# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:02:02 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)CN1CN(c2ccccc2)C3(CCN(CC3)C(=O)c4ccc5n[nH]cc5c4)C1=O
#
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
 D6W  D6W  2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide  ligand  59  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D6W
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
 D6W  C4   C  CH2   0  -0.449   0.3361  -0.4049  -0.0221
 D6W  C5   C  CH2   0  -0.332  -0.7257  -1.0924   0.8280
 D6W  C8   C  CH2   0  -0.069   3.5618   0.6629  -0.2422
 D6W  C10  C  CR5   0   0.585   2.4390  -0.7251   1.2419
 D6W  C13  C  CR16  0  -0.340   0.4941   2.7719  -0.7087
 D6W  C15  C  CR16  0  -0.294   0.9785   4.4456  -2.3858
 D6W  C17  C  CR16  0  -0.371   2.6767   2.8701  -1.6984
 D6W  C20  C  CR6   0  -0.081  -3.3389   0.2543   0.6038
 D6W  C21  C  CR16  0  -0.328  -3.9430  -0.9718   0.7064
 D6W  C22  C  CR56  0  -0.093  -5.0110  -1.2603  -0.1655
 D6W  C24  C  CR16  0  -0.283  -4.8047   0.9514  -1.2221
 D6W  C26  C  CR15  0  -0.007  -5.8560  -2.3497  -0.3638
 D6W  C1   C  CH2   0  -0.330  -0.2264   0.2551   2.7588
 D6W  C2   C  CH2   0  -0.454   0.8780   1.0380   2.0584
 D6W  C3   C  CR5   0  -0.015   1.4226   0.3206   0.8040
 D6W  N6   N  NT    0  -0.444  -1.2511  -0.1568   1.8126
 D6W  N7   N  NR5   0  -0.590   2.2407   1.2005  -0.0201
 D6W  N9   N  NR5   0  -0.471   3.6217  -0.4357   0.6787
 D6W  O11  O  O     0  -0.468   2.2168  -1.6637   1.9829
 D6W  C12  C  CR6   0   0.404   1.7989   2.2531  -0.7893
 D6W  C14  C  CR16  0  -0.248   0.1018   3.8433  -1.4944
 D6W  C16  C  CR16  0  -0.237   2.2685   3.9437  -2.4743
 D6W  C18  C  C     0   0.515  -2.2834   0.6870   1.5662
 D6W  O19  O  O     0  -0.484  -2.3974   1.7691   2.1285
 D6W  C23  C  CR56  0   0.247  -5.4392  -0.3096  -1.1352
 D6W  C25  C  CR16  0  -0.283  -3.7890   1.2157  -0.3513
 D6W  N27  N  NR15  0  -0.398  -6.6614  -1.9933  -1.3639
 D6W  N28  N  N     0  -0.312  -6.4540  -0.7820  -1.8610
 D6W  C29  C  CH2   0  -0.452   4.7139  -1.3575   0.6645
 D6W  C30  C  C     0   0.542   4.5256  -2.4160  -0.4236
 D6W  O31  O  O     0  -0.484   3.4885  -2.5027  -1.0617
 D6W  N32  N  NH1   0  -0.624   5.5718  -3.2277  -0.5980
 D6W  C33  C  CH3   0  -0.513   5.5667  -4.3022  -1.5640
 D6W  H1   H  HCH2  0   0.265   0.8160  -1.1322  -0.6817
 D6W  H2   H  HCH2  0   0.256  -0.1666   0.3084  -0.6772
 D6W  H3   H  HCH2  0   0.280  -1.5158  -1.4647   0.1828
 D6W  H4   H  HCH2  0   0.263  -0.3154  -1.9509   1.3593
 D6W  H5   H  HCH2  0   0.237   3.7087   0.3197  -1.2755
 D6W  H6   H  HCH2  0   0.251   4.3431   1.3974  -0.0191
 D6W  H7   H  HCR6  0   0.253  -0.2353   2.3556  -0.0311
 D6W  H8   H  HCR6  0   0.248   0.6643   5.2831  -2.9938
 D6W  H9   H  HCR6  0   0.272   3.6932   2.5203  -1.8147
 D6W  H10  H  HCR6  0   0.272  -3.6241  -1.6964   1.4456
 D6W  H11  H  HCR6  0   0.262  -5.1238   1.6862  -1.9494
 D6W  H12  H  HCR5  0   0.301  -5.9281  -3.3107   0.1172
 D6W  H13  H  HCH2  0   0.262   0.1717  -0.6456   3.2274
