# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 07:50:27 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 7-isoquinolin-4-yl-2-phenyl-5,7-diazaspiro[3.4]octane-6,8-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@]2(C[C@H](C2)c3ccccc3)C(=O)N1c4cncc5ccccc45
#
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
 V1B  V1B  "7-isoquinolin-4-yl-2-phenyl-5,7-diazaspiro[3.4]octane-6,8-dione"
  ligand  43  26  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V1B
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
 V1B  C4   C  C     0  -0.357  11.3173  -0.0545  22.9701
 V1B  C14  C  CR16  0  -0.088   7.1513   0.6458  18.4075
 V1B  C5   C  CR6   0   0.213  12.3541  -0.5307  23.9402
 V1B  C6   C  CR16  0  -0.324  13.5801   0.1223  24.0406
 V1B  C11  C  C     0  -0.422   9.8870   0.2290  23.4800
 V1B  C7   C  CR16  0  -0.237  14.5537  -0.3145  24.9303
 V1B  C8   C  CR16  0  -0.270  14.3136  -1.4175  25.7372
 V1B  C9   C  CR16  0  -0.236  13.0936  -2.0771  25.6483
 V1B  C10  C  CR16  0  -0.337  12.1251  -1.6371  24.7583
 V1B  C12  C  CR5   0   0.558   8.9433   0.5763  21.1294
 V1B  C13  C  CR6   0   0.195   6.9435   0.9210  19.7295
 V1B  N1   N  NR15  0  -0.709   8.1611  -1.2472  22.2643
 V1B  N2   N  NR5   0  -0.695   7.6827   0.2330  20.7131
 V1B  C3   C  C     0  -0.421  10.7138  -1.0683  21.9725
 V1B  N3   N  N     0  -0.405   6.4943   1.2674  17.4077
 V1B  C1   C  CR5   0   0.678   7.1947  -0.8952  21.3988
 V1B  C2   C  C     0   0.056   9.3290  -0.4231  22.1973
 V1B  O2   O  O     0  -0.407   9.5993   1.4989  20.7166
 V1B  C15  C  CR16  0  -0.085   5.6112   2.1739  17.7266
 V1B  C16  C  CR66  0  -0.022   5.3050   2.5490  19.0549
 V1B  C17  C  CR16  0  -0.294   4.3422   3.5380  19.3507
 V1B  C18  C  CR16  0  -0.251   4.0842   3.8734  20.6509
 V1B  C19  C  CR16  0  -0.235   4.7805   3.2346  21.6985
 V1B  C20  C  CR16  0  -0.312   5.7180   2.2707  21.4404
 V1B  C21  C  CR66  0   0.234   5.9990   1.9057  20.1062
 V1B  H1   H  H     0   0.268  11.6974   0.8141  22.4313
 V1B  H2   H  HCR6  0   0.281   7.8757  -0.1077  18.1192
 V1B  H3   H  HCR6  0   0.247  13.7762   0.9841  23.4129
 V1B  H4   H  H     0   0.270   9.6135   1.2647  23.6789
 V1B  H5   H  H     0   0.265   9.6291  -0.3782  24.3494
 V1B  H6   H  HCR6  0   0.252  15.5002   0.2077  24.9900
 V1B  H7   H  HCR6  0   0.252  15.0701  -1.7618  26.4305
 V1B  H8   H  HCR6  0   0.252  12.8963  -2.9385  26.2737
 V1B  H9   H  HCR6  0   0.246  11.1810  -2.1680  24.7062
 V1B  H10  H  HNR5  0   0.413   8.0828  -2.0556  22.8612
 V1B  H11  H  H     0   0.265  10.7181  -2.0859  22.3665
 V1B  H12  H  H     0   0.270  11.1078  -1.0810  20.9567
 V1B  H13  H  HCR6  0   0.277   5.0865   2.6635  16.9109
 V1B  H14  H  HCR6  0   0.267   3.8169   4.0225  18.5368
 V1B  H15  H  HCR6  0   0.269   3.3474   4.6305  20.8834
 V1B  H16  H  HCR6  0   0.272   4.5690   3.5136  22.7224
 V1B  H17  H  HCR6  0   0.262   6.2453   1.7983  22.2588
