# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 05:18:35 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N2CCC(CC2)C1=O
#
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
 QNN  QNN  "(2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one"
  ligand  23  10  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QNN
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
 QNN  C1   C  CH3   0  -0.664  153.9842  -5.1921  37.2010
 QNN  C6   C  CH2   0  -0.335  157.4175  -5.6225  35.7227
 QNN  C2   C  CH1   0  -0.232  155.0952  -5.5996  36.2407
 QNN  C7   C  CH2   0  -0.339  156.4088  -3.5851  36.3978
 QNN  C8   C  CH2   0  -0.470  156.0348  -3.1982  34.9474
 QNN  C3   C  C     0   0.430  154.7491  -5.2630  34.7938
 QNN  C4   C  CH1   0  -0.387  155.8550  -4.4883  34.1300
 QNN  C5   C  CH2   0  -0.465  157.1452  -5.3145  34.2299
 QNN  N1   N  NT    0  -0.397  156.3981  -5.0335  36.5853
 QNN  O1   O  O     0  -0.396  153.7043  -5.5748  34.2696
 QNN  H1   H  HCH3  0   0.242  154.2772  -5.4193  38.2253
 QNN  H2   H  HCH3  0   0.233  153.7470  -4.1298  37.1408
 QNN  H3   H  HCH3  0   0.243  153.0744  -5.7464  36.9777
 QNN  H5   H  HCH2  0   0.245  158.3904  -5.2332  36.0283
 QNN  H6   H  HCH1  0   0.283  155.1967  -6.6913  36.2987
 QNN  H7   H  HCH2  0   0.247  157.4087  -3.2268  36.6486
 QNN  H8   H  HCH2  0   0.250  155.7302  -3.1205  37.1138
 QNN  H9   H  HCH2  0   0.253  156.8186  -2.5966  34.4821
 QNN  H10  H  HCH2  0   0.250  155.1217  -2.6000  34.9185
 QNN  H11  H  HCH1  0   0.264  155.6012  -4.2682  33.0925
 QNN  H12  H  HCH2  0   0.250  157.0600  -6.2322  33.6451
 QNN  H13  H  HCH2  0   0.250  157.9611  -4.7368  33.7904
 QNN  H4   H  HCH2  0   0.245  157.4398  -6.7000  35.8998

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
 QNN  C4  C5   single  1.535  0.020  1.535
 QNN  C4  C3   single  1.505  0.020  1.505
 QNN  C4  C8   single  1.538  0.020  1.538
 QNN  C5  C6   single  1.548  0.020  1.548
 QNN  O1  C3   double  1.210  0.020  1.210
 QNN  C3  C2   single  1.525  0.020  1.525
 QNN  C8  C7   single  1.547  0.020  1.547
 QNN  C6  N1   single  1.460  0.020  1.460
 QNN  C2  N1   single  1.462  0.020  1.462
 QNN  C2  C1   single  1.524  0.020  1.524
 QNN  C7  N1   single  1.460  0.020  1.460
 QNN  C1  H1   single  0.970  0.020  1.090
 QNN  C1  H2   single  0.970  0.020  1.090
 QNN  C1  H3   single  0.970  0.020  1.090
 QNN  C6  H4   single  0.970  0.020  1.090
 QNN  C6  H5   single  0.970  0.020  1.090
 QNN  C2  H6   single  0.970  0.020  1.090
 QNN  C7  H7   single  0.970  0.020  1.090
 QNN  C7  H8   single  0.970  0.020  1.090
 QNN  C8  H9   single  0.970  0.020  1.090
 QNN  C8  H10  single  0.970  0.020  1.090
 QNN  C4  H11  single  0.970  0.020  1.090
 QNN  C5  H12  single  0.970  0.020  1.090
 QNN  C5  H13  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
 QNN  H3   C1  H2   107.63  3.000
 QNN  H3   C1  H1   108.15  3.000
