# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:00:59 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-(cyclopropylmethyl)-2'-methyl-5'-(5-methyl-1,3,4-oxadiazol-2-yl)biphenyl-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(nn1)c2ccc(C)c(c2)c3ccc(cc3)C(=O)NCC4CC4
#
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
 GK4  GK4  N-(cyclopropylmethyl)-2'-methyl-5'-(5-methyl-1,3,4-oxadiazol-2-yl)biphenyl-4-carboxamide  ligand  47  26  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GK4
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
 GK4  O2    O  O     0  -0.493   4.9827  -1.8191  -0.8854
 GK4  C17   C  C     0   0.533   4.3573  -0.8741  -0.4205
 GK4  N3    N  NH1   0  -0.651   4.9461   0.2701  -0.0412
 GK4  C18   C  CH2   0  -0.260   6.3737   0.4963  -0.1519
 GK4  C19   C  CH1   0  -0.288   6.7932   1.6192   0.7534
 GK4  C21   C  CH2   0  -0.491   7.9541   2.4781   0.3635
 GK4  C20   C  CH2   0  -0.486   6.5652   3.0401   0.3290
 GK4  C14   C  CR6   0  -0.045   2.8739  -0.9474  -0.2435
 GK4  C13   C  CR16  0  -0.276   2.1868  -0.1953   0.7057
 GK4  C12   C  CR16  0  -0.280   0.8133  -0.3241   0.8448
 GK4  C15   C  CR16  0  -0.255   2.1587  -1.8376  -1.0414
 GK4  C16   C  CR16  0  -0.276   0.7873  -1.9610  -0.9049
 GK4  C11   C  CR6   0   0.033   0.0954  -1.2086   0.0433
 GK4  C9    C  CR6   0   0.071  -1.3744  -1.3216   0.1895
 GK4  C7    C  CR6   0   0.075  -1.9910  -2.5381   0.5244
 GK4  C8    C  CH3   0  -0.744  -1.2032  -3.7895   0.7772
 GK4  C6    C  CR16  0  -0.282  -3.3775  -2.5612   0.6504
 GK4  C5    C  CR16  0  -0.279  -4.1508  -1.4299   0.4546
 GK4  C10   C  CR16  0  -0.310  -2.1477  -0.1832   0.0068
 GK4  C4    C  CR6   0  -0.019  -3.5347  -0.2242   0.1325
 GK4  C3    C  CR5   0   0.475  -4.3012   0.9914  -0.0756
 GK4  N2    N  N     0  -0.319  -3.8760   2.1707  -0.3705
 GK4  N1    N  N     0  -0.310  -4.9794   2.9765  -0.4608
 GK4  O1    O  O     0  -0.412  -5.6387   0.9687   0.0361
 GK4  C2    C  CR5   0   0.458  -6.0036   2.2392  -0.2160
 GK4  C1    C  CH3   0  -0.757  -7.4318   2.6042  -0.1836
 GK4  HN3   H  HNH1  0   0.406   4.3762   1.0743   0.1681
 GK4  H18   H  HCH2  0   0.252   6.8967  -0.4218   0.1186
 GK4  H18A  H  HCH2  0   0.234   6.6472   0.7258  -1.1879
 GK4  H19   H  HCH1  0   0.266   6.6818   1.4105   1.8126
 GK4  H21   H  HCH2  0   0.255   8.6258   2.8129   1.1430
 GK4  H21A  H  HCH2  0   0.248   8.4385   2.2722  -0.5832
 GK4  H20   H  HCH2  0   0.249   6.1153   3.2205  -0.6402
 GK4  H20A  H  HCH2  0   0.254   6.2858   3.7590   1.0883
 GK4  H13   H  HCR6  0   0.259   2.7128   0.4781   1.3708
 GK4  H12   H  HCR6  0   0.262   0.2984   0.2568   1.5998
 GK4  H15   H  HCR6  0   0.261   2.6757  -2.4307  -1.7840
 GK4  H16   H  HCR6  0   0.262   0.2489  -2.6411  -1.5529
 GK4  H8    H  HCH3  0   0.256  -0.8673  -4.2498  -0.1531
 GK4  H8A   H  HCH3  0   0.251  -0.3147  -3.5939   1.3773
 GK4  H8B   H  HCH3  0   0.256  -1.8098  -4.5260   1.3019
 GK4  H6    H  HCR6  0   0.261  -3.8660  -3.4890   0.9212
 GK4  H5    H  HCR6  0   0.264  -5.2249  -1.4989   0.5622
 GK4  H10   H  HCR6  0   0.263  -1.6632   0.7500  -0.2526
 GK4  H1    H  HCH3  0   0.277  -7.8659   2.3914   0.7934
 GK4  H1A   H  HCH3  0   0.276  -7.5395   3.6652  -0.3908
