# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:22:28 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (3~{a}~{R})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~{H}-benzo[de]isoquinolin-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N(C[C@@H]2CCCc3cccc1c23)[C@@H]4CN5CCC4CC5
#
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
 7A9  7A9  (3~{a}~{R})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~{H}-benzo[de]isoquinolin-1-one  ligand  46  22  .  2022-07-23  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_7A9
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
 7A9  C22  C  CH2   0  -0.334   4.7627  -0.3947  -0.2611
 7A9  C13  C  CR16  0  -0.306  -2.3525  -2.3610  -0.2610
 7A9  C21  C  CH2   0  -0.458   4.1562   0.7570  -1.1009
 7A9  C14  C  CH2   0  -0.495  -4.3809   1.4038   0.2606
 7A9  C11  C  CR16  0  -0.302  -4.3587  -1.1097   0.1509
 7A9  C16  C  CH2   0  -0.330   2.6549  -1.1307   0.5627
 7A9  C20  C  CH1   0  -0.322   2.7818   1.0983  -0.5102
 7A9  C19  C  CH2   0  -0.466   3.0260   1.6466   0.9025
 7A9  C06  C  C     0   0.543  -0.1773  -1.2282  -0.6233
 7A9  N05  N  NT    0  -0.516   0.5432  -0.1144  -0.3648
 7A9  C15  C  CH1   0  -0.028   1.9979  -0.2220  -0.5113
 7A9  C18  C  CH2   0  -0.327   3.8375   0.5962   1.6934
 7A9  N17  N  NT    0  -0.393   3.9740  -0.6434   0.9402
 7A9  C04  C  CH2   0  -0.270  -0.0943   1.0559   0.2218
 7A9  C08  C  CR6   0  -0.057  -1.6436  -1.1692  -0.3585
 7A9  C12  C  CR16  0  -0.248  -3.7140  -2.3277  -0.0039
 7A9  C10  C  CR6   0   0.056  -3.6654   0.0944   0.0485
 7A9  C01  C  CH2   0  -0.452  -3.5899   2.6022  -0.2458
 7A9  C09  C  CR6   0   0.112  -2.2966   0.0556  -0.2139
 7A9  C03  C  CH1   0  -0.337  -1.4680   1.2980  -0.3752
 7A9  C02  C  CH2   0  -0.433  -2.1434   2.5244   0.2221
 7A9  H1   H  HCH2  0   0.237   4.7985  -1.3203  -0.8407
 7A9  H2   H  HCH2  0   0.240   5.7888  -0.1645   0.0331
 7A9  H4   H  HCH2  0   0.238   4.7917   1.6450  -1.0694
 7A9  H5   H  HCH2  0   0.242   4.0630   0.4673  -2.1498
 7A9  H6   H  HCH2  0   0.251  -5.3658   1.3653  -0.2102
 7A9  H7   H  HCH2  0   0.246  -4.5649   1.5267   1.3333
 7A9  H8   H  HCR6  0   0.252  -5.4232  -1.0907   0.3552
 7A9  H9   H  HCH2  0   0.235   2.0293  -1.1633   1.4598
 7A9  H10  H  HCH2  0   0.248   2.7430  -2.1526   0.1920
 7A9  H11  H  HCH1  0   0.253   2.2892   1.8437  -1.1388
 7A9  H12  H  HCH2  0   0.242   3.5745   2.5883   0.8239
 7A9  H13  H  HCH2  0   0.245   2.0954   1.8843   1.4177
 7A9  H14  H  HCH1  0   0.249   2.1602  -0.6745  -1.4933
 7A9  H15  H  HCH2  0   0.236   4.8389   0.9653   1.9258
 7A9  H16  H  HCH2  0   0.238   3.3565   0.3714   2.6479
 7A9  H18  H  HCH2  0   0.237  -0.1724   0.9533   1.3114
 7A9  H19  H  HCH2  0   0.269   0.5200   1.9294   0.0211
