# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:07:48 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-amino-N-[5-(4-ethynylphenyl)-1,3,4-oxadiazol-2-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1)C(=O)Nc2oc(nn2)c3ccc(cc3)C#C
#
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
 KKL  KKL  4-amino-N-[5-(4-ethynylphenyl)-1,3,4-oxadiazol-2-yl]benzamide  ligand  35  23  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KKL
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
 KKL  C01  C  CR16  0  -0.248  245.4839  228.4330  207.9076
 KKL  C02  C  CR16  0  -0.317  246.0282  227.7262  206.8601
 KKL  C03  C  CR6   0   0.346  247.3275  227.1950  206.9508
 KKL  C04  C  CR16  0  -0.314  248.0440  227.4092  208.1407
 KKL  C05  C  CR16  0  -0.281  247.4829  228.1106  209.1858
 KKL  C06  C  CR6   0  -0.099  246.1890  228.6346  209.0992
 KKL  C07  C  C     0   0.538  245.5389  229.4195  210.1618
 KKL  C10  C  CR5   0   0.707  245.7258  230.0149  212.5130
 KKL  C12  C  CR5   0   0.488  245.6905  230.4939  214.5648
 KKL  C15  C  CR6   0  -0.021  245.9721  230.3680  215.9821
 KKL  C16  C  CR16  0  -0.257  245.4501  231.3164  216.8641
 KKL  C17  C  CR16  0  -0.261  245.6896  231.2141  218.2191
 KKL  C18  C  CR6   0  -0.052  246.4572  230.1595  218.7236
 KKL  C19  C  CR16  0  -0.261  246.9813  229.2155  217.8388
 KKL  C20  C  CR16  0  -0.273  246.7421  229.3177  216.4804
 KKL  C21  C  CSP   0   0.313  246.6974  230.0498  220.1241
 KKL  C22  C  CSP1  0  -0.542  246.8865  229.9605  221.3093
 KKL  N09  N  NH1   0  -0.770  246.0947  229.2880  211.4255
 KKL  N13  N  N     0  -0.304  244.9879  231.3810  213.9578
 KKL  N14  N  N     0  -0.323  245.0063  231.0803  212.6211
 KKL  N23  N  NH2   0  -0.852  247.8888  226.5368  205.9061
 KKL  O08  O  O     0  -0.423  244.5746  230.1290  209.9700
 KKL  O11  O  O     0  -0.432  246.1895  229.5894  213.6942
 KKL  H1   H  HCR6  0   0.259  244.4829  228.8307  207.8035
 KKL  H2   H  HCR6  0   0.264  245.4517  227.5774  205.9552
 KKL  H3   H  HCR6  0   0.266  249.0521  227.0243  208.2344
 KKL  H4   H  HCR6  0   0.255  248.0976  228.2632  210.0647
 KKL  H6   H  HCR6  0   0.271  244.8530  232.1363  216.4881
 KKL  H7   H  HCR6  0   0.271  245.2800  231.9529  218.8945
 KKL  H8   H  HCR6  0   0.272  247.5773  228.3962  218.2172
 KKL  H9   H  HCR6  0   0.271  247.1592  228.5702  215.8192
 KKL  H10  H  H     0   0.283  247.0480  229.8756  222.3600
 KKL  H11  H  HNH1  0   0.439  246.7670  228.5532  211.5935
 KKL  H16  H  HNH2  0   0.394  248.7083  225.9771  206.0709
 KKL  H17  H  HNH2  0   0.394  247.2919  226.2025  205.1685

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
 KKL  C01  C02  aromatic  1.376  0.020  1.376
 KKL  C01  C06  aromatic  1.399  0.020  1.399
 KKL  C02  C03  aromatic  1.407  0.020  1.407
 KKL  C03  C04  aromatic  1.405  0.020  1.405
 KKL  C03  N23  single    1.356  0.020  1.356
 KKL  C04  C05  aromatic  1.378  0.020  1.378
 KKL  C05  C06  aromatic  1.399  0.020  1.399
 KKL  C06  C07  single    1.472  0.020  1.472
 KKL  C07  N09  single    1.387  0.020  1.387
 KKL  C07  O08  double    1.212  0.020  1.212
 KKL  C10  N09  single    1.359  0.020  1.359
 KKL  C10  N14  aromatic  1.290  0.020  1.290
 KKL  C10  O11  aromatic  1.338  0.020  1.338
 KKL  C12  C15  single    1.450  0.020  1.450
 KKL  C12  N13  aromatic  1.284  0.020  1.284