 GK4  H1B   H  HCH3  0   0.277  -7.9935   2.0435  -0.9310

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
 GK4  C8   C7    single    1.500  0.020  1.500
 GK4  C21  C20   single    1.499  0.020  1.499
 GK4  C21  C19   single    1.496  0.020  1.496
 GK4  C7   C6    aromatic  1.392  0.020  1.392
 GK4  C7   C9    aromatic  1.404  0.020  1.404
 GK4  C6   C5    aromatic  1.384  0.020  1.384
 GK4  C20  C19   single    1.500  0.020  1.500
 GK4  C19  C18   single    1.502  0.020  1.502
 GK4  C12  C13   aromatic  1.386  0.020  1.386
 GK4  C12  C11   aromatic  1.393  0.020  1.393
 GK4  C13  C14   aromatic  1.392  0.020  1.392
 GK4  C9   C11   single    1.481  0.020  1.481
 GK4  C9   C10   aromatic  1.388  0.020  1.388
 GK4  C11  C16   aromatic  1.394  0.020  1.394
 GK4  N3   C18   single    1.450  0.020  1.450
 GK4  N3   C17   single    1.341  0.020  1.341
 GK4  C5   C4    aromatic  1.392  0.020  1.392
 GK4  C14  C17   single    1.496  0.020  1.496
 GK4  C14  C15   aromatic  1.393  0.020  1.393
 GK4  C16  C15   aromatic  1.384  0.020  1.384
 GK4  C17  O2    double    1.225  0.020  1.225
 GK4  C10  C4    aromatic  1.393  0.020  1.393
 GK4  C4   C3    single    1.452  0.020  1.452
 GK4  C3   O1    aromatic  1.342  0.020  1.342
 GK4  C3   N2    aromatic  1.288  0.020  1.288
 GK4  O1   C2    aromatic  1.346  0.020  1.346
 GK4  N2   N1    aromatic  1.369  0.020  1.369
 GK4  C2   C1    single    1.474  0.020  1.474
 GK4  C2   N1    aromatic  1.285  0.020  1.285
 GK4  N3   HN3   single    0.860  0.020  1.020
 GK4  C18  H18   single    0.970  0.020  1.090
 GK4  C18  H18A  single    0.970  0.020  1.090
 GK4  C19  H19   single    0.970  0.020  1.090
 GK4  C21  H21   single    0.970  0.020  1.090
 GK4  C21  H21A  single    0.970  0.020  1.090
 GK4  C20  H20   single    0.970  0.020  1.090
 GK4  C20  H20A  single    0.970  0.020  1.090
 GK4  C13  H13   single    0.930  0.020  1.080
 GK4  C12  H12   single    0.930  0.020  1.080
 GK4  C15  H15   single    0.930  0.020  1.080
 GK4  C16  H16   single    0.930  0.020  1.080
 GK4  C8   H8    single    0.970  0.020  1.090
 GK4  C8   H8A   single    0.970  0.020  1.090
 GK4  C8   H8B   single    0.970  0.020  1.090
 GK4  C6   H6    single    0.930  0.020  1.080
 GK4  C5   H5    single    0.930  0.020  1.080
 GK4  C10  H10   single    0.930  0.020  1.080
 GK4  C1   H1    single    0.970  0.020  1.090
 GK4  C1   H1A   single    0.970  0.020  1.090
 GK4  C1   H1B   single    0.970  0.020  1.090

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
 GK4  C14   C17  N3   116.34  3.000
 GK4  C14   C17  O2   120.89  3.000
 GK4  N3    C17  O2   122.77  3.000
 GK4  HN3   N3   C18  116.63  3.000
 GK4  HN3   N3   C17  119.42  3.000
 GK4  C18   N3   C17  122.94  3.000
 GK4  H18A  C18  H18  106.92  3.000
 GK4  H18A  C18  C19  110.09  3.000
 GK4  H18   C18  C19  110.23  3.000
 GK4  H18A  C18  N3   110.53  3.000
 GK4  H18   C18  N3   108.78  3.000
 GK4  C19   C18  N3   110.22  3.000
 GK4  H19   C19  C20  116.27  3.000
 GK4  H19   C19  C21  116.39  3.000
 GK4  C20   C19  C21   60.02  3.000
 GK4  H19   C19  C18  114.57  3.000
 GK4  C20   C19  C18  119.67  3.000
 GK4  C21   C19  C18  119.26  3.000