 7A9  H20  H  HCR6  0   0.255  -4.2737  -3.2501   0.0793
 7A9  H21  H  HCH2  0   0.226  -3.6176   2.6340  -1.3394
 7A9  H22  H  HCH2  0   0.242  -4.0562   3.5245   0.1049
 7A9  H23  H  HCH1  0   0.262  -1.3332   1.4767  -1.4507
 7A9  H24  H  HCH2  0   0.244  -1.5952   3.4225  -0.0705
 7A9  H25  H  HCH2  0   0.225  -2.1112   2.4734   1.3159
 7A9  H3   H  HCR6  0   0.252  -1.8420  -3.3071  -0.3808
 7A9  O07  O  O     0  -0.500   0.3376  -2.2600  -1.0438

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
 7A9  C22  N17  single    1.458  0.020  1.458
 7A9  C22  C21  single    1.549  0.020  1.549
 7A9  N17  C18  single    1.457  0.020  1.457
 7A9  N17  C16  single    1.456  0.020  1.456
 7A9  C18  C19  single    1.545  0.020  1.545
 7A9  C16  C15  single    1.553  0.020  1.553
 7A9  C21  C20  single    1.534  0.020  1.534
 7A9  C19  C20  single    1.535  0.020  1.535
 7A9  C15  C20  single    1.535  0.020  1.535
 7A9  C15  N05  single    1.466  0.020  1.466
 7A9  C04  N05  single    1.456  0.020  1.456
 7A9  C04  C03  single    1.517  0.020  1.517
 7A9  N05  C06  single    1.351  0.020  1.351
 7A9  O07  C06  double    1.227  0.020  1.227
 7A9  C06  C08  single    1.491  0.020  1.491
 7A9  C02  C03  single    1.522  0.020  1.522
 7A9  C02  C01  single    1.522  0.020  1.522
 7A9  C03  C09  single    1.502  0.020  1.502
 7A9  C08  C09  aromatic  1.396  0.020  1.396
 7A9  C08  C13  aromatic  1.390  0.020  1.390
 7A9  C09  C10  aromatic  1.394  0.020  1.394
 7A9  C01  C14  single    1.523  0.020  1.523
 7A9  C13  C12  aromatic  1.386  0.020  1.386
 7A9  C10  C14  single    1.507  0.020  1.507
 7A9  C10  C11  aromatic  1.393  0.020  1.393
 7A9  C12  C11  aromatic  1.387  0.020  1.387
 7A9  C22  H1   single    0.970  0.020  1.090
 7A9  C22  H2   single    0.970  0.020  1.090
 7A9  C13  H3   single    0.930  0.020  1.080
 7A9  C21  H4   single    0.970  0.020  1.090
 7A9  C21  H5   single    0.970  0.020  1.090
 7A9  C14  H6   single    0.970  0.020  1.090
 7A9  C14  H7   single    0.970  0.020  1.090
 7A9  C11  H8   single    0.930  0.020  1.080
 7A9  C16  H9   single    0.970  0.020  1.090
 7A9  C16  H10  single    0.970  0.020  1.090
 7A9  C20  H11  single    0.970  0.020  1.090
 7A9  C19  H12  single    0.970  0.020  1.090
 7A9  C19  H13  single    0.970  0.020  1.090
 7A9  C15  H14  single    0.970  0.020  1.090
 7A9  C18  H15  single    0.970  0.020  1.090
 7A9  C18  H16  single    0.970  0.020  1.090
 7A9  C04  H18  single    0.970  0.020  1.090
 7A9  C04  H19  single    0.970  0.020  1.090
 7A9  C12  H20  single    0.930  0.020  1.080
 7A9  C01  H21  single    0.970  0.020  1.090
 7A9  C01  H22  single    0.970  0.020  1.090
 7A9  C03  H23  single    0.970  0.020  1.090
 7A9  C02  H24  single    0.970  0.020  1.090
