
 2KW  C24  H8   single    0.970  0.020  1.090
 2KW  C17  H9   single    0.970  0.020  1.090
 2KW  C17  H10  single    0.970  0.020  1.090
 2KW  N20  H11  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
 2KW  C13  C8   C9   120.86  3.000
 2KW  C13  C8   C7   119.58  3.000
 2KW  C9   C8   C7   119.56  3.000
 2KW  O    C7   C12  116.42  3.000
 2KW  O    C7   C8   121.20  3.000
 2KW  C12  C7   C8   122.38  3.000
 2KW  H1   C9   C10  119.16  3.000
 2KW  H1   C9   C8   122.39  3.000
 2KW  C10  C9   C8   118.42  3.000
 2KW  H2   C10  N11  116.22  3.000
 2KW  H2   C10  C9   121.87  3.000
 2KW  N11  C10  C9   121.91  3.000
 2KW  H3   C5   C    121.42  3.000
 2KW  H3   C5   C4   120.93  3.000
 2KW  C    C5   C4   117.64  3.000
 2KW  C3   C4   C5   121.90  3.000
 2KW  C5   C4   C6   119.00  3.000
 2KW  C3   C4   C6   119.10  3.000
 2KW  H4   C3   C2   120.43  3.000
 2KW  H4   C3   C4   120.98  3.000
 2KW  C2   C3   C4   118.59  3.000
 2KW  O    C2   C1   122.93  3.000
 2KW  C1   C2   C3   120.99  3.000
 2KW  O    C2   C3   116.07  3.000
 2KW  H5   C1   C    119.45  3.000
 2KW  H5   C1   C2   121.79  3.000
 2KW  C    C1   C2   118.76  3.000
 2KW  F15  C13  F14  107.24  3.000
 2KW  F14  C13  F    107.20  3.000
 2KW  F15  C13  F    107.56  3.000
 2KW  F14  C13  C8   111.65  3.000
 2KW  F    C13  C8   111.38  3.000
 2KW  F15  C13  C8   111.56  3.000
 2KW  O16  C12  N11  121.92  3.000
 2KW  O16  C12  C7   123.81  3.000
 2KW  N11  C12  C7   114.24  3.000
 2KW  N22  C18  N19  111.95  3.000
 2KW  N22  C18  C17  123.75  3.000
 2KW  N19  C18  C17  124.30  3.000
 2KW  O23  C21  N22  127.87  3.000
 2KW  N22  C21  N20  102.41  3.000
 2KW  O23  C21  N20  129.73  3.000
 2KW  CL   C    C1   118.73  3.000
 2KW  CL   C    C5   119.15  3.000
 2KW  C1   C    C5   122.12  3.000
 2KW  C2   O    C7   118.63  3.000
 2KW  C17  N11  C12  116.32  3.000
 2KW  C12  N11  C10  123.33  3.000
 2KW  C17  N11  C10  120.01  3.000
 2KW  N20  N19  C18  104.48  3.000
 2KW  H11  N20  N19  120.24  3.000
 2KW  H11  N20  C21  126.27  3.000
 2KW  N19  N20  C21  113.46  3.000
 2KW  C21  N22  C18  107.70  3.000
 2KW  C18  N22  C24  127.52  3.000
 2KW  C21  N22  C24  124.78  3.000
 2KW  H10  C17  H9   107.13  3.000
 2KW  H10  C17  N11  110.09  3.000
 2KW  H9   C17  N11  109.00  3.000
 2KW  H10  C17  C18  110.86  3.000
 2KW  H9   C17  C18  110.74  3.000
 2KW  N11  C17  C18  108.99  3.000
 2KW  N    C6   C4   180.00  3.000
 2KW  H8   C24  H7   108.52  3.000
 2KW  H8   C24  H6   109.41  3.000
 2KW  H7   C24  H6   108.70  3.000
 2KW  H8   C24  N22  110.81  3.000
 2KW  H7   C24  N22  108.34  3.000
 2KW  H6   C24  N22  110.99  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
 2KW  CONST_01  C2   C1   C    C5     0.00   0.0  0
 2KW  CONST_02  C2   C3   C4   C5     0.00   0.0  0
