# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 03:12:55 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 2,2-dimethylpropyl (1S)-1-methyl-8-[(7-methyl-1H-indazol-5-yl)carbonyl]-2,8-diazaspiro[4.5]decane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N(CCC12CCN(CC2)C(=O)c3cc(C)c4[nH]ncc4c3)C(=O)OCC(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
 57L  57L  '2,2-dimethylpropyl (1S)-1-methyl-8-[(7-methyl-1H-indazol-5-yl)carbonyl]-2,8-diazaspiro[4.5]decane-2-carboxylate'  ligand  65  31  .  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_57L
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
 57L  N3   N  NT    0  -0.444   1.9058  -1.4640  -1.1481
 57L  C4   C  CR6   0  -0.073   3.8663  -0.3536  -0.2021
 57L  N2   N  N     0  -0.224   6.1199   3.5979  -0.5380
 57L  C7   C  CR56  0   0.398   5.4469   1.7657   0.5467
 57L  C6   C  CR56  0  -0.074   4.9021   1.7199  -0.7463
 57L  C9   C  C     0   0.517   3.1184  -1.5961  -0.5681
 57L  C13  C  CH2   0  -0.431   0.0273  -2.9851  -0.6963
 57L  C20  C  CH2   0  -0.119  -5.9236   0.7370   1.0596
 57L  C21  C  CT    0  -0.147  -6.4931   1.9403   0.3145
 57L  C8   C  CR15  0  -0.129   5.3748   2.9090  -1.3646
 57L  C18  C  CH3   0  -0.671  -2.5954  -3.5020   0.5064
 57L  C16  C  CH2   0  -0.267  -2.9438  -0.7103  -1.3307
 57L  C19  C  C     0   0.760  -4.0367  -0.6891   0.9000
 57L  C2   C  CR6   0   0.091   5.2312   0.7602   1.5043
 57L  C3   C  CR16  0  -0.352   4.4491  -0.2922   1.0865
 57L  C5   C  CR16  0  -0.351   4.0918   0.6437  -1.1261
 57L  N1   N  NR15  0  -0.553   6.1609   2.9124   0.6072
 57L  O1   O  O     0  -0.493   3.6459  -2.6847  -0.3690
 57L  C10  C  CH2   0  -0.326   1.0518  -0.2915  -1.0370
 57L  C11  C  CH2   0  -0.408  -0.1362  -0.5746  -0.1236
 57L  C12  C  CT    0  -0.127  -0.9401  -1.8138  -0.5472
 57L  C14  C  CH2   0  -0.322   1.1931  -2.6428  -1.6145
 57L  C15  C  CH2   0  -0.479  -1.7495  -1.5244  -1.8196
 57L  N4   N  NT    0  -0.502  -3.0873  -1.1268   0.0591
 57L  C17  C  CH1   0  -0.031  -2.0614  -2.0747   0.4816
 57L  O2   O  O     0  -0.536  -4.1563  -1.0429   2.0599
 57L  O3   O  O2    0  -0.481  -4.8422   0.1950   0.3066
 57L  C22  C  CH3   0  -0.640  -6.9796   1.5366  -1.0781
 57L  C23  C  CH3   0  -0.647  -7.6770   2.4496   1.1394
 57L  C24  C  CH3   0  -0.642  -5.4390   3.0425   0.2053
 57L  H12  H  HCH2  0   0.239   0.4227  -3.2653   0.2857
 57L  H13  H  HCH2  0   0.246  -0.4859  -3.8618  -1.0964
 57L  H25  H  HCH2  0   0.229  -5.5823   1.0424   2.0524
 57L  H24  H  HCH2  0   0.227  -6.6968  -0.0281   1.1891
 57L  H7   H  HCR5  0   0.271   5.1898   3.2640  -2.3671
 57L  H21  H  HCH3  0   0.233  -1.8346  -4.1983   0.8595
 57L  H22  H  HCH3  0   0.244  -3.4438  -3.5715   1.1864
 57L  H23  H  HCH3  0   0.226  -2.9263  -3.8302  -0.4801
 57L  H18  H  HCH2  0   0.238  -2.7522   0.3633  -1.3998
 57L  H19  H  HCH2  0   0.251  -3.8434  -0.9179  -1.9117
 57L  H3   H  HCH3  0   0.250   5.5407   1.7647   3.3793
 57L  H4   H  HCH3  0   0.257   5.5116   0.0064   3.4914
