# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:04:27 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (1~{R},5~{S})-9-[2-(4-chlorophenyl)ethyl]-9-azabicyclo[3.3.1]nonan-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CCN2[C@@H]3CCC[C@H]2CC(=O)C3)cc1
#
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
 GO5  GO5  (1~{R},5~{S})-9-[2-(4-chlorophenyl)ethyl]-9-azabicyclo[3.3.1]nonan-3-one  ligand  39  19  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GO5
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
 GO5  C4   C   CH2   0  -0.415   4.0554  -1.3198  -0.9428
 GO5  C5   C   C     0  -0.562   2.7364   1.4559   0.8935
 GO5  C6   C   CR6   0   0.392   3.4206   1.7627  -0.4110
 GO5  C7   C   CR16  0  -0.140   2.7498  -0.5660  -1.1902
 GO5  C8   C   C     0  -0.560   2.9860   0.9102  -1.5720
 GO5  N    N   NR6   0  -0.409   1.8954  -0.7003  -0.0212
 GO5  C1   C   CR16  0  -0.141   2.5002  -0.0510   1.1322
 GO5  C2   C   CH2   0  -0.414   3.7868  -0.7919   1.4969
 GO5  C3   C   CH2   0  -0.478   4.7633  -0.8549   0.3269
 GO5  O    O   O     0  -0.418   4.2187   2.6697  -0.5295
 GO5  CA   C   CH2   0  -0.272   0.5014  -0.3727  -0.2431
 GO5  CB   C   CH2   0  -0.524  -0.4223  -1.1186   0.7238
 GO5  CG   C   CR6   0   0.140  -1.8607  -0.7599   0.4838
 GO5  CD1  C   CR16  0  -0.311  -2.3955   0.4173   1.0037
 GO5  CE1  C   CR16  0  -0.197  -3.7088   0.7864   0.7549
 GO5  CZ   C   CR6   0  -0.058  -4.5021  -0.0380  -0.0279
 GO5  CL1  CL  CL    0  -0.136  -6.1494   0.4090  -0.3433
 GO5  CE2  C   CR16  0  -0.196  -4.0012  -1.2155  -0.5589
 GO5  CD2  C   CR16  0  -0.318  -2.6832  -1.5645  -0.2997
 GO5  H1   H   HCH2  0   0.229   3.8171  -2.3833  -0.8540
 GO5  H2   H   HCH2  0   0.233   4.7118  -1.2133  -1.8095
 GO5  H3   H   H     0   0.267   3.2857   1.9071   1.7217
 GO5  H4   H   H     0   0.276   1.7659   1.9658   0.8548
 GO5  H5   H   HCR6  0   0.254   2.2413  -1.0437  -2.0315
 GO5  H6   H   H     0   0.277   2.0364   1.3317  -1.9256
 GO5  H7   H   H     0   0.265   3.6970   1.0017  -2.3959
 GO5  H9   H   HCR6  0   0.256   1.8153  -0.1405   1.9784
 GO5  H10  H   HCH2  0   0.232   4.2537  -0.3199   2.3646
 GO5  H11  H   HCH2  0   0.229   3.5118  -1.8071   1.7954
 GO5  H12  H   HCH2  0   0.248   5.5835  -1.5359   0.5635
 GO5  H13  H   HCH2  0   0.227   5.2368   0.1181   0.1703
 GO5  H14  H   HCH2  0   0.208   0.2917   0.7066  -0.1811
 GO5  H15  H   HCH2  0   0.244   0.2412  -0.6729  -1.2614
 GO5  H16  H   HCH2  0   0.247  -0.2718  -2.1923   0.5953
 GO5  H17  H   HCH2  0   0.251  -0.1563  -0.8807   1.7569
 GO5  H18  H   HCR6  0   0.258  -1.7785   1.0609   1.6202
 GO5  H19  H   HCR6  0   0.277  -4.1070   1.7027   1.1693
 GO5  H20  H   HCR6  0   0.278  -4.6258  -1.8557  -1.1671
 GO5  H21  H   HCR6  0   0.259  -2.2956  -2.4869  -0.7151

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
 GO5  C8   C7   single    1.543  0.020  1.543
 GO5  C8   C6   single    1.505  0.020  1.505
 GO5  C4   C7   single    1.528  0.020  1.528
 GO5  C4   C3   single    1.526  0.020  1.526
 GO5  C7   N    single    1.454  0.020  1.454