 7A9  C02  H25  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
 7A9  H2   C22  H1   106.90  3.000
 7A9  H2   C22  N17  108.79  3.000
 7A9  H1   C22  N17  108.07  3.000
 7A9  H2   C22  C21  110.93  3.000
 7A9  H1   C22  C21  110.80  3.000
 7A9  N17  C22  C21  111.20  3.000
 7A9  H3   C13  C12  120.34  3.000
 7A9  H3   C13  C08  120.09  3.000
 7A9  C12  C13  C08  119.56  3.000
 7A9  H5   C21  H4   107.04  3.000
 7A9  H5   C21  C20  110.63  3.000
 7A9  H4   C21  C20  109.22  3.000
 7A9  H5   C21  C22  110.91  3.000
 7A9  H4   C21  C22  111.16  3.000
 7A9  C20  C21  C22  107.90  3.000
 7A9  H7   C14  H6   105.94  3.000
 7A9  H7   C14  C01  108.94  3.000
 7A9  H6   C14  C01  110.66  3.000
 7A9  H7   C14  C10  108.37  3.000
 7A9  H6   C14  C10  109.68  3.000
 7A9  C01  C14  C10  112.98  3.000
 7A9  H8   C11  C10  119.17  3.000
 7A9  H8   C11  C12  119.53  3.000
 7A9  C10  C11  C12  121.30  3.000
 7A9  H10  C16  H9   107.28  3.000
 7A9  H10  C16  N17  109.18  3.000
 7A9  H9   C16  N17  108.38  3.000
 7A9  H10  C16  C15  110.33  3.000
 7A9  H9   C16  C15  110.04  3.000
 7A9  N17  C16  C15  111.52  3.000
 7A9  H11  C20  C15  110.86  3.000
 7A9  H11  C20  C19  110.95  3.000
 7A9  C15  C20  C19  112.90  3.000
 7A9  H11  C20  C21  109.52  3.000
 7A9  C15  C20  C21  105.41  3.000
 7A9  C19  C20  C21  106.93  3.000
 7A9  H13  C19  H12  105.94  3.000
 7A9  H13  C19  C18  110.78  3.000
 7A9  H12  C19  C18  111.05  3.000
 7A9  H13  C19  C20  112.15  3.000
 7A9  H12  C19  C20  108.76  3.000
 7A9  C18  C19  C20  108.17  3.000
 7A9  C08  C06  N05  117.24  3.000
 7A9  C08  C06  O07  120.43  3.000
 7A9  N05  C06  O07  122.32  3.000
 7A9  C04  N05  C15  122.26  3.000
 7A9  C04  N05  C06  120.40  3.000
 7A9  C15  N05  C06  116.71  3.000
 7A9  H14  C15  N05  105.51  3.000
 7A9  H14  C15  C20  106.30  3.000
 7A9  N05  C15  C20  116.32  3.000
 7A9  H14  C15  C16  108.44  3.000
 7A9  N05  C15  C16  113.18  3.000
 7A9  C20  C15  C16  106.66  3.000
 7A9  H16  C18  H15  106.70  3.000
 7A9  H16  C18  N17  108.53  3.000
 7A9  H15  C18  N17  108.15  3.000
 7A9  H16  C18  C19  110.86  3.000
 7A9  H15  C18  C19  111.14  3.000
 7A9  N17  C18  C19  111.29  3.000
 7A9  C18  N17  C16  109.50  3.000
 7A9  C16  N17  C22  109.48  3.000
 7A9  C18  N17  C22  109.36  3.000
 7A9  H19  C04  H18  107.39  3.000
 7A9  H19  C04  C03  108.12  3.000
 7A9  H18  C04  C03  109.95  3.000
 7A9  H19  C04  N05  108.92  3.000
 7A9  H18  C04  N05  110.86  3.000
 7A9  C03  C04  N05  111.48  3.000
 7A9  C09  C08  C06  120.88  3.000
 7A9  C09  C08  C13  120.44  3.000
 7A9  C06  C08  C13  118.69  3.000
 7A9  H20  C12  C11  119.97  3.000
 7A9  H20  C12  C13  120.12  3.000
 7A9  C11  C12  C13  119.90  3.000
 7A9  C09  C10  C11  118.58  3.000
