# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 17:50:10 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1-[2-[(1~{R},3~{S},5~{R})-3-[(6-bromanylpyridin-2-yl)carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]indazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1nn(CC(=O)N2[C@@H]3C[C@@H]3C[C@H]2C(=O)Nc4cccc(Br)n4)c5ccccc15
#
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
 8NQ  8NQ  1-[2-[(1~{R},3~{S},5~{R})-3-[(6-bromanylpyridin-2-yl)carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]indazole-3-carboxamide  ligand  50  31  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8NQ
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
 8NQ  C4   C   CR15  0  -0.275  -0.6505  -5.0310   0.6473
 8NQ  C14  C   CR56  0  -0.082   4.1108   1.1381   0.0948
 8NQ  C5   C   CR15  0  -0.106   0.5336  -4.1446   0.7950
 8NQ  C6   C   CH2   0  -0.482   0.5842  -5.2994  -0.1628
 8NQ  C11  C   CR16  0  -0.264   2.8674   2.0368   2.4019
 8NQ  C8   C   CH2   0  -0.450   2.4349  -2.0297   0.5309
 8NQ  C9   C   CR56  0   0.470   3.2636   0.3084   0.8456
 8NQ  C10  C   CR16  0  -0.298   2.6230   0.7406   2.0101
 8NQ  C12  C   CR16  0  -0.262   3.7201   2.8853   1.6659
 8NQ  C13  C   CR16  0  -0.331   4.3457   2.4540   0.5184
 8NQ  N1   N   NR5   0  -0.462   0.1836  -2.8788   0.2168
 8NQ  N2   N   NR5   0  -0.384   3.2465  -0.8952   0.2113
 8NQ  C3   C   CH2   0  -0.457  -1.7757  -4.2188   0.0440
 8NQ  C1   C   C     0   0.546  -1.9532  -1.6969   0.1678
 8NQ  C2   C   CR15  0  -0.220  -1.1404  -2.8712  -0.3741
 8NQ  C15  C   CR5   0   0.095   4.5208   0.3120  -0.9896
 8NQ  C16  C   C     0   0.476   5.4208   0.6727  -2.1057
 8NQ  O2   O   O     0  -0.477   5.9097   1.7934  -2.1670
 8NQ  N4   N   N     0  -0.254   3.9796  -0.8801  -0.8913
 8NQ  O3   O   O     0  -0.471   0.6947  -0.8688  -0.6459
 8NQ  N5   N   NH1   0  -0.733  -2.8298  -1.1982  -0.7538
 8NQ  C17  C   CR6   0   0.533  -3.7923  -0.2117  -0.6042
 8NQ  C18  C   CR16  0  -0.398  -4.5339   0.1619  -1.7291
 8NQ  C19  C   CR16  0  -0.137  -5.4955   1.1391  -1.5776
 8NQ  C20  C   CR16  0  -0.293  -5.7034   1.7248  -0.3336
 8NQ  C21  C   CR6   0   0.085  -4.9028   1.2635   0.6936
 8NQ  BR1  BR  BR    0  -0.044  -5.1201   2.0056   2.4283
 8NQ  N6   N   N     0  -0.395  -3.9837   0.3365   0.5843
 8NQ  H1   H   HCR5  0   0.282  -0.9004  -5.7275   1.4368
 8NQ  H2   H   HCR5  0   0.292   1.1353  -4.1253   1.6949
 8NQ  H3   H   HCH2  0   0.271   1.1797  -6.1572   0.1219
 8NQ  H4   H   HCH2  0   0.261   0.5843  -5.0836  -1.2252
 8NQ  H6   H   HCH2  0   0.309   2.4026  -2.1574   1.6150
 8NQ  H7   H   HCH2  0   0.324   2.9097  -2.9225   0.1214
 8NQ  H8   H   HCR6  0   0.273   1.9644   0.0964   2.5772
 8NQ  H9   H   HCR6  0   0.260   3.8805   3.8968   2.0145