 2KW  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 2KW  CONST_04  C1   C    C5   C4     0.00   0.0  0
 2KW  CONST_05  C    C1   C2   C3     0.00   0.0  0
 2KW  CONST_06  C    C5   C4   C3     0.00   0.0  0
 2KW  CONST_07  C10  N11  C12  C7     0.00   0.0  0
 2KW  CONST_08  C21  N20  N19  C18    0.00   0.0  0
 2KW  CONST_09  N20  C21  N22  C18    0.00   0.0  0
 2KW  CONST_10  N19  C18  N22  C21    0.00   0.0  0
 2KW  CONST_11  N22  C21  N20  N19    0.00   0.0  0
 2KW  CONST_12  N22  C18  N19  N20    0.00   0.0  0
 2KW  CONST_13  C2   C3   C4   C6   180.00   0.0  0
 2KW  CONST_14  C    C5   C4   C6   180.00   0.0  0
 2KW  CONST_15  O    C2   C3   C4   180.00   0.0  0
 2KW  CONST_16  CL   C    C5   C4   180.00   0.0  0
 2KW  CONST_17  CL   C    C1   C2   180.00   0.0  0
 2KW  CONST_18  O    C2   C1   C    180.00   0.0  0
 2KW  CONST_19  C17  N11  C12  C7   180.00   0.0  0
 2KW  CONST_20  O16  C12  N11  C10  180.00   0.0  0
 2KW  CONST_21  N20  C21  N22  C24  180.00   0.0  0
 2KW  CONST_22  N19  C18  N22  C24  180.00   0.0  0
 2KW  CONST_23  O23  C21  N22  C18  180.00   0.0  0
 2KW  CONST_24  N20  N19  C18  C17  180.00   0.0  0
 2KW  CONST_25  C21  N22  C18  C17  180.00   0.0  0
 2KW  CONST_26  O23  C21  N20  N19  180.00   0.0  0
 2KW  CONST_27  H5   C1   C    C5   180.00   0.0  0
 2KW  CONST_28  H4   C3   C4   C5   180.00   0.0  0
 2KW  CONST_29  H3   C5   C4   C3   180.00   0.0  0
 2KW  CONST_30  H11  N20  N19  C18  180.00   0.0  0
 2KW  CONST_31  O23  C21  N22  C24    0.00   0.0  0
 2KW  CONST_32  C17  C18  N22  C24    0.00   0.0  0
 2KW  CONST_33  O16  C12  N11  C17    0.00   0.0  0
 2KW  Var_01    C1   C2   O    C7    14.37  30.0  2
 2KW  Var_02    C18  C17  N11  C10  102.03  30.0  1
 2KW  Var_03    C12  C7   O    C2    65.46  30.0  2
 2KW  Var_04    N19  C18  C17  N11  -11.52  30.0  2
 2KW  Var_05    F15  C13  C8   C7   -63.00  30.0  3
 2KW  Var_06    H6   C24  N22  C18   64.13  30.0  3

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
 2KW  plan-1  C18  0.020
 2KW  plan-1  C21  0.020
 2KW  plan-1  N19  0.020
 2KW  plan-1  N20  0.020
 2KW  plan-1  N22  0.020
 2KW  plan-1  O23  0.020
 2KW  plan-1  H11  0.020
 2KW  plan-1  C17  0.020
 2KW  plan-1  C24  0.020
 2KW  plan-2  C8   0.020
 2KW  plan-2  C7   0.020
 2KW  plan-2  C9   0.020
 2KW  plan-2  C10  0.020
 2KW  plan-2  C13  0.020
 2KW  plan-2  C12  0.020
 2KW  plan-2  O    0.020
 2KW  plan-2  N11  0.020
 2KW  plan-2  O16  0.020
 2KW  plan-2  H1   0.020
 2KW  plan-2  H2   0.020
 2KW  plan-2  C17  0.020
 2KW  plan-3  C5   0.020
 2KW  plan-3  C4   0.020
 2KW  plan-3  C3   0.020
 2KW  plan-3  C2   0.020
 2KW  plan-3  C1   0.020
 2KW  plan-3  C    0.020
 2KW  plan-3  N    0.020
 2KW  plan-3  O    0.020
 2KW  plan-3  CL   0.020
 2KW  plan-3  H3   0.020
 2KW  plan-3  H4   0.020
 2KW  plan-3  H5   0.020
 2KW  plan-3  C6   0.020