 57L  H2   H  HCH3  0   0.252   6.9225   0.8293   2.8292
 57L  H5   H  HCR6  0   0.255   4.2617  -1.1021   1.7816
 57L  H6   H  HCR6  0   0.268   3.6670   0.5959  -2.1213
 57L  H1   H  HNR5  0   0.420   6.6995   3.2695   1.3793
 57L  H8   H  HCH2  0   0.277   1.6111   0.5492  -0.6384
 57L  H9   H  HCH2  0   0.246   0.7155  -0.0032  -2.0370
 57L  H11  H  HCH2  0   0.238   0.2374  -0.7212   0.8950
 57L  H10  H  HCH2  0   0.251  -0.7693   0.3166  -0.0949
 57L  H14  H  HCH2  0   0.249   0.8318  -2.4428  -2.6283
 57L  H15  H  HCH2  0   0.267   1.8831  -3.4790  -1.6817
 57L  H16  H  HCH2  0   0.249  -2.0825  -2.4608  -2.2738
 57L  H17  H  HCH2  0   0.257  -1.1912  -0.9825  -2.5827
 57L  H20  H  HCH1  0   0.248  -1.7130  -1.8156   1.4852
 57L  H28  H  HCH3  0   0.222  -7.7287   0.7442  -1.0202
 57L  H27  H  HCH3  0   0.225  -7.4378   2.3883  -1.5844
 57L  H26  H  HCH3  0   0.232  -6.1628   1.1818  -1.7078
 57L  H29  H  HCH3  0   0.227  -7.3718   2.7230   2.1519
 57L  H30  H  HCH3  0   0.233  -8.1137   3.3361   0.6758
 57L  H31  H  HCH3  0   0.227  -8.4646   1.6968   1.2192
 57L  H32  H  HCH3  0   0.231  -4.5731   2.7219  -0.3755
 57L  H34  H  HCH3  0   0.226  -5.8551   3.9241  -0.2857
 57L  H33  H  HCH3  0   0.222  -5.0851   3.3503   1.1919
 57L  C1   C  CH3   0  -0.730   5.8315   0.8426   2.8724

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
 57L  N2   N1   aromatic  1.335  0.020  1.335
 57L  N2   C8   aromatic  1.309  0.020  1.309
 57L  N1   C7   aromatic  1.352  0.020  1.352
 57L  C8   C6   aromatic  1.421  0.020  1.421
 57L  C7   C6   aromatic  1.404  0.020  1.404
 57L  C7   C2   aromatic  1.405  0.020  1.405
 57L  C6   C5   aromatic  1.400  0.020  1.400
 57L  C1   C2   single    1.496  0.020  1.496
 57L  C2   C3   aromatic  1.376  0.020  1.376
 57L  C5   C4   aromatic  1.378  0.020  1.378
 57L  C3   C4   aromatic  1.416  0.020  1.416
 57L  C4   C9   single    1.496  0.020  1.496
 57L  C9   O1   double    1.226  0.020  1.226
 57L  C9   N3   single    1.351  0.020  1.351
 57L  C10  N3   single    1.455  0.020  1.455
 57L  C10  C11  single    1.525  0.020  1.525
 57L  N3   C14  single    1.454  0.020  1.454
 57L  C14  C13  single    1.523  0.020  1.523
 57L  C11  C12  single    1.537  0.020  1.537
 57L  C15  C12  single    1.535  0.020  1.535
 57L  C15  C16  single    1.526  0.020  1.526
 57L  C13  C12  single    1.526  0.020  1.526
 57L  C12  C17  single    1.544  0.020  1.544
 57L  C16  N4   single    1.458  0.020  1.458
 57L  C24  C21  single    1.529  0.020  1.529
 57L  N4   C17  single    1.459  0.020  1.459
 57L  N4   C19  single    1.342  0.020  1.342
 57L  C17  C18  single    1.524  0.020  1.524
 57L  O3   C19  single    1.335  0.020  1.335
 57L  O3   C20  single    1.425  0.020  1.425
 57L  C19  O2   double    1.219  0.020  1.219
 57L  C21  C20  single    1.526  0.020  1.526
 57L  C21  C22  single    1.529  0.020  1.529
 57L  C21  C23  single    1.530  0.020  1.530
 57L  C13  H12  single    0.970  0.020  1.090
 57L  C13  H13  single    0.970  0.020  1.090
 57L  C20  H25  single    0.970  0.020  1.090
