# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 00:09:09 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 2-(biphenyl-4-yl)-8-[(1-methyl-1H-imidazol-2-yl)methyl]-2,8-diazaspiro[4.5]decan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccnc1CN2CCC3(CC2)CCN(c4ccc(cc4)c5ccccc5)C3=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
 4JR  4JR  2-(biphenyl-4-yl)-8-[(1-methyl-1H-imidazol-2-yl)methyl]-2,8-diazaspiro[4.5]decan-1-one  ligand  58  30  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4JR
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
 4JR  N1   N  NR5   0  -0.427  -7.2890  -0.1559   0.7264
 4JR  N3   N  NT    0  -0.410  -4.1683   0.3437  -0.6905
 4JR  C4   C  CR5   0   0.428  -6.5313  -0.2076  -0.3958
 4JR  C5   C  CH2   0  -0.364  -5.5311   0.8345  -0.7765
 4JR  C6   C  CH2   0  -0.287  -3.2439   1.2733  -1.3131
 4JR  C7   C  CH2   0  -0.422  -1.8282   0.7172  -1.3318
 4JR  C8   C  CR5   0  -0.276  -1.3510   0.3458   0.0839
 4JR  C10  C  CH2   0  -0.294   0.4330   1.8725   0.6121
 4JR  C13  C  CR16  0  -0.309   3.2031   1.3921  -0.0984
 4JR  C15  C  CR6   0   0.079   5.1462  -0.0487   0.0395
 4JR  C17  C  CR16  0  -0.282   2.9186  -0.9260   0.4489
 4JR  C20  C  CR16  0  -0.240   8.5013  -1.6329  -0.6510
 4JR  C21  C  CR16  0  -0.268   9.3760  -0.6357  -0.2394
 4JR  C22  C  CR16  0  -0.239   8.8660   0.5536   0.2647
 4JR  C24  C  CH2   0  -0.414  -2.3903  -0.5759   0.7149
 4JR  C1   C  CH3   0  -0.538  -7.2811   0.8794   1.7386
 4JR  C2   C  CR15  0  -0.117  -8.0752  -1.2733   0.7363
 4JR  C3   C  CR15  0  -0.228  -7.7510  -1.9600  -0.3979
 4JR  N2   N  N     0  -0.452  -6.7925  -1.2874  -1.0947
 4JR  C25  C  CH2   0  -0.302  -3.7747   0.0491   0.6748
 4JR  C11  C  CR5   0   0.605   0.0023  -0.3388  -0.0339
 4JR  O    O  O     0  -0.467   0.1835  -1.4797  -0.4109
 4JR  C9   C  CH2   0  -0.456  -1.0276   1.5815   0.9274
 4JR  N4   N  NR5   0  -0.578   0.9747   0.5530   0.3096
 4JR  C12  C  CR6   0   0.350   2.3544   0.3293   0.2115
 4JR  C14  C  CR16  0  -0.305   4.5722   1.2025  -0.1798
 4JR  C16  C  CR16  0  -0.307   4.2883  -1.1023   0.3576
 4JR  C18  C  CR6   0   0.095   6.6046  -0.2508  -0.0552
 4JR  C23  C  CR16  0  -0.315   7.4951   0.7431   0.3570
 4JR  C19  C  CR16  0  -0.314   7.1304  -1.4419  -0.5606
 4JR  H2   H  HCH2  0   0.225  -5.6851   1.7442  -0.1735
 4JR  H3   H  HCH2  0   0.266  -5.7204   1.1232  -1.8133
 4JR  H4   H  HCH2  0   0.247  -3.5676   1.4531  -2.3413
 4JR  H5   H  HCH2  0   0.198  -3.2540   2.2555  -0.8096
 4JR  H6   H  HCH2  0   0.244  -1.8028  -0.1738  -1.9641
 4JR  H7   H  HCH2  0   0.248  -1.1616   1.4542  -1.7882
 4JR  H8   H  HCH2  0   0.251   0.5351   2.5437  -0.2452
 4JR  H9   H  HCH2  0   0.268   0.9654   2.3178   1.4523
 4JR  H11  H  HCR6  0   0.270   2.3031  -1.7670   0.7278
 4JR  H12  H  HCR6  0   0.258   8.8865  -2.5612  -1.0523
 4JR  H13  H  HCR6  0   0.257  10.4455  -0.7848  -0.3109
