# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:53:08 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 2-[4,6-difluoro-1-(2-hydroxyethyl)-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl]-5,6,7,8-tetrahydroquinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCN1CC2(CCN(CC2)C3=NC4=C(CCCC4)C(=O)N3)c5c(F)cc(F)cc15
#
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
 9H9  9H9  2-[4,6-difluoro-1-(2-hydroxyethyl)-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl]-5,6,7,8-tetrahydroquinazolin-4(3H)-one  ligand  56  30  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9H9
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
 9H9  C10  C  CR5   0  -0.153   1.1837  -0.3871   0.6890
 9H9  C11  C  CR56  0  -0.141   2.1380   0.5149  -0.0523
 9H9  C12  C  CR6   0   0.508   1.9301   1.6979  -0.7212
 9H9  C14  C  CR16  0  -0.593   2.9452   2.3650  -1.3908
 9H9  C15  C  CR6   0   0.555   4.1962   1.7803  -1.3612
 9H9  C01  C  CH2   0  -0.475  -6.2726   1.2083  -0.4285
 9H9  C02  C  CR6   0  -0.181  -5.0039   0.5582   0.0455
 9H9  C03  C  CR6   0   0.526  -4.5070   0.8940   1.3468
 9H9  C06  C  CR6   0   0.758  -2.6692  -0.6198   0.8869
 9H9  C08  C  CH2   0  -0.340  -0.7503  -2.0070   0.4081
 9H9  C09  C  CH2   0  -0.426   0.2813  -1.1425  -0.3063
 9H9  C17  C  CR16  0  -0.501   4.4765   0.5890  -0.7185
 9H9  C18  C  CR56  0   0.389   3.4187  -0.0515  -0.0762
 9H9  C21  C  CH2   0  -0.195   5.3573  -2.4149  -0.5168
 9H9  C23  C  CH2   0  -0.277   2.1932  -1.3457   1.3739
 9H9  C24  C  CH2   0  -0.425   0.3207   0.3399   1.7274
 9H9  C25  C  CH2   0  -0.376  -0.6899  -0.6085   2.3641
 9H9  C27  C  CR6   0   0.265  -4.3020  -0.3563  -0.6912
 9H9  C28  C  CH2   0  -0.503  -4.7663  -0.7820  -2.0531
 9H9  C29  C  CH2   0  -0.446  -6.2154  -0.4129  -2.3355
 9H9  C30  C  CH2   0  -0.446  -6.4846   1.0278  -1.9265
 9H9  F13  F  F     0  -0.307   0.7004   2.2358  -0.7557
 9H9  F16  F  F     0  -0.316   5.2042   2.4161  -1.9783
 9H9  N05  N  NR16  0  -0.733  -3.3199   0.2581   1.6923
 9H9  N07  N  NT    0  -0.479  -1.5335  -1.2064   1.3392
 9H9  N19  N  NR5   0  -0.526   3.4605  -1.2287   0.6501
 9H9  N26  N  N     0  -0.529  -3.1424  -0.9304  -0.2890
 9H9  O04  O  O     0  -0.492  -5.0276   1.6651   2.1449
 9H9  O22  O  OH1   0  -0.670   6.2813  -1.9081   0.4174
 9H9  H1   H  HCR6  0   0.292   2.7651   3.3005  -1.9029
 9H9  H2   H  HCH2  0   0.233  -7.1268   0.7891   0.1154
 9H9  H3   H  HCH2  0   0.240  -6.2581   2.2722  -0.1788
 9H9  H4   H  HCH2  0   0.279  -1.4105  -2.4929  -0.3033
 9H9  H5   H  HCH2  0   0.257  -0.2643  -2.7951   0.9883
 9H9  H6   H  HCH2  0   0.248  -0.2398  -0.4266  -0.9484
 9H9  H7   H  HCH2  0   0.251   0.8939  -1.7681  -0.9614