 57L  C20  H24  single    0.970  0.020  1.090
 57L  C8   H7   single    0.930  0.020  1.080
 57L  C18  H21  single    0.970  0.020  1.090
 57L  C18  H22  single    0.970  0.020  1.090
 57L  C18  H23  single    0.970  0.020  1.090
 57L  C16  H18  single    0.970  0.020  1.090
 57L  C16  H19  single    0.970  0.020  1.090
 57L  C1   H3   single    0.970  0.020  1.090
 57L  C1   H4   single    0.970  0.020  1.090
 57L  C1   H2   single    0.970  0.020  1.090
 57L  C3   H5   single    0.930  0.020  1.080
 57L  C5   H6   single    0.930  0.020  1.080
 57L  N1   H1   single    0.860  0.020  1.020
 57L  C10  H8   single    0.970  0.020  1.090
 57L  C10  H9   single    0.970  0.020  1.090
 57L  C11  H11  single    0.970  0.020  1.090
 57L  C11  H10  single    0.970  0.020  1.090
 57L  C14  H14  single    0.970  0.020  1.090
 57L  C14  H15  single    0.970  0.020  1.090
 57L  C15  H16  single    0.970  0.020  1.090
 57L  C15  H17  single    0.970  0.020  1.090
 57L  C17  H20  single    0.970  0.020  1.090
 57L  C22  H28  single    0.970  0.020  1.090
 57L  C22  H27  single    0.970  0.020  1.090
 57L  C22  H26  single    0.970  0.020  1.090
 57L  C23  H29  single    0.970  0.020  1.090
 57L  C23  H30  single    0.970  0.020  1.090
 57L  C23  H31  single    0.970  0.020  1.090
 57L  C24  H32  single    0.970  0.020  1.090
 57L  C24  H34  single    0.970  0.020  1.090
 57L  C24  H33  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
 57L  C14  N3   C10  112.96  3.000
 57L  C14  N3   C9   119.89  3.000
 57L  C10  N3   C9   124.97  3.000
 57L  C5   C4   C3   120.77  3.000
 57L  C3   C4   C9   117.69  3.000
 57L  C5   C4   C9   121.26  3.000
 57L  N1   N2   C8   106.79  3.000
 57L  N1   C7   C2   131.11  3.000
 57L  C2   C7   C6   123.01  3.000
 57L  N1   C7   C6   105.89  3.000
 57L  C5   C6   C8   135.88  3.000
 57L  C5   C6   C7   119.98  3.000
 57L  C8   C6   C7   104.14  3.000
 57L  O1   C9   C4   118.87  3.000
 57L  O1   C9   N3   122.88  3.000
 57L  C4   C9   N3   118.21  3.000
 57L  H13  C13  H12  107.03  3.000
 57L  H13  C13  C14  108.62  3.000
 57L  H12  C13  C14  108.77  3.000
 57L  H13  C13  C12  110.74  3.000
 57L  H12  C13  C12  109.73  3.000
 57L  C14  C13  C12  111.81  3.000
 57L  H24  C20  H25  107.94  3.000
 57L  H24  C20  O3   109.43  3.000
 57L  H25  C20  O3   110.44  3.000
 57L  H24  C20  C21  110.19  3.000
 57L  H25  C20  C21  109.85  3.000
 57L  O3   C20  C21  108.98  3.000
 57L  C24  C21  C23  109.39  3.000
 57L  C23  C21  C22  109.43  3.000
 57L  C24  C21  C22  110.15  3.000
 57L  C23  C21  C20  106.75  3.000
 57L  C22  C21  C20  110.81  3.000
 57L  C24  C21  C20  110.25  3.000
 57L  H7   C8   C6   128.48  3.000
 57L  H7   C8   N2   120.73  3.000
 57L  C6   C8   N2   110.79  3.000
 57L  H23  C18  H22  108.00  3.000
 57L  H23  C18  H21  108.21  3.000
 57L  H22  C18  H21  107.49  3.000
 57L  H23  C18  C17  111.92  3.000
 57L  H22  C18  C17  110.04  3.000
 57L  H21  C18  C17  111.03  3.000
 57L  H19  C16  H18  107.33  3.000
 57L  H19  C16  N4   111.86  3.000
 57L  H18  C16  N4   110.99  3.000