 4JR  H14  H  HCR6  0   0.257   9.5373   1.3357   0.5957
 4JR  H15  H  HCH2  0   0.237  -2.4158  -1.5253   0.1751
 4JR  H16  H  HCH2  0   0.243  -2.1202  -0.7973   1.7504
 4JR  H17  H  HCH3  0   0.259  -6.2928   0.9816   2.1829
 4JR  H18  H  HCH3  0   0.263  -7.5810   1.8382   1.3201
 4JR  H19  H  HCH3  0   0.271  -7.9830   0.6105   2.5223
 4JR  H20  H  HCR5  0   0.285  -8.7775  -1.4727   1.5285
 4JR  H21  H  HCR5  0   0.246  -8.1614  -2.8957  -0.7454
 4JR  H22  H  HCH2  0   0.201  -3.7975   0.9555   1.3065
 4JR  H23  H  HCH2  0   0.251  -4.4872  -0.6549   1.1122
 4JR  H24  H  HCH2  0   0.262  -1.6655   2.4373   0.7111
 4JR  H25  H  HCH2  0   0.257  -1.1396   1.3501   1.9893
 4JR  H26  H  HCR6  0   0.257   5.1955   2.0480  -0.4433
 4JR  H27  H  HCR6  0   0.256   4.6947  -2.0834   0.5706
 4JR  H28  H  HCR6  0   0.253   7.1166   1.6677   0.7746
 4JR  H29  H  HCR6  0   0.253   6.4636  -2.2225  -0.9058
 4JR  H10  H  HCR6  0   0.273   2.8037   2.3779  -0.2958

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
 4JR  C20  C21  aromatic  1.389  0.020  1.389
 4JR  C20  C19  aromatic  1.387  0.020  1.387
 4JR  C21  C22  aromatic  1.389  0.020  1.389
 4JR  C19  C18  aromatic  1.397  0.020  1.397
 4JR  C22  C23  aromatic  1.387  0.020  1.387
 4JR  C18  C23  aromatic  1.397  0.020  1.397
 4JR  C18  C15  single    1.475  0.020  1.475
 4JR  C14  C15  aromatic  1.394  0.020  1.394
 4JR  C14  C13  aromatic  1.385  0.020  1.385
 4JR  C15  C16  aromatic  1.395  0.020  1.395
 4JR  C13  C12  aromatic  1.395  0.020  1.395
 4JR  C16  C17  aromatic  1.384  0.020  1.384
 4JR  C12  C17  aromatic  1.397  0.020  1.397
 4JR  C12  N4   single    1.401  0.020  1.401
 4JR  C10  N4   single    1.458  0.020  1.458
 4JR  C10  C9   single    1.522  0.020  1.522
 4JR  N4   C11  single    1.363  0.020  1.363
 4JR  C9   C8   single    1.531  0.020  1.531
 4JR  C24  C8   single    1.526  0.020  1.526
 4JR  C24  C25  single    1.519  0.020  1.519
 4JR  C11  O    double    1.215  0.020  1.215
 4JR  C11  C8   single    1.521  0.020  1.521
 4JR  C8   C7   single    1.539  0.020  1.539
 4JR  C25  N3   single    1.451  0.020  1.451
 4JR  C1   N1   single    1.448  0.020  1.448
 4JR  N1   C2   aromatic  1.366  0.020  1.366
 4JR  N1   C4   aromatic  1.355  0.020  1.355
 4JR  N3   C5   single    1.451  0.020  1.451
 4JR  N3   C6   single    1.451  0.020  1.451
 4JR  C7   C6   single    1.521  0.020  1.521
 4JR  C2   C3   aromatic  1.365  0.020  1.365
 4JR  C5   C4   single    1.494  0.020  1.494
 4JR  C4   N2   aromatic  1.312  0.020  1.312
 4JR  C3   N2   aromatic  1.363  0.020  1.363
 4JR  C5   H2   single    0.970  0.020  1.090
 4JR  C5   H3   single    0.970  0.020  1.090
 4JR  C6   H4   single    0.970  0.020  1.090
 4JR  C6   H5   single    0.970  0.020  1.090
 4JR  C7   H6   single    0.970  0.020  1.090
 4JR  C7   H7   single    0.970  0.020  1.090
 4JR  C10  H8   single    0.970  0.020  1.090
 4JR  C10  H9   single    0.970  0.020  1.090