 D6W  H14  H  HCH2  0   0.268  -0.6699   0.8605   3.5456
 D6W  H15  H  HCH2  0   0.260   0.4944   2.0213   1.7893
 D6W  H16  H  HCH2  0   0.262   1.6997   1.2180   2.7556
 D6W  H17  H  HCR6  0   0.252  -0.9133   4.2084  -1.4004
 D6W  H18  H  HCR6  0   0.254   2.9780   4.3879  -3.1609
 D6W  H19  H  HCR6  0   0.255  -3.3022   2.1820  -0.3859
 D6W  H20  H  HNR5  0   0.434  -7.3958  -2.5636  -1.7574
 D6W  H21  H  HCH2  0   0.301   5.6492  -0.8149   0.5160
 D6W  H22  H  HCH2  0   0.307   4.7875  -1.8493   1.6362
 D6W  H23  H  HNH1  0   0.409   6.3977  -3.0933  -0.0382
 D6W  H24  H  HCH3  0   0.240   4.7853  -5.0320  -1.3502
 D6W  H25  H  HCH3  0   0.240   5.4207  -3.9287  -2.5777
 D6W  H26  H  HCH3  0   0.253   6.5270  -4.8074  -1.5211

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
 D6W  N32  C33  single    1.445  0.020  1.445
 D6W  N32  C30  single    1.336  0.020  1.336
 D6W  C29  C30  single    1.530  0.020  1.530
 D6W  C29  N9   single    1.429  0.020  1.429
 D6W  O11  C10  double    1.216  0.020  1.216
 D6W  C30  O31  double    1.221  0.020  1.221
 D6W  N9   C10  single    1.342  0.020  1.342
 D6W  N9   C8   single    1.435  0.020  1.435
 D6W  C10  C3   single    1.523  0.020  1.523
 D6W  C1   C2   single    1.524  0.020  1.524
 D6W  C1   N6   single    1.454  0.020  1.454
 D6W  C2   C3   single    1.544  0.020  1.544
 D6W  C3   C4   single    1.546  0.020  1.546
 D6W  C3   N7   single    1.457  0.020  1.457
 D6W  N6   C5   single    1.456  0.020  1.456
 D6W  N6   C18  single    1.356  0.020  1.356
 D6W  C5   C4   single    1.524  0.020  1.524
 D6W  C8   N7   single    1.443  0.020  1.443
 D6W  O19  C18  double    1.225  0.020  1.225
 D6W  N7   C12  single    1.377  0.020  1.377
 D6W  C18  C20  single    1.492  0.020  1.492
 D6W  C25  C20  aromatic  1.428  0.020  1.428
 D6W  C25  C24  aromatic  1.364  0.020  1.364
 D6W  C20  C21  aromatic  1.371  0.020  1.371
 D6W  C12  C17  aromatic  1.406  0.020  1.406
 D6W  C12  C13  aromatic  1.406  0.020  1.406
 D6W  C24  C23  aromatic  1.414  0.020  1.414
 D6W  C21  C22  aromatic  1.409  0.020  1.409
 D6W  C17  C16  aromatic  1.386  0.020  1.386
 D6W  C13  C14  aromatic  1.385  0.020  1.385
 D6W  C23  C22  aromatic  1.424  0.020  1.424
 D6W  C23  N28  aromatic  1.334  0.020  1.334
 D6W  C22  C26  aromatic  1.393  0.020  1.393
 D6W  C16  C15  aromatic  1.387  0.020  1.387
 D6W  C14  C15  aromatic  1.388  0.020  1.388
 D6W  N28  N27  aromatic  1.326  0.020  1.326
 D6W  C26  N27  aromatic  1.333  0.020  1.333
 D6W  C4   H1   single    0.970  0.020  1.090
 D6W  C4   H2   single    0.970  0.020  1.090
 D6W  C5   H3   single    0.970  0.020  1.090
 D6W  C5   H4   single    0.970  0.020  1.090
 D6W  C8   H5   single    0.970  0.020  1.090
 D6W  C8   H6   single    0.970  0.020  1.090
 D6W  C13  H7   single    0.930  0.020  1.080
 D6W  C15  H8   single    0.930  0.020  1.080
 D6W  C17  H9   single    0.930  0.020  1.080
 D6W  C21  H10  single    0.930  0.020  1.080
 D6W  C24  H11  single    0.930  0.020  1.080
