# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 13:47:21 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 1'-(2H-indazol-5-ylcarbonyl)-1-(propan-2-yl)-1,4-dihydrospiro[indazole-5,4'-piperidin]-7(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1ncc2CC3(CCN(CC3)C(=O)c4ccc5n[nH]cc5c4)CC(=O)c12
#
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
 3W7  3W7  1'-(2H-indazol-5-ylcarbonyl)-1-(propan-2-yl)-1,4-dihydrospiro[indazole-5,4'-piperidin]-7(6H)-one  ligand  54  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3W7
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
 3W7  C1   C  CR16  0  -0.279  -4.1666   0.6678  -1.4586
 3W7  C2   C  CR16  0  -0.285  -5.0450  -0.3004  -1.8474
 3W7  C3   C  CR16  0  -0.323  -3.8569  -0.3084   0.7489
 3W7  C4   C  CR15  0  -0.009  -5.3306  -2.4215   1.0085
 3W7  C5   C  CR15  0  -0.100   4.2651   0.4294  -2.0954
 3W7  C6   C  CR56  0  -0.090  -4.7802  -1.3069   0.3807
 3W7  C7   C  CR6   0  -0.098  -3.5530   0.6623  -0.1697
 3W7  C8   C  CR56  0  -0.139   3.4332   0.8873  -1.0720
 3W7  C9   C  CR56  0   0.245  -5.3691  -1.3139  -0.9153
 3W7  C10  C  CR56  0   0.342   3.7486   0.0786   0.0062
 3W7  C11  C  CR6   0   0.370   3.0792   0.1796   1.2968
 3W7  C12  C  C     0   0.518  -2.6911   1.8291   0.1912
 3W7  C13  C  C     0  -0.483   2.4094   1.9654  -1.0184
 3W7  C14  C  C     0  -0.564   2.1331   1.3564   1.3865
 3W7  C15  C  CH2   0  -0.417   0.5158   2.9397   0.2899
 3W7  C16  C  CH2   0  -0.399   0.4530   0.5337  -0.3251
 3W7  C17  C  CH2   0  -0.332  -0.6682   2.6972   1.2160
 3W7  C18  C  CH2   0  -0.323  -0.7378   0.3457   0.6102
 3W7  C19  C  CR6   0  -0.154   1.3779   1.6891   0.0862
 3W7  C20  C  CH3   0  -0.649   4.7549  -3.2076  -0.1190
 3W7  C21  C  CH3   0  -0.652   6.8653  -1.8401   0.1248
 3W7  N23  N  NR15  0  -0.399  -6.1434  -2.9696   0.1053
 3W7  N24  N  N     0  -0.250   5.0251  -0.5724  -1.6723
 3W7  N25  N  N     0  -0.313  -6.2025  -2.3455  -1.0629
 3W7  N26  N  NR5   0  -0.340   4.7172  -0.7787  -0.4105
 3W7  N27  N  NT    0  -0.444  -1.4842   1.5877   0.7482
 3W7  O28  O  O     0  -0.405   3.2641  -0.5754   2.2316
 3W7  O29  O  O     0  -0.492  -3.1252   2.9607   0.0083
 3W7  H1   H  HCR6  0   0.259  -3.9143   1.4606  -2.1510
 3W7  H2   H  HCR6  0   0.261  -5.4874  -0.2910  -2.8348
 3W7  H3   H  HCR6  0   0.270  -3.4124  -0.3064   1.7367
 3W7  H4   H  HCR5  0   0.300  -5.2014  -2.8393   1.9929
 3W7  H5   H  HCR5  0   0.267   4.3421   0.7818  -3.1128
 3W7  H6   H  H     0   0.260   2.8962   2.9268  -0.8180
 3W7  H7   H  H     0   0.257   1.9085   2.0714  -1.9839
 3W7  H8   H  H     0   0.272   1.4558   1.1807   2.2234
 3W7  H9   H  H     0   0.287   2.7416   2.2255   1.6697
 3W7  H10  H  HCH2  0   0.244   0.1399   3.2749  -0.6821