 KKL  C12  O11  aromatic  1.351  0.020  1.351
 KKL  C15  C16  aromatic  1.396  0.020  1.396
 KKL  C15  C20  aromatic  1.394  0.020  1.394
 KKL  C16  C17  aromatic  1.380  0.020  1.380
 KKL  C17  C18  aromatic  1.399  0.020  1.399
 KKL  C18  C19  aromatic  1.396  0.020  1.396
 KKL  C18  C21  single    1.425  0.020  1.425
 KKL  C19  C20  aromatic  1.383  0.020  1.383
 KKL  C21  C22  triple    1.204  0.020  1.204
 KKL  C01  H1   single    0.929  0.020  1.085
 KKL  C02  H2   single    0.929  0.020  1.085
 KKL  C04  H3   single    0.929  0.020  1.085
 KKL  C05  H4   single    0.929  0.020  1.085
 KKL  C16  H6   single    0.929  0.020  1.085
 KKL  C17  H7   single    0.929  0.020  1.085
 KKL  C19  H8   single    0.929  0.020  1.085
 KKL  C20  H9   single    0.929  0.020  1.085
 KKL  C22  H10  single    0.913  0.020  1.066
 KKL  N09  H11  single    0.868  0.020  1.013
 KKL  N23  H16  single    0.868  0.020  1.013
 KKL  N23  H17  single    0.868  0.020  1.013
 KKL  N14  N13  aromatic  1.370  0.020  1.370

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
 KKL  H1   C01  C06  119.67  3.000
 KKL  H1   C01  C02  118.79  3.000
 KKL  C06  C01  C02  121.54  3.000
 KKL  H2   C02  C03  119.58  3.000
 KKL  H2   C02  C01  119.74  3.000
 KKL  C03  C02  C01  120.69  3.000
 KKL  N23  C03  C04  121.01  3.000
 KKL  N23  C03  C02  121.05  3.000
 KKL  C04  C03  C02  117.90  3.000
 KKL  H3   C04  C05  119.62  3.000
 KKL  H3   C04  C03  119.57  3.000
 KKL  C05  C04  C03  120.81  3.000
 KKL  H4   C05  C06  121.50  3.000
 KKL  H4   C05  C04  117.13  3.000
 KKL  C06  C05  C04  121.35  3.000
 KKL  C07  C06  C05  124.29  3.000
 KKL  C07  C06  C01  117.97  3.000
 KKL  C05  C06  C01  117.71  3.000
 KKL  O08  C07  N09  121.23  3.000
 KKL  O08  C07  C06  123.29  3.000
 KKL  N09  C07  C06  115.48  3.000
 KKL  O11  C10  N14  112.45  3.000
 KKL  O11  C10  N09  116.24  3.000
 KKL  N14  C10  N09  131.31  3.000
 KKL  O11  C12  N13  111.09  3.000
 KKL  O11  C12  C15  119.99  3.000
 KKL  N13  C12  C15  128.91  3.000
 KKL  C20  C15  C16  119.49  3.000
 KKL  C20  C15  C12  121.45  3.000
 KKL  C16  C15  C12  119.05  3.000
 KKL  H6   C16  C17  119.56  3.000
 KKL  H6   C16  C15  120.11  3.000
 KKL  C17  C16  C15  120.33  3.000
 KKL  H7   C17  C18  119.85  3.000
 KKL  H7   C17  C16  119.79  3.000
 KKL  C18  C17  C16  120.36  3.000
 KKL  C21  C18  C19  120.50  3.000
 KKL  C21  C18  C17  120.34  3.000
 KKL  C19  C18  C17  119.16  3.000
 KKL  H8   C19  C20  119.66  3.000
 KKL  H8   C19  C18  119.83  3.000
 KKL  C20  C19  C18  120.51  3.000
 KKL  H9   C20  C19  118.86  3.000
 KKL  H9   C20  C15  121.00  3.000
 KKL  C19  C20  C15  120.14  3.000
 KKL  C22  C21  C18  180.00  3.000
 KKL  H10  C22  C21  180.00  3.000
 KKL  H11  N09  C10  115.89  3.000
 KKL  H11  N09  C07  119.17  3.000
 KKL  C10  N09  C07  124.72  3.000
 KKL  N14  N13  C12  107.59  3.000
 KKL  N13  N14  C10  105.69  3.000
 KKL  H17  N23  H16  114.74  3.000
 KKL  H17  N23  C03  118.72  3.000
 KKL  H16  N23  C03  118.75  3.000
 KKL  C12  O11  C10  103.18  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
 KKL  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 KKL  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 KKL  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 KKL  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 KKL  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 KKL  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 KKL  CONST_07  C12  N13  N14  C10    0.00   0.0  0
