# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:22:11 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 3-{[5-amino-1-(2-fluoro-6-methoxybenzene-1-carbonyl)-1H-1,2,4-triazol-3-yl]amino}-N-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cccc(Nc2nn(c(N)n2)C(=O)c3c(F)cccc3OC)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
 NKY  NKY  3-{[5-amino-1-(2-fluoro-6-methoxybenzene-1-carbonyl)-1H-1,2,4-triazol-3-yl]amino}-N-methylbenzamide  ligand  45  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NKY
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
 NKY  C18  C  CR16  0  -0.355  -3.1653   0.3647  -0.0315
 NKY  C19  C  CR6   0  -0.008  -4.5348   0.6133  -0.0168
 NKY  C25  C  CR16  0  -0.232  -4.1461   2.7356   1.0217
 NKY  C22  C  CH3   0  -0.514  -7.6571  -1.4086  -0.6598
 NKY  C15  C  CR5   0   0.605  -0.1204   0.0902   0.1525
 NKY  C12  C  CR5   0   0.729   0.4841  -1.7426  -0.6703
 NKY  O28  O  O     0  -0.419   3.2412  -2.5283  -0.6217
 NKY  C02  C  CR6   0   0.570   4.5296  -0.6650   1.5067
 NKY  C03  C  CR16  0  -0.439   5.4612   0.2196   2.0165
 NKY  C04  C  CR16  0  -0.224   5.7200   1.3689   1.2876
 NKY  C05  C  CR16  0  -0.402   5.0749   1.6336   0.0860
 NKY  C06  C  CR6   0   0.458   4.1397   0.7259  -0.4027
 NKY  C08  C  CH3   0  -0.437   3.6606   2.0327  -2.3187
 NKY  C09  C  CR6   0  -0.362   3.8578  -0.4373   0.3231
 NKY  C17  C  CR6   0   0.386  -2.2744   1.2962   0.5021
 NKY  C20  C  C     0   0.522  -5.4250  -0.4345  -0.6128
 NKY  C24  C  CR16  0  -0.331  -5.0345   1.8028   0.5042
 NKY  C26  C  CR16  0  -0.353  -2.7867   2.4898   1.0277
 NKY  N11  N  NR5   0  -0.402   1.5791  -1.0695  -0.1728
 NKY  N13  N  NH2   0  -0.851   0.5265  -2.9305  -1.2535
 NKY  N14  N  N     0  -0.565  -0.5937  -1.0185  -0.4735
 NKY  N16  N  NH1   0  -0.800  -0.9003   1.1319   0.5503
 NKY  N21  N  NH1   0  -0.642  -6.6894  -0.4558  -0.1713
 NKY  N27  N  N     0  -0.341   1.1669   0.1233   0.3673
 NKY  O07  O  O2    0  -0.456   3.4754   0.8558  -1.5543
 NKY  O23  O  O     0  -0.495  -5.0103  -1.2233  -1.4536
 NKY  H1   H  HCR6  0   0.288  -2.7972  -0.5563  -0.4545
 NKY  H2   H  HCR6  0   0.264  -4.5168   3.6698   1.4219
 NKY  H3   H  HCH3  0   0.236  -7.4070  -2.4317  -0.3736
 NKY  H4   H  HCH3  0   0.250  -8.6259  -1.1604  -0.2361
 NKY  H5   H  HCH3  0   0.240  -7.7369  -1.3685  -1.7456
 NKY  H6   H  HCR6  0   0.280   5.9601   0.0155   2.9538
 NKY  H7   H  HCR6  0   0.276   6.4445   2.0798   1.6616
 NKY  H8   H  HCR6  0   0.288   5.3118   2.5400  -0.4534
 NKY  H9   H  HCH3  0   0.235   3.3760   2.9264  -1.7590
 NKY  H10  H  HCH3  0   0.233   4.6941   2.1365  -2.6573
 NKY  H11  H  HCH3  0   0.263   3.0139   1.9381  -3.1868
 NKY  H12  H  HCR6  0   0.255  -6.0930   2.0282   0.4921
 NKY  H13  H  HCR6  0   0.271  -2.1105   3.2298   1.4399
 NKY  H14  H  HNH2  0   0.438   1.3894  -3.4321  -1.3728
 NKY  H15  H  HNH2  0   0.434  -0.3302  -3.3341  -1.5931
 NKY  H16  H  HNH1  0   0.428  -0.3850   1.8884   0.9754
 NKY  H17  H  HNH1  0   0.422  -6.9532   0.1203   0.6095