 9H9  H8   H  HCR6  0   0.281   5.4896   0.2180  -0.6804
 9H9  H9   H  HCH2  0   0.225   3.3056  -2.8883  -0.6605
 9H9  H10  H  HCH2  0   0.249   4.0001  -3.1956   0.9244
 9H9  H11  H  HCH2  0   0.234   5.6057  -3.4397  -0.8220
 9H9  H12  H  HCH2  0   0.209   5.3348  -1.8176  -1.4353
 9H9  H13  H  HCH2  0   0.251   2.3414  -1.0548   2.4197
 9H9  H14  H  HCH2  0   0.248   1.8518  -2.3819   1.3764
 9H9  H15  H  HCH2  0   0.255   0.9554   0.7752   2.5024
 9H9  H16  H  HCH2  0   0.251  -0.2271   1.1631   1.2642
 9H9  H17  H  HCH2  0   0.276  -0.1883  -1.4219   2.8946
 9H9  H18  H  HCH2  0   0.269  -1.2717  -0.0921   3.1258
 9H9  H19  H  HCH2  0   0.252  -4.1092  -0.3118  -2.7933
 9H9  H20  H  HCH2  0   0.253  -4.6054  -1.8576  -2.1543
 9H9  H21  H  HCH2  0   0.238  -6.4320  -0.5639  -3.3946
 9H9  H22  H  HCH2  0   0.223  -6.8827  -1.0806  -1.7815
 9H9  H23  H  HCH2  0   0.235  -7.5011   1.3236  -2.1926
 9H9  H24  H  HCH2  0   0.221  -5.8104   1.6918  -2.4767
 9H9  H25  H  HNR6  0   0.418  -2.9761   0.4621   2.6199
 9H9  H26  H  HOH1  0   0.459   7.1485  -1.8940   0.0022
 9H9  C20  C  CH2   0  -0.317   3.9805  -2.4765   0.1033

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
 9H9  C30  C01  single    1.524  0.020  1.524
 9H9  C30  C29  single    1.522  0.020  1.522
 9H9  C01  C02  single    1.502  0.020  1.502
 9H9  C29  C28  single    1.522  0.020  1.522
 9H9  O04  C03  double    1.226  0.020  1.226
 9H9  C02  C03  single    1.433  0.020  1.433
 9H9  C02  C27  double    1.368  0.020  1.368
 9H9  C03  N05  single    1.390  0.020  1.390
 9H9  C28  C27  single    1.501  0.020  1.501
 9H9  C27  N26  single    1.355  0.020  1.355
 9H9  N05  C06  single    1.357  0.020  1.357
 9H9  N26  C06  double    1.305  0.020  1.305
 9H9  C06  N07  single    1.356  0.020  1.356
 9H9  N07  C08  single    1.456  0.020  1.456
 9H9  N07  C25  single    1.456  0.020  1.456
 9H9  C08  C09  single    1.524  0.020  1.524
 9H9  C25  C24  single    1.525  0.020  1.525
 9H9  C09  C10  single    1.541  0.020  1.541
 9H9  C24  C10  single    1.534  0.020  1.534
 9H9  C10  C23  single    1.551  0.020  1.551
 9H9  C10  C11  single    1.508  0.020  1.508
 9H9  C23  N19  single    1.464  0.020  1.464
 9H9  F13  C12  single    1.343  0.020  1.343
 9H9  C11  C12  aromatic  1.375  0.020  1.375
 9H9  C11  C18  aromatic  1.401  0.020  1.401
 9H9  C12  C14  aromatic  1.387  0.020  1.387
 9H9  N19  C18  single    1.384  0.020  1.384
 9H9  N19  C20  single    1.458  0.020  1.458
 9H9  C18  C17  aromatic  1.394  0.020  1.394
 9H9  O22  C21  single    1.408  0.020  1.408
 9H9  C20  C21  single    1.511  0.020  1.511
 9H9  C14  C15  aromatic  1.381  0.020  1.381