 KKL  CONST_08  C15  C12  O11  C10  180.00   0.0  0
 KKL  CONST_09  N13  C12  O11  C10    0.00   0.0  0
 KKL  CONST_10  C17  C16  C15  C12  180.00   0.0  0
 KKL  CONST_11  C19  C20  C15  C12  180.00   0.0  0
 KKL  CONST_12  N14  C10  O11  C12    0.00   0.0  0
 KKL  CONST_13  N14  N13  C12  C15  180.00   0.0  0
 KKL  CONST_14  C18  C17  C16  C15    0.00   0.0  0
 KKL  CONST_15  C18  C19  C20  C15    0.00   0.0  0
 KKL  CONST_16  N13  C12  C15  C16    0.00   0.0  0
 KKL  CONST_17  O11  C12  C15  C16  180.00   0.0  0
 KKL  CONST_18  C19  C20  C15  C16    0.00   0.0  0
 KKL  CONST_19  C19  C18  C17  C16    0.00   0.0  0
 KKL  CONST_20  C20  C15  C16  C17    0.00   0.0  0
 KKL  CONST_21  C20  C19  C18  C17    0.00   0.0  0
 KKL  CONST_22  N13  C12  C15  C20  180.00   0.0  0
 KKL  CONST_23  O11  C12  C15  C20    0.00   0.0  0
 KKL  CONST_24  O11  C10  N14  N13    0.00   0.0  0
 KKL  CONST_25  O11  C12  N13  N14    0.00   0.0  0
 KKL  CONST_26  N23  C03  C02  C01  180.00   0.0  0
 KKL  CONST_27  C07  C06  C01  C02  180.00   0.0  0
 KKL  CONST_28  C07  C06  C05  C04  180.00   0.0  0
 KKL  CONST_29  N23  C03  C04  C05  180.00   0.0  0
 KKL  CONST_30  N09  C10  O11  C12  180.00   0.0  0
 KKL  CONST_31  C21  C18  C17  C16  180.00   0.0  0
 KKL  CONST_32  C21  C18  C19  C20  180.00   0.0  0
 KKL  CONST_33  N13  N14  C10  N09  180.00   0.0  0
 KKL  CONST_34  H4   C05  C06  C01  180.00   0.0  0
 KKL  CONST_35  H3   C04  C03  C02  180.00   0.0  0
 KKL  CONST_36  H1   C01  C02  C03  180.00   0.0  0
 KKL  CONST_37  H2   C02  C03  C04  180.00   0.0  0
 KKL  CONST_38  H6   C16  C15  C12    0.00   0.0  0
 KKL  CONST_39  H9   C20  C15  C12    0.00   0.0  0
 KKL  CONST_40  H7   C17  C16  C15  180.00   0.0  0
 KKL  CONST_41  H8   C19  C20  C15  180.00   0.0  0
 KKL  CONST_42  C10  N09  C07  C06  180.00   0.0  0
 KKL  CONST_43  N14  C10  N09  C07    0.00   0.0  0
 KKL  CONST_44  O11  C10  N09  C07  180.00   0.0  0
 KKL  CONST_47  H11  N09  C10  N14  180.00   0.0  0
 KKL  CONST_48  O08  C07  N09  C10    0.00   0.0  0
 KKL  Var_01    N09  C07  C06  C01  163.04  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
 KKL  plan-1  C10  0.020
 KKL  plan-1  C12  0.020
 KKL  plan-1  C15  0.020
 KKL  plan-1  N09  0.020
 KKL  plan-1  N13  0.020
 KKL  plan-1  N14  0.020
 KKL  plan-1  O11  0.020
 KKL  plan-2  C01  0.020
 KKL  plan-2  C02  0.020
 KKL  plan-2  C03  0.020
 KKL  plan-2  C04  0.020
 KKL  plan-2  C05  0.020
 KKL  plan-2  C06  0.020
 KKL  plan-2  C07  0.020
 KKL  plan-2  N23  0.020
 KKL  plan-2  H1   0.020
 KKL  plan-2  H2   0.020
 KKL  plan-2  H3   0.020
 KKL  plan-2  H4   0.020
 KKL  plan-3  C12  0.020
 KKL  plan-3  C15  0.020
 KKL  plan-3  C16  0.020
 KKL  plan-3  C17  0.020
 KKL  plan-3  C18  0.020
 KKL  plan-3  C19  0.020
 KKL  plan-3  C20  0.020
 KKL  plan-3  C21  0.020
 KKL  plan-3  C22  0.020
 KKL  plan-3  H6   0.020
 KKL  plan-3  H7   0.020
 KKL  plan-3  H8   0.020
 KKL  plan-3  H9   0.020
 KKL  plan-4  C06  0.020
 KKL  plan-4  C07  0.020
 KKL  plan-4  C10  0.020
 KKL  plan-4  N09  0.020
 KKL  plan-4  O08  0.020
 KKL  plan-4  H11  0.020
 KKL  plan-5  C03  0.020
 KKL  plan-5  N23  0.020
 KKL  plan-5  H16  0.020
 KKL  plan-5  H17  0.020

