# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 06:37:43 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (3R)-8-[(3-chloro-4-fluorophenyl)methyl]-6-hydroxy-1,5,7-trioxo-1,2',3',5,7,8,9,10-octahydro-2H-spiro[imidazo[5,1-a][2,6]naphthyridine-3,1'-indene]-7'-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C2C(=O)N(CCC2=C3N(C1=O)[C@@]4(CCc5cccc(C#N)c45)NC3=O)Cc6ccc(F)c(Cl)c6
#
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
 8G1  8G1  (3R)-8-[(3-chloro-4-fluorophenyl)methyl]-6-hydroxy-1,5,7-trioxo-1,2',3',5,7,8,9,10-octahydro-2H-spiro[imidazo[5,1-a][2,6]naphthyridine-3,1'-indene]-7'-carbonitrile  ligand  54  36  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8G1
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
 8G1  C1   C   CR6   0  -0.053  -0.1120   1.1285  -0.7386
 8G1  C2   C   CR6   0   0.205   0.8558   1.0458  -1.7029
 8G1  C3   C   CR6   0   0.490   2.2656   0.8449  -1.3568
 8G1  C7   C   CH2   0  -0.469   4.8921   1.6104   0.1611
 8G1  C8   C   CH2   0  -0.496   5.8998   0.9925  -0.8161
 8G1  C9   C   CR56  0   0.082   5.6399  -0.4801  -0.7293
 8G1  C10  C   CR56  0   0.240   4.4876  -0.7515  -0.0194
 8G1  C11  C   CR6   0  -0.008   4.0375  -2.0593   0.1394
 8G1  C12  C   CR16  0  -0.271   4.7749  -3.1054  -0.4118
 8G1  C13  C   CR16  0  -0.243   5.9435  -2.8284  -1.1099
 8G1  C14  C   CR16  0  -0.297   6.3798  -1.5212  -1.2763
 8G1  C15  C   CSP   0   0.016   2.8268  -2.3373   0.8421
 8G1  C16  C   C     0   0.588  -1.5474   1.3039  -1.1136
 8G1  C19  C   CH2   0  -0.413  -3.7404   2.1025  -0.4297
 8G1  C20  C   CR6   0   0.114  -4.6583   1.0795   0.1898
 8G1  C21  C   CR16  0  -0.288  -5.5532   1.4321   1.1919
 8G1  C22  C   CR16  0  -0.403  -6.3938   0.4868   1.7656
 8G1  C24  C   CR6   0  -0.213  -5.4403  -1.1918   0.3307
 8G1  O3   O   O     0  -0.482  -1.9593   0.9911  -2.2218
 8G1  N3   N   NT    0  -0.473  -2.3436   1.8195  -0.1546
 8G1  C25  C   CR16  0  -0.244  -4.6079  -0.2455  -0.2380
 8G1  CL   CL  CL    0  -0.092  -5.3976  -2.8347  -0.1881
 8G1  C23  C   CR6   0   0.601  -6.3283  -0.8180   1.3290
 8G1  F    F   F     0  -0.294  -7.1271  -1.7428   1.8656
 8G1  C17  C   CH2   0  -0.295  -1.8553   2.1556   1.1729
 8G1  C18  C   CH2   0  -0.540  -0.8457   1.1345   1.6511
 8G1  C    C   CR6   0   0.006   0.2529   1.0237   0.6423
 8G1  C4   C   CR56  0   0.175   1.5530   0.8220   0.9451
 8G1  C5   C   CR5   0   0.525   2.2426   0.6415   2.2378
 8G1  O    O   O     0  -0.445   1.7611   0.6554   3.3522
 8G1  N1   N   NR15  0  -0.686   3.5408   0.4523   1.9175
 8G1  C6   C   C     0   0.248   3.8576   0.5133   0.5149
 8G1  N    N   N     0  -0.627   2.5122   0.7345  -0.0350
 8G1  O1   O   O     0  -0.487   3.1296   0.7858  -2.2268
 8G1  O2   O   OH1   0  -0.574   0.6288   1.1605  -2.9994
 8G1  N2   N   NS    0  -0.240   1.8432  -2.5688   1.3959