 NKY  C10  C  C     0   0.545   2.8988  -1.4452  -0.2031
 NKY  F01  F  F     0  -0.290   4.2417  -1.7771   2.1879

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
 NKY  O28  C10  double    1.211  0.020  1.211
 NKY  N13  C12  single    1.324  0.020  1.324
 NKY  C10  C09  single    1.487  0.020  1.487
 NKY  C10  N11  single    1.372  0.020  1.372
 NKY  C12  N11  aromatic  1.378  0.020  1.378
 NKY  C12  N14  aromatic  1.313  0.020  1.313
 NKY  F01  C02  single    1.336  0.020  1.336
 NKY  C09  C02  aromatic  1.380  0.020  1.380
 NKY  C09  C06  aromatic  1.400  0.020  1.400
 NKY  O07  C06  single    1.336  0.020  1.336
 NKY  O07  C08  single    1.416  0.020  1.416
 NKY  N11  N27  aromatic  1.373  0.020  1.373
 NKY  C02  C03  aromatic  1.382  0.020  1.382
 NKY  C06  C05  aromatic  1.392  0.020  1.392
 NKY  N14  C15  aromatic  1.358  0.020  1.358
 NKY  C03  C04  aromatic  1.385  0.020  1.385
 NKY  C05  C04  aromatic  1.389  0.020  1.389
 NKY  N27  C15  aromatic  1.306  0.020  1.306
 NKY  C15  N16  single    1.361  0.020  1.361
 NKY  N16  C17  single    1.385  0.020  1.385
 NKY  C26  C17  aromatic  1.401  0.020  1.401
 NKY  C26  C25  aromatic  1.381  0.020  1.381
 NKY  C17  C18  aromatic  1.395  0.020  1.395
 NKY  C25  C24  aromatic  1.388  0.020  1.388
 NKY  C18  C19  aromatic  1.392  0.020  1.392
 NKY  C24  C19  aromatic  1.391  0.020  1.391
 NKY  C19  C20  single    1.499  0.020  1.499
 NKY  C20  O23  double    1.225  0.020  1.225
 NKY  C20  N21  single    1.339  0.020  1.339
 NKY  N21  C22  single    1.443  0.020  1.443
 NKY  C18  H1   single    0.930  0.020  1.080
 NKY  C25  H2   single    0.930  0.020  1.080
 NKY  C22  H3   single    0.970  0.020  1.090
 NKY  C22  H4   single    0.970  0.020  1.090
 NKY  C22  H5   single    0.970  0.020  1.090
 NKY  C03  H6   single    0.930  0.020  1.080
 NKY  C04  H7   single    0.930  0.020  1.080
 NKY  C05  H8   single    0.930  0.020  1.080
 NKY  C08  H9   single    0.970  0.020  1.090
 NKY  C08  H10  single    0.970  0.020  1.090
 NKY  C08  H11  single    0.970  0.020  1.090
 NKY  C24  H12  single    0.930  0.020  1.080
 NKY  C26  H13  single    0.930  0.020  1.080
 NKY  N13  H14  single    0.860  0.020  1.020
 NKY  N13  H15  single    0.860  0.020  1.020
 NKY  N16  H16  single    0.860  0.020  1.020
 NKY  N21  H17  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
 NKY  H1   C18  C17  120.16  3.000
 NKY  H1   C18  C19  119.50  3.000
 NKY  C17  C18  C19  120.34  3.000
 NKY  C24  C19  C20  122.23  3.000
 NKY  C20  C19  C18  117.09  3.000
 NKY  C24  C19  C18  120.66  3.000
 NKY  H2   C25  C26  119.29  3.000
 NKY  H2   C25  C24  119.93  3.000
 NKY  C26  C25  C24  120.78  3.000
 NKY  H5   C22  H4   108.37  3.000
 NKY  H5   C22  H3   108.22  3.000
 NKY  H4   C22  H3   108.45  3.000
 NKY  H5   C22  N21  111.23  3.000
 NKY  H4   C22  N21  108.37  3.000
 NKY  H3   C22  N21  112.11  3.000
 NKY  N27  C15  N16  119.85  3.000
 NKY  N16  C15  N14  124.05  3.000
 NKY  N27  C15  N14  116.11  3.000
 NKY  N14  C12  N13  125.94  3.000