 D6W  C26  H12  single    0.930  0.020  1.080
 D6W  C1   H13  single    0.970  0.020  1.090
 D6W  C1   H14  single    0.970  0.020  1.090
 D6W  C2   H15  single    0.970  0.020  1.090
 D6W  C2   H16  single    0.970  0.020  1.090
 D6W  C14  H17  single    0.930  0.020  1.080
 D6W  C16  H18  single    0.930  0.020  1.080
 D6W  C25  H19  single    0.930  0.020  1.080
 D6W  N27  H20  single    0.860  0.020  1.020
 D6W  C29  H21  single    0.970  0.020  1.090
 D6W  C29  H22  single    0.970  0.020  1.090
 D6W  N32  H23  single    0.860  0.020  1.020
 D6W  C33  H24  single    0.970  0.020  1.090
 D6W  C33  H25  single    0.970  0.020  1.090
 D6W  C33  H26  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
 D6W  H2   C4   H1   105.96  3.000
 D6W  H2   C4   C3   109.75  3.000
 D6W  H1   C4   C3   109.04  3.000
 D6W  H2   C4   C5   107.99  3.000
 D6W  H1   C4   C5   110.02  3.000
 D6W  C3   C4   C5   113.79  3.000
 D6W  H4   C5   H3   107.07  3.000
 D6W  H4   C5   N6   108.20  3.000
 D6W  H3   C5   N6   111.07  3.000
 D6W  H4   C5   C4   111.41  3.000
 D6W  H3   C5   C4   109.28  3.000
 D6W  N6   C5   C4   109.79  3.000
 D6W  H6   C8   H5   107.80  3.000
 D6W  H6   C8   N9   110.67  3.000
 D6W  H5   C8   N9   111.03  3.000
 D6W  H6   C8   N7   111.82  3.000
 D6W  H5   C8   N7   112.55  3.000
 D6W  N9   C8   N7   102.98  3.000
 D6W  O11  C10  N9   125.68  3.000
 D6W  N9   C10  C3   108.64  3.000
 D6W  O11  C10  C3   125.68  3.000
 D6W  H7   C13  C14  117.58  3.000
 D6W  H7   C13  C12  121.38  3.000
 D6W  C14  C13  C12  121.03  3.000
 D6W  H8   C15  C16  120.96  3.000
 D6W  H8   C15  C14  120.91  3.000
 D6W  C16  C15  C14  118.13  3.000
 D6W  H9   C17  C16  117.85  3.000
 D6W  H9   C17  C12  120.96  3.000
 D6W  C16  C17  C12  121.18  3.000
 D6W  C25  C20  C18  117.32  3.000
 D6W  C25  C20  C21  120.88  3.000
 D6W  C18  C20  C21  121.52  3.000
 D6W  H10  C21  C22  120.57  3.000
 D6W  H10  C21  C20  121.31  3.000
 D6W  C22  C21  C20  118.11  3.000
 D6W  C23  C22  C26  104.05  3.000
 D6W  C26  C22  C21  135.10  3.000
 D6W  C23  C22  C21  120.84  3.000
 D6W  H11  C24  C25  121.15  3.000
 D6W  H11  C24  C23  120.97  3.000
 D6W  C25  C24  C23  117.88  3.000
 D6W  H12  C26  N27  122.23  3.000
 D6W  H12  C26  C22  132.44  3.000
 D6W  N27  C26  C22  105.33  3.000
 D6W  H14  C1   H13  107.33  3.000
 D6W  H14  C1   N6   109.95  3.000
 D6W  H13  C1   N6   107.63  3.000
 D6W  H14  C1   C2   110.00  3.000
 D6W  H13  C1   C2   110.93  3.000
 D6W  N6   C1   C2   110.91  3.000
 D6W  H16  C2   H15  105.89  3.000
 D6W  H16  C2   C3   109.25  3.000
 D6W  H15  C2   C3   110.06  3.000
 D6W  H16  C2   C1   109.65  3.000
 D6W  H15  C2   C1   108.79  3.000
 D6W  C3   C2   C1   112.97  3.000
 D6W  N7   C3   C2   112.14  3.000
 D6W  N7   C3   C10  101.69  3.000
 D6W  C2   C3   C10  108.72  3.000
 D6W  N7   C3   C4   112.07  3.000
 D6W  C2   C3   C4   113.85  3.000
 D6W  C10  C3   C4   107.50  3.000
 D6W  C18  N6   C1   118.58  3.000
 D6W  C18  N6   C5   123.48  3.000
 D6W  C1   N6   C5   111.57  3.000
 D6W  C12  N7   C3   126.70  3.000