 9H9  C17  C15  aromatic  1.382  0.020  1.382
 9H9  C15  F16  single    1.342  0.020  1.342
 9H9  C14  H1   single    0.930  0.020  1.080
 9H9  C01  H2   single    0.970  0.020  1.090
 9H9  C01  H3   single    0.970  0.020  1.090
 9H9  C08  H4   single    0.970  0.020  1.090
 9H9  C08  H5   single    0.970  0.020  1.090
 9H9  C09  H6   single    0.970  0.020  1.090
 9H9  C09  H7   single    0.970  0.020  1.090
 9H9  C17  H8   single    0.930  0.020  1.080
 9H9  C20  H9   single    0.970  0.020  1.090
 9H9  C20  H10  single    0.970  0.020  1.090
 9H9  C21  H11  single    0.970  0.020  1.090
 9H9  C21  H12  single    0.970  0.020  1.090
 9H9  C23  H13  single    0.970  0.020  1.090
 9H9  C23  H14  single    0.970  0.020  1.090
 9H9  C24  H15  single    0.970  0.020  1.090
 9H9  C24  H16  single    0.970  0.020  1.090
 9H9  C25  H17  single    0.970  0.020  1.090
 9H9  C25  H18  single    0.970  0.020  1.090
 9H9  C28  H19  single    0.970  0.020  1.090
 9H9  C28  H20  single    0.970  0.020  1.090
 9H9  C29  H21  single    0.970  0.020  1.090
 9H9  C29  H22  single    0.970  0.020  1.090
 9H9  C30  H23  single    0.970  0.020  1.090
 9H9  C30  H24  single    0.970  0.020  1.090
 9H9  N05  H25  single    0.860  0.020  1.020
 9H9  O22  H26  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
 9H9  C24  C10  C23  111.11  3.000
 9H9  C23  C10  C09  111.30  3.000
 9H9  C24  C10  C09  109.88  3.000
 9H9  C23  C10  C11  100.07  3.000
 9H9  C24  C10  C11  113.92  3.000
 9H9  C09  C10  C11  110.26  3.000
 9H9  C18  C11  C12  118.55  3.000
 9H9  C18  C11  C10  110.19  3.000
 9H9  C12  C11  C10  131.16  3.000
 9H9  F13  C12  C14  117.72  3.000
 9H9  C14  C12  C11  122.55  3.000
 9H9  F13  C12  C11  119.72  3.000
 9H9  H1   C14  C15  121.81  3.000
 9H9  H1   C14  C12  121.51  3.000
 9H9  C15  C14  C12  116.67  3.000
 9H9  F16  C15  C17  118.02  3.000
 9H9  F16  C15  C14  118.02  3.000
 9H9  C17  C15  C14  123.95  3.000
 9H9  H3   C01  H2   105.63  3.000
 9H9  H3   C01  C30  109.98  3.000
 9H9  H2   C01  C30  109.52  3.000
 9H9  H3   C01  C02  109.76  3.000
 9H9  H2   C01  C02  109.64  3.000
 9H9  C30  C01  C02  112.11  3.000
 9H9  C27  C02  C03  117.89  3.000
 9H9  C27  C02  C01  123.55  3.000
 9H9  C03  C02  C01  118.55  3.000
 9H9  O04  C03  N05  119.25  3.000
 9H9  N05  C03  C02  114.49  3.000
 9H9  O04  C03  C02  126.26  3.000
 9H9  N26  C06  N07  120.09  3.000
 9H9  N07  C06  N05  118.90  3.000
 9H9  N26  C06  N05  120.98  3.000
 9H9  H5   C08  H4   107.20  3.000
 9H9  H5   C08  N07  107.23  3.000
 9H9  H4   C08  N07  109.76  3.000
 9H9  H5   C08  C09  110.92  3.000
 9H9  H4   C08  C09  111.01  3.000
 9H9  N07  C08  C09  110.61  3.000
