# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 21:53:21 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1'-(4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-yl)-2H-spiro[1-benzofuran-3,4'-piperidin]-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=NC2=C1CCCC2)N3CCC4(CC3)C(=O)Oc5ccccc45
#
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
 9H3  9H3  1'-(4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-yl)-2H-spiro[1-benzofuran-3,4'-piperidin]-2-one  ligand  47  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9H3
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
 9H3  C10  C  CR5   0  -0.388   2.3114   0.3709   0.3682
 9H3  C11  C  CR56  0   0.153   3.1994  -0.5499  -0.4119
 9H3  C12  C  CR16  0  -0.336   2.9247  -1.5007  -1.3750
 9H3  C13  C  CR16  0  -0.252   3.9850  -2.2269  -1.9130
 9H3  C14  C  CR16  0  -0.262   5.2890  -1.9992  -1.4871
 9H3  C15  C  CR16  0  -0.330   5.5767  -1.0411  -0.5174
 9H3  C01  C  CH2   0  -0.474  -5.2187  -0.5611  -1.2383
 9H3  C02  C  CR6   0  -0.182  -3.9254  -0.0740  -0.6506
 9H3  C03  C  CR6   0   0.528  -3.2790   1.0462  -1.2655
 9H3  C06  C  CR6   0   0.764  -1.5536   0.8029   0.4201
 9H3  C08  C  CH2   0  -0.335   0.3011   0.4841   1.9454
 9H3  C09  C  CH2   0  -0.416   1.3308  -0.4123   1.2690
 9H3  C16  C  CR56  0   0.349   4.5045  -0.3419  -0.0102
 9H3  C18  C  CR5   0   0.615   3.3480   1.1085   1.2146
 9H3  C20  C  CH2   0  -0.407   1.5403   1.3533  -0.5372
 9H3  C21  C  CH2   0  -0.371   0.5038   2.1623   0.2341
 9H3  C23  C  CR6   0   0.266  -3.3335  -0.6313   0.4499
 9H3  C24  C  CH2   0  -0.504  -3.9605  -1.7949   1.1617
 9H3  C25  C  CH2   0  -0.446  -5.4295  -1.9836   0.8122
 9H3  C26  C  CH2   0  -0.447  -5.6194  -1.9276  -0.6970
 9H3  N05  N  NR16  0  -0.736  -2.0821   1.4216  -0.6661
 9H3  N07  N  NT    0  -0.485  -0.4015   1.2804   0.9512
 9H3  N22  N  N     0  -0.532  -2.1572  -0.2124   0.9762
 9H3  O17  O  O     0  -0.461   4.5910   0.6366   0.9495
 9H3  O19  O  O     0  -0.386   3.1895   1.9812   2.0157
 9H3  H1   H  HCR6  0   0.261   1.9103  -1.6831  -1.7073
 9H3  H2   H  HCR6  0   0.264   3.7939  -2.9780  -2.6675
 9H3  H3   H  HCR6  0   0.268   6.0985  -2.5772  -1.9124
 9H3  H4   H  HCR6  0   0.279   6.5889  -0.8613  -0.1812
 9H3  H5   H  HCH2  0   0.233  -6.0134   0.1651  -1.0322
 9H3  H6   H  HCH2  0   0.240  -5.1360  -0.6008  -2.3274
 9H3  H7   H  HCH2  0   0.284  -0.4099  -0.1178   2.5022
 9H3  H8   H  HCH2  0   0.262   0.8068  -1.1352   0.6371
 9H3  H9   H  HCH2  0   0.273   2.2329   2.0219  -1.0520
 9H3  H10  H  HCH2  0   0.265   1.0346   0.7674  -1.3102
 9H3  H11  H  HCH2  0   0.284   0.9818   2.8121   0.9672
 9H3  H12  H  HCH2  0   0.273  -0.0229   2.8359  -0.4393
 9H3  H13  H  HCH2  0   0.252  -3.3969  -2.6957   0.8936
 9H3  H14  H  HCH2  0   0.253  -3.8195  -1.6626   2.2367
 9H3  H15  H  HCH2  0   0.237  -5.7838  -2.9340   1.2151