 4JR  C13  H10  single    0.930  0.020  1.080
 4JR  C17  H11  single    0.930  0.020  1.080
 4JR  C20  H12  single    0.930  0.020  1.080
 4JR  C21  H13  single    0.930  0.020  1.080
 4JR  C22  H14  single    0.930  0.020  1.080
 4JR  C24  H15  single    0.970  0.020  1.090
 4JR  C24  H16  single    0.970  0.020  1.090
 4JR  C1   H17  single    0.970  0.020  1.090
 4JR  C1   H18  single    0.970  0.020  1.090
 4JR  C1   H19  single    0.970  0.020  1.090
 4JR  C2   H20  single    0.930  0.020  1.080
 4JR  C3   H21  single    0.930  0.020  1.080
 4JR  C25  H22  single    0.970  0.020  1.090
 4JR  C25  H23  single    0.970  0.020  1.090
 4JR  C9   H24  single    0.970  0.020  1.090
 4JR  C9   H25  single    0.970  0.020  1.090
 4JR  C14  H26  single    0.930  0.020  1.080
 4JR  C16  H27  single    0.930  0.020  1.080
 4JR  C23  H28  single    0.930  0.020  1.080
 4JR  C19  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
 4JR  C2   N1   C1   125.65  3.000
 4JR  C2   N1   C4   107.25  3.000
 4JR  C1   N1   C4   127.10  3.000
 4JR  C25  N3   C6   111.16  3.000
 4JR  C6   N3   C5   110.86  3.000
 4JR  C25  N3   C5   112.28  3.000
 4JR  N2   C4   C5   124.85  3.000
 4JR  N2   C4   N1   111.17  3.000
 4JR  C5   C4   N1   123.98  3.000
 4JR  H3   C5   H2   106.07  3.000
 4JR  H3   C5   C4   108.07  3.000
 4JR  H2   C5   C4   110.05  3.000
 4JR  H3   C5   N3   107.96  3.000
 4JR  H2   C5   N3   112.21  3.000
 4JR  C4   C5   N3   112.20  3.000
 4JR  H5   C6   H4   106.26  3.000
 4JR  H5   C6   C7   109.84  3.000
 4JR  H4   C6   C7   108.92  3.000
 4JR  H5   C6   N3   111.62  3.000
 4JR  H4   C6   N3   108.68  3.000
 4JR  C7   C6   N3   111.34  3.000
 4JR  H7   C7   H6   107.09  3.000
 4JR  H7   C7   C8   110.94  3.000
 4JR  H6   C7   C8   109.16  3.000
 4JR  H7   C7   C6   109.03  3.000
 4JR  H6   C7   C6   109.08  3.000
 4JR  C8   C7   C6   111.43  3.000
 4JR  C9   C8   C11  102.60  3.000
 4JR  C11  C8   C24  111.48  3.000
 4JR  C9   C8   C24  113.81  3.000
 4JR  C11  C8   C7   108.25  3.000
 4JR  C24  C8   C7   108.35  3.000
 4JR  C9   C8   C7   112.18  3.000
 4JR  H9   C10  H8   107.94  3.000
 4JR  H9   C10  N4   110.38  3.000
 4JR  H8   C10  N4   110.98  3.000
 4JR  H9   C10  C9   112.78  3.000
 4JR  H8   C10  C9   111.67  3.000
 4JR  N4   C10  C9   103.09  3.000
 4JR  H10  C13  C14  118.63  3.000
 4JR  H10  C13  C12  120.68  3.000
 4JR  C14  C13  C12  120.68  3.000
 4JR  C18  C15  C16  121.26  3.000
 4JR  C16  C15  C14  117.41  3.000
 4JR  C18  C15  C14  121.33  3.000
 4JR  H11  C17  C16  118.84  3.000
 4JR  H11  C17  C12  120.94  3.000
 4JR  C16  C17  C12  120.20  3.000
 4JR  H12  C20  C19  119.61  3.000
 4JR  H12  C20  C21  120.11  3.000
 4JR  C19  C20  C21  120.28  3.000
 4JR  H13  C21  C22  120.32  3.000
 4JR  H13  C21  C20  120.26  3.000
 4JR  C22  C21  C20  119.42  3.000
 4JR  H14  C22  C23  119.60  3.000
 4JR  H14  C22  C21  120.13  3.000
 4JR  C23  C22  C21  120.27  3.000