 7A9  C11  C10  C14  120.28  3.000
 7A9  C09  C10  C14  121.12  3.000
 7A9  H22  C01  H21  106.60  3.000
 7A9  H22  C01  C02  110.51  3.000
 7A9  H21  C01  C02  109.43  3.000
 7A9  H22  C01  C14  109.65  3.000
 7A9  H21  C01  C14  110.01  3.000
 7A9  C02  C01  C14  110.56  3.000
 7A9  C03  C09  C10  122.60  3.000
 7A9  C10  C09  C08  120.22  3.000
 7A9  C03  C09  C08  117.17  3.000
 7A9  H23  C03  C02  107.91  3.000
 7A9  H23  C03  C09  107.90  3.000
 7A9  C02  C03  C09  112.30  3.000
 7A9  H23  C03  C04  107.46  3.000
 7A9  C09  C03  C04  108.98  3.000
 7A9  C02  C03  C04  112.08  3.000
 7A9  H25  C02  H24  106.92  3.000
 7A9  H25  C02  C03  109.95  3.000
 7A9  H24  C02  C03  109.55  3.000
 7A9  H25  C02  C01  109.71  3.000
 7A9  H24  C02  C01  110.64  3.000
 7A9  C03  C02  C01  110.01  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
 7A9  CONST_01  C10  C09  C08  C13     0.00   0.0  0
 7A9  CONST_02  C10  C11  C12  C13     0.00   0.0  0
 7A9  CONST_03  C08  C09  C10  C11     0.00   0.0  0
 7A9  CONST_04  C08  C13  C12  C11     0.00   0.0  0
 7A9  CONST_05  C09  C08  C13  C12     0.00   0.0  0
 7A9  CONST_06  C09  C10  C11  C12     0.00   0.0  0
 7A9  CONST_07  C08  C06  N05  C15   180.00   0.0  0
 7A9  CONST_08  C08  C06  N05  C04     0.00   0.0  0
 7A9  CONST_09  C15  N05  C06  O07     0.00   0.0  0
 7A9  CONST_10  C04  N05  C06  O07   180.00   0.0  0
 7A9  CONST_11  H8   C11  C12  C13   180.00   0.0  0
 7A9  CONST_12  H3   C13  C12  C11   180.00   0.0  0
 7A9  CONST_13  H20  C12  C13  C08   180.00   0.0  0
 7A9  Var_01    C19  C18  N17  C22    64.83  30.0  1
 7A9  Var_02    C15  C16  N17  C22   -50.06  30.0  3
 7A9  Var_03    N05  C06  C08  C13  -162.85  30.0  1
 7A9  Var_04    C18  N17  C22  C21   -54.65  30.0  1
 7A9  Var_05    C03  C02  C01  C14    63.45  30.0  1
 7A9  Var_06    C01  C14  C10  C11  -164.57  30.0  1
 7A9  Var_07    N17  C22  C21  C20    -9.62  30.0  1
 7A9  Var_08    N17  C18  C19  C20    -7.35  30.0  1
 7A9  Var_09    C03  C04  N05  C06   -40.34  30.0  1
 7A9  Var_10    C02  C01  C14  C10   -46.87  30.0  1

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
 7A9  chir_01  C20  C21  C19  C15  positiv
 7A9  chir_02  C15  N05  C20  C16  negativ
 7A9  chir_03  C03  C04  C02  C09  positiv

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
 7A9  plan-1  C06  0.020
 7A9  plan-1  N05  0.020
 7A9  plan-1  C15  0.020
 7A9  plan-1  C04  0.020
 7A9  plan-1  C08  0.020
 7A9  plan-1  O07  0.020
 7A9  plan-2  C13  0.020
 7A9  plan-2  C14  0.020
 7A9  plan-2  C11  0.020
 7A9  plan-2  C06  0.020
 7A9  plan-2  C08  0.020
 7A9  plan-2  C12  0.020
 7A9  plan-2  C10  0.020
 7A9  plan-2  C09  0.020
 7A9  plan-2  C03  0.020
 7A9  plan-2  H8   0.020
 7A9  plan-2  H20  0.020
 7A9  plan-2  H3   0.020

