# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 00:49:12 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (1S,3R,6S)-4-oxo-6-{4-[(2-phenylquinolin-4-yl)methoxy]phenyl}-5-azaspiro[2.4]heptane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1C[C@@]12C[C@H](NC2=O)c3ccc(OCc4cc(nc5ccccc45)c6ccccc6)cc3
#
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
 642  642  '(1S,3R,6S)-4-oxo-6-{4-[(2-phenylquinolin-4-yl)methoxy]phenyl}-5-azaspiro[2.4]heptane-1-carboxylic acid'  ligand  58  35  .  2022-09-22  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_642
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
 642  C1    C  CH1    0  -0.395  -7.5606   0.9807  -0.3964
 642  C2    C  CT     0  -0.169  -6.5883   0.0400   0.2657
 642  C3    C  CH2    0  -0.457  -7.9454  -0.4417  -0.1440
 642  C4    C  C      0   0.433  -7.2988   1.4666  -1.8107
 642  O1    O  O      0  -0.603  -6.8920   0.6307  -2.6414
 642  O2    O  OC    -1  -0.615  -7.5201   2.6770  -2.0175
 642  C5    C  C      0   0.570  -6.3272   0.1980   1.7277
 642  N1    N  NH1    0  -0.643  -5.1208  -0.3495   1.9763
 642  O3    O  O      0  -0.493  -7.0639   0.7133   2.5534
 642  C6    C  CH1    0  -0.119  -4.5454  -1.0698   0.8556
 642  C7    C  CH2    0  -0.449  -5.2958  -0.4560  -0.3429
 642  C8    C  CR6    0   0.125  -3.0504  -0.9287   0.7755
 642  C9    C  CR16   0  -0.283  -2.4397   0.3257   0.8259
 642  C10   C  CR16   0  -0.336  -1.0706   0.4590   0.7116
 642  C11   C  CR6    0   0.393  -0.2686  -0.6721   0.5417
 642  C12   C  CR16   0  -0.363  -0.8584  -1.9295   0.5003
 642  C13   C  CR16   0  -0.313  -2.2408  -2.0416   0.6190
 642  O4    O  O2     0  -0.481   1.0585  -0.4456   0.4283
 642  C14   C  CH2    0  -0.226   1.9160  -1.5445   0.2618
 642  C15   C  CR6    0   0.171   3.3233  -1.0593   0.0803
 642  N2    N  N      0  -0.474   5.9664  -0.1986  -0.2788
 642  C16   C  CR6    0   0.228   4.9931   0.6657  -0.1457
 642  C17   C  CR16   0  -0.420   3.6457   0.2667   0.0486
 642  C18   C  CR66   0   0.202   5.6822  -1.5190  -0.2413
 642  C19   C  CR66   0   0.069   4.3661  -2.0139  -0.0712
 642  C20   C  CR16   0  -0.346   4.1555  -3.4107  -0.0544
 642  C21   C  CR16   0  -0.244   5.2080  -4.2757  -0.1967
 642  C22   C  CR16   0  -0.260   6.5168  -3.7824  -0.3634
 642  C23   C  CR16   0  -0.299   6.7499  -2.4343  -0.3863
 642  C24   C  CR6    0   0.070   5.3531   2.1010  -0.1956
 642  C25   C  CR16   0  -0.283   6.6623   2.5003   0.0818
 642  C26   C  CR16   0  -0.240   7.0182   3.8385   0.0358
 642  C27   C  CR16   0  -0.260   6.0749   4.8033  -0.2968
 642  C28   C  CR16   0  -0.238   4.7728   4.4173  -0.5830
 642  C29   C  CR16   0  -0.321   4.4142   3.0779  -0.5308
 642  H1    H  HCH1   0   0.238  -8.0031   1.7104   0.2744
 642  H3    H  HCH2   0   0.252  -8.6714  -0.6476   0.6332
 642  H3A   H  HCH2   0   0.254  -7.9819  -1.1065  -0.9978
 642  HN1   H  HNH1   0   0.392  -4.7943  -0.4961   2.9197
 642  H6    H  HCH1   0   0.258  -4.7883  -2.1359   0.9373
 642  H7    H  HCH2   0   0.259  -5.4320  -1.1811  -1.1400
 642  H7A   H  HCH2   0   0.243  -4.7191   0.3782  -0.7472
 642  H9    H  HCR6   0   0.254  -3.0443   1.2153   0.9580
 642  H10   H  HCR6   0   0.264  -0.6108   1.4389   0.7499