 D6W  C12  N7   C8   119.51  3.000
 D6W  C3   N7   C8   112.09  3.000
 D6W  C29  N9   C10  122.59  3.000
 D6W  C10  N9   C8   113.45  3.000
 D6W  C29  N9   C8   121.29  3.000
 D6W  N7   C12  C17  119.76  3.000
 D6W  C17  C12  C13  117.02  3.000
 D6W  N7   C12  C13  123.22  3.000
 D6W  H17  C14  C15  120.11  3.000
 D6W  H17  C14  C13  118.49  3.000
 D6W  C15  C14  C13  121.40  3.000
 D6W  H18  C16  C17  118.67  3.000
 D6W  H18  C16  C15  120.10  3.000
 D6W  C17  C16  C15  121.23  3.000
 D6W  O19  C18  N6   122.50  3.000
 D6W  O19  C18  C20  119.10  3.000
 D6W  N6   C18  C20  118.37  3.000
 D6W  N28  C23  C24  128.57  3.000
 D6W  N28  C23  C22  111.27  3.000
 D6W  C24  C23  C22  120.15  3.000
 D6W  H19  C25  C24  119.17  3.000
 D6W  H19  C25  C20  118.72  3.000
 D6W  C24  C25  C20  122.10  3.000
 D6W  H20  N27  N28  118.93  3.000
 D6W  H20  N27  C26  125.53  3.000
 D6W  N28  N27  C26  115.54  3.000
 D6W  N27  N28  C23  103.80  3.000
 D6W  H22  C29  H21  106.70  3.000
 D6W  H22  C29  C30  109.26  3.000
 D6W  H21  C29  C30  110.65  3.000
 D6W  H22  C29  N9   109.47  3.000
 D6W  H21  C29  N9   109.60  3.000
 D6W  C30  C29  N9   111.06  3.000
 D6W  N32  C30  O31  123.64  3.000
 D6W  O31  C30  C29  121.70  3.000
 D6W  N32  C30  C29  114.65  3.000
 D6W  H23  N32  C33  118.28  3.000
 D6W  H23  N32  C30  119.27  3.000
 D6W  C33  N32  C30  122.45  3.000
 D6W  H26  C33  H25  108.33  3.000
 D6W  H26  C33  H24  108.33  3.000
 D6W  H25  C33  H24  108.40  3.000
 D6W  H26  C33  N32  108.45  3.000
 D6W  H25  C33  N32  111.55  3.000
 D6W  H24  C33  N32  111.67  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
 D6W  CONST_01  C16  C17  C12  C13     0.00   0.0  0
 D6W  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 D6W  CONST_03  C12  C17  C16  C15     0.00   0.0  0
 D6W  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 D6W  CONST_05  C14  C13  C12  C17     0.00   0.0  0
 D6W  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 D6W  CONST_07  C23  C24  C25  C20     0.00   0.0  0
 D6W  CONST_08  C23  C22  C21  C20     0.00   0.0  0
 D6W  CONST_09  C26  C22  C21  C20   180.00   0.0  0
 D6W  CONST_10  C24  C25  C20  C21     0.00   0.0  0
 D6W  CONST_11  C24  C23  C22  C21     0.00   0.0  0
 D6W  CONST_12  N28  C23  C22  C21   180.00   0.0  0
 D6W  CONST_13  N27  C26  C22  C21   180.00   0.0  0
 D6W  CONST_14  C25  C20  C21  C22     0.00   0.0  0
 D6W  CONST_15  C25  C24  C23  C22     0.00   0.0  0
 D6W  CONST_16  N27  N28  C23  C22     0.00   0.0  0
 D6W  CONST_17  N28  N27  C26  C22     0.00   0.0  0
 D6W  CONST_18  C26  C22  C23  C24   180.00   0.0  0
 D6W  CONST_19  N27  N28  C23  C24   180.00   0.0  0
 D6W  CONST_20  N28  C23  C22  C26     0.00   0.0  0
 D6W  CONST_21  C23  N28  N27  C26     0.00   0.0  0
 D6W  CONST_22  N27  C26  C22  C23     0.00   0.0  0
 D6W  CONST_23  N28  C23  C24  C25   180.00   0.0  0
 D6W  CONST_24  C16  C17  C12  N7    180.00   0.0  0
 D6W  CONST_25  C14  C13  C12  N7    180.00   0.0  0
 D6W  CONST_26  C3   C10  N9   C8      0.00   0.0  0