 8G1  H1   H   HCH2  0   0.283   5.3949   1.8936   1.0860
 8G1  H2   H   HCH2  0   0.280   4.4098   2.5072  -0.2232
 8G1  H3   H   HCH2  0   0.272   5.7370   1.3394  -1.8373
 8G1  H4   H   HCH2  0   0.268   6.9274   1.2400  -0.5486
 8G1  H5   H   HCR6  0   0.285   4.4381  -4.1258  -0.2926
 8G1  H6   H   HCR6  0   0.278   6.5151  -3.6455  -1.5285
 8G1  H7   H   HCR6  0   0.271   7.2872  -1.3174  -1.8304
 8G1  H8   H   HCH2  0   0.287  -3.8891   2.1431  -1.5069
 8G1  H9   H   HCH2  0   0.283  -3.9724   3.0947  -0.0380
 8G1  H10  H   HCR6  0   0.275  -5.6032   2.4581   1.5340
 8G1  H11  H   HCR6  0   0.292  -7.0912   0.7602   2.5465
 8G1  H12  H   HCR6  0   0.285  -3.9258  -0.5427  -1.0244
 8G1  H13  H   HCH2  0   0.263  -1.4238   3.1613   1.1787
 8G1  H14  H   HCH2  0   0.272  -2.7066   2.1646   1.8531
 8G1  H15  H   HCH2  0   0.281  -0.4655   1.4244   2.6269
 8G1  H16  H   HCH2  0   0.271  -1.3375   0.1637   1.7681
 8G1  H17  H   HNR5  0   0.421   4.2649   0.3342   2.6108
 8G1  H18  H   HOH1  0   0.478   1.4851   1.0960  -3.4571

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
 8G1  O2   C2   single    1.321  0.020  1.321
 8G1  O1   C3   double    1.228  0.020  1.228
 8G1  C14  C13  aromatic  1.388  0.020  1.388
 8G1  C14  C9   aromatic  1.389  0.020  1.389
 8G1  C8   C9   single    1.498  0.020  1.498
 8G1  C8   C7   single    1.534  0.020  1.534
 8G1  C13  C12  aromatic  1.389  0.020  1.389
 8G1  C9   C10  aromatic  1.380  0.020  1.380
 8G1  C3   C2   single    1.466  0.020  1.466
 8G1  C3   N    single    1.349  0.020  1.349
 8G1  C2   C1   double    1.369  0.020  1.369
 8G1  O3   C16  double    1.223  0.020  1.223
 8G1  CL   C24  single    1.723  0.020  1.723
 8G1  C7   C6   single    1.549  0.020  1.549
 8G1  C12  C11  aromatic  1.393  0.020  1.393
 8G1  C10  C6   single    1.511  0.020  1.511
 8G1  C10  C11  aromatic  1.392  0.020  1.392
 8G1  N    C6   single    1.470  0.020  1.470
 8G1  N    C4   single    1.374  0.020  1.374
 8G1  C16  C1   single    1.494  0.020  1.494
 8G1  C16  N3   single    1.349  0.020  1.349
 8G1  C1   C    single    1.432  0.020  1.432
 8G1  C6   N1   single    1.439  0.020  1.439
 8G1  C11  C15  single    1.427  0.020  1.427
 8G1  C25  C24  aromatic  1.383  0.020  1.383
 8G1  C25  C20  aromatic  1.393  0.020  1.393
 8G1  C24  C23  aromatic  1.387  0.020  1.387
 8G1  C4   C    double    1.350  0.020  1.350
 8G1  C4   C5   single    1.476  0.020  1.476
 8G1  N3   C19  single    1.452  0.020  1.452
 8G1  N3   C17  single    1.454  0.020  1.454
 8G1  C    C18  single    1.496  0.020  1.496
 8G1  C19  C20  single    1.508  0.020  1.508
 8G1  C20  C21  aromatic  1.389  0.020  1.389
 8G1  C15  N2   triple    1.152  0.020  1.152
 8G1  N1   C5   single    1.350  0.020  1.350
 8G1  C23  F    single    1.335  0.020  1.335
 8G1  C23  C22  aromatic  1.377  0.020  1.377
 8G1  C5   O    double    1.214  0.020  1.214