 4JR  H16  C24  H15  107.34  3.000
 4JR  H16  C24  C25  109.48  3.000
 4JR  H15  C24  C25  108.86  3.000
 4JR  H16  C24  C8   110.23  3.000
 4JR  H15  C24  C8   109.67  3.000
 4JR  C25  C24  C8   111.18  3.000
 4JR  H19  C1   H18  108.51  3.000
 4JR  H19  C1   H17  108.40  3.000
 4JR  H18  C1   H17  108.93  3.000
 4JR  H19  C1   N1   108.90  3.000
 4JR  H18  C1   N1   111.08  3.000
 4JR  H17  C1   N1   110.95  3.000
 4JR  H20  C2   C3   132.28  3.000
 4JR  H20  C2   N1   122.13  3.000
 4JR  C3   C2   N1   105.59  3.000
 4JR  H21  C3   N2   122.06  3.000
 4JR  H21  C3   C2   127.84  3.000
 4JR  N2   C3   C2   110.10  3.000
 4JR  C3   N2   C4   105.89  3.000
 4JR  H23  C25  H22  106.63  3.000
 4JR  H23  C25  C24  108.57  3.000
 4JR  H22  C25  C24  109.94  3.000
 4JR  H23  C25  N3   109.30  3.000
 4JR  H22  C25  N3   111.45  3.000
 4JR  C24  C25  N3   110.82  3.000
 4JR  N4   C11  O    125.87  3.000
 4JR  O    C11  C8   125.40  3.000
 4JR  N4   C11  C8   108.70  3.000
 4JR  H25  C9   H24  107.43  3.000
 4JR  H25  C9   C10  109.88  3.000
 4JR  H24  C9   C10  111.75  3.000
 4JR  H25  C9   C8   110.06  3.000
 4JR  H24  C9   C8   113.66  3.000
 4JR  C10  C9   C8   104.06  3.000
 4JR  C12  N4   C11  125.46  3.000
 4JR  C11  N4   C10  112.29  3.000
 4JR  C12  N4   C10  121.66  3.000
 4JR  N4   C12  C17  121.96  3.000
 4JR  N4   C12  C13  119.54  3.000
 4JR  C17  C12  C13  118.48  3.000
 4JR  H26  C14  C15  120.14  3.000
 4JR  H26  C14  C13  118.45  3.000
 4JR  C15  C14  C13  121.39  3.000
 4JR  H27  C16  C17  118.28  3.000
 4JR  H27  C16  C15  119.87  3.000
 4JR  C17  C16  C15  121.82  3.000
 4JR  C19  C18  C23  118.27  3.000
 4JR  C23  C18  C15  120.92  3.000
 4JR  C19  C18  C15  120.81  3.000
 4JR  H28  C23  C18  119.91  3.000
 4JR  H28  C23  C22  119.19  3.000
 4JR  C18  C23  C22  120.89  3.000
 4JR  H29  C19  C18  119.88  3.000
 4JR  H29  C19  C20  119.24  3.000
 4JR  C18  C19  C20  120.87  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
 4JR  CONST_01  N2   C3   C2   N1     0.00   0.0  0
 4JR  CONST_02  C3   N2   C4   N1     0.00   0.0  0
 4JR  CONST_03  C3   C2   N1   C4     0.00   0.0  0
 4JR  CONST_04  C2   C3   N2   C4     0.00   0.0  0
 4JR  CONST_05  C18  C15  C14  C13  180.00   0.0  0
 4JR  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 4JR  CONST_07  C16  C17  C12  C13    0.00   0.0  0
 4JR  CONST_08  C20  C19  C18  C15  180.00   0.0  0
 4JR  CONST_09  C22  C23  C18  C15  180.00   0.0  0
 4JR  CONST_10  C12  C13  C14  C15    0.00   0.0  0
 4JR  CONST_11  C12  C17  C16  C15    0.00   0.0  0
 4JR  CONST_12  C18  C15  C16  C17  180.00   0.0  0
 4JR  CONST_13  C14  C15  C16  C17    0.00   0.0  0
 4JR  CONST_14  C14  C13  C12  C17    0.00   0.0  0
 4JR  CONST_15  C23  C22  C21  C20    0.00   0.0  0
 4JR  CONST_16  C23  C18  C19  C20    0.00   0.0  0
 4JR  CONST_17  C18  C19  C20  C21    0.00   0.0  0
 4JR  CONST_18  C18  C23  C22  C21    0.00   0.0  0
