# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 05:26:19 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: tert-butyl 7-[(7-methyl-1H-indazol-5-yl)carbonyl]-2,7-diazaspiro[3.5]nonane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(cc2cn[nH]c12)C(=O)N3CCC4(CC3)CN(C4)C(=O)OC(C)(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
 57K  57K  'tert-butyl 7-[(7-methyl-1H-indazol-5-yl)carbonyl]-2,7-diazaspiro[3.5]nonane-2-carboxylate'  ligand  56  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_57K
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
 57K  N3   N  NT    0  -0.450  -1.2519   1.2321  -0.6704
 57K  C4   C  CR6   0  -0.067  -3.5559   0.7970  -0.0017
 57K  N2   N  N     0  -0.218  -6.9761  -1.9645  -1.2240
 57K  C7   C  CR56  0   0.407  -5.8729  -0.6658   0.2244
 57K  C6   C  CR56  0  -0.070  -5.1644  -0.6573  -0.9871
 57K  C9   C  C     0   0.523  -2.3768   1.7110  -0.0933
 57K  C13  C  CH2   0  -0.444   0.2754  -0.4146   0.3113
 57K  C8   C  CR15  0  -0.130  -5.9255  -1.4963  -1.8460
 57K  C18  C  CT    0   0.193   6.8153  -0.7938   0.5900
 57K  C16  C  C     0  -0.229   2.3037   0.0849  -1.2033
 57K  C19  C  CH3   0  -0.672   7.1337  -2.1963   0.0849
 57K  C2   C  CR6   0   0.106  -5.4596   0.0580   1.3549
 57K  C3   C  CR16  0  -0.330  -4.3059   0.7911   1.1972
 57K  C5   C  CR16  0  -0.336  -3.9825   0.0806  -1.0988
 57K  N1   N  NR15  0  -0.547  -6.9433  -1.4662   0.0159
 57K  O1   O  O     0  -0.486  -2.4865   2.8673   0.2953
 57K  C10  C  CH2   0  -0.308  -0.1501   2.1351  -0.9610
 57K  C11  C  CH2   0  -0.421   0.9985   1.9488   0.0206
 57K  C12  C  C     0  -0.137   1.4579   0.4996   0.0360
 57K  C14  C  CH2   0  -0.310  -0.8585  -0.1711  -0.6788
 57K  C15  C  C     0  -0.208   2.7092   0.2262   0.9048
 57K  N4   N  N     0  -0.470   3.4102  -0.1486  -0.3057
 57K  C17  C  C     0   0.739   4.6799  -0.4862  -0.5712
 57K  O2   O  O     0  -0.548   5.0812  -0.7039  -1.7024
 57K  O3   O  O2    0  -0.486   5.3798  -0.5520   0.5502
 57K  H13  H  HCH2  0   0.268   0.5806  -1.4620   0.2497
 57K  H12  H  HCH2  0   0.262  -0.0904  -0.2418   1.3278
 57K  H24  H  HCH3  0   0.258   6.9238   0.3054   2.4558
 57K  H23  H  HCH3  0   0.244   6.5735  -1.4210   2.6529
 57K  H25  H  HCH3  0   0.254   8.2038  -0.8867   2.2294
 57K  H27  H  HCH3  0   0.217   7.4199   0.1828  -1.2655
 57K  H26  H  HCH3  0   0.262   7.2759   1.2723   0.1248
 57K  H28  H  HCH3  0   0.264   8.6398   0.1679   0.0027
 57K  H7   H  HCR5  0   0.291  -5.7284  -1.7591  -2.8741
 57K  H18  H  H     0   0.243   1.9544  -0.8074  -1.7310
 57K  H19  H  H     0   0.218   2.4791   0.8760  -1.9392
 57K  H21  H  HCH3  0   0.227   8.1921  -2.3983   0.2546