 8G1  C17  C18  single    1.514  0.020  1.514
 8G1  C21  C22  aromatic  1.389  0.020  1.389
 8G1  C7   H1   single    0.970  0.020  1.090
 8G1  C7   H2   single    0.970  0.020  1.090
 8G1  C8   H3   single    0.970  0.020  1.090
 8G1  C8   H4   single    0.970  0.020  1.090
 8G1  C12  H5   single    0.930  0.020  1.080
 8G1  C13  H6   single    0.930  0.020  1.080
 8G1  C14  H7   single    0.930  0.020  1.080
 8G1  C19  H8   single    0.970  0.020  1.090
 8G1  C19  H9   single    0.970  0.020  1.090
 8G1  C21  H10  single    0.930  0.020  1.080
 8G1  C22  H11  single    0.930  0.020  1.080
 8G1  C25  H12  single    0.930  0.020  1.080
 8G1  C17  H13  single    0.970  0.020  1.090
 8G1  C17  H14  single    0.970  0.020  1.090
 8G1  C18  H15  single    0.970  0.020  1.090
 8G1  C18  H16  single    0.970  0.020  1.090
 8G1  N1   H17  single    0.860  0.020  1.020
 8G1  O2   H18  single    0.850  0.020  0.980

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
 8G1  C    C1   C16  119.70  3.000
 8G1  C    C1   C2   119.65  3.000
 8G1  C16  C1   C2   120.64  3.000
 8G1  O2   C2   C3   114.13  3.000
 8G1  C3   C2   C1   121.48  3.000
 8G1  O2   C2   C1   124.38  3.000
 8G1  O1   C3   N    124.18  3.000
 8G1  N    C3   C2   114.73  3.000
 8G1  O1   C3   C2   121.09  3.000
 8G1  H2   C7   H1   106.85  3.000
 8G1  H2   C7   C6   111.61  3.000
 8G1  H1   C7   C6   107.36  3.000
 8G1  H2   C7   C8   113.46  3.000
 8G1  H1   C7   C8   110.01  3.000
 8G1  C6   C7   C8   107.40  3.000
 8G1  H4   C8   H3   107.35  3.000
 8G1  H4   C8   C9   111.87  3.000
 8G1  H3   C8   C9   109.94  3.000
 8G1  H4   C8   C7   111.81  3.000
 8G1  H3   C8   C7   111.73  3.000
 8G1  C9   C8   C7   104.19  3.000
 8G1  C14  C9   C10  119.98  3.000
 8G1  C10  C9   C8   111.59  3.000
 8G1  C14  C9   C8   128.42  3.000
 8G1  C6   C10  C11  127.69  3.000
 8G1  C11  C10  C9   120.88  3.000
 8G1  C6   C10  C9   111.43  3.000
 8G1  C15  C11  C12  119.83  3.000
 8G1  C15  C11  C10  120.89  3.000
 8G1  C12  C11  C10  119.28  3.000
 8G1  H5   C12  C13  120.38  3.000
 8G1  H5   C12  C11  120.00  3.000
 8G1  C13  C12  C11  119.62  3.000
 8G1  H6   C13  C14  119.93  3.000
 8G1  H6   C13  C12  119.24  3.000
 8G1  C14  C13  C12  120.83  3.000
 8G1  H7   C14  C13  120.14  3.000
 8G1  H7   C14  C9   120.45  3.000
 8G1  C13  C14  C9   119.41  3.000
 8G1  N2   C15  C11  180.00  3.000
 8G1  N3   C16  O3   122.90  3.000
 8G1  N3   C16  C1   115.69  3.000
 8G1  O3   C16  C1   121.40  3.000
 8G1  H9   C19  H8   106.99  3.000
 8G1  H9   C19  N3   108.28  3.000
 8G1  H8   C19  N3   109.05  3.000
 8G1  H9   C19  C20  109.87  3.000
 8G1  H8   C19  C20  110.42  3.000
 8G1  N3   C19  C20  112.07  3.000
 8G1  C25  C20  C21  119.09  3.000
 8G1  C21  C20  C19  121.10  3.000
 8G1  C25  C20  C19  119.81  3.000
 8G1  H10  C21  C22  119.11  3.000
 8G1  H10  C21  C20  119.89  3.000