 3W7  H11  H  HCH2  0   0.243   1.1228   3.7543   0.6943
 3W7  H12  H  HCH2  0   0.246   0.9981  -0.4120  -0.3847
 3W7  H13  H  HCH2  0   0.241   0.0701   0.7304  -1.3315
 3W7  H14  H  HCH2  0   0.252  -0.3240   2.4632   2.2275
 3W7  H15  H  HCH2  0   0.270  -1.2803   3.5916   1.2887
 3W7  H16  H  HCH2  0   0.279  -1.3768  -0.4350   0.2096
 3W7  H17  H  HCH2  0   0.247  -0.4146   0.0117   1.6002
 3W7  H18  H  HCH3  0   0.238   5.2075  -4.0211   0.4478
 3W7  H19  H  HCH3  0   0.238   3.6791  -3.2330   0.0565
 3W7  H20  H  HCH3  0   0.232   4.9374  -3.3902  -1.1786
 3W7  H21  H  HCH3  0   0.234   7.1484  -2.0406  -0.9077
 3W7  H22  H  HCH3  0   0.240   7.2803  -0.8755   0.4172
 3W7  H23  H  HCH3  0   0.239   7.3199  -2.6055   0.7534
 3W7  H24  H  HCH1  0   0.271   5.1325  -1.7122   1.3651
 3W7  H25  H  HNR5  0   0.434  -6.6967  -3.8028   0.2424
 3W7  C22  C  CH1   0  -0.121   5.3573  -1.8784   0.3147

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
 3W7  C20  C22  single    1.522  0.020  1.522
 3W7  C21  C22  single    1.520  0.020  1.520
 3W7  C22  N26  single    1.465  0.020  1.465
 3W7  N26  N24  aromatic  1.315  0.020  1.315
 3W7  N26  C10  aromatic  1.359  0.020  1.359
 3W7  O28  C11  double    1.216  0.020  1.216
 3W7  N24  C5   aromatic  1.327  0.020  1.327
 3W7  C10  C11  single    1.457  0.020  1.457
 3W7  C10  C8   aromatic  1.384  0.020  1.384
 3W7  C11  C14  single    1.513  0.020  1.513
 3W7  C5   C8   aromatic  1.396  0.020  1.396
 3W7  C8   C13  single    1.488  0.020  1.488
 3W7  C14  C19  single    1.540  0.020  1.540
 3W7  C13  C19  single    1.536  0.020  1.536
 3W7  C19  C16  single    1.536  0.020  1.536
 3W7  C19  C15  single    1.533  0.020  1.533
 3W7  C16  C18  single    1.526  0.020  1.526
 3W7  C15  C17  single    1.523  0.020  1.523
 3W7  C18  N27  single    1.456  0.020  1.456
 3W7  C17  N27  single    1.454  0.020  1.454
 3W7  N27  C12  single    1.351  0.020  1.351
 3W7  C12  C7   single    1.495  0.020  1.495
 3W7  C12  O29  double    1.226  0.020  1.226
 3W7  C7   C3   aromatic  1.371  0.020  1.371
 3W7  C7   C1   aromatic  1.427  0.020  1.427
 3W7  C3   C6   aromatic  1.409  0.020  1.409
 3W7  C1   C2   aromatic  1.364  0.020  1.364
 3W7  C6   C4   aromatic  1.393  0.020  1.393
 3W7  C6   C9   aromatic  1.424  0.020  1.424
 3W7  C4   N23  aromatic  1.333  0.020  1.333
 3W7  C2   C9   aromatic  1.415  0.020  1.415
 3W7  C9   N25  aromatic  1.334  0.020  1.334
 3W7  N23  N25  aromatic  1.326  0.020  1.326
 3W7  C1   H1   single    0.930  0.020  1.080
 3W7  C2   H2   single    0.930  0.020  1.080
 3W7  C3   H3   single    0.930  0.020  1.080
 3W7  C4   H4   single    0.930  0.020  1.080
 3W7  C5   H5   single    0.930  0.020  1.080
 3W7  C13  H6   single    0.970  0.020  1.090