 GK4  H21A  C21  H21  114.25  3.000
 GK4  H21A  C21  C20  117.75  3.000
 GK4  H21   C21  C20  118.42  3.000
 GK4  H21A  C21  C19  117.76  3.000
 GK4  H21   C21  C19  118.14  3.000
 GK4  C20   C21  C19   60.14  3.000
 GK4  H20A  C20  H20  114.19  3.000
 GK4  H20A  C20  C21  118.18  3.000
 GK4  H20   C20  C21  117.89  3.000
 GK4  H20A  C20  C19  118.02  3.000
 GK4  H20   C20  C19  118.28  3.000
 GK4  C21   C20  C19   59.84  3.000
 GK4  C15   C14  C13  118.83  3.000
 GK4  C15   C14  C17  118.21  3.000
 GK4  C13   C14  C17  122.93  3.000
 GK4  H13   C13  C12  118.51  3.000
 GK4  H13   C13  C14  120.99  3.000
 GK4  C12   C13  C14  120.47  3.000
 GK4  H12   C12  C11  119.78  3.000
 GK4  H12   C12  C13  119.42  3.000
 GK4  C11   C12  C13  120.79  3.000
 GK4  H15   C15  C16  119.50  3.000
 GK4  H15   C15  C14  119.87  3.000
 GK4  C16   C15  C14  120.62  3.000
 GK4  H16   C16  C11  119.95  3.000
 GK4  H16   C16  C15  119.33  3.000
 GK4  C11   C16  C15  120.72  3.000
 GK4  C9    C11  C16  121.23  3.000
 GK4  C16   C11  C12  118.57  3.000
 GK4  C9    C11  C12  120.20  3.000
 GK4  C10   C9   C7   119.81  3.000
 GK4  C10   C9   C11  118.50  3.000
 GK4  C7    C9   C11  121.68  3.000
 GK4  C6    C7   C8   119.59  3.000
 GK4  C6    C7   C9   118.24  3.000
 GK4  C8    C7   C9   122.15  3.000
 GK4  H8B   C8   H8A  108.07  3.000
 GK4  H8B   C8   H8   107.28  3.000
 GK4  H8A   C8   H8   107.11  3.000
 GK4  H8B   C8   C7   110.66  3.000
 GK4  H8A   C8   C7   111.79  3.000
 GK4  H8    C8   C7   111.71  3.000
 GK4  H6    C6   C5   118.92  3.000
 GK4  H6    C6   C7   119.08  3.000
 GK4  C5    C6   C7   122.00  3.000
 GK4  H5    C5   C4   121.19  3.000
 GK4  H5    C5   C6   119.24  3.000
 GK4  C4    C5   C6   119.57  3.000
 GK4  H10   C10  C4   119.49  3.000
 GK4  H10   C10  C9   119.27  3.000
 GK4  C4    C10  C9   121.23  3.000
 GK4  C3    C4   C10  119.20  3.000
 GK4  C3    C4   C5   121.65  3.000
 GK4  C10   C4   C5   119.15  3.000
 GK4  O1    C3   N2   111.31  3.000
 GK4  N2    C3   C4   128.69  3.000
 GK4  O1    C3   C4   119.99  3.000
 GK4  N1    N2   C3   106.74  3.000
 GK4  C2    N1   N2   106.97  3.000
 GK4  C2    O1   C3   103.81  3.000
 GK4  C1    C2   O1   119.49  3.000
 GK4  C1    C2   N1   129.34  3.000
 GK4  O1    C2   N1   111.17  3.000
 GK4  H1B   C1   H1A  108.69  3.000
 GK4  H1B   C1   H1   107.99  3.000
 GK4  H1A   C1   H1   108.79  3.000
 GK4  H1B   C1   C2   110.90  3.000
 GK4  H1A   C1   C2   109.49  3.000
 GK4  H1    C1   C2   110.93  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
 GK4  CONST_01  C11  C12  C13  C14     0.00   0.0  0
 GK4  CONST_02  C11  C16  C15  C14     0.00   0.0  0
 GK4  CONST_03  C9   C11  C12  C13   180.00   0.0  0
 GK4  CONST_04  C16  C11  C12  C13     0.00   0.0  0
 GK4  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 GK4  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 GK4  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 GK4  CONST_10  C9   C11  C16  C15   180.00   0.0  0
 GK4  CONST_13  C6   C7   C9   C11   180.00   0.0  0
 GK4  CONST_14  C4   C10  C9   C11   180.00   0.0  0
 GK4  CONST_15  C5   C6   C7   C9      0.00   0.0  0
 GK4  CONST_16  C5   C4   C10  C9      0.00   0.0  0
 GK4  CONST_17  C3   C4   C10  C9    180.00   0.0  0