 9H9  H7   C09  H6   106.84  3.000
 9H9  H7   C09  C08  109.61  3.000
 9H9  H6   C09  C08  108.90  3.000
 9H9  H7   C09  C10  109.83  3.000
 9H9  H6   C09  C10  109.71  3.000
 9H9  C08  C09  C10  111.82  3.000
 9H9  H8   C17  C18  122.56  3.000
 9H9  H8   C17  C15  120.19  3.000
 9H9  C18  C17  C15  117.16  3.000
 9H9  N19  C18  C17  127.59  3.000
 9H9  C17  C18  C11  121.07  3.000
 9H9  N19  C18  C11  111.27  3.000
 9H9  H12  C21  H11  106.29  3.000
 9H9  H12  C21  O22  111.92  3.000
 9H9  H11  C21  O22  111.83  3.000
 9H9  H12  C21  C20  110.33  3.000
 9H9  H11  C21  C20  106.39  3.000
 9H9  O22  C21  C20  109.89  3.000
 9H9  H14  C23  H13  107.00  3.000
 9H9  H14  C23  N19  110.36  3.000
 9H9  H13  C23  N19  109.48  3.000
 9H9  H14  C23  C10  112.59  3.000
 9H9  H13  C23  C10  110.21  3.000
 9H9  N19  C23  C10  107.19  3.000
 9H9  H16  C24  H15  106.98  3.000
 9H9  H16  C24  C25  108.27  3.000
 9H9  H15  C24  C25  109.68  3.000
 9H9  H16  C24  C10  110.64  3.000
 9H9  H15  C24  C10  110.02  3.000
 9H9  C25  C24  C10  111.15  3.000
 9H9  H18  C25  H17  105.00  3.000
 9H9  H18  C25  N07  112.18  3.000
 9H9  H17  C25  N07  107.57  3.000
 9H9  H18  C25  C24  110.56  3.000
 9H9  H17  C25  C24  111.18  3.000
 9H9  N07  C25  C24  110.21  3.000
 9H9  N26  C27  C28  114.46  3.000
 9H9  N26  C27  C02  124.23  3.000
 9H9  C28  C27  C02  121.30  3.000
 9H9  H20  C28  H19  105.76  3.000
 9H9  H20  C28  C29  111.21  3.000
 9H9  H19  C28  C29  109.97  3.000
 9H9  H20  C28  C27  108.54  3.000
 9H9  H19  C28  C27  107.81  3.000
 9H9  C29  C28  C27  113.23  3.000
 9H9  H22  C29  H21  106.60  3.000
 9H9  H22  C29  C30  109.49  3.000
 9H9  H21  C29  C30  110.89  3.000
 9H9  H22  C29  C28  109.80  3.000
 9H9  H21  C29  C28  109.60  3.000
 9H9  C30  C29  C28  110.38  3.000
 9H9  H24  C30  H23  106.66  3.000
 9H9  H24  C30  C29  109.28  3.000
 9H9  H23  C30  C29  110.85  3.000
 9H9  H24  C30  C01  109.67  3.000
 9H9  H23  C30  C01  109.70  3.000
 9H9  C29  C30  C01  110.60  3.000
 9H9  H25  N05  C06  120.81  3.000
 9H9  H25  N05  C03  115.24  3.000
 9H9  C06  N05  C03  123.90  3.000
 9H9  C25  N07  C08  111.35  3.000
 9H9  C25  N07  C06  122.86  3.000
 9H9  C08  N07  C06  118.35  3.000
 9H9  C23  N19  C20  115.19  3.000
 9H9  C20  N19  C18  122.81  3.000
 9H9  C23  N19  C18  107.53  3.000
 9H9  C27  N26  C06  118.48  3.000
 9H9  H26  O22  C21  108.09  3.000
 9H9  H10  C20  H9   106.67  3.000
 9H9  H10  C20  N19  106.74  3.000
 9H9  H9   C20  N19  111.24  3.000
 9H9  H10  C20  C21  108.61  3.000
 9H9  H9   C20  C21  106.83  3.000
 9H9  N19  C20  C21  116.35  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
 9H9  CONST_01  C15  C14  C12  C11     0.00   0.0  0