 8G1  C22  C21  C20  121.01  3.000
 8G1  H11  C22  C23  119.92  3.000
 8G1  H11  C22  C21  121.07  3.000
 8G1  C23  C22  C21  119.01  3.000
 8G1  C23  C24  CL   119.30  3.000
 8G1  C23  C24  C25  119.79  3.000
 8G1  CL   C24  C25  120.91  3.000
 8G1  C17  N3   C19  116.82  3.000
 8G1  C17  N3   C16  122.64  3.000
 8G1  C19  N3   C16  120.52  3.000
 8G1  H12  C25  C24  119.35  3.000
 8G1  H12  C25  C20  120.46  3.000
 8G1  C24  C25  C20  120.19  3.000
 8G1  F    C23  C24  119.06  3.000
 8G1  F    C23  C22  120.03  3.000
 8G1  C24  C23  C22  120.91  3.000
 8G1  H14  C17  H13  107.29  3.000
 8G1  H14  C17  C18  109.24  3.000
 8G1  H13  C17  C18  110.81  3.000
 8G1  H14  C17  N3   108.03  3.000
 8G1  H13  C17  N3   110.47  3.000
 8G1  C18  C17  N3   110.89  3.000
 8G1  H16  C18  H15  107.33  3.000
 8G1  H16  C18  C    109.66  3.000
 8G1  H15  C18  C    111.62  3.000
 8G1  H16  C18  C17  109.41  3.000
 8G1  H15  C18  C17  109.70  3.000
 8G1  C    C18  C17  109.08  3.000
 8G1  C4   C    C18  124.55  3.000
 8G1  C18  C    C1   117.24  3.000
 8G1  C4   C    C1   118.20  3.000
 8G1  N    C4   C5   106.90  3.000
 8G1  C5   C4   C    131.65  3.000
 8G1  N    C4   C    121.45  3.000
 8G1  N1   C5   O    126.91  3.000
 8G1  O    C5   C4   128.11  3.000
 8G1  N1   C5   C4   104.98  3.000
 8G1  H17  N1   C6   121.09  3.000
 8G1  H17  N1   C5   122.90  3.000
 8G1  C6   N1   C5   115.90  3.000
 8G1  N    C6   N1    99.76  3.000
 8G1  N1   C6   C10  113.64  3.000
 8G1  N    C6   C10  112.05  3.000
 8G1  N1   C6   C7   113.55  3.000
 8G1  N    C6   C7   114.78  3.000
 8G1  C10  C6   C7   103.51  3.000
 8G1  C6   N    C4   112.43  3.000
 8G1  C4   N    C3   124.48  3.000
 8G1  C6   N    C3   123.09  3.000
 8G1  H18  O2   C2   107.74  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
 8G1  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 8G1  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 8G1  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 8G1  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 8G1  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 8G1  CONST_06  C14  C9   C10  C11     0.00   0.0  0
 8G1  CONST_07  C23  C24  C25  C20     0.00   0.0  0
 8G1  CONST_08  C23  C22  C21  C20     0.00   0.0  0
 8G1  CONST_09  C24  C25  C20  C21     0.00   0.0  0
 8G1  CONST_10  C24  C23  C22  C21     0.00   0.0  0
 8G1  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 8G1  CONST_12  C25  C20  C21  C22     0.00   0.0  0
 8G1  CONST_13  C6   C10  C9   C8      0.00   0.0  0
 8G1  CONST_14  C6   C10  C11  C12   180.00   0.0  0
 8G1  CONST_15  C6   C10  C9   C14   180.00   0.0  0
 8G1  CONST_16  C17  N3   C16  C1      0.00   0.0  0
 8G1  CONST_17  C6   N    C3   C2    180.00   0.0  0
 8G1  CONST_18  C4   N    C3   C2      0.00   0.0  0
 8G1  CONST_19  C6   N1   C5   C4      0.00   0.0  0