 3W7  C13  H7   single    0.970  0.020  1.090
 3W7  C14  H8   single    0.970  0.020  1.090
 3W7  C14  H9   single    0.970  0.020  1.090
 3W7  C15  H10  single    0.970  0.020  1.090
 3W7  C15  H11  single    0.970  0.020  1.090
 3W7  C16  H12  single    0.970  0.020  1.090
 3W7  C16  H13  single    0.970  0.020  1.090
 3W7  C17  H14  single    0.970  0.020  1.090
 3W7  C17  H15  single    0.970  0.020  1.090
 3W7  C18  H16  single    0.970  0.020  1.090
 3W7  C18  H17  single    0.970  0.020  1.090
 3W7  C20  H18  single    0.970  0.020  1.090
 3W7  C20  H19  single    0.970  0.020  1.090
 3W7  C20  H20  single    0.970  0.020  1.090
 3W7  C21  H21  single    0.970  0.020  1.090
 3W7  C21  H22  single    0.970  0.020  1.090
 3W7  C21  H23  single    0.970  0.020  1.090
 3W7  C22  H24  single    0.970  0.020  1.090
 3W7  N23  H25  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
 3W7  H1   C1   C7   118.70  3.000
 3W7  H1   C1   C2   119.19  3.000
 3W7  C7   C1   C2   122.11  3.000
 3W7  H2   C2   C9   120.92  3.000
 3W7  H2   C2   C1   121.15  3.000
 3W7  C9   C2   C1   117.92  3.000
 3W7  H3   C3   C7   121.27  3.000
 3W7  H3   C3   C6   120.56  3.000
 3W7  C7   C3   C6   118.17  3.000
 3W7  H4   C4   N23  122.20  3.000
 3W7  H4   C4   C6   132.45  3.000
 3W7  N23  C4   C6   105.34  3.000
 3W7  H5   C5   N24  120.41  3.000
 3W7  H5   C5   C8   128.78  3.000
 3W7  N24  C5   C8   110.81  3.000
 3W7  C9   C6   C4   104.06  3.000
 3W7  C9   C6   C3   120.83  3.000
 3W7  C4   C6   C3   135.11  3.000
 3W7  C12  C7   C3   121.25  3.000
 3W7  C3   C7   C1   120.84  3.000
 3W7  C12  C7   C1   117.57  3.000
 3W7  C13  C8   C10  123.52  3.000
 3W7  C13  C8   C5   132.38  3.000
 3W7  C10  C8   C5   104.10  3.000
 3W7  N25  C9   C6   111.27  3.000
 3W7  N25  C9   C2   128.62  3.000
 3W7  C6   C9   C2   120.11  3.000
 3W7  N26  C10  C11  129.99  3.000
 3W7  C11  C10  C8   123.00  3.000
 3W7  N26  C10  C8   106.98  3.000
 3W7  O28  C11  C14  122.19  3.000
 3W7  C14  C11  C10  113.19  3.000
 3W7  O28  C11  C10  124.61  3.000
 3W7  O29  C12  N27  122.88  3.000
 3W7  O29  C12  C7   118.71  3.000
 3W7  N27  C12  C7   118.38  3.000
 3W7  H7   C13  H6   106.27  3.000
 3W7  H7   C13  C19  110.18  3.000
 3W7  H6   C13  C19  108.93  3.000
 3W7  H7   C13  C8   110.73  3.000
 3W7  H6   C13  C8   109.67  3.000
 3W7  C19  C13  C8   110.95  3.000
 3W7  H9   C14  H8   105.88  3.000
 3W7  H9   C14  C19  108.58  3.000
 3W7  H8   C14  C19  112.21  3.000
 3W7  H9   C14  C11  106.53  3.000
 3W7  H8   C14  C11  107.97  3.000
 3W7  C19  C14  C11  115.13  3.000
 3W7  H11  C15  H10  106.91  3.000
 3W7  H11  C15  C19  110.17  3.000
 3W7  H10  C15  C19  108.97  3.000
 3W7  H11  C15  C17  108.99  3.000