 NKY  N14  C12  N11  109.19  3.000
 NKY  N13  C12  N11  124.87  3.000
 NKY  F01  C02  C09  118.03  3.000
 NKY  C09  C02  C03  122.61  3.000
 NKY  F01  C02  C03  119.35  3.000
 NKY  H6   C03  C04  121.76  3.000
 NKY  H6   C03  C02  120.66  3.000
 NKY  C04  C03  C02  117.57  3.000
 NKY  H7   C04  C05  119.00  3.000
 NKY  H7   C04  C03  119.24  3.000
 NKY  C05  C04  C03  121.76  3.000
 NKY  H8   C05  C06  121.25  3.000
 NKY  H8   C05  C04  119.31  3.000
 NKY  C06  C05  C04  119.43  3.000
 NKY  O07  C06  C09  115.32  3.000
 NKY  O07  C06  C05  124.99  3.000
 NKY  C09  C06  C05  119.68  3.000
 NKY  H11  C08  H10  108.89  3.000
 NKY  H11  C08  H9   109.00  3.000
 NKY  H10  C08  H9   109.12  3.000
 NKY  H11  C08  O07  106.33  3.000
 NKY  H10  C08  O07  111.72  3.000
 NKY  H9   C08  O07  111.68  3.000
 NKY  C06  C09  C02  118.94  3.000
 NKY  C06  C09  C10  120.63  3.000
 NKY  C02  C09  C10  120.36  3.000
 NKY  N16  C17  C26  116.80  3.000
 NKY  C26  C17  C18  118.60  3.000
 NKY  N16  C17  C18  124.60  3.000
 NKY  O23  C20  N21  122.38  3.000
 NKY  N21  C20  C19  116.15  3.000
 NKY  O23  C20  C19  121.47  3.000
 NKY  H12  C24  C25  119.35  3.000
 NKY  H12  C24  C19  121.68  3.000
 NKY  C25  C24  C19  118.96  3.000
 NKY  H13  C26  C17  119.75  3.000
 NKY  H13  C26  C25  119.61  3.000
 NKY  C17  C26  C25  120.65  3.000
 NKY  N27  N11  C10  122.36  3.000
 NKY  N27  N11  C12  109.14  3.000
 NKY  C10  N11  C12  128.48  3.000
 NKY  H15  N13  H14  119.39  3.000
 NKY  H15  N13  C12  118.77  3.000
 NKY  H14  N13  C12  121.84  3.000
 NKY  C12  N14  C15  103.48  3.000
 NKY  H16  N16  C17  115.62  3.000
 NKY  H16  N16  C15  113.85  3.000
 NKY  C17  N16  C15  130.49  3.000
 NKY  H17  N21  C20  119.64  3.000
 NKY  H17  N21  C22  117.72  3.000
 NKY  C20  N21  C22  122.13  3.000
 NKY  N11  N27  C15  102.09  3.000
 NKY  C08  O07  C06  118.78  3.000
 NKY  N11  C10  C09  115.26  3.000
 NKY  N11  C10  O28  121.64  3.000
 NKY  C09  C10  O28  123.10  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
 NKY  CONST_01  C25  C26  C17  C18    0.00   0.0  0
 NKY  CONST_02  C25  C24  C19  C18    0.00   0.0  0
 NKY  CONST_03  C26  C17  C18  C19    0.00   0.0  0
 NKY  CONST_04  C26  C25  C24  C19    0.00   0.0  0
 NKY  CONST_05  N11  C12  N14  C15    0.00   0.0  0
 NKY  CONST_06  C12  N11  N27  C15    0.00   0.0  0
 NKY  CONST_07  N27  C15  N14  C12    0.00   0.0  0
 NKY  CONST_08  C05  C06  C09  C02    0.00   0.0  0
 NKY  CONST_09  C05  C04  C03  C02    0.00   0.0  0
 NKY  CONST_10  C06  C09  C02  C03    0.00   0.0  0
 NKY  CONST_11  C06  C05  C04  C03    0.00   0.0  0
 NKY  CONST_12  C09  C02  C03  C04    0.00   0.0  0
 NKY  CONST_13  C09  C06  C05  C04    0.00   0.0  0
 NKY  CONST_14  C24  C25  C26  C17    0.00   0.0  0
 NKY  CONST_15  C24  C19  C18  C17    0.00   0.0  0
 NKY  CONST_16  N14  C15  N27  N11    0.00   0.0  0
 NKY  CONST_17  N27  N11  C12  N14    0.00   0.0  0
 NKY  CONST_18  N16  C17  C18  C19  180.00   0.0  0
 NKY  CONST_19  N16  C17  C26  C25  180.00   0.0  0
 NKY  CONST_20  C20  C19  C24  C25  180.00   0.0  0