 V1B  O1   O  O     0  -0.455   6.1143  -1.3981  21.2047

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
 V1B  N3   C15  aromatic  1.305  0.020  1.305
 V1B  N3   C14  aromatic  1.348  0.020  1.348
 V1B  C15  C16  aromatic  1.414  0.020  1.414
 V1B  C14  C13  aromatic  1.366  0.020  1.366
 V1B  C16  C17  aromatic  1.412  0.020  1.412
 V1B  C16  C21  aromatic  1.414  0.020  1.414
 V1B  C17  C18  aromatic  1.367  0.020  1.367
 V1B  C13  C21  aromatic  1.415  0.020  1.415
 V1B  C13  N2   single    1.410  0.020  1.410
 V1B  C21  C20  aromatic  1.411  0.020  1.411
 V1B  C18  C19  aromatic  1.411  0.020  1.411
 V1B  O2   C12  double    1.205  0.020  1.205
 V1B  N2   C12  single    1.371  0.020  1.371
 V1B  N2   C1   single    1.408  0.020  1.408
 V1B  C12  C2   single    1.513  0.020  1.513
 V1B  C20  C19  aromatic  1.369  0.020  1.369
 V1B  O1   C1   double    1.207  0.020  1.207
 V1B  C1   N1   single    1.344  0.020  1.344
 V1B  C3   C2   single    1.544  0.020  1.544
 V1B  C3   C4   single    1.545  0.020  1.545
 V1B  C2   N1   single    1.431  0.020  1.431
 V1B  C2   C11  single    1.543  0.020  1.543
 V1B  C4   C11  single    1.545  0.020  1.545
 V1B  C4   C5   single    1.498  0.020  1.498
 V1B  C5   C6   aromatic  1.393  0.020  1.393
 V1B  C5   C10  aromatic  1.395  0.020  1.395
 V1B  C6   C7   aromatic  1.389  0.020  1.389
 V1B  C10  C9   aromatic  1.387  0.020  1.387
 V1B  C7   C8   aromatic  1.388  0.020  1.388
 V1B  C9   C8   aromatic  1.390  0.020  1.390
 V1B  C4   H1   single    0.970  0.020  1.090
 V1B  C14  H2   single    0.930  0.020  1.080
 V1B  C6   H3   single    0.930  0.020  1.080
 V1B  C11  H4   single    0.970  0.020  1.090
 V1B  C11  H5   single    0.970  0.020  1.090
 V1B  C7   H6   single    0.930  0.020  1.080
 V1B  C8   H7   single    0.930  0.020  1.080
 V1B  C9   H8   single    0.930  0.020  1.080
 V1B  C10  H9   single    0.930  0.020  1.080
 V1B  N1   H10  single    0.860  0.020  1.020
 V1B  C3   H11  single    0.970  0.020  1.090
 V1B  C3   H12  single    0.970  0.020  1.090
 V1B  C15  H13  single    0.930  0.020  1.080
 V1B  C17  H14  single    0.930  0.020  1.080
 V1B  C18  H15  single    0.930  0.020  1.080
 V1B  C19  H16  single    0.930  0.020  1.080
 V1B  C20  H17  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
 V1B  H1   C4   C3   109.86  3.000
 V1B  H1   C4   C11  109.86  3.000
 V1B  C3   C4   C11   88.39  3.000
 V1B  H1   C4   C5   109.39  3.000
 V1B  C11  C4   C5   119.05  3.000
 V1B  C3   C4   C5   118.69  3.000
 V1B  H2   C14  N3   116.67  3.000
 V1B  H2   C14  C13  119.92  3.000
 V1B  N3   C14  C13  123.41  3.000
 V1B  C10  C5   C6   118.31  3.000
 V1B  C10  C5   C4   121.23  3.000
 V1B  C6   C5   C4   120.46  3.000
 V1B  H3   C6   C7   119.60  3.000
 V1B  H3   C6   C5   119.36  3.000
 V1B  C7   C6   C5   121.04  3.000
 V1B  H5   C11  H4   108.91  3.000
 V1B  H5   C11  C2   109.97  3.000