 QNN  H2   C1  H1   108.28  3.000
 QNN  H3   C1  C2   110.11  3.000
 QNN  H2   C1  C2   112.61  3.000
 QNN  H1   C1  C2   109.92  3.000
 QNN  H5   C6  H4   106.76  3.000
 QNN  H5   C6  N1   108.25  3.000
 QNN  H4   C6  N1   108.46  3.000
 QNN  H5   C6  C5   110.84  3.000
 QNN  H4   C6  C5   110.86  3.000
 QNN  N1   C6  C5   111.51  3.000
 QNN  H6   C2  N1   106.88  3.000
 QNN  H6   C2  C3   106.89  3.000
 QNN  N1   C2  C3   109.90  3.000
 QNN  H6   C2  C1   107.46  3.000
 QNN  N1   C2  C1   113.43  3.000
 QNN  C3   C2  C1   111.92  3.000
 QNN  H8   C7  H7   106.23  3.000
 QNN  H8   C7  N1   109.49  3.000
 QNN  H7   C7  N1   107.63  3.000
 QNN  H8   C7  C8   111.01  3.000
 QNN  H7   C7  C8   110.78  3.000
 QNN  N1   C7  C8   111.51  3.000
 QNN  H10  C8  H9   106.68  3.000
 QNN  H10  C8  C4   110.35  3.000
 QNN  H9   C8  C4   108.64  3.000
 QNN  H10  C8  C7   111.34  3.000
 QNN  H9   C8  C7   111.33  3.000
 QNN  C4   C8  C7   108.47  3.000
 QNN  O1   C3  C4   125.19  3.000
 QNN  O1   C3  C2   123.38  3.000
 QNN  C4   C3  C2   111.43  3.000
 QNN  H11  C4  C5   111.47  3.000
 QNN  H11  C4  C3   110.65  3.000
 QNN  C5   C4  C3   108.18  3.000
 QNN  H11  C4  C8   111.32  3.000
 QNN  C3   C4  C8   106.46  3.000
 QNN  C5   C4  C8   108.58  3.000
 QNN  H13  C5  H12  106.70  3.000
 QNN  H13  C5  C4   108.48  3.000
 QNN  H12  C5  C4   110.61  3.000
 QNN  H13  C5  C6   111.22  3.000
 QNN  H12  C5  C6   111.29  3.000
 QNN  C4   C5  C6   108.51  3.000
 QNN  C7   N1  C2   111.12  3.000
 QNN  C7   N1  C6   108.62  3.000
 QNN  C2   N1  C6   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
 QNN  Var_01  C8   C7  N1  C6    62.92  30.0  1
 QNN  Var_02  C5   C6  N1  C2    60.95  30.0  1
 QNN  Var_03  C8   C7  N1  C2   -57.07  30.0  1
 QNN  Var_04  C5   C6  N1  C7   -60.30  30.0  1
 QNN  Var_05  N1   C6  C5  C4    -0.77  30.0  1
 QNN  Var_06  N1   C7  C8  C4    -3.59  30.0  1
 QNN  Var_07  H7   C7  N1  C6   -58.77  30.0  1
 QNN  Var_08  H8   C7  N1  C6  -173.82  30.0  1
 QNN  Var_09  H4   C6  N1  C2   -61.39  30.0  1
 QNN  Var_10  H5   C6  N1  C2  -176.87  30.0  1
 QNN  Var_11  H7   C7  N1  C2  -178.76  30.0  1
 QNN  Var_12  H8   C7  N1  C2    66.18  30.0  1
 QNN  Var_13  H4   C6  N1  C7   177.35  30.0  1
 QNN  Var_14  H5   C6  N1  C7    61.87  30.0  1
 QNN  Var_15  H4   C6  C5  C4   120.18  30.0  1
 QNN  Var_16  H5   C6  C5  C4  -121.45  30.0  1
 QNN  Var_17  H7   C7  C8  C4   116.26  30.0  1
 QNN  Var_18  H8   C7  C8  C4  -125.97  30.0  1
 QNN  Var_19  H12  C5  C6  N1  -122.70  30.0  1
 QNN  Var_20  H13  C5  C6  N1   118.47  30.0  1
 QNN  Var_21  H9   C8  C7  N1  -123.07  30.0  1
 QNN  Var_22  H10  C8  C7  N1   118.02  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
 QNN  chir_01  C2  C3  N1  C1  negativ
 QNN  chir_02  C4  C8  C3  C5  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
 QNN  plan-1  C2  0.020
 QNN  plan-1  C3  0.020
 QNN  plan-1  C4  0.020
 QNN  plan-1  O1  0.020