 8NQ  H10  H   HCR6  0   0.261   4.9992   3.1076  -0.0408
 8NQ  H11  H   HCH2  0   0.271  -2.2498  -4.7041  -0.8086
 8NQ  H12  H   HCH2  0   0.269  -2.5451  -4.0683   0.8024
 8NQ  H13  H   HNH2  0   0.411   5.2106  -1.1964  -2.9306
 8NQ  H14  H   HNH2  0   0.406   6.2270  -0.1123  -3.8075
 8NQ  H15  H   HCR5  0   0.294  -1.0592  -2.8091  -1.4634
 8NQ  H16  H   HNH1  0   0.425  -2.7643  -1.5843  -1.6837
 8NQ  H17  H   HCR6  0   0.290  -4.3595  -0.3030  -2.6902
 8NQ  H18  H   HCR6  0   0.290  -6.0892   1.4508  -2.4263
 8NQ  H19  H   HCR6  0   0.291  -6.4482   2.4929  -0.1880
 8NQ  C7   C   C     0   0.552   1.0272  -1.8660  -0.0300
 8NQ  O1   O   O     0  -0.415  -1.8472  -1.3226   1.3097
 8NQ  H5   H   HCR6  0   0.265   2.3917   2.4170   3.2962
 8NQ  N3   N   NH2   0  -0.811   5.6444  -0.2921  -3.0068

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
 8NQ  C6   C5   single    1.501  0.020  1.501
 8NQ  C6   C4   single    1.501  0.020  1.501
 8NQ  C8   N2   single    1.431  0.020  1.431
 8NQ  C8   C7   single    1.524  0.020  1.524
 8NQ  O2   C16  double    1.224  0.020  1.224
 8NQ  C5   C4   single    1.487  0.020  1.487
 8NQ  C5   N1   single    1.435  0.020  1.435
 8NQ  N4   N2   aromatic  1.324  0.020  1.324
 8NQ  N4   C15  aromatic  1.313  0.020  1.313
 8NQ  N2   C9   aromatic  1.361  0.020  1.361
 8NQ  C4   C3   single    1.513  0.020  1.513
 8NQ  C15  C16  single    1.478  0.020  1.478
 8NQ  C15  C14  aromatic  1.424  0.020  1.424
 8NQ  C16  N3   single    1.339  0.020  1.339
 8NQ  C9   C10  aromatic  1.398  0.020  1.398
 8NQ  C9   C14  aromatic  1.403  0.020  1.403
 8NQ  C10  C11  aromatic  1.376  0.020  1.376
 8NQ  C14  C13  aromatic  1.402  0.020  1.402
 8NQ  C11  C12  aromatic  1.410  0.020  1.410
 8NQ  C13  C12  aromatic  1.376  0.020  1.376
 8NQ  N1   C7   single    1.341  0.020  1.341
 8NQ  N1   C2   single    1.450  0.020  1.450
 8NQ  C7   O3   double    1.218  0.020  1.218
 8NQ  C3   C2   single    1.547  0.020  1.547
 8NQ  C2   C1   single    1.528  0.020  1.528
 8NQ  O1   C1   double    1.206  0.020  1.206
 8NQ  C1   N5   single    1.366  0.020  1.366
 8NQ  N5   C17  single    1.386  0.020  1.386
 8NQ  C17  C18  aromatic  1.398  0.020  1.398
 8NQ  C17  N6   aromatic  1.323  0.020  1.323
 8NQ  C18  C19  aromatic  1.379  0.020  1.379
 8NQ  N6   C21  aromatic  1.310  0.020  1.310
 8NQ  C19  C20  aromatic  1.391  0.020  1.391
 8NQ  C21  C20  aromatic  1.382  0.020  1.382
 8NQ  C21  BR1  single    1.899  0.020  1.899
 8NQ  C4   H1   single    0.970  0.020  1.090
 8NQ  C5   H2   single    0.970  0.020  1.090
 8NQ  C6   H3   single    0.970  0.020  1.090
 8NQ  C6   H4   single    0.970  0.020  1.090
 8NQ  C11  H5   single    0.930  0.020  1.080
 8NQ  C8   H6   single    0.970  0.020  1.090
 8NQ  C8   H7   single    0.970  0.020  1.090