 9H9  CONST_02  C15  C17  C18  C11     0.00   0.0  0
 9H9  CONST_03  C17  C18  C11  C12     0.00   0.0  0
 9H9  CONST_04  C17  C15  C14  C12     0.00   0.0  0
 9H9  CONST_05  C18  C11  C12  C14     0.00   0.0  0
 9H9  CONST_06  C18  C17  C15  C14     0.00   0.0  0
 9H9  CONST_07  C06  N05  C03  C02     0.00   0.0  0
 9H9  CONST_08  N26  C06  N05  C03     0.00   0.0  0
 9H9  CONST_09  N07  C06  N05  C03   180.00   0.0  0
 9H9  CONST_10  N05  C06  N07  C08   180.00   0.0  0
 9H9  CONST_11  N26  C06  N07  C08     0.00   0.0  0
 9H9  CONST_14  N05  C06  N26  C27     0.00   0.0  0
 9H9  CONST_15  N07  C06  N26  C27   180.00   0.0  0
 9H9  CONST_16  F13  C12  C11  C10     0.00   0.0  0
 9H9  CONST_17  F16  C15  C14  C12   180.00   0.0  0
 9H9  CONST_18  F13  C12  C14  C15   180.00   0.0  0
 9H9  CONST_19  F13  C12  C11  C18   180.00   0.0  0
 9H9  CONST_20  F16  C15  C17  C18   180.00   0.0  0
 9H9  CONST_21  O04  C03  N05  C06   180.00   0.0  0
 9H9  CONST_22  H1   C14  C12  C11   180.00   0.0  0
 9H9  CONST_23  H8   C17  C18  C11   180.00   0.0  0
 9H9  CONST_24  H25  N05  C03  C02   180.00   0.0  0
 9H9  Var_01    N07  C08  C09  C10    55.02  30.0  1
 9H9  Var_02    N07  C25  C24  C10   -57.53  30.0  1
 9H9  Var_03    C18  N19  C23  C10    18.07  30.0  1
 9H9  Var_04    C08  C09  C10  C11  -176.82  30.0  3
 9H9  Var_05    C25  C24  C10  C11   175.79  30.0  3
 9H9  Var_06    N19  C23  C10  C11   -18.82  30.0  1
 9H9  Var_07    C23  N19  C18  C11    -9.32  30.0  1
 9H9  Var_08    C09  C10  C11  C12    72.80  30.0  1
 9H9  Var_09    C28  C29  C30  C01   -62.24  30.0  1
 9H9  Var_10    C29  C30  C01  C02    45.60  30.0  1
 9H9  Var_11    C29  C28  C27  C02   -15.77  30.0  1
 9H9  Var_12    C30  C01  C02  C03   165.83  30.0  1
 9H9  Var_13    C09  C08  N07  C06    89.86  30.0  1
 9H9  Var_14    C24  C25  N07  C06   -87.04  30.0  1
 9H9  Var_15    C30  C29  C28  C27    46.30  30.0  1
 9H9  Var_16    C21  C20  N19  C18    52.07  30.0  3
 9H9  Var_17    O22  C21  C20  N19    55.79  30.0  3

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
 9H9  plan-1  C10  0.020
 9H9  plan-1  C11  0.020
 9H9  plan-1  C12  0.020
 9H9  plan-1  C14  0.020
 9H9  plan-1  C15  0.020
 9H9  plan-1  C17  0.020
 9H9  plan-1  C18  0.020
 9H9  plan-1  F13  0.020
 9H9  plan-1  F16  0.020
 9H9  plan-1  N19  0.020
 9H9  plan-1  H1   0.020
 9H9  plan-1  H8   0.020
 9H9  plan-2  C01  0.020
 9H9  plan-2  C02  0.020
 9H9  plan-2  C03  0.020
 9H9  plan-2  C06  0.020
 9H9  plan-2  C08  0.020
 9H9  plan-2  C25  0.020
 9H9  plan-2  C27  0.020
 9H9  plan-2  C28  0.020
 9H9  plan-2  N05  0.020
 9H9  plan-2  N07  0.020
 9H9  plan-2  N26  0.020
 9H9  plan-2  O04  0.020
 9H9  plan-2  H25  0.020