 GO5  O    C6   double    1.214  0.020  1.214
 GO5  C3   C2   single    1.525  0.020  1.525
 GO5  C6   C5   single    1.505  0.020  1.505
 GO5  CD1  CE1  aromatic  1.387  0.020  1.387
 GO5  CD1  CG   aromatic  1.394  0.020  1.394
 GO5  N    CA   single    1.449  0.020  1.449
 GO5  N    C1   single    1.455  0.020  1.455
 GO5  CB   CA   single    1.531  0.020  1.531
 GO5  CB   CG   single    1.502  0.020  1.502
 GO5  CE1  CZ   aromatic  1.386  0.020  1.386
 GO5  C2   C1   single    1.529  0.020  1.529
 GO5  C5   C1   single    1.544  0.020  1.544
 GO5  CG   CD2  aromatic  1.392  0.020  1.392
 GO5  CZ   CL1  single    1.736  0.020  1.736
 GO5  CZ   CE2  aromatic  1.385  0.020  1.385
 GO5  CD2  CE2  aromatic  1.388  0.020  1.388
 GO5  C4   H1   single    0.970  0.020  1.090
 GO5  C4   H2   single    0.970  0.020  1.090
 GO5  C5   H3   single    0.970  0.020  1.090
 GO5  C5   H4   single    0.970  0.020  1.090
 GO5  C7   H5   single    0.970  0.020  1.090
 GO5  C8   H6   single    0.970  0.020  1.090
 GO5  C8   H7   single    0.970  0.020  1.090
 GO5  C1   H9   single    0.970  0.020  1.090
 GO5  C2   H10  single    0.970  0.020  1.090
 GO5  C2   H11  single    0.970  0.020  1.090
 GO5  C3   H12  single    0.970  0.020  1.090
 GO5  C3   H13  single    0.970  0.020  1.090
 GO5  CA   H14  single    0.970  0.020  1.090
 GO5  CA   H15  single    0.970  0.020  1.090
 GO5  CB   H16  single    0.970  0.020  1.090
 GO5  CB   H17  single    0.970  0.020  1.090
 GO5  CD1  H18  single    0.930  0.020  1.080
 GO5  CE1  H19  single    0.930  0.020  1.080
 GO5  CE2  H20  single    0.930  0.020  1.080
 GO5  CD2  H21  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
 GO5  H2   C4   H1   106.87  3.000
 GO5  H2   C4   C3   110.59  3.000
 GO5  H1   C4   C3   109.26  3.000
 GO5  H2   C4   C7   109.69  3.000
 GO5  H1   C4   C7   107.86  3.000
 GO5  C3   C4   C7   112.38  3.000
 GO5  H4   C5   H3   106.25  3.000
 GO5  H4   C5   C1   108.89  3.000
 GO5  H3   C5   C1   111.29  3.000
 GO5  H4   C5   C6   106.08  3.000
 GO5  H3   C5   C6   110.16  3.000
 GO5  C1   C5   C6   113.74  3.000
 GO5  O    C6   C8   122.55  3.000
 GO5  O    C6   C5   122.41  3.000
 GO5  C8   C6   C5   114.97  3.000
 GO5  H5   C7   N    107.76  3.000
 GO5  H5   C7   C8   107.39  3.000
 GO5  N    C7   C8   112.16  3.000
 GO5  H5   C7   C4   107.86  3.000
 GO5  N    C7   C4   109.05  3.000
 GO5  C8   C7   C4   112.41  3.000
 GO5  H7   C8   H6   106.74  3.000
 GO5  H7   C8   C7   111.50  3.000
 GO5  H6   C8   C7   108.35  3.000
 GO5  H7   C8   C6   110.28  3.000
 GO5  H6   C8   C6   106.31  3.000
 GO5  C7   C8   C6   113.29  3.000
 GO5  CA   N    C1   114.86  3.000
 GO5  C1   N    C7   110.59  3.000
 GO5  CA   N    C7   114.91  3.000
 GO5  H9   C1   C2   107.65  3.000
 GO5  H9   C1   N    108.47  3.000
 GO5  C2   C1   N    108.82  3.000
 GO5  H9   C1   C5   107.20  3.000
 GO5  C2   C1   C5   112.40  3.000
 GO5  N    C1   C5   112.12  3.000
 GO5  H11  C2   H10  106.96  3.000
 GO5  H11  C2   C3   109.39  3.000
 GO5  H10  C2   C3   110.70  3.000
 GO5  H11  C2   C1   107.67  3.000