 642  H12   H  HCR6   0   0.282  -0.2712  -2.8299   0.3826
 642  H13   H  HCR6   0   0.256  -2.6855  -3.0296   0.5867
 642  H14   H  HCH2   0   0.256   1.8631  -2.2132   1.1304
 642  H14A  H  HCH2   0   0.256   1.6286  -2.1347  -0.6178
 642  H17   H  HCR6   0   0.266   2.8809   1.0160   0.1845
 642  H20   H  HCR6   0   0.261   3.1573  -3.8097   0.0722
 642  H21   H  HCR6   0   0.266   5.0352  -5.3435  -0.1816
 642  H22   H  HCR6   0   0.266   7.3388  -4.4771  -0.4747
 642  H23   H  HCR6   0   0.262   7.7499  -2.0407  -0.5167
 642  H25   H  HCR6   0   0.252   7.4015   1.7541   0.3402
 642  H26   H  HCR6   0   0.259   8.0352   4.1303   0.2637
 642  H27   H  HCR6   0   0.261   6.3532   5.8485  -0.3335
 642  H28   H  HCR6   0   0.261   4.0320   5.1589  -0.8523
 642  H29   H  HCR6   0   0.254   3.3970   2.8033  -0.7784

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
 642  C3   C1    single    1.495  0.020  1.495
 642  C2   C1    single    1.506  0.020  1.506
 642  C1   C4    single    1.518  0.020  1.518
 642  C1   H1    single    0.970  0.020  1.090
 642  C3   C2    single    1.497  0.020  1.497
 642  C2   C5    single    1.494  0.020  1.494
 642  C2   C7    single    1.512  0.020  1.512
 642  C3   H3    single    0.970  0.020  1.090
 642  C3   H3A   single    0.970  0.020  1.090
 642  O1   C4    deloc     1.247  0.020  1.247
 642  C4   O2    deloc     1.248  0.020  1.248
 642  O3   C5    double    1.221  0.020  1.221
 642  C5   N1    single    1.348  0.020  1.348
 642  N1   C6    single    1.451  0.020  1.451
 642  N1   HN1   single    0.860  0.020  1.020
 642  C7   C6    single    1.542  0.020  1.542
 642  C6   C8    single    1.504  0.020  1.504
 642  C6   H6    single    0.970  0.020  1.090
 642  C7   H7    single    0.970  0.020  1.090
 642  C7   H7A   single    0.970  0.020  1.090
 642  C8   C13   aromatic  1.385  0.020  1.385
 642  C8   C9    aromatic  1.396  0.020  1.396
 642  C9   C10   aromatic  1.380  0.020  1.380
 642  C9   H9    single    0.930  0.020  1.080
 642  C10  C11   aromatic  1.397  0.020  1.397
 642  C10  H10   single    0.930  0.020  1.080
 642  C12  C11   aromatic  1.389  0.020  1.389
 642  C11  O4    single    1.351  0.020  1.351
 642  C13  C12   aromatic  1.392  0.020  1.392
 642  C12  H12   single    0.930  0.020  1.080
 642  C13  H13   single    0.930  0.020  1.080
 642  O4   C14   single    1.404  0.020  1.404
 642  C14  C15   single    1.500  0.020  1.500
 642  C14  H14   single    0.970  0.020  1.090
 642  C14  H14A  single    0.970  0.020  1.090
 642  C17  C15   aromatic  1.365  0.020  1.365
 642  C15  C19   aromatic  1.422  0.020  1.422
 642  C16  N2    aromatic  1.308  0.020  1.308
 642  N2   C18   aromatic  1.351  0.020  1.351
 642  C17  C16   aromatic  1.419  0.020  1.419
 642  C24  C16   single    1.481  0.020  1.481
 642  C17  H17   single    0.930  0.020  1.080
 642  C19  C18   aromatic  1.416  0.020  1.416
 642  C18  C23   aromatic  1.414  0.020  1.414
 642  C19  C20   aromatic  1.413  0.020  1.413
 642  C20  C21   aromatic  1.370  0.020  1.370
 642  C20  H20   single    0.930  0.020  1.080
 642  C21  C22   aromatic  1.409  0.020  1.409
 642  C21  H21   single    0.930  0.020  1.080