 V1B  H4   C11  C2   117.56  3.000
 V1B  H5   C11  C4   112.31  3.000
 V1B  H4   C11  C4   117.85  3.000
 V1B  C2   C11  C4    89.02  3.000
 V1B  H6   C7   C8   120.18  3.000
 V1B  H6   C7   C6   119.76  3.000
 V1B  C8   C7   C6   120.07  3.000
 V1B  H7   C8   C9   120.24  3.000
 V1B  H7   C8   C7   120.29  3.000
 V1B  C9   C8   C7   119.47  3.000
 V1B  H8   C9   C10  119.73  3.000
 V1B  H8   C9   C8   120.04  3.000
 V1B  C10  C9   C8   120.23  3.000
 V1B  H9   C10  C9   118.91  3.000
 V1B  H9   C10  C5   120.20  3.000
 V1B  C9   C10  C5   120.89  3.000
 V1B  O2   C12  C2   127.51  3.000
 V1B  C2   C12  N2   106.45  3.000
 V1B  O2   C12  N2   126.03  3.000
 V1B  C21  C13  N2   120.25  3.000
 V1B  N2   C13  C14  119.81  3.000
 V1B  C21  C13  C14  119.94  3.000
 V1B  H10  N1   C2   123.57  3.000
 V1B  H10  N1   C1   122.38  3.000
 V1B  C2   N1   C1   113.94  3.000
 V1B  C1   N2   C13  123.32  3.000
 V1B  C1   N2   C12  111.81  3.000
 V1B  C13  N2   C12  124.87  3.000
 V1B  H12  C3   H11  108.92  3.000
 V1B  H12  C3   C2   117.70  3.000
 V1B  H11  C3   C2   109.91  3.000
 V1B  H12  C3   C4   117.93  3.000
 V1B  H11  C3   C4   112.16  3.000
 V1B  C2   C3   C4    88.98  3.000
 V1B  C15  N3   C14  117.95  3.000
 V1B  O1   C1   N2   124.45  3.000
 V1B  O1   C1   N1   129.63  3.000
 V1B  N2   C1   N1   105.92  3.000
 V1B  C3   C2   N1   119.88  3.000
 V1B  N1   C2   C12  101.86  3.000
 V1B  C3   C2   C12  113.70  3.000
 V1B  N1   C2   C11  119.97  3.000
 V1B  C3   C2   C11   88.47  3.000
 V1B  C12  C2   C11  113.56  3.000
 V1B  H13  C15  C16  118.77  3.000
 V1B  H13  C15  N3   117.15  3.000
 V1B  C16  C15  N3   124.08  3.000
 V1B  C21  C16  C17  119.84  3.000
 V1B  C21  C16  C15  118.12  3.000
 V1B  C17  C16  C15  122.04  3.000
 V1B  H14  C17  C18  120.88  3.000
 V1B  H14  C17  C16  119.13  3.000
 V1B  C18  C17  C16  119.99  3.000
 V1B  H15  C18  C19  119.57  3.000
 V1B  H15  C18  C17  120.31  3.000
 V1B  C19  C18  C17  120.13  3.000
 V1B  H16  C19  C20  119.58  3.000
 V1B  H16  C19  C18  119.30  3.000
 V1B  C20  C19  C18  121.11  3.000
 V1B  H17  C20  C21  120.33  3.000
 V1B  H17  C20  C19  119.89  3.000
 V1B  C21  C20  C19  119.77  3.000
 V1B  C20  C21  C16  119.16  3.000
 V1B  C20  C21  C13  124.35  3.000
 V1B  C16  C21  C13  116.49  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
 V1B  CONST_01  C16  C15  N3   C14     0.00   0.0  0
 V1B  CONST_02  C16  C21  C13  C14     0.00   0.0  0
 V1B  CONST_03  C20  C21  C13  C14   180.00   0.0  0
 V1B  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 V1B  CONST_05  C8   C9   C10  C5      0.00   0.0  0
 V1B  CONST_06  C9   C10  C5   C6      0.00   0.0  0
 V1B  CONST_07  C9   C8   C7   C6      0.00   0.0  0
 V1B  CONST_08  C10  C5   C6   C7      0.00   0.0  0
 V1B  CONST_09  C10  C9   C8   C7      0.00   0.0  0
 V1B  CONST_10  C15  N3   C14  C13     0.00   0.0  0
 V1B  CONST_11  C15  C16  C21  C13     0.00   0.0  0