 57L  H19  C16  C15  111.92  3.000
 57L  H18  C16  C15  111.51  3.000
 57L  N4   C16  C15  103.30  3.000
 57L  O3   C19  O2   123.78  3.000
 57L  O2   C19  N4   124.84  3.000
 57L  O3   C19  N4   111.37  3.000
 57L  C3   C2   C1   123.21  3.000
 57L  C3   C2   C7   115.31  3.000
 57L  C1   C2   C7   121.47  3.000
 57L  H5   C3   C2   118.37  3.000
 57L  H5   C3   C4   118.70  3.000
 57L  C2   C3   C4   122.93  3.000
 57L  H6   C5   C6   120.68  3.000
 57L  H6   C5   C4   121.33  3.000
 57L  C6   C5   C4   117.99  3.000
 57L  H1   N1   C7   128.13  3.000
 57L  H1   N1   N2   119.48  3.000
 57L  C7   N1   N2   112.39  3.000
 57L  H9   C10  H8   106.86  3.000
 57L  H9   C10  C11  110.91  3.000
 57L  H8   C10  C11  108.98  3.000
 57L  H9   C10  N3   108.86  3.000
 57L  H8   C10  N3   110.48  3.000
 57L  C11  C10  N3   110.69  3.000
 57L  H10  C11  H11  106.40  3.000
 57L  H10  C11  C12  111.20  3.000
 57L  H11  C11  C12  109.09  3.000
 57L  H10  C11  C10  108.38  3.000
 57L  H11  C11  C10  108.44  3.000
 57L  C12  C11  C10  113.09  3.000
 57L  C17  C12  C15  101.61  3.000
 57L  C17  C12  C11  109.42  3.000
 57L  C15  C12  C11  110.62  3.000
 57L  C17  C12  C13  113.31  3.000
 57L  C15  C12  C13  113.44  3.000
 57L  C11  C12  C13  108.31  3.000
 57L  H15  C14  H14  107.04  3.000
 57L  H15  C14  C13  110.52  3.000
 57L  H14  C14  C13  110.29  3.000
 57L  H15  C14  N3   109.42  3.000
 57L  H14  C14  N3   108.10  3.000
 57L  C13  C14  N3   111.34  3.000
 57L  H17  C15  H16  106.92  3.000
 57L  H17  C15  C12  113.82  3.000
 57L  H16  C15  C12  110.09  3.000
 57L  H17  C15  C16  111.10  3.000
 57L  H16  C15  C16  110.60  3.000
 57L  C12  C15  C16  104.34  3.000
 57L  C17  N4   C19  121.87  3.000
 57L  C19  N4   C16  125.02  3.000
 57L  C17  N4   C16  113.10  3.000
 57L  H20  C17  N4   109.62  3.000
 57L  H20  C17  C12  109.89  3.000
 57L  N4   C17  C12  102.00  3.000
 57L  H20  C17  C18  108.57  3.000
 57L  N4   C17  C18  111.51  3.000
 57L  C12  C17  C18  115.06  3.000
 57L  C19  O3   C20  118.35  3.000
 57L  H26  C22  H27  107.48  3.000
 57L  H26  C22  H28  107.95  3.000
 57L  H27  C22  H28  107.63  3.000
 57L  H26  C22  C21  111.93  3.000
 57L  H27  C22  C21  110.49  3.000
 57L  H28  C22  C21  111.19  3.000
 57L  H31  C23  H30  107.59  3.000
 57L  H31  C23  H29  107.83  3.000
 57L  H30  C23  H29  107.59  3.000
 57L  H31  C23  C21  111.58  3.000
 57L  H30  C23  C21  110.54  3.000
 57L  H29  C23  C21  111.52  3.000
 57L  H33  C24  H34  107.59  3.000
 57L  H33  C24  H32  107.86  3.000
 57L  H34  C24  H32  107.49  3.000
 57L  H33  C24  C21  111.22  3.000
 57L  H34  C24  C21  110.58  3.000
 57L  H32  C24  C21  111.92  3.000
 57L  H2   C1   H4   107.87  3.000
 57L  H2   C1   H3   107.14  3.000
 57L  H4   C1   H3   107.85  3.000
 57L  H2   C1   C2   111.35  3.000
 57L  H4   C1   C2   111.09  3.000
 57L  H3   C1   C2   111.36  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
 57L  CONST_01  C8   C6   C5   C4   180.00   0.0  0
 57L  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 57L  CONST_03  C7   C2   C3   C4     0.00   0.0  0