 642  C23  C22   aromatic  1.368  0.020  1.368
 642  C22  H22   single    0.930  0.020  1.080
 642  C23  H23   single    0.930  0.020  1.080
 642  C29  C24   aromatic  1.396  0.020  1.396
 642  C25  C24   aromatic  1.397  0.020  1.397
 642  C26  C25   aromatic  1.385  0.020  1.385
 642  C25  H25   single    0.930  0.020  1.080
 642  C27  C26   aromatic  1.390  0.020  1.390
 642  C26  H26   single    0.930  0.020  1.080
 642  C28  C27   aromatic  1.388  0.020  1.388
 642  C27  H27   single    0.930  0.020  1.080
 642  C28  C29   aromatic  1.388  0.020  1.388
 642  C28  H28   single    0.930  0.020  1.080
 642  C29  H29   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
 642  H1    C1   C4   115.52  3.000
 642  H1    C1   C3   115.48  3.000
 642  C4    C1   C3   120.41  3.000
 642  H1    C1   C2   114.29  3.000
 642  C4    C1   C2   119.88  3.000
 642  C3    C1   C2    59.85  3.000
 642  C7    C2   C5   106.21  3.000
 642  C7    C2   C3   123.99  3.000
 642  C5    C2   C3   117.41  3.000
 642  C7    C2   C1   125.42  3.000
 642  C5    C2   C1   118.50  3.000
 642  C3    C2   C1    59.70  3.000
 642  H3A   C3   H3   115.24  3.000
 642  H3A   C3   C2   116.35  3.000
 642  H3    C3   C2   118.18  3.000
 642  H3A   C3   C1   117.37  3.000
 642  H3    C3   C1   118.33  3.000
 642  C2    C3   C1    60.45  3.000
 642  O2    C4   O1   126.72  3.000
 642  O2    C4   C1   115.74  3.000
 642  O1    C4   C1   117.54  3.000
 642  O3    C5   N1   125.94  3.000
 642  N1    C5   C2   107.10  3.000
 642  O3    C5   C2   126.96  3.000
 642  HN1   N1   C6   121.45  3.000
 642  HN1   N1   C5   121.40  3.000
 642  C6    N1   C5   114.46  3.000
 642  H6    C6   C8   108.39  3.000
 642  H6    C6   C7   109.71  3.000
 642  C8    C6   C7   113.90  3.000
 642  H6    C6   N1   109.71  3.000
 642  C8    C6   N1   112.88  3.000
 642  C7    C6   N1   102.11  3.000
 642  H7A   C7   H7   107.73  3.000
 642  H7A   C7   C6   109.57  3.000
 642  H7    C7   C6   111.45  3.000
 642  H7A   C7   C2   110.48  3.000
 642  H7    C7   C2   114.03  3.000
 642  C6    C7   C2   103.52  3.000
 642  C13   C8   C9   118.06  3.000
 642  C9    C8   C6   121.15  3.000
 642  C13   C8   C6   120.78  3.000
 642  H9    C9   C10  118.96  3.000
 642  H9    C9   C8   119.87  3.000
 642  C10   C9   C8   121.18  3.000
 642  H10   C10  C11  119.54  3.000
 642  H10   C10  C9   120.37  3.000
 642  C11   C10  C9   120.09  3.000
 642  O4    C11  C12  124.48  3.000
 642  O4    C11  C10  116.00  3.000
 642  C12   C11  C10  119.52  3.000
 642  H12   C12  C13  118.78  3.000
 642  H12   C12  C11  121.75  3.000
 642  C13   C12  C11  119.46  3.000
 642  H13   C13  C12  118.57  3.000
 642  H13   C13  C8   119.73  3.000
 642  C12   C13  C8   121.70  3.000
 642  C14   O4   C11  118.60  3.000
 642  H14A  C14  H14  107.10  3.000
 642  H14A  C14  C15  108.83  3.000
 642  H14   C14  C15  109.76  3.000
 642  H14A  C14  O4   110.86  3.000
 642  H14   C14  O4   110.71  3.000
 642  C15   C14  O4   109.53  3.000
 642  C19   C15  C17  118.46  3.000
 642  C19   C15  C14  118.94  3.000
 642  C17   C15  C14  122.60  3.000
 642  C18   N2   C16  119.10  3.000
 642  C24   C16  C17  120.54  3.000
 642  C24   C16  N2   117.14  3.000