 GK4  CONST_18  C4   C5   C6   C7      0.00   0.0  0
 GK4  CONST_19  C4   C10  C9   C7      0.00   0.0  0
 GK4  CONST_20  C10  C9   C7   C6      0.00   0.0  0
 GK4  CONST_21  C10  C4   C5   C6      0.00   0.0  0
 GK4  CONST_22  C3   C4   C5   C6    180.00   0.0  0
 GK4  CONST_23  O1   C3   C4   C5      0.00   0.0  0
 GK4  CONST_24  N2   C3   C4   C5    180.00   0.0  0
 GK4  CONST_25  O1   C3   C4   C10   180.00   0.0  0
 GK4  CONST_26  N2   C3   C4   C10     0.00   0.0  0
 GK4  CONST_27  C2   O1   C3   C4    180.00   0.0  0
 GK4  CONST_28  N1   N2   C3   C4    180.00   0.0  0
 GK4  CONST_29  N1   C2   O1   C3      0.00   0.0  0
 GK4  CONST_30  C2   N1   N2   C3      0.00   0.0  0
 GK4  CONST_31  C2   O1   C3   N2      0.00   0.0  0
 GK4  CONST_32  O1   C2   N1   N2      0.00   0.0  0
 GK4  CONST_33  O1   C3   N2   N1      0.00   0.0  0
 GK4  CONST_34  C12  C13  C14  C17   180.00   0.0  0
 GK4  CONST_35  C16  C15  C14  C17   180.00   0.0  0
 GK4  CONST_36  C8   C7   C9   C11     0.00   0.0  0
 GK4  CONST_37  C5   C6   C7   C8    180.00   0.0  0
 GK4  CONST_38  C10  C9   C7   C8    180.00   0.0  0
 GK4  CONST_39  C1   C2   O1   C3    180.00   0.0  0
 GK4  CONST_40  C1   C2   N1   N2    180.00   0.0  0
 GK4  CONST_41  H12  C12  C13  C14   180.00   0.0  0
 GK4  CONST_42  H16  C16  C15  C14   180.00   0.0  0
 GK4  CONST_43  H15  C15  C14  C13   180.00   0.0  0
 GK4  CONST_44  H13  C13  C14  C15   180.00   0.0  0
 GK4  CONST_45  H10  C10  C9   C11     0.00   0.0  0
 GK4  CONST_46  H6   C6   C7   C9    180.00   0.0  0
 GK4  CONST_47  H5   C5   C6   C7    180.00   0.0  0
 GK4  CONST_48  C14  C17  N3   C18   180.00   0.0  0
 GK4  CONST_49  HN3  N3   C17  C14     0.00   0.0  0
 GK4  CONST_50  C18  N3   C17  O2      0.00   0.0  0
 GK4  Var_01    C20  C21  C19  C18   109.38  30.0  1
 GK4  Var_02    H20  C20  C21  C19  -108.20  30.0  1
 GK4  Var_03    C13  C14  C17  O2    154.17  30.0  2
 GK4  Var_04    C21  C19  C18  N3   -149.43  30.0  1
 GK4  Var_05    H8   C8   C7   C9    -77.53  30.0  2
 GK4  Var_06    H1   C1   C2   N1   -121.14  30.0  2
 GK4  Var_07    C19  C18  N3   C17  -160.55  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 GK4  chir_01  C19  C21  C20  C18  both

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
 GK4  plan-1  C4   0.020
 GK4  plan-1  C3   0.020
 GK4  plan-1  N2   0.020
 GK4  plan-1  N1   0.020
 GK4  plan-1  O1   0.020
 GK4  plan-1  C2   0.020
 GK4  plan-1  C1   0.020
 GK4  plan-2  C17  0.020
 GK4  plan-2  C14  0.020
 GK4  plan-2  C13  0.020
 GK4  plan-2  C12  0.020
 GK4  plan-2  C15  0.020
 GK4  plan-2  C16  0.020
 GK4  plan-2  C11  0.020
 GK4  plan-2  C9   0.020
 GK4  plan-2  H13  0.020
 GK4  plan-2  H12  0.020
 GK4  plan-2  H15  0.020
 GK4  plan-2  H16  0.020
 GK4  plan-3  C11  0.020
 GK4  plan-3  C9   0.020
 GK4  plan-3  C7   0.020
 GK4  plan-3  C8   0.020
 GK4  plan-3  C6   0.020
 GK4  plan-3  C5   0.020
 GK4  plan-3  C10  0.020
 GK4  plan-3  C4   0.020
 GK4  plan-3  C3   0.020
 GK4  plan-3  H6   0.020
 GK4  plan-3  H5   0.020
 GK4  plan-3  H10  0.020
 GK4  plan-4  O2   0.020
 GK4  plan-4  C17  0.020
 GK4  plan-4  N3   0.020
 GK4  plan-4  C18  0.020
 GK4  plan-4  C14  0.020
 GK4  plan-4  HN3  0.020