 V1B  CONST_12  C17  C16  C21  C13   180.00   0.0  0
 V1B  CONST_13  C19  C20  C21  C13   180.00   0.0  0
 V1B  CONST_14  C17  C16  C15  N3    180.00   0.0  0
 V1B  CONST_15  C21  C16  C15  N3      0.00   0.0  0
 V1B  CONST_16  C21  C13  C14  N3      0.00   0.0  0
 V1B  CONST_17  C18  C17  C16  C15   180.00   0.0  0
 V1B  CONST_18  C20  C21  C16  C15   180.00   0.0  0
 V1B  CONST_19  C19  C18  C17  C16     0.00   0.0  0
 V1B  CONST_20  C19  C20  C21  C16     0.00   0.0  0
 V1B  CONST_21  C20  C21  C16  C17     0.00   0.0  0
 V1B  CONST_22  C20  C19  C18  C17     0.00   0.0  0
 V1B  CONST_23  C21  C16  C17  C18     0.00   0.0  0
 V1B  CONST_24  C21  C20  C19  C18     0.00   0.0  0
 V1B  CONST_25  C7   C6   C5   C4    180.00   0.0  0
 V1B  CONST_26  C9   C10  C5   C4    180.00   0.0  0
 V1B  CONST_27  N3   C14  C13  N2    180.00   0.0  0
 V1B  CONST_28  C16  C21  C13  N2    180.00   0.0  0
 V1B  CONST_29  C20  C21  C13  N2      0.00   0.0  0
 V1B  CONST_30  N1   C1   N2   C12     0.00   0.0  0
 V1B  CONST_31  C1   N1   C2   C12     0.00   0.0  0
 V1B  CONST_32  C2   C12  N2   C13   180.00   0.0  0
 V1B  CONST_33  N1   C1   N2   C13   180.00   0.0  0
 V1B  CONST_34  N2   C12  C2   N1      0.00   0.0  0
 V1B  CONST_35  C2   N1   C1   N2      0.00   0.0  0
 V1B  CONST_36  C2   C12  N2   C1      0.00   0.0  0
 V1B  CONST_37  O1   C1   N2   C12   180.00   0.0  0
 V1B  CONST_38  O2   C12  N2   C13     0.00   0.0  0
 V1B  CONST_39  O1   C1   N2   C13     0.00   0.0  0
 V1B  CONST_40  C2   N1   C1   O1    180.00   0.0  0
 V1B  CONST_41  O2   C12  N2   C1    180.00   0.0  0
 V1B  CONST_42  H3   C6   C5   C4      0.00   0.0  0
 V1B  CONST_43  H9   C10  C5   C4      0.00   0.0  0
 V1B  CONST_44  H13  C15  N3   C14   180.00   0.0  0
 V1B  CONST_45  H6   C7   C6   C5    180.00   0.0  0
 V1B  CONST_46  H8   C9   C10  C5    180.00   0.0  0
 V1B  CONST_47  H9   C10  C5   C6    180.00   0.0  0
 V1B  CONST_48  H7   C8   C7   C6    180.00   0.0  0
 V1B  CONST_49  H8   C9   C8   C7    180.00   0.0  0
 V1B  CONST_50  H3   C6   C7   C8    180.00   0.0  0
 V1B  CONST_51  H9   C10  C9   C8    180.00   0.0  0
 V1B  CONST_52  H6   C7   C8   C9    180.00   0.0  0
 V1B  CONST_53  H3   C6   C5   C10   180.00   0.0  0
 V1B  CONST_54  H7   C8   C9   C10   180.00   0.0  0
 V1B  CONST_55  H17  C20  C21  C13     0.00   0.0  0
 V1B  CONST_56  H2   C14  C13  N2      0.00   0.0  0
 V1B  CONST_57  H2   C14  N3   C15   180.00   0.0  0
 V1B  CONST_58  H14  C17  C16  C15     0.00   0.0  0
 V1B  CONST_59  H15  C18  C17  C16   180.00   0.0  0
 V1B  CONST_60  H17  C20  C21  C16   180.00   0.0  0
 V1B  CONST_61  H13  C15  C16  C17     0.00   0.0  0
 V1B  CONST_62  H16  C19  C18  C17   180.00   0.0  0
 V1B  CONST_63  H17  C20  C19  C18   180.00   0.0  0
 V1B  CONST_64  H14  C17  C18  C19   180.00   0.0  0
 V1B  CONST_65  H15  C18  C19  C20   180.00   0.0  0
 V1B  CONST_66  H13  C15  C16  C21   180.00   0.0  0