 9H3  H16  H  HCH2  0   0.224  -6.0274  -1.1987   1.2857
 9H3  H17  H  HCH2  0   0.236  -6.6551  -2.1415  -0.9668
 9H3  H18  H  HCH2  0   0.222  -5.0056  -2.7044  -1.1637
 9H3  H19  H  HNR6  0   0.419  -1.6220   2.2166  -1.0862
 9H3  H20  H  HCH2  0   0.267   0.7756   1.1687   2.6494
 9H3  H21  H  HCH2  0   0.269   1.8779  -0.9894   2.0174
 9H3  O04  O  O     0  -0.491  -3.6832   1.6720  -2.2388

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
 9H3  C26  C01  single    1.524  0.020  1.524
 9H3  C26  C25  single    1.522  0.020  1.522
 9H3  C01  C02  single    1.502  0.020  1.502
 9H3  C25  C24  single    1.522  0.020  1.522
 9H3  O04  C03  double    1.226  0.020  1.226
 9H3  C02  C03  single    1.432  0.020  1.432
 9H3  C02  C23  double    1.368  0.020  1.368
 9H3  C03  N05  single    1.390  0.020  1.390
 9H3  C24  C23  single    1.501  0.020  1.501
 9H3  C23  N22  single    1.355  0.020  1.355
 9H3  N05  C06  single    1.357  0.020  1.357
 9H3  N22  C06  double    1.306  0.020  1.306
 9H3  C06  N07  single    1.355  0.020  1.355
 9H3  N07  C21  single    1.453  0.020  1.453
 9H3  N07  C08  single    1.455  0.020  1.455
 9H3  C21  C20  single    1.524  0.020  1.524
 9H3  C08  C09  single    1.524  0.020  1.524
 9H3  C20  C10  single    1.543  0.020  1.543
 9H3  C09  C10  single    1.545  0.020  1.545
 9H3  O19  C18  double    1.195  0.020  1.195
 9H3  C10  C18  single    1.528  0.020  1.528
 9H3  C10  C11  single    1.498  0.020  1.498
 9H3  C18  O17  single    1.356  0.020  1.356
 9H3  C11  C12  aromatic  1.381  0.020  1.381
 9H3  C11  C16  aromatic  1.381  0.020  1.381
 9H3  O17  C16  single    1.373  0.020  1.373
 9H3  C12  C13  aromatic  1.393  0.020  1.393
 9H3  C16  C15  aromatic  1.377  0.020  1.377
 9H3  C13  C14  aromatic  1.391  0.020  1.391
 9H3  C15  C14  aromatic  1.393  0.020  1.393
 9H3  C12  H1   single    0.930  0.020  1.080
 9H3  C13  H2   single    0.930  0.020  1.080
 9H3  C14  H3   single    0.930  0.020  1.080
 9H3  C15  H4   single    0.930  0.020  1.080
 9H3  C01  H5   single    0.970  0.020  1.090
 9H3  C01  H6   single    0.970  0.020  1.090
 9H3  C08  H7   single    0.970  0.020  1.090
 9H3  C09  H8   single    0.970  0.020  1.090
 9H3  C20  H9   single    0.970  0.020  1.090
 9H3  C20  H10  single    0.970  0.020  1.090
 9H3  C21  H11  single    0.970  0.020  1.090
 9H3  C21  H12  single    0.970  0.020  1.090
 9H3  C24  H13  single    0.970  0.020  1.090
 9H3  C24  H14  single    0.970  0.020  1.090
 9H3  C25  H15  single    0.970  0.020  1.090
 9H3  C25  H16  single    0.970  0.020  1.090
 9H3  C26  H17  single    0.970  0.020  1.090
 9H3  C26  H18  single    0.970  0.020  1.090
 9H3  N05  H19  single    0.860  0.020  1.020
 9H3  C08  H20  single    0.970  0.020  1.090
 9H3  C09  H21  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
 9H3  C20  C10  C18  110.91  3.000
 9H3  C18  C10  C09  110.63  3.000