 642  C17   C16  N2   122.32  3.000
 642  H17   C17  C16  119.68  3.000
 642  H17   C17  C15  120.27  3.000
 642  C16   C17  C15  120.05  3.000
 642  C23   C18  C19  119.20  3.000
 642  C23   C18  N2   118.10  3.000
 642  C19   C18  N2   122.70  3.000
 642  C20   C19  C18  119.04  3.000
 642  C20   C19  C15  123.59  3.000
 642  C18   C19  C15  117.37  3.000
 642  H20   C20  C21  119.21  3.000
 642  H20   C20  C19  120.22  3.000
 642  C21   C20  C19  120.57  3.000
 642  H21   C21  C22  119.72  3.000
 642  H21   C21  C20  119.94  3.000
 642  C22   C21  C20  120.34  3.000
 642  H22   C22  C23  120.10  3.000
 642  H22   C22  C21  119.55  3.000
 642  C23   C22  C21  120.35  3.000
 642  H23   C23  C22  121.17  3.000
 642  H23   C23  C18  118.33  3.000
 642  C22   C23  C18  120.50  3.000
 642  C29   C24  C25  118.57  3.000
 642  C25   C24  C16  119.89  3.000
 642  C29   C24  C16  121.54  3.000
 642  H25   C25  C26  119.91  3.000
 642  H25   C25  C24  119.39  3.000
 642  C26   C25  C24  120.69  3.000
 642  H26   C26  C27  120.07  3.000
 642  H26   C26  C25  119.66  3.000
 642  C27   C26  C25  120.27  3.000
 642  H27   C27  C28  120.19  3.000
 642  H27   C27  C26  120.26  3.000
 642  C28   C27  C26  119.54  3.000
 642  H28   C28  C29  119.60  3.000
 642  H28   C28  C27  120.19  3.000
 642  C29   C28  C27  120.21  3.000
 642  H29   C29  C28  118.63  3.000
 642  H29   C29  C24  120.63  3.000
 642  C28   C29  C24  120.72  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
 642  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 642  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 642  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 642  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 642  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 642  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 642  CONST_07  N2   C16  C17  C15     0.00   0.0  0
 642  CONST_08  C24  C16  C17  C15   180.00   0.0  0
 642  CONST_09  N2   C18  C19  C15     0.00   0.0  0
 642  CONST_10  C23  C18  C19  C15   180.00   0.0  0
 642  CONST_11  C21  C20  C19  C15   180.00   0.0  0
 642  CONST_14  C20  C19  C18  N2    180.00   0.0  0
 642  CONST_15  C22  C23  C18  N2    180.00   0.0  0
 642  CONST_16  C19  C18  N2   C16     0.00   0.0  0
 642  CONST_17  C23  C18  N2   C16   180.00   0.0  0
 642  CONST_18  C19  C15  C17  C16     0.00   0.0  0
 642  CONST_19  C28  C29  C24  C16   180.00   0.0  0
 642  CONST_20  C26  C25  C24  C16   180.00   0.0  0
 642  CONST_21  C18  C19  C15  C17     0.00   0.0  0
 642  CONST_22  C20  C19  C15  C17   180.00   0.0  0
 642  CONST_23  C18  N2   C16  C17     0.00   0.0  0
 642  CONST_26  C24  C16  N2   C18   180.00   0.0  0
 642  CONST_27  C21  C20  C19  C18     0.00   0.0  0
 642  CONST_28  C21  C22  C23  C18     0.00   0.0  0
 642  CONST_29  C22  C23  C18  C19     0.00   0.0  0
 642  CONST_30  C22  C21  C20  C19     0.00   0.0  0
 642  CONST_31  C23  C18  C19  C20     0.00   0.0  0
 642  CONST_32  C23  C22  C21  C20     0.00   0.0  0
 642  CONST_33  C27  C28  C29  C24     0.00   0.0  0
 642  CONST_34  C27  C26  C25  C24     0.00   0.0  0
 642  CONST_35  C28  C29  C24  C25     0.00   0.0  0
 642  CONST_36  C28  C27  C26  C25     0.00   0.0  0