 8NQ  C10  H8   single    0.930  0.020  1.080
 8NQ  C12  H9   single    0.930  0.020  1.080
 8NQ  C13  H10  single    0.930  0.020  1.080
 8NQ  C3   H11  single    0.970  0.020  1.090
 8NQ  C3   H12  single    0.970  0.020  1.090
 8NQ  N3   H13  single    0.860  0.020  1.020
 8NQ  N3   H14  single    0.860  0.020  1.020
 8NQ  C2   H15  single    0.970  0.020  1.090
 8NQ  N5   H16  single    0.860  0.020  1.020
 8NQ  C18  H17  single    0.930  0.020  1.080
 8NQ  C19  H18  single    0.930  0.020  1.080
 8NQ  C20  H19  single    0.930  0.020  1.080

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
 8NQ  H1   C4   C3   117.69  3.000
 8NQ  H1   C4   C6   117.95  3.000
 8NQ  C3   C4   C6   119.51  3.000
 8NQ  H1   C4   C5   119.69  3.000
 8NQ  C3   C4   C5   108.17  3.000
 8NQ  C6   C4   C5    60.33  3.000
 8NQ  C15  C14  C13  136.59  3.000
 8NQ  C13  C14  C9   119.63  3.000
 8NQ  C15  C14  C9   103.78  3.000
 8NQ  H2   C5   N1   117.05  3.000
 8NQ  H2   C5   C6   121.69  3.000
 8NQ  N1   C5   C6   115.45  3.000
 8NQ  H2   C5   C4   122.41  3.000
 8NQ  N1   C5   C4   106.96  3.000
 8NQ  C6   C5   C4    60.31  3.000
 8NQ  H4   C6   H3   114.55  3.000
 8NQ  H4   C6   C5   118.18  3.000
 8NQ  H3   C6   C5   117.42  3.000
 8NQ  H4   C6   C4   119.56  3.000
 8NQ  H3   C6   C4   116.90  3.000
 8NQ  C5   C6   C4    59.36  3.000
 8NQ  H5   C11  C12  119.07  3.000
 8NQ  H5   C11  C10  119.22  3.000
 8NQ  C12  C11  C10  121.71  3.000
 8NQ  H7   C8   H6   106.85  3.000
 8NQ  H7   C8   N2   108.55  3.000
 8NQ  H6   C8   N2   109.34  3.000
 8NQ  H7   C8   C7   110.59  3.000
 8NQ  H6   C8   C7   110.52  3.000
 8NQ  N2   C8   C7   110.88  3.000
 8NQ  N2   C9   C10  131.01  3.000
 8NQ  C10  C9   C14  122.65  3.000
 8NQ  N2   C9   C14  106.33  3.000
 8NQ  H8   C10  C9   122.12  3.000
 8NQ  H8   C10  C11  121.32  3.000
 8NQ  C9   C10  C11  116.56  3.000
 8NQ  H9   C12  C13  119.63  3.000
 8NQ  H9   C12  C11  118.94  3.000
 8NQ  C13  C12  C11  121.43  3.000
 8NQ  H10  C13  C12  121.13  3.000
 8NQ  H10  C13  C14  120.85  3.000
 8NQ  C12  C13  C14  118.02  3.000
 8NQ  C2   N1   C7   119.70  3.000
 8NQ  C2   N1   C5   113.05  3.000
 8NQ  C7   N1   C5   125.94  3.000
 8NQ  N4   N2   C9   111.78  3.000
 8NQ  C9   N2   C8   127.18  3.000
 8NQ  N4   N2   C8   120.60  3.000
 8NQ  H12  C3   H11  107.38  3.000
 8NQ  H12  C3   C2   110.94  3.000
 8NQ  H11  C3   C2   110.80  3.000
 8NQ  H12  C3   C4   108.74  3.000
 8NQ  H11  C3   C4   113.35  3.000
 8NQ  C2   C3   C4   105.66  3.000
 8NQ  N5   C1   C2   112.51  3.000
 8NQ  N5   C1   O1   125.57  3.000
 8NQ  C2   C1   O1   121.84  3.000
 8NQ  H15  C2   C1   110.43  3.000
 8NQ  H15  C2   C3   110.42  3.000
 8NQ  C1   C2   C3   110.80  3.000
 8NQ  H15  C2   N1   109.77  3.000
 8NQ  C1   C2   N1   110.20  3.000
 8NQ  C3   C2   N1   105.09  3.000