 D6W  CONST_27  C18  C20  C21  C22   180.00   0.0  0
 D6W  CONST_28  C18  C20  C25  C24   180.00   0.0  0
 D6W  CONST_30  C1   N6   C18  C20   180.00   0.0  0
 D6W  CONST_31  O11  C10  N9   C8    180.00   0.0  0
 D6W  CONST_32  C29  N9   C10  C3    180.00   0.0  0
 D6W  CONST_33  H9   C17  C12  C13   180.00   0.0  0
 D6W  CONST_34  H8   C15  C14  C13   180.00   0.0  0
 D6W  CONST_35  H7   C13  C14  C15   180.00   0.0  0
 D6W  CONST_36  H11  C24  C25  C20   180.00   0.0  0
 D6W  CONST_37  H19  C25  C20  C21   180.00   0.0  0
 D6W  CONST_38  H12  C26  C22  C21     0.00   0.0  0
 D6W  CONST_39  H20  N27  C26  C22   180.00   0.0  0
 D6W  CONST_40  H10  C21  C22  C26     0.00   0.0  0
 D6W  CONST_41  H18  C16  C17  C12   180.00   0.0  0
 D6W  CONST_42  H17  C14  C13  C12   180.00   0.0  0
 D6W  CONST_44  O19  C18  N6   C1      0.00   0.0  0
 D6W  CONST_45  C29  N9   C10  O11     0.00   0.0  0
 D6W  CONST_46  C33  N32  C30  C29   180.00   0.0  0
 D6W  CONST_47  C33  N32  C30  O31     0.00   0.0  0
 D6W  CONST_48  H23  N32  C30  C29     0.00   0.0  0
 D6W  Var_01    N9   C10  C3   C4    116.30  30.0  3
 D6W  Var_02    C1   C2   C3   C4     38.13  30.0  1
 D6W  Var_03    C8   N7   C3   C4   -106.58  30.0  3
 D6W  Var_04    C1   N6   C5   C4    -64.24  30.0  1
 D6W  Var_05    C2   C1   N6   C5     64.55  30.0  1
 D6W  Var_06    C10  C3   C4   C5     81.67  30.0  1
 D6W  Var_07    C17  C12  N7   C8     -5.64  30.0  2
 D6W  Var_08    N7   C8   N9   C10     9.98  30.0  1
 D6W  Var_09    N6   C1   C2   C3    -50.17  30.0  1
 D6W  Var_10    N6   C5   C4   C3     50.66  30.0  1
 D6W  Var_11    N9   C8   N7   C3    -10.95  30.0  1
 D6W  Var_12    N6   C18  C20  C21    49.90  30.0  2
 D6W  Var_13    C30  C29  N9   C8    -81.45  30.0  3
 D6W  Var_14    N32  C30  C29  N9    173.07  30.0  3
 D6W  Var_15    H24  C33  N32  C30   -61.17  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
 D6W  plan-1  C13  0.020
 D6W  plan-1  C15  0.020
 D6W  plan-1  C17  0.020
 D6W  plan-1  N7   0.020
 D6W  plan-1  C12  0.020
 D6W  plan-1  C14  0.020
 D6W  plan-1  C16  0.020
 D6W  plan-1  H7   0.020
 D6W  plan-1  H8   0.020
 D6W  plan-1  H9   0.020
 D6W  plan-1  H17  0.020
 D6W  plan-1  H18  0.020
 D6W  plan-2  C20  0.020
 D6W  plan-2  C21  0.020
 D6W  plan-2  C22  0.020
 D6W  plan-2  C24  0.020
 D6W  plan-2  C26  0.020
 D6W  plan-2  C18  0.020
 D6W  plan-2  C23  0.020
 D6W  plan-2  C25  0.020
 D6W  plan-2  N27  0.020
 D6W  plan-2  N28  0.020
 D6W  plan-2  H10  0.020
 D6W  plan-2  H11  0.020
 D6W  plan-2  H12  0.020
 D6W  plan-2  H19  0.020
 D6W  plan-2  H20  0.020
 D6W  plan-3  C5   0.020
 D6W  plan-3  C20  0.020
 D6W  plan-3  C1   0.020
 D6W  plan-3  N6   0.020
 D6W  plan-3  C18  0.020
 D6W  plan-3  O19  0.020
 D6W  plan-4  C29  0.020
 D6W  plan-4  C30  0.020
 D6W  plan-4  O31  0.020
 D6W  plan-4  N32  0.020
 D6W  plan-4  C33  0.020
 D6W  plan-4  H23  0.020
 D6W  plan-5  C8   0.020
 D6W  plan-5  C10  0.020
 D6W  plan-5  C3   0.020
 D6W  plan-5  N9   0.020
 D6W  plan-5  O11  0.020
 D6W  plan-5  C29  0.020