 57K  H22  H  HCH3  0   0.221   6.5616  -2.9490   0.6309
 57K  H20  H  HCH3  0   0.233   6.9366  -2.3108  -0.9794
 57K  H2   H  HCH3  0   0.235  -6.3118  -0.9842   3.0337
 57K  H3   H  HCH3  0   0.248  -5.7787   0.6523   3.3916
 57K  H4   H  HCH3  0   0.234  -7.2614   0.3920   2.4826
 57K  H5   H  HCR6  0   0.230  -3.9473   1.3827   2.0305
 57K  H6   H  HCR6  0   0.249  -3.4266   0.0956  -2.0280
 57K  H1   H  HNR5  0   0.386  -7.6730  -1.7167   0.6586
 57K  H9   H  HCH2  0   0.232   0.1935   1.9205  -1.9792
 57K  H8   H  HCH2  0   0.260  -0.5100   3.1602  -0.9548
 57K  H11  H  HCH2  0   0.234   1.8222   2.6133  -0.2551
 57K  H10  H  HCH2  0   0.237   0.6723   2.2393   1.0236
 57K  H14  H  HCH2  0   0.268  -1.7022  -0.8055  -0.4268
 57K  H15  H  HCH2  0   0.237  -0.5481  -0.4446  -1.6920
 57K  H17  H  H     0   0.233   3.1222   1.1010   1.4136
 57K  H16  H  H     0   0.234   2.6001  -0.5804   1.6335
 57K  C1   C  CH3   0  -0.717  -6.2421   0.0282   2.6299
 57K  C20  C  CH3   0  -0.677   7.1430  -0.6923   2.0732
 57K  C21  C  CH3   0  -0.684   7.5719   0.2714  -0.1917

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
 57K  C21  C18  single    1.523  0.020  1.523
 57K  C18  C19  single    1.524  0.020  1.524
 57K  C18  C20  single    1.522  0.020  1.522
 57K  C18  O3   single    1.456  0.020  1.456
 57K  O2   C17  double    1.220  0.020  1.220
 57K  C17  O3   single    1.323  0.020  1.323
 57K  C17  N4   single    1.340  0.020  1.340
 57K  N4   C16  single    1.444  0.020  1.444
 57K  N4   C15  single    1.448  0.020  1.448
 57K  C16  C12  single    1.557  0.020  1.557
 57K  C15  C12  single    1.548  0.020  1.548
 57K  C12  C13  single    1.520  0.020  1.520
 57K  C12  C11  single    1.520  0.020  1.520
 57K  C13  C14  single    1.525  0.020  1.525
 57K  C11  C10  single    1.522  0.020  1.522
 57K  C14  N3   single    1.457  0.020  1.457
 57K  C10  N3   single    1.454  0.020  1.454
 57K  N3   C9   single    1.352  0.020  1.352
 57K  C9   O1   double    1.225  0.020  1.225
 57K  C9   C4   single    1.495  0.020  1.495
 57K  C4   C3   aromatic  1.414  0.020  1.414
 57K  C4   C5   aromatic  1.378  0.020  1.378
 57K  C3   C2   aromatic  1.376  0.020  1.376
 57K  C5   C6   aromatic  1.398  0.020  1.398
 57K  C2   C1   single    1.496  0.020  1.496
 57K  C2   C7   aromatic  1.405  0.020  1.405
 57K  C6   C7   aromatic  1.404  0.020  1.404
 57K  C6   C8   aromatic  1.422  0.020  1.422
 57K  C7   N1   aromatic  1.353  0.020  1.353
 57K  C8   N2   aromatic  1.308  0.020  1.308
 57K  N1   N2   aromatic  1.337  0.020  1.337
 57K  C13  H13  single    0.970  0.020  1.090
 57K  C13  H12  single    0.970  0.020  1.090
 57K  C20  H24  single    0.970  0.020  1.090