 V1B  CONST_67  H14  C17  C16  C21   180.00   0.0  0
 V1B  CONST_68  H2   C14  C13  C21   180.00   0.0  0
 V1B  CONST_69  H16  C19  C20  C21   180.00   0.0  0
 V1B  CONST_70  H10  N1   C2   C12   180.00   0.0  0
 V1B  CONST_71  H10  N1   C1   N2    180.00   0.0  0
 V1B  CONST_72  H10  N1   C1   O1      0.00   0.0  0
 V1B  Var_01    C12  C2   C3   C4     98.10  30.0  3
 V1B  Var_02    N1   C2   C3   C4   -141.17  30.0  3
 V1B  Var_03    C11  C2   C3   C4    -17.05  30.0  3
 V1B  Var_04    C12  C2   C11  C4    -98.22  30.0  3
 V1B  Var_05    N1   C2   C11  C4    141.10  30.0  3
 V1B  Var_06    C12  N2   C13  C14    83.56  30.0  2
 V1B  Var_07    C1   N2   C13  C14   -97.10  30.0  2
 V1B  Var_08    N2   C12  C2   C11  -131.05  30.0  1
 V1B  Var_09    C1   N1   C2   C11   127.48  30.0  1
 V1B  Var_10    C21  C13  N2   C12   -95.70  30.0  3
 V1B  Var_11    C3   C2   C12  N2    129.77  30.0  1
 V1B  Var_12    C1   N1   C2   C3   -125.32  30.0  1
 V1B  Var_13    C21  C13  N2   C1     83.63  30.0  3
 V1B  Var_14    O2   C12  C2   C11    48.78  30.0  1
 V1B  Var_15    O2   C12  C2   C3    -50.40  30.0  1
 V1B  Var_16    H11  C3   C2   C11    96.21  30.0  3
 V1B  Var_17    H12  C3   C2   C11  -138.36  30.0  3
 V1B  Var_18    H10  N1   C2   C11   -56.21  30.0  1
 V1B  Var_19    H11  C3   C2   C12  -148.64  30.0  3
 V1B  Var_20    H12  C3   C2   C12   -23.22  30.0  3
 V1B  Var_21    H4   C11  C2   C12    22.98  30.0  3
 V1B  Var_22    H5   C11  C2   C12   148.33  30.0  3
 V1B  Var_23    H11  C3   C2   N1    -27.91  30.0  3
 V1B  Var_24    H12  C3   C2   N1     97.51  30.0  3
 V1B  Var_25    H4   C11  C2   N1    -97.70  30.0  3
 V1B  Var_26    H5   C11  C2   N1     27.65  30.0  3
 V1B  Var_27    H10  N1   C2   C3     50.99  30.0  1
 V1B  Var_28    H4   C11  C2   C3    138.26  30.0  3
 V1B  Var_29    H5   C11  C2   C3    -96.39  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
 V1B  chir_01  C4  C3  C11  C5  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
 V1B  plan-1  C4   0.020
 V1B  plan-1  C5   0.020
 V1B  plan-1  C6   0.020
 V1B  plan-1  C7   0.020
 V1B  plan-1  C8   0.020
 V1B  plan-1  C9   0.020
 V1B  plan-1  C10  0.020
 V1B  plan-1  H3   0.020
 V1B  plan-1  H6   0.020
 V1B  plan-1  H7   0.020
 V1B  plan-1  H8   0.020
 V1B  plan-1  H9   0.020
 V1B  plan-2  C14  0.020
 V1B  plan-2  C13  0.020
 V1B  plan-2  N2   0.020
 V1B  plan-2  N3   0.020
 V1B  plan-2  C15  0.020
 V1B  plan-2  C16  0.020
 V1B  plan-2  C17  0.020
 V1B  plan-2  C18  0.020
 V1B  plan-2  C19  0.020
 V1B  plan-2  C20  0.020
 V1B  plan-2  C21  0.020
 V1B  plan-2  H2   0.020
 V1B  plan-2  H13  0.020
 V1B  plan-2  H14  0.020
 V1B  plan-2  H15  0.020
 V1B  plan-2  H16  0.020
 V1B  plan-2  H17  0.020
 V1B  plan-3  C12  0.020
 V1B  plan-3  C13  0.020
 V1B  plan-3  N1   0.020
 V1B  plan-3  N2   0.020
 V1B  plan-3  C1   0.020
 V1B  plan-3  C2   0.020
 V1B  plan-3  O2   0.020
 V1B  plan-3  H10  0.020
 V1B  plan-3  O1   0.020