 GO5  H10  C2   C1   109.86  3.000
 GO5  C3   C2   C1   112.08  3.000
 GO5  H13  C3   H12  105.11  3.000
 GO5  H13  C3   C2   110.51  3.000
 GO5  H12  C3   C2   109.90  3.000
 GO5  H13  C3   C4   110.65  3.000
 GO5  H12  C3   C4   109.79  3.000
 GO5  C2   C3   C4   110.72  3.000
 GO5  H15  CA   H14  106.04  3.000
 GO5  H15  CA   CB   108.11  3.000
 GO5  H14  CA   CB   109.08  3.000
 GO5  H15  CA   N    108.04  3.000
 GO5  H14  CA   N    113.34  3.000
 GO5  CB   CA   N    111.93  3.000
 GO5  H17  CB   H16  106.97  3.000
 GO5  H17  CB   CG   109.40  3.000
 GO5  H16  CB   CG   110.37  3.000
 GO5  H17  CB   CA   110.12  3.000
 GO5  H16  CB   CA   108.75  3.000
 GO5  CG   CB   CA   111.13  3.000
 GO5  CD2  CG   CD1  118.14  3.000
 GO5  CD2  CG   CB   121.18  3.000
 GO5  CD1  CG   CB   120.64  3.000
 GO5  H18  CD1  CE1  118.89  3.000
 GO5  H18  CD1  CG   119.69  3.000
 GO5  CE1  CD1  CG   121.42  3.000
 GO5  H19  CE1  CZ   120.63  3.000
 GO5  H19  CE1  CD1  120.36  3.000
 GO5  CZ   CE1  CD1  119.01  3.000
 GO5  CE2  CZ   CL1  119.50  3.000
 GO5  CE2  CZ   CE1  120.99  3.000
 GO5  CL1  CZ   CE1  119.51  3.000
 GO5  H20  CE2  CD2  120.30  3.000
 GO5  H20  CE2  CZ   120.65  3.000
 GO5  CD2  CE2  CZ   119.05  3.000
 GO5  H21  CD2  CE2  118.83  3.000
 GO5  H21  CD2  CG   119.78  3.000
 GO5  CE2  CD2  CG   121.39  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
 GO5  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 GO5  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 GO5  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 GO5  CONST_04  CE2  CD2  CG   CD1    0.00   0.0  0
 GO5  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 GO5  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 GO5  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 GO5  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 GO5  CONST_09  CL1  CZ   CE1  CD1  180.00   0.0  0
 GO5  CONST_10  CD2  CE2  CZ   CL1  180.00   0.0  0
 GO5  CONST_11  H19  CE1  CD1  CG   180.00   0.0  0
 GO5  CONST_12  H20  CE2  CD2  CG   180.00   0.0  0
 GO5  CONST_13  H21  CD2  CG   CD1  180.00   0.0  0
 GO5  CONST_14  H18  CD1  CE1  CZ   180.00   0.0  0
 GO5  Var_01    C1   C2   C3   C4   -48.52  30.0  1
 GO5  Var_02    C7   C8   C6   C5   -39.11  30.0  3
 GO5  Var_03    C2   C3   C4   C7    48.06  30.0  1
 GO5  Var_04    C1   C5   C6   C8    38.67  30.0  3
 GO5  Var_05    CB   CA   N    C7   153.02  30.0  3
 GO5  Var_06    CG   CB   CA   N    179.66  30.0  1
 GO5  Var_07    CD1  CG   CB   CA   -80.81  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
 GO5  chir_01  C7  C8  C4  N   negativ
 GO5  chir_02  C1  N   C5  C2  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
 GO5  plan-1  CB   0.020
 GO5  plan-1  CG   0.020
 GO5  plan-1  CD1  0.020
 GO5  plan-1  CE1  0.020
 GO5  plan-1  CZ   0.020
 GO5  plan-1  CL1  0.020
 GO5  plan-1  CE2  0.020
 GO5  plan-1  CD2  0.020
 GO5  plan-1  H18  0.020
 GO5  plan-1  H19  0.020
 GO5  plan-1  H20  0.020
 GO5  plan-1  H21  0.020
 GO5  plan-2  C5   0.020
 GO5  plan-2  C6   0.020
 GO5  plan-2  C8   0.020
 GO5  plan-2  O    0.020