 8G1  CONST_20  C15  C11  C10  C9    180.00   0.0  0
 8G1  CONST_21  C15  C11  C12  C13   180.00   0.0  0
 8G1  CONST_22  C6   C10  C11  C15     0.00   0.0  0
 8G1  CONST_23  C24  C25  C20  C19   180.00   0.0  0
 8G1  CONST_24  C22  C21  C20  C19   180.00   0.0  0
 8G1  CONST_25  CL   C24  C25  C20   180.00   0.0  0
 8G1  CONST_26  F    C23  C22  C21   180.00   0.0  0
 8G1  CONST_27  CL   C24  C23  C22   180.00   0.0  0
 8G1  CONST_28  F    C23  C24  C25   180.00   0.0  0
 8G1  CONST_29  C19  N3   C16  C1    180.00   0.0  0
 8G1  CONST_30  C17  N3   C16  O3    180.00   0.0  0
 8G1  CONST_31  O1   C3   N    C4    180.00   0.0  0
 8G1  CONST_32  C6   N1   C5   O     180.00   0.0  0
 8G1  CONST_33  O1   C3   N    C6      0.00   0.0  0
 8G1  CONST_34  H7   C14  C9   C8      0.00   0.0  0
 8G1  CONST_35  H6   C13  C14  C9    180.00   0.0  0
 8G1  CONST_36  H5   C12  C11  C10   180.00   0.0  0
 8G1  CONST_37  H11  C22  C21  C20   180.00   0.0  0
 8G1  CONST_38  H12  C25  C20  C21   180.00   0.0  0
 8G1  CONST_39  H10  C21  C20  C25   180.00   0.0  0
 8G1  CONST_40  H17  N1   C5   C4    180.00   0.0  0
 8G1  CONST_41  O3   C16  N3   C19     0.00   0.0  0
 8G1  Var_01    C17  C18  C    C1    -36.70  30.0  1
 8G1  Var_02    N3   C16  C1   C2   -158.31  30.0  1
 8G1  Var_03    C14  C9   C8   C7   -171.03  30.0  1
 8G1  Var_04    C6   C7   C8   C9    -13.70  30.0  1
 8G1  Var_05    C18  C17  N3   C16   -38.08  30.0  1
 8G1  Var_06    C    C18  C17  N3     55.28  30.0  1
 8G1  Var_07    C20  C19  N3   C16   104.61  30.0  3
 8G1  Var_08    N3   C19  C20  C21   115.26  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
 8G1  chir_01  C6  C10  N  N1  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
 8G1  plan-1  C19  0.020
 8G1  plan-1  C20  0.020
 8G1  plan-1  C21  0.020
 8G1  plan-1  C22  0.020
 8G1  plan-1  C24  0.020
 8G1  plan-1  C25  0.020
 8G1  plan-1  CL   0.020
 8G1  plan-1  C23  0.020
 8G1  plan-1  F    0.020
 8G1  plan-1  H10  0.020
 8G1  plan-1  H11  0.020
 8G1  plan-1  H12  0.020
 8G1  plan-2  C8   0.020
 8G1  plan-2  C9   0.020
 8G1  plan-2  C10  0.020
 8G1  plan-2  C11  0.020
 8G1  plan-2  C12  0.020
 8G1  plan-2  C13  0.020
 8G1  plan-2  C14  0.020
 8G1  plan-2  C15  0.020
 8G1  plan-2  C6   0.020
 8G1  plan-2  N2   0.020
 8G1  plan-2  H5   0.020
 8G1  plan-2  H6   0.020
 8G1  plan-2  H7   0.020
 8G1  plan-3  C1   0.020
 8G1  plan-3  C16  0.020
 8G1  plan-3  C19  0.020
 8G1  plan-3  O3   0.020
 8G1  plan-3  N3   0.020
 8G1  plan-3  C17  0.020
 8G1  plan-4  C1   0.020
 8G1  plan-4  C2   0.020
 8G1  plan-4  C3   0.020
 8G1  plan-4  C16  0.020
 8G1  plan-4  C18  0.020
 8G1  plan-4  C    0.020
 8G1  plan-4  C4   0.020
 8G1  plan-4  C5   0.020
 8G1  plan-4  O    0.020
 8G1  plan-4  N1   0.020
 8G1  plan-4  C6   0.020
 8G1  plan-4  N    0.020
 8G1  plan-4  O1   0.020
 8G1  plan-4  O2   0.020
 8G1  plan-4  H17  0.020