 642  CONST_37  C29  C24  C25  C26     0.00   0.0  0
 642  CONST_38  C29  C28  C27  C26     0.00   0.0  0
 642  CONST_39  C12  C13  C8   C6    180.00   0.0  0
 642  CONST_40  C10  C9   C8   C6    180.00   0.0  0
 642  CONST_41  C6   N1   C5   C2      0.00   0.0  0
 642  CONST_42  O4   C11  C10  C9    180.00   0.0  0
 642  CONST_43  O4   C11  C12  C13   180.00   0.0  0
 642  CONST_44  C16  C17  C15  C14   180.00   0.0  0
 642  CONST_45  C18  C19  C15  C14   180.00   0.0  0
 642  CONST_46  C20  C19  C15  C14     0.00   0.0  0
 642  CONST_47  C6   N1   C5   O3    180.00   0.0  0
 642  CONST_48  H13  C13  C8   C6      0.00   0.0  0
 642  CONST_49  H9   C9   C8   C6      0.00   0.0  0
 642  CONST_50  H12  C12  C13  C8    180.00   0.0  0
 642  CONST_51  H10  C10  C9   C8    180.00   0.0  0
 642  CONST_52  H20  C20  C19  C15     0.00   0.0  0
 642  CONST_53  H17  C17  C16  N2    180.00   0.0  0
 642  CONST_54  H23  C23  C18  N2      0.00   0.0  0
 642  CONST_55  H29  C29  C24  C16     0.00   0.0  0
 642  CONST_56  H25  C25  C24  C16     0.00   0.0  0
 642  CONST_57  H22  C22  C23  C18   180.00   0.0  0
 642  CONST_58  H21  C21  C20  C19   180.00   0.0  0
 642  CONST_59  H28  C28  C29  C24   180.00   0.0  0
 642  CONST_60  H26  C26  C25  C24   180.00   0.0  0
 642  CONST_61  H27  C27  C26  C25   180.00   0.0  0
 642  CONST_62  HN1  N1   C5   C2    180.00   0.0  0
 642  Var_01    C5   C2   C3   C1    108.63  30.0  3
 642  Var_02    N1   C5   C2   C1   -156.82  30.0  1
 642  Var_03    C6   C7   C2   C1    166.13  30.0  1
 642  Var_04    C4   C1   C3   C2    109.09  30.0  1
 642  Var_05    O1   C4   C1   C2     42.51  30.0  3
 642  Var_06    C15  C14  O4   C11   176.79  30.0  3
 642  Var_07    C17  C15  C14  O4     -1.92  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
 642  chir_03  C6  N1  C7  C8  negativ
 642  chir_04  C1  C3  C2  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
 642  plan-1  C6   0.020
 642  plan-1  C8   0.020
 642  plan-1  C9   0.020
 642  plan-1  C10  0.020
 642  plan-1  C11  0.020
 642  plan-1  C12  0.020
 642  plan-1  C13  0.020
 642  plan-1  O4   0.020
 642  plan-1  H9   0.020
 642  plan-1  H10  0.020
 642  plan-1  H12  0.020
 642  plan-1  H13  0.020
 642  plan-2  C16  0.020
 642  plan-2  C24  0.020
 642  plan-2  C25  0.020
 642  plan-2  C26  0.020
 642  plan-2  C27  0.020
 642  plan-2  C28  0.020
 642  plan-2  C29  0.020
 642  plan-2  H25  0.020
 642  plan-2  H26  0.020
 642  plan-2  H27  0.020
 642  plan-2  H28  0.020
 642  plan-2  H29  0.020
 642  plan-3  C14  0.020
 642  plan-3  C15  0.020
 642  plan-3  N2   0.020
 642  plan-3  C16  0.020
 642  plan-3  C17  0.020
 642  plan-3  C18  0.020
 642  plan-3  C19  0.020
 642  plan-3  C20  0.020
 642  plan-3  C21  0.020
 642  plan-3  C22  0.020
 642  plan-3  C23  0.020
 642  plan-3  C24  0.020
 642  plan-3  H17  0.020
 642  plan-3  H20  0.020
 642  plan-3  H21  0.020
 642  plan-3  H22  0.020
 642  plan-3  H23  0.020
 642  plan-4  C2   0.020
 642  plan-4  C5   0.020
 642  plan-4  N1   0.020
 642  plan-4  O3   0.020
 642  plan-4  C6   0.020
 642  plan-4  HN1  0.020
 642  plan-5  C1   0.020
 642  plan-5  C4   0.020
 642  plan-5  O1   0.020
 642  plan-5  O2   0.020