 4JR  CONST_19  C19  C20  C21  C22    0.00   0.0  0
 4JR  CONST_20  C19  C18  C23  C22    0.00   0.0  0
 4JR  CONST_21  N2   C4   N1   C2     0.00   0.0  0
 4JR  CONST_26  C14  C13  C12  N4   180.00   0.0  0
 4JR  CONST_27  C16  C17  C12  N4   180.00   0.0  0
 4JR  CONST_28  C12  N4   C11  C8   180.00   0.0  0
 4JR  CONST_29  C10  N4   C11  C8     0.00   0.0  0
 4JR  CONST_30  C2   N1   C4   C5   180.00   0.0  0
 4JR  CONST_31  C3   N2   C4   C5   180.00   0.0  0
 4JR  CONST_32  C3   C2   N1   C1   180.00   0.0  0
 4JR  CONST_33  N2   C4   N1   C1   180.00   0.0  0
 4JR  CONST_34  O    C11  N4   C10  180.00   0.0  0
 4JR  CONST_35  C12  N4   C11  O      0.00   0.0  0
 4JR  CONST_36  H21  C3   C2   N1   180.00   0.0  0
 4JR  CONST_37  H20  C2   N1   C4   180.00   0.0  0
 4JR  CONST_38  H11  C17  C12  C13  180.00   0.0  0
 4JR  CONST_39  H29  C19  C18  C15    0.00   0.0  0
 4JR  CONST_40  H28  C23  C18  C15    0.00   0.0  0
 4JR  CONST_41  H10  C13  C14  C15  180.00   0.0  0
 4JR  CONST_42  H14  C22  C21  C20  180.00   0.0  0
 4JR  CONST_43  H12  C20  C21  C22  180.00   0.0  0
 4JR  CONST_44  H26  C14  C13  C12  180.00   0.0  0
 4JR  CONST_45  H27  C16  C17  C12  180.00   0.0  0
 4JR  CONST_46  H13  C21  C22  C23  180.00   0.0  0
 4JR  Var_01    C8   C24  C25  N3    58.50  30.0  1
 4JR  Var_02    C8   C7   C6   N3   -56.02  30.0  1
 4JR  Var_03    C24  C25  N3   C6   -60.15  30.0  1
 4JR  Var_04    C9   C8   C7   C6   -73.60  30.0  1
 4JR  Var_05    C10  C9   C8   C7   -88.03  30.0  3
 4JR  Var_06    C25  C24  C8   C7   -54.04  30.0  1
 4JR  Var_07    N4   C11  C8   C7   102.49  30.0  3
 4JR  Var_08    C25  N3   C6   C7    59.07  30.0  1
 4JR  Var_09    N4   C10  C9   C8   -29.62  30.0  1
 4JR  Var_10    C13  C12  N4   C10  -24.09  30.0  2
 4JR  Var_11    C9   C10  N4   C11   20.71  30.0  1
 4JR  Var_12    N3   C5   C4   N1   111.21  30.0  2
 4JR  Var_13    H17  C1   N1   C4   -59.17  30.0  2

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
 4JR  plan-1  N1   0.020
 4JR  plan-1  C4   0.020
 4JR  plan-1  C5   0.020
 4JR  plan-1  C1   0.020
 4JR  plan-1  C2   0.020
 4JR  plan-1  C3   0.020
 4JR  plan-1  N2   0.020
 4JR  plan-1  H20  0.020
 4JR  plan-1  H21  0.020
 4JR  plan-2  C15  0.020
 4JR  plan-2  C20  0.020
 4JR  plan-2  C21  0.020
 4JR  plan-2  C22  0.020
 4JR  plan-2  C18  0.020
 4JR  plan-2  C23  0.020
 4JR  plan-2  C19  0.020
 4JR  plan-2  H12  0.020
 4JR  plan-2  H13  0.020
 4JR  plan-2  H14  0.020
 4JR  plan-2  H28  0.020
 4JR  plan-2  H29  0.020
 4JR  plan-3  C8   0.020
 4JR  plan-3  C10  0.020
 4JR  plan-3  C11  0.020
 4JR  plan-3  O    0.020
 4JR  plan-3  N4   0.020
 4JR  plan-3  C12  0.020
 4JR  plan-4  C13  0.020
 4JR  plan-4  C15  0.020
 4JR  plan-4  C17  0.020
 4JR  plan-4  N4   0.020
 4JR  plan-4  C12  0.020
 4JR  plan-4  C14  0.020
 4JR  plan-4  C16  0.020
 4JR  plan-4  C18  0.020
 4JR  plan-4  H11  0.020
 4JR  plan-4  H26  0.020
 4JR  plan-4  H27  0.020
 4JR  plan-4  H10  0.020