 9H3  C20  C10  C09  110.36  3.000
 9H3  C18  C10  C11  100.54  3.000
 9H3  C09  C10  C11  111.60  3.000
 9H3  C20  C10  C11  112.46  3.000
 9H3  C16  C11  C12  119.63  3.000
 9H3  C16  C11  C10  108.42  3.000
 9H3  C12  C11  C10  131.94  3.000
 9H3  H1   C12  C13  120.44  3.000
 9H3  H1   C12  C11  121.08  3.000
 9H3  C13  C12  C11  118.48  3.000
 9H3  H2   C13  C14  119.54  3.000
 9H3  H2   C13  C12  119.79  3.000
 9H3  C14  C13  C12  120.67  3.000
 9H3  H3   C14  C15  119.12  3.000
 9H3  H3   C14  C13  119.59  3.000
 9H3  C15  C14  C13  121.30  3.000
 9H3  H4   C15  C16  121.99  3.000
 9H3  H4   C15  C14  121.60  3.000
 9H3  C16  C15  C14  116.41  3.000
 9H3  H6   C01  H5   105.45  3.000
 9H3  H6   C01  C26  109.96  3.000
 9H3  H5   C01  C26  109.68  3.000
 9H3  H6   C01  C02  109.67  3.000
 9H3  H5   C01  C02  109.63  3.000
 9H3  C26  C01  C02  112.23  3.000
 9H3  C23  C02  C03  117.95  3.000
 9H3  C23  C02  C01  123.73  3.000
 9H3  C03  C02  C01  118.32  3.000
 9H3  O04  C03  N05  119.24  3.000
 9H3  N05  C03  C02  114.50  3.000
 9H3  O04  C03  C02  126.26  3.000
 9H3  N22  C06  N07  120.00  3.000
 9H3  N07  C06  N05  118.94  3.000
 9H3  N22  C06  N05  121.02  3.000
 9H3  H20  C08  H7   107.58  3.000
 9H3  H20  C08  N07  107.92  3.000
 9H3  H7   C08  N07  109.75  3.000
 9H3  H20  C08  C09  111.21  3.000
 9H3  H7   C08  C09  110.13  3.000
 9H3  N07  C08  C09  110.18  3.000
 9H3  H21  C09  H8   106.67  3.000
 9H3  H21  C09  C08  110.20  3.000
 9H3  H8   C09  C08  108.75  3.000
 9H3  H21  C09  C10  110.46  3.000
 9H3  H8   C09  C10  107.59  3.000
 9H3  C08  C09  C10  112.92  3.000
 9H3  O17  C16  C15  124.76  3.000
 9H3  C15  C16  C11  123.52  3.000
 9H3  O17  C16  C11  111.72  3.000
 9H3  O19  C18  O17  120.45  3.000
 9H3  O17  C18  C10  110.22  3.000
 9H3  O19  C18  C10  129.32  3.000
 9H3  H10  C20  H9   106.74  3.000
 9H3  H10  C20  C21  109.12  3.000
 9H3  H9   C20  C21  110.18  3.000
 9H3  H10  C20  C10  107.75  3.000
 9H3  H9   C20  C10  110.46  3.000
 9H3  C21  C20  C10  112.39  3.000
 9H3  H12  C21  H11  105.03  3.000
 9H3  H12  C21  N07  112.30  3.000
 9H3  H11  C21  N07  107.64  3.000
 9H3  H12  C21  C20  110.14  3.000
 9H3  H11  C21  C20  111.01  3.000
 9H3  N07  C21  C20  110.56  3.000
 9H3  N22  C23  C24  114.71  3.000
 9H3  N22  C23  C02  124.20  3.000
 9H3  C24  C23  C02  121.09  3.000
 9H3  H14  C24  H13  105.90  3.000
 9H3  H14  C24  C25  111.45  3.000
 9H3  H13  C24  C25  109.78  3.000
 9H3  H14  C24  C23  108.59  3.000
 9H3  H13  C24  C23  107.84  3.000
 9H3  C25  C24  C23  112.98  3.000
 9H3  H16  C25  H15  106.71  3.000
 9H3  H16  C25  C26  109.54  3.000
 9H3  H15  C25  C26  110.95  3.000
 9H3  H16  C25  C24  109.82  3.000
 9H3  H15  C25  C24  109.67  3.000
 9H3  C26  C25  C24  110.09  3.000
 9H3  H18  C26  H17  106.72  3.000
 9H3  H18  C26  C25  109.07  3.000
 9H3  H17  C26  C25  110.87  3.000
 9H3  H18  C26  C01  109.73  3.000