 NKY  CONST_21  N13  C12  N14  C15  180.00   0.0  0
 NKY  CONST_22  C10  N11  N27  C15  180.00   0.0  0
 NKY  CONST_23  N16  C15  N14  C12  180.00   0.0  0
 NKY  CONST_24  C03  C02  C09  C10  180.00   0.0  0
 NKY  CONST_25  C05  C06  C09  C10  180.00   0.0  0
 NKY  CONST_26  N14  C12  N11  C10  180.00   0.0  0
 NKY  CONST_27  O07  C06  C09  C02  180.00   0.0  0
 NKY  CONST_28  F01  C02  C03  C04  180.00   0.0  0
 NKY  CONST_29  O07  C06  C05  C04  180.00   0.0  0
 NKY  CONST_30  F01  C02  C09  C06  180.00   0.0  0
 NKY  CONST_31  C20  C19  C18  C17  180.00   0.0  0
 NKY  CONST_32  N16  C15  N27  N11  180.00   0.0  0
 NKY  CONST_33  N27  N11  C12  N13  180.00   0.0  0
 NKY  CONST_34  C09  C10  N11  C12  180.00   0.0  0
 NKY  CONST_35  N27  N11  C10  C09    0.00   0.0  0
 NKY  CONST_36  H13  C26  C17  C18  180.00   0.0  0
 NKY  CONST_37  H12  C24  C19  C18  180.00   0.0  0
 NKY  CONST_38  H2   C25  C24  C19  180.00   0.0  0
 NKY  CONST_39  H7   C04  C03  C02  180.00   0.0  0
 NKY  CONST_40  H8   C05  C04  C03  180.00   0.0  0
 NKY  CONST_41  H6   C03  C04  C05  180.00   0.0  0
 NKY  CONST_42  H1   C18  C19  C24  180.00   0.0  0
 NKY  CONST_43  O28  C10  N11  C12    0.00   0.0  0
 NKY  CONST_44  N27  N11  C10  O28  180.00   0.0  0
 NKY  CONST_45  H14  N13  C12  N11    0.00   0.0  0
 NKY  CONST_46  H15  N13  C12  N11  180.00   0.0  0
 NKY  CONST_47  C22  N21  C20  C19  180.00   0.0  0
 NKY  CONST_48  H17  N21  C20  C19    0.00   0.0  0
 NKY  CONST_49  O23  C20  N21  C22    0.00   0.0  0
 NKY  Var_01    C15  N16  C17  C18   -1.68  30.0  2
 NKY  Var_02    N11  C10  C09  C02  110.92  30.0  2
 NKY  Var_03    N14  C15  N16  C17    4.03  30.0  2
 NKY  Var_04    O23  C20  C19  C18  -24.14  30.0  2
 NKY  Var_05    C09  C06  O07  C08  177.26  30.0  2
 NKY  Var_06    H9   C08  O07  C06  -59.74  30.0  3
 NKY  Var_07    H3   C22  N21  C20   66.31  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
 NKY  plan-1  C15  0.020
 NKY  plan-1  C12  0.020
 NKY  plan-1  O28  0.020
 NKY  plan-1  C09  0.020
 NKY  plan-1  N11  0.020
 NKY  plan-1  N13  0.020
 NKY  plan-1  N14  0.020
 NKY  plan-1  N16  0.020
 NKY  plan-1  N27  0.020
 NKY  plan-1  C10  0.020
 NKY  plan-2  C02  0.020
 NKY  plan-2  C03  0.020
 NKY  plan-2  C04  0.020
 NKY  plan-2  C05  0.020
 NKY  plan-2  C06  0.020
 NKY  plan-2  C09  0.020
 NKY  plan-2  O07  0.020
 NKY  plan-2  H6   0.020
 NKY  plan-2  H7   0.020
 NKY  plan-2  H8   0.020
 NKY  plan-2  C10  0.020
 NKY  plan-2  F01  0.020
 NKY  plan-3  C18  0.020
 NKY  plan-3  C19  0.020
 NKY  plan-3  C25  0.020
 NKY  plan-3  C17  0.020
 NKY  plan-3  C20  0.020
 NKY  plan-3  C24  0.020
 NKY  plan-3  C26  0.020
 NKY  plan-3  N16  0.020
 NKY  plan-3  H1   0.020
 NKY  plan-3  H2   0.020
 NKY  plan-3  H12  0.020
 NKY  plan-3  H13  0.020
 NKY  plan-4  C19  0.020
 NKY  plan-4  C22  0.020
 NKY  plan-4  C20  0.020
 NKY  plan-4  N21  0.020
 NKY  plan-4  O23  0.020
 NKY  plan-4  H17  0.020
 NKY  plan-5  C12  0.020
 NKY  plan-5  N13  0.020
 NKY  plan-5  H14  0.020
 NKY  plan-5  H15  0.020