 3W7  H10  C15  C17  108.77  3.000
 3W7  C19  C15  C17  112.85  3.000
 3W7  H13  C16  H12  106.24  3.000
 3W7  H13  C16  C19  108.76  3.000
 3W7  H12  C16  C19  111.41  3.000
 3W7  H13  C16  C18  108.22  3.000
 3W7  H12  C16  C18  108.42  3.000
 3W7  C19  C16  C18  113.48  3.000
 3W7  H15  C17  H14  106.96  3.000
 3W7  H15  C17  N27  109.48  3.000
 3W7  H14  C17  N27  108.11  3.000
 3W7  H15  C17  C15  110.35  3.000
 3W7  H14  C17  C15  110.60  3.000
 3W7  N27  C17  C15  111.23  3.000
 3W7  H17  C18  H16  106.76  3.000
 3W7  H17  C18  N27  109.04  3.000
 3W7  H16  C18  N27  110.29  3.000
 3W7  H17  C18  C16  111.22  3.000
 3W7  H16  C18  C16  108.77  3.000
 3W7  N27  C18  C16  110.68  3.000
 3W7  C16  C19  C15  108.10  3.000
 3W7  C15  C19  C14  109.87  3.000
 3W7  C16  C19  C14  111.03  3.000
 3W7  C15  C19  C13  109.05  3.000
 3W7  C16  C19  C13  110.31  3.000
 3W7  C14  C19  C13  108.46  3.000
 3W7  H20  C20  H19  108.52  3.000
 3W7  H20  C20  H18  108.11  3.000
 3W7  H19  C20  H18  107.97  3.000
 3W7  H20  C20  C22  110.90  3.000
 3W7  H19  C20  C22  111.40  3.000
 3W7  H18  C20  C22  109.83  3.000
 3W7  H23  C21  H22  107.94  3.000
 3W7  H23  C21  H21  108.00  3.000
 3W7  H22  C21  H21  108.55  3.000
 3W7  H23  C21  C22  108.91  3.000
 3W7  H22  C21  C22  111.49  3.000
 3W7  H21  C21  C22  111.81  3.000
 3W7  H25  N23  N25  118.94  3.000
 3W7  H25  N23  C4   125.55  3.000
 3W7  N25  N23  C4   115.51  3.000
 3W7  N26  N24  C5   106.88  3.000
 3W7  N23  N25  C9   103.81  3.000
 3W7  N24  N26  C22  119.38  3.000
 3W7  N24  N26  C10  111.23  3.000
 3W7  C22  N26  C10  129.30  3.000
 3W7  C18  N27  C17  113.19  3.000
 3W7  C17  N27  C12  119.84  3.000
 3W7  C18  N27  C12  124.85  3.000
 3W7  H24  C22  N26  105.86  3.000
 3W7  H24  C22  C21  108.78  3.000
 3W7  N26  C22  C21  110.66  3.000
 3W7  H24  C22  C20  109.08  3.000
 3W7  N26  C22  C20  109.97  3.000
 3W7  C21  C22  C20  112.26  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
 3W7  CONST_01  C6   C3   C7   C1      0.00   0.0  0
 3W7  CONST_02  C6   C9   C2   C1      0.00   0.0  0
 3W7  CONST_03  N25  C9   C2   C1    180.00   0.0  0
 3W7  CONST_04  C3   C7   C1   C2      0.00   0.0  0
 3W7  CONST_05  C3   C6   C9   C2      0.00   0.0  0
 3W7  CONST_06  C4   C6   C9   C2    180.00   0.0  0
 3W7  CONST_07  N23  N25  C9   C2    180.00   0.0  0
 3W7  CONST_08  N23  C4   C6   C3    180.00   0.0  0
 3W7  CONST_09  N25  C9   C6   C3    180.00   0.0  0
 3W7  CONST_10  C7   C3   C6   C4    180.00   0.0  0
 3W7  CONST_11  N25  C9   C6   C4      0.00   0.0  0
 3W7  CONST_12  C9   N25  N23  C4      0.00   0.0  0
 3W7  CONST_13  C10  N26  N24  C5      0.00   0.0  0
 3W7  CONST_14  N26  C10  C8   C5      0.00   0.0  0
 3W7  CONST_15  N25  N23  C4   C6      0.00   0.0  0