 9H3  H17  C26  C01  109.72  3.000
 9H3  C25  C26  C01  110.64  3.000
 9H3  H19  N05  C06  120.95  3.000
 9H3  H19  N05  C03  115.17  3.000
 9H3  C06  N05  C03  123.87  3.000
 9H3  C21  N07  C08  111.63  3.000
 9H3  C08  N07  C06  119.04  3.000
 9H3  C21  N07  C06  123.37  3.000
 9H3  C23  N22  C06  118.45  3.000
 9H3  C18  O17  C16  109.08  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
 9H3  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 9H3  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 9H3  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 9H3  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 9H3  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 9H3  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 9H3  CONST_07  C06  N05  C03  C02     0.00   0.0  0
 9H3  CONST_08  N22  C06  N05  C03     0.00   0.0  0
 9H3  CONST_09  N07  C06  N05  C03   180.00   0.0  0
 9H3  CONST_10  N05  C06  N07  C08   180.00   0.0  0
 9H3  CONST_11  N22  C06  N07  C08     0.00   0.0  0
 9H3  CONST_14  N05  C06  N22  C23     0.00   0.0  0
 9H3  CONST_15  N07  C06  N22  C23   180.00   0.0  0
 9H3  CONST_16  O04  C03  N05  C06   180.00   0.0  0
 9H3  CONST_17  H1   C12  C11  C10     0.00   0.0  0
 9H3  CONST_18  H2   C13  C12  C11   180.00   0.0  0
 9H3  CONST_19  H4   C15  C16  C11   180.00   0.0  0
 9H3  CONST_20  H3   C14  C13  C12   180.00   0.0  0
 9H3  CONST_21  H19  N05  C03  C02   180.00   0.0  0
 9H3  Var_01    N07  C21  C20  C10   -54.84  30.0  1
 9H3  Var_02    N07  C08  C09  C10    54.34  30.0  1
 9H3  Var_03    C21  C20  C10  C11   172.44  30.0  3
 9H3  Var_04    C08  C09  C10  C11  -172.95  30.0  3
 9H3  Var_05    O17  C18  C10  C11    -1.12  30.0  1
 9H3  Var_06    C20  C10  C11  C12   -61.72  30.0  1
 9H3  Var_07    C24  C25  C26  C01   -62.59  30.0  1
 9H3  Var_08    C25  C26  C01  C02    44.59  30.0  1
 9H3  Var_09    C25  C24  C23  C02   -17.13  30.0  1
 9H3  Var_10    C26  C01  C02  C03   166.83  30.0  1
 9H3  Var_11    C20  C21  N07  C06   -89.97  30.0  1
 9H3  Var_12    C09  C08  N07  C06    91.80  30.0  1
 9H3  Var_13    C26  C25  C24  C23    47.81  30.0  1

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
 9H3  plan-1  C10  0.020
 9H3  plan-1  C11  0.020
 9H3  plan-1  C12  0.020
 9H3  plan-1  C13  0.020
 9H3  plan-1  C14  0.020
 9H3  plan-1  C15  0.020
 9H3  plan-1  C16  0.020
 9H3  plan-1  O17  0.020
 9H3  plan-1  H1   0.020
 9H3  plan-1  H2   0.020
 9H3  plan-1  H3   0.020
 9H3  plan-1  H4   0.020
 9H3  plan-2  C01  0.020
 9H3  plan-2  C02  0.020
 9H3  plan-2  C03  0.020
 9H3  plan-2  C06  0.020
 9H3  plan-2  C08  0.020
 9H3  plan-2  C21  0.020
 9H3  plan-2  C23  0.020
 9H3  plan-2  C24  0.020
 9H3  plan-2  N05  0.020
 9H3  plan-2  N07  0.020
 9H3  plan-2  N22  0.020
 9H3  plan-2  H19  0.020
 9H3  plan-2  O04  0.020
 9H3  plan-3  C10  0.020
 9H3  plan-3  C18  0.020
 9H3  plan-3  O17  0.020
 9H3  plan-3  O19  0.020