 8NQ  N4   C15  C16  121.94  3.000
 8NQ  C16  C15  C14  127.50  3.000
 8NQ  N4   C15  C14  110.56  3.000
 8NQ  O2   C16  C15  120.29  3.000
 8NQ  C15  C16  N3   115.71  3.000
 8NQ  O2   C16  N3   124.00  3.000
 8NQ  C15  N4   N2   107.52  3.000
 8NQ  H16  N5   C17  114.64  3.000
 8NQ  H16  N5   C1   116.12  3.000
 8NQ  C17  N5   C1   129.23  3.000
 8NQ  N6   C17  C18  122.37  3.000
 8NQ  N6   C17  N5   119.49  3.000
 8NQ  C18  C17  N5   118.14  3.000
 8NQ  H17  C18  C19  120.96  3.000
 8NQ  H17  C18  C17  120.96  3.000
 8NQ  C19  C18  C17  118.08  3.000
 8NQ  H18  C19  C20  119.90  3.000
 8NQ  H18  C19  C18  120.05  3.000
 8NQ  C20  C19  C18  120.06  3.000
 8NQ  H19  C20  C21  122.48  3.000
 8NQ  H19  C20  C19  121.56  3.000
 8NQ  C21  C20  C19  115.96  3.000
 8NQ  N6   C21  BR1  115.66  3.000
 8NQ  BR1  C21  C20  118.83  3.000
 8NQ  N6   C21  C20  125.51  3.000
 8NQ  C21  N6   C17  118.02  3.000
 8NQ  O3   C7   N1   122.65  3.000
 8NQ  O3   C7   C8   121.74  3.000
 8NQ  N1   C7   C8   115.60  3.000
 8NQ  H14  N3   H13  118.08  3.000
 8NQ  H14  N3   C16  120.22  3.000
 8NQ  H13  N3   C16  121.65  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
 8NQ  CONST_01  N2   N4   C15  C14     0.00   0.0  0
 8NQ  CONST_02  N4   N2   C9   C14     0.00   0.0  0
 8NQ  CONST_03  C11  C10  C9   C14     0.00   0.0  0
 8NQ  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 8NQ  CONST_05  N2   C9   C10  C11   180.00   0.0  0
 8NQ  CONST_06  C15  N4   N2   C9      0.00   0.0  0
 8NQ  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 8NQ  CONST_08  N4   C15  C14  C9      0.00   0.0  0
 8NQ  CONST_09  C12  C13  C14  C9      0.00   0.0  0
 8NQ  CONST_10  N4   N2   C9   C10   180.00   0.0  0
 8NQ  CONST_11  C15  C14  C9   C10   180.00   0.0  0
 8NQ  CONST_12  C13  C14  C9   C10     0.00   0.0  0
 8NQ  CONST_13  C13  C12  C11  C10     0.00   0.0  0
 8NQ  CONST_14  C15  C14  C13  C12   180.00   0.0  0
 8NQ  CONST_15  N4   C15  C14  C13   180.00   0.0  0
 8NQ  CONST_16  N2   C9   C14  C13   180.00   0.0  0
 8NQ  CONST_17  C15  C14  C9   N2      0.00   0.0  0
 8NQ  CONST_18  C20  C19  C18  C17     0.00   0.0  0
 8NQ  CONST_19  C20  C21  N6   C17     0.00   0.0  0
 8NQ  CONST_20  C21  N6   C17  C18     0.00   0.0  0
 8NQ  CONST_21  C21  C20  C19  C18     0.00   0.0  0
 8NQ  CONST_22  N6   C17  C18  C19     0.00   0.0  0
 8NQ  CONST_23  N6   C21  C20  C19     0.00   0.0  0
 8NQ  CONST_24  C8   N2   C9   C14   180.00   0.0  0
 8NQ  CONST_25  C15  N4   N2   C8    180.00   0.0  0
 8NQ  CONST_26  C10  C9   N2   C8      0.00   0.0  0
 8NQ  CONST_27  C16  C15  C14  C9    180.00   0.0  0
 8NQ  CONST_28  C16  C15  C14  C13     0.00   0.0  0
 8NQ  CONST_29  C16  C15  N4   N2    180.00   0.0  0
 8NQ  CONST_30  C19  C18  C17  N5    180.00   0.0  0