 57K  C20  H23  single    0.970  0.020  1.090
 57K  C20  H25  single    0.970  0.020  1.090
 57K  C21  H27  single    0.970  0.020  1.090
 57K  C21  H26  single    0.970  0.020  1.090
 57K  C21  H28  single    0.970  0.020  1.090
 57K  C8   H7   single    0.930  0.020  1.080
 57K  C16  H18  single    0.970  0.020  1.090
 57K  C16  H19  single    0.970  0.020  1.090
 57K  C19  H21  single    0.970  0.020  1.090
 57K  C19  H22  single    0.970  0.020  1.090
 57K  C19  H20  single    0.970  0.020  1.090
 57K  C1   H2   single    0.970  0.020  1.090
 57K  C1   H3   single    0.970  0.020  1.090
 57K  C1   H4   single    0.970  0.020  1.090
 57K  C3   H5   single    0.930  0.020  1.080
 57K  C5   H6   single    0.930  0.020  1.080
 57K  N1   H1   single    0.860  0.020  1.020
 57K  C10  H9   single    0.970  0.020  1.090
 57K  C10  H8   single    0.970  0.020  1.090
 57K  C11  H11  single    0.970  0.020  1.090
 57K  C11  H10  single    0.970  0.020  1.090
 57K  C14  H14  single    0.970  0.020  1.090
 57K  C14  H15  single    0.970  0.020  1.090
 57K  C15  H17  single    0.970  0.020  1.090
 57K  C15  H16  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
 57K  C14  N3   C10  113.10  3.000
 57K  C10  N3   C9   119.73  3.000
 57K  C14  N3   C9   124.62  3.000
 57K  C5   C4   C3   120.57  3.000
 57K  C5   C4   C9   120.88  3.000
 57K  C3   C4   C9   118.22  3.000
 57K  N1   N2   C8   106.74  3.000
 57K  N1   C7   C2   131.44  3.000
 57K  N1   C7   C6   105.66  3.000
 57K  C2   C7   C6   122.89  3.000
 57K  C5   C6   C8   135.72  3.000
 57K  C8   C6   C7   104.34  3.000
 57K  C5   C6   C7   119.94  3.000
 57K  O1   C9   C4   119.16  3.000
 57K  C4   C9   N3   117.77  3.000
 57K  O1   C9   N3   122.98  3.000
 57K  H12  C13  H13  107.29  3.000
 57K  H12  C13  C14  109.23  3.000
 57K  H13  C13  C14  108.91  3.000
 57K  H12  C13  C12  109.48  3.000
 57K  H13  C13  C12  110.43  3.000
 57K  C14  C13  C12  111.40  3.000
 57K  H7   C8   C6   128.42  3.000
 57K  H7   C8   N2   120.84  3.000
 57K  C6   C8   N2   110.74  3.000
 57K  O3   C18  C19  110.47  3.000
 57K  O3   C18  C21  111.08  3.000
 57K  C19  C18  C21  111.70  3.000
 57K  O3   C18  C20  103.17  3.000
 57K  C19  C18  C20  109.82  3.000
 57K  C21  C18  C20  110.27  3.000
 57K  H19  C16  H18  108.44  3.000
 57K  H19  C16  N4   114.33  3.000
 57K  H18  C16  N4   114.38  3.000
 57K  H19  C16  C12  115.45  3.000
 57K  H18  C16  C12  115.34  3.000
 57K  N4   C16  C12   87.97  3.000
 57K  H20  C19  H22  108.75  3.000
 57K  H20  C19  H21  107.96  3.000
 57K  H22  C19  H21  107.64  3.000
 57K  H20  C19  C18  112.51  3.000
 57K  H22  C19  C18  111.05  3.000
 57K  H21  C19  C18  108.76  3.000