 3W7  CONST_16  N23  N25  C9   C6      0.00   0.0  0
 3W7  CONST_17  C9   C6   C3   C7      0.00   0.0  0
 3W7  CONST_18  C9   C2   C1   C7      0.00   0.0  0
 3W7  CONST_19  N24  N26  C10  C8      0.00   0.0  0
 3W7  CONST_20  N26  N24  C5   C8      0.00   0.0  0
 3W7  CONST_21  N23  C4   C6   C9      0.00   0.0  0
 3W7  CONST_22  N24  C5   C8   C10     0.00   0.0  0
 3W7  CONST_23  C12  C7   C1   C2    180.00   0.0  0
 3W7  CONST_24  C22  N26  N24  C5    180.00   0.0  0
 3W7  CONST_25  C12  C7   C3   C6    180.00   0.0  0
 3W7  CONST_26  C22  N26  C10  C8    180.00   0.0  0
 3W7  CONST_27  C22  N26  C10  C11     0.00   0.0  0
 3W7  CONST_29  C17  N27  C12  C7    180.00   0.0  0
 3W7  CONST_30  H3   C3   C7   C1    180.00   0.0  0
 3W7  CONST_31  H1   C1   C7   C3    180.00   0.0  0
 3W7  CONST_32  H4   C4   C6   C3      0.00   0.0  0
 3W7  CONST_33  H25  N23  C4   C6    180.00   0.0  0
 3W7  CONST_34  H2   C2   C9   C6    180.00   0.0  0
 3W7  CONST_35  H5   C5   C8   C10   180.00   0.0  0
 3W7  CONST_36  O29  C12  N27  C17     0.00   0.0  0
 3W7  Var_01    C19  C13  C8   C5    155.37  30.0  1
 3W7  Var_02    C14  C11  C10  C8     -6.93  30.0  1
 3W7  Var_03    C14  C19  C13  C8     49.37  30.0  1
 3W7  Var_04    C19  C14  C11  C10    35.84  30.0  1
 3W7  Var_05    C13  C19  C14  C11   -57.85  30.0  1
 3W7  Var_06    C18  C16  C19  C13  -170.57  30.0  3
 3W7  Var_07    C17  C15  C19  C13   171.40  30.0  3
 3W7  Var_08    C18  N27  C17  C15    57.29  30.0  1
 3W7  Var_09    C17  N27  C18  C16   -56.58  30.0  1
 3W7  Var_10    N27  C18  C16  C19    54.43  30.0  1
 3W7  Var_11    N27  C17  C15  C19   -55.20  30.0  1
 3W7  Var_12    N27  C12  C7   C1   -133.51  30.0  2
 3W7  Var_13    C20  C22  N26  C10   101.08  30.0  1
 3W7  Var_14    H18  C20  C22  N26  -177.97  30.0  3
 3W7  Var_15    H21  C21  C22  N26   -66.34  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
 3W7  plan-1  C1   0.020
 3W7  plan-1  C2   0.020
 3W7  plan-1  C3   0.020
 3W7  plan-1  C4   0.020
 3W7  plan-1  C6   0.020
 3W7  plan-1  C7   0.020
 3W7  plan-1  C9   0.020
 3W7  plan-1  C12  0.020
 3W7  plan-1  N23  0.020
 3W7  plan-1  N25  0.020
 3W7  plan-1  H1   0.020
 3W7  plan-1  H2   0.020
 3W7  plan-1  H3   0.020
 3W7  plan-1  H4   0.020
 3W7  plan-1  H25  0.020
 3W7  plan-2  C5   0.020
 3W7  plan-2  C8   0.020
 3W7  plan-2  C10  0.020
 3W7  plan-2  C11  0.020
 3W7  plan-2  C13  0.020
 3W7  plan-2  N24  0.020
 3W7  plan-2  N26  0.020
 3W7  plan-2  H5   0.020
 3W7  plan-2  C22  0.020
 3W7  plan-3  C7   0.020
 3W7  plan-3  C12  0.020
 3W7  plan-3  C17  0.020
 3W7  plan-3  C18  0.020
 3W7  plan-3  N27  0.020
 3W7  plan-3  O29  0.020
 3W7  plan-4  C10  0.020
 3W7  plan-4  C11  0.020
 3W7  plan-4  C14  0.020
 3W7  plan-4  O28  0.020