 8NQ  CONST_31  C21  N6   C17  N5    180.00   0.0  0
 8NQ  CONST_32  BR1  C21  N6   C17   180.00   0.0  0
 8NQ  CONST_33  BR1  C21  C20  C19   180.00   0.0  0
 8NQ  CONST_34  H8   C10  C9   C14   180.00   0.0  0
 8NQ  CONST_35  H9   C12  C13  C14   180.00   0.0  0
 8NQ  CONST_36  H10  C13  C12  C11   180.00   0.0  0
 8NQ  CONST_37  H5   C11  C10  C9    180.00   0.0  0
 8NQ  CONST_38  H18  C19  C18  C17   180.00   0.0  0
 8NQ  CONST_39  H19  C20  C19  C18   180.00   0.0  0
 8NQ  CONST_40  H17  C18  C19  C20   180.00   0.0  0
 8NQ  CONST_41  C8   C7   N1   C5      0.00   0.0  0
 8NQ  CONST_42  O3   C7   N1   C5    180.00   0.0  0
 8NQ  CONST_43  C2   N1   C7   C8    180.00   0.0  0
 8NQ  CONST_44  O3   C7   N1   C2      0.00   0.0  0
 8NQ  CONST_45  C17  N5   C1   C2    180.00   0.0  0
 8NQ  CONST_46  C18  C17  N5   C1    180.00   0.0  0
 8NQ  CONST_47  N6   C17  N5   C1      0.00   0.0  0
 8NQ  CONST_48  H16  N5   C17  C18     0.00   0.0  0
 8NQ  CONST_49  C17  N5   C1   O1      0.00   0.0  0
 8NQ  CONST_50  H13  N3   C16  C15     0.00   0.0  0
 8NQ  CONST_51  H14  N3   C16  C15   180.00   0.0  0
 8NQ  Var_01    N1   C5   C6   C4    -95.77  30.0  1
 8NQ  Var_02    C2   N1   C5   C4     -2.91  30.0  1
 8NQ  Var_03    C3   C4   C6   C5     95.16  30.0  1
 8NQ  Var_04    C2   C3   C4   C5      8.97  30.0  1
 8NQ  Var_05    O2   C16  C15  C14     0.20  30.0  2
 8NQ  Var_06    N4   N2   C8   C7    -91.59  30.0  2
 8NQ  Var_07    N2   C8   C7   N1   -179.93  30.0  2

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
 8NQ  chir_03  C2  N1  C3  C1  negativ
 8NQ  chir_04  C4  C6  C5  C3  both
 8NQ  chir_05  C5  N1  C6  C4  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
 8NQ  plan-1  N5   0.020
 8NQ  plan-1  C17  0.020
 8NQ  plan-1  C18  0.020
 8NQ  plan-1  C19  0.020
 8NQ  plan-1  C20  0.020
 8NQ  plan-1  C21  0.020
 8NQ  plan-1  BR1  0.020
 8NQ  plan-1  N6   0.020
 8NQ  plan-1  H17  0.020
 8NQ  plan-1  H18  0.020
 8NQ  plan-1  H19  0.020
 8NQ  plan-2  C14  0.020
 8NQ  plan-2  C11  0.020
 8NQ  plan-2  C8   0.020
 8NQ  plan-2  C9   0.020
 8NQ  plan-2  C10  0.020
 8NQ  plan-2  C12  0.020
 8NQ  plan-2  C13  0.020
 8NQ  plan-2  N2   0.020
 8NQ  plan-2  C15  0.020
 8NQ  plan-2  C16  0.020
 8NQ  plan-2  N4   0.020
 8NQ  plan-2  H8   0.020
 8NQ  plan-2  H9   0.020
 8NQ  plan-2  H10  0.020
 8NQ  plan-2  H5   0.020
 8NQ  plan-3  C15  0.020
 8NQ  plan-3  C16  0.020
 8NQ  plan-3  O2   0.020
 8NQ  plan-3  H13  0.020
 8NQ  plan-3  H14  0.020
 8NQ  plan-3  N3   0.020
 8NQ  plan-4  C5   0.020
 8NQ  plan-4  C8   0.020
 8NQ  plan-4  N1   0.020
 8NQ  plan-4  C2   0.020
 8NQ  plan-4  O3   0.020
 8NQ  plan-4  C7   0.020
 8NQ  plan-5  C1   0.020
 8NQ  plan-5  C2   0.020
 8NQ  plan-5  N5   0.020
 8NQ  plan-5  C17  0.020
 8NQ  plan-5  H16  0.020
 8NQ  plan-5  O1   0.020