 57K  C3   C2   C1   123.15  3.000
 57K  C1   C2   C7   121.44  3.000
 57K  C3   C2   C7   115.41  3.000
 57K  H5   C3   C2   118.71  3.000
 57K  H5   C3   C4   118.32  3.000
 57K  C2   C3   C4   122.96  3.000
 57K  H6   C5   C6   120.66  3.000
 57K  H6   C5   C4   121.14  3.000
 57K  C6   C5   C4   118.20  3.000
 57K  H1   N1   C7   128.61  3.000
 57K  H1   N1   N2   118.87  3.000
 57K  C7   N1   N2   112.52  3.000
 57K  H8   C10  H9   107.10  3.000
 57K  H8   C10  C11  111.21  3.000
 57K  H9   C10  C11  109.79  3.000
 57K  H8   C10  N3   109.50  3.000
 57K  H9   C10  N3   107.55  3.000
 57K  C11  C10  N3   111.52  3.000
 57K  H10  C11  H11  107.12  3.000
 57K  H10  C11  C12  109.50  3.000
 57K  H11  C11  C12  110.74  3.000
 57K  H10  C11  C10  109.50  3.000
 57K  H11  C11  C10  109.35  3.000
 57K  C12  C11  C10  110.56  3.000
 57K  C15  C12  C11  114.73  3.000
 57K  C11  C12  C16  114.21  3.000
 57K  C15  C12  C16   87.74  3.000
 57K  C11  C12  C13  109.89  3.000
 57K  C15  C12  C13  114.90  3.000
 57K  C16  C12  C13  113.99  3.000
 57K  H15  C14  H14  106.82  3.000
 57K  H15  C14  C13  110.50  3.000
 57K  H14  C14  C13  109.51  3.000
 57K  H15  C14  N3   108.81  3.000
 57K  H14  C14  N3   110.59  3.000
 57K  C13  C14  N3   110.54  3.000
 57K  H16  C15  H17  108.55  3.000
 57K  H16  C15  N4   114.51  3.000
 57K  H17  C15  N4   114.41  3.000
 57K  H16  C15  C12  115.10  3.000
 57K  H17  C15  C12  115.18  3.000
 57K  N4   C15  C12   88.16  3.000
 57K  C17  N4   C15  133.57  3.000
 57K  C15  N4   C16   96.13  3.000
 57K  C17  N4   C16  130.06  3.000
 57K  O3   C17  O2   127.08  3.000
 57K  O3   C17  N4   110.22  3.000
 57K  O2   C17  N4   122.70  3.000
 57K  C17  O3   C18  123.55  3.000
 57K  H4   C1   H3   107.50  3.000
 57K  H4   C1   H2   107.40  3.000
 57K  H3   C1   H2   107.46  3.000
 57K  H4   C1   C2   111.50  3.000
 57K  H3   C1   C2   111.24  3.000
 57K  H2   C1   C2   111.52  3.000
 57K  H25  C20  H23  108.22  3.000
 57K  H25  C20  H24  107.97  3.000
 57K  H23  C20  H24  108.62  3.000
 57K  H25  C20  C18  109.72  3.000
 57K  H23  C20  C18  111.14  3.000
 57K  H24  C20  C18  111.07  3.000
 57K  H28  C21  H26  107.53  3.000
 57K  H28  C21  H27  107.76  3.000
 57K  H26  C21  H27  108.86  3.000
 57K  H28  C21  C18  109.19  3.000
 57K  H26  C21  C18  110.99  3.000
 57K  H27  C21  C18  112.35  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
 57K  CONST_01  C7   C2   C3   C4      0.00   0.0  0
 57K  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 57K  CONST_03  C8   C6   C5   C4    180.00   0.0  0
 57K  CONST_04  C5   C6   C8   N2    180.00   0.0  0
 57K  CONST_05  C7   C6   C8   N2      0.00   0.0  0
 57K  CONST_06  C2   C7   N1   N2    180.00   0.0  0