 57L  CONST_04  C6   C7   N1   N2     0.00   0.0  0
 57L  CONST_05  C2   C7   N1   N2   180.00   0.0  0
 57L  CONST_06  C7   C6   C8   N2     0.00   0.0  0
 57L  CONST_07  C5   C6   C8   N2   180.00   0.0  0
 57L  CONST_08  C8   N2   N1   C7     0.00   0.0  0
 57L  CONST_09  N1   N2   C8   C6     0.00   0.0  0
 57L  CONST_10  C3   C2   C7   C6     0.00   0.0  0
 57L  CONST_11  C3   C4   C5   C6     0.00   0.0  0
 57L  CONST_12  N1   C7   C6   C8     0.00   0.0  0
 57L  CONST_13  C2   C7   C6   C8   180.00   0.0  0
 57L  CONST_14  C5   C6   C7   C2     0.00   0.0  0
 57L  CONST_15  C5   C4   C3   C2     0.00   0.0  0
 57L  CONST_16  N1   C7   C2   C3   180.00   0.0  0
 57L  CONST_17  N1   C7   C6   C5   180.00   0.0  0
 57L  CONST_18  C1   C2   C3   C4   180.00   0.0  0
 57L  CONST_19  C1   C2   C7   C6   180.00   0.0  0
 57L  CONST_20  C9   C4   C5   C6   180.00   0.0  0
 57L  CONST_21  C2   C3   C4   C9   180.00   0.0  0
 57L  CONST_22  N1   C7   C2   C1     0.00   0.0  0
 57L  CONST_24  C14  N3   C9   C4   180.00   0.0  0
 57L  CONST_25  H7   C8   C6   C7   180.00   0.0  0
 57L  CONST_26  H6   C5   C6   C7   180.00   0.0  0
 57L  CONST_27  H5   C3   C2   C7   180.00   0.0  0
 57L  CONST_28  H1   N1   C7   C6   180.00   0.0  0
 57L  CONST_30  C14  N3   C9   O1     0.00   0.0  0
 57L  Var_01    C12  C11  C10  N3   -54.28  30.0  1
 57L  Var_02    C12  C13  C14  N3    56.45  30.0  1
 57L  Var_03    C10  N3   C14  C13  -57.86  30.0  1
 57L  Var_04    C10  C11  C12  C13   52.39  30.0  1
 57L  Var_05    C16  C15  C12  C13  160.56  30.0  3
 57L  Var_06    C14  N3   C10  C11   56.30  30.0  1
 57L  Var_07    C14  C13  C12  C11  -52.85  30.0  1
 57L  Var_08    N4   C16  C15  C12  -25.81  30.0  1
 57L  Var_09    C17  N4   C16  C15    2.41  30.0  1
 57L  Var_10    C5   C4   C9   N3   -52.64  30.0  2
 57L  Var_11    O3   C19  N4   C16   -0.46  30.0  2
 57L  Var_12    H3   C1   C2   C7    56.60  30.0  2
 57L  Var_13    N4   C19  O3   C20  178.74  30.0  3
 57L  Var_14    C24  C21  C20  O3   -63.25  30.0  3
 57L  Var_15    H32  C24  C21  C20   62.84  30.0  3
 57L  Var_16    H28  C22  C21  C20   57.32  30.0  3
 57L  Var_17    H29  C23  C21  C20   58.51  30.0  3
 57L  Var_18    H25  C20  O3   C19   46.01  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
 57L  chir_01  C17  C12  N4  C18  negativ

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
 57L  plan-1  N3   0.020
 57L  plan-1  C4   0.020
 57L  plan-1  C9   0.020
 57L  plan-1  O1   0.020
 57L  plan-1  C10  0.020
 57L  plan-1  C14  0.020
 57L  plan-2  C4   0.020
 57L  plan-2  N2   0.020
 57L  plan-2  C7   0.020
 57L  plan-2  C6   0.020
 57L  plan-2  C9   0.020
 57L  plan-2  C8   0.020
 57L  plan-2  C2   0.020
 57L  plan-2  C3   0.020
 57L  plan-2  C5   0.020
 57L  plan-2  N1   0.020
 57L  plan-2  H7   0.020
 57L  plan-2  H5   0.020
 57L  plan-2  H6   0.020
 57L  plan-2  H1   0.020
 57L  plan-2  C1   0.020
 57L  plan-3  C19  0.020
 57L  plan-3  N4   0.020
 57L  plan-3  O2   0.020
 57L  plan-3  O3   0.020