 57K  CONST_07  C6   C7   N1   N2      0.00   0.0  0
 57K  CONST_08  C8   N2   N1   C7      0.00   0.0  0
 57K  CONST_09  C3   C4   C5   C6      0.00   0.0  0
 57K  CONST_10  C3   C2   C7   C6      0.00   0.0  0
 57K  CONST_11  N1   N2   C8   C6      0.00   0.0  0
 57K  CONST_12  C2   C7   C6   C8    180.00   0.0  0
 57K  CONST_13  N1   C7   C6   C8      0.00   0.0  0
 57K  CONST_14  C5   C4   C3   C2      0.00   0.0  0
 57K  CONST_15  C5   C6   C7   C2      0.00   0.0  0
 57K  CONST_16  N1   C7   C2   C3    180.00   0.0  0
 57K  CONST_17  N1   C7   C6   C5    180.00   0.0  0
 57K  CONST_18  C1   C2   C3   C4    180.00   0.0  0
 57K  CONST_19  C9   C4   C5   C6    180.00   0.0  0
 57K  CONST_20  C1   C2   C7   C6    180.00   0.0  0
 57K  CONST_21  C2   C3   C4   C9    180.00   0.0  0
 57K  CONST_22  N1   C7   C2   C1      0.00   0.0  0
 57K  CONST_24  C10  N3   C9   C4    180.00   0.0  0
 57K  CONST_25  H5   C3   C2   C7    180.00   0.0  0
 57K  CONST_26  H6   C5   C6   C7    180.00   0.0  0
 57K  CONST_27  H7   C8   C6   C7    180.00   0.0  0
 57K  CONST_28  H1   N1   C7   C6    180.00   0.0  0
 57K  CONST_30  C10  N3   C9   O1      0.00   0.0  0
 57K  Var_01    C12  C13  C14  N3    -55.32  30.0  1
 57K  Var_02    C12  C11  C10  N3     55.45  30.0  1
 57K  Var_03    N4   C16  C12  C13  -116.04  30.0  3
 57K  Var_04    N4   C15  C12  C13   115.19  30.0  3
 57K  Var_05    C10  C11  C12  C13   -54.12  30.0  1
 57K  Var_06    C10  N3   C14  C13    56.76  30.0  1
 57K  Var_07    C12  C15  N4   C16     0.32  30.0  1
 57K  Var_08    C14  C13  C12  C16   -75.10  30.0  1
 57K  Var_09    C14  N3   C10  C11   -57.34  30.0  1
 57K  Var_10    C3   C4   C9   N3    138.22  30.0  2
 57K  Var_11    O2   C17  N4   C16    -2.95  30.0  1
 57K  Var_12    H2   C1   C2   C7     60.55  30.0  2
 57K  Var_13    N4   C17  O3   C18  -175.08  30.0  1
 57K  Var_14    H27  C21  C18  C20   175.74  30.0  3
 57K  Var_15    H21  C19  C18  C20   -59.12  30.0  3
 57K  Var_16    H24  C20  C18  C21    56.39  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
 57K  plan-1  N3   0.020
 57K  plan-1  C4   0.020
 57K  plan-1  C9   0.020
 57K  plan-1  O1   0.020
 57K  plan-1  C10  0.020
 57K  plan-1  C14  0.020
 57K  plan-2  C4   0.020
 57K  plan-2  N2   0.020
 57K  plan-2  C7   0.020
 57K  plan-2  C6   0.020
 57K  plan-2  C9   0.020
 57K  plan-2  C8   0.020
 57K  plan-2  C2   0.020
 57K  plan-2  C3   0.020
 57K  plan-2  C5   0.020
 57K  plan-2  N1   0.020
 57K  plan-2  H7   0.020
 57K  plan-2  H5   0.020
 57K  plan-2  H6   0.020
 57K  plan-2  H1   0.020
 57K  plan-2  C1   0.020
 57K  plan-3  N4   0.020
 57K  plan-3  C17  0.020
 57K  plan-3  O2   0.020
 57K  plan-3  O3   0.020

