# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 05:18:37 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2~{R})-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
 QN8  QN8  "(2~{R})-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_QN8
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
 QN8  C1   C  CH3   0  -0.666  168.8764  -8.3030  35.2177
 QN8  C2   C  CH1   0  -0.232  167.6258  -7.6908  34.5980
 QN8  C3   C  C     0   0.430  167.2272  -8.4030  33.3089
 QN8  C4   C  CH1   0  -0.387  167.0566  -7.4306  32.1734
 QN8  C5   C  CH2   0  -0.469  168.4016  -6.7058  32.0035
 QN8  C6   C  CH2   0  -0.339  168.7308  -5.9692  33.3239
 QN8  C7   C  CH2   0  -0.335  166.4441  -5.7440  33.9187
 QN8  C8   C  CH2   0  -0.465  165.9941  -6.4035  32.5914
 QN8  N1   N  NT    0  -0.397  167.7390  -6.2541  34.3577
 QN8  O1   O  O     0  -0.396  167.0804  -9.6011  33.2288
 QN8  H1   H  HCH3  0   0.243  169.1635  -7.7422  36.1066
 QN8  H2   H  HCH3  0   0.243  168.6807  -9.3316  35.5156
 QN8  H3   H  HCH3  0   0.233  169.7237  -8.3137  34.5316
 QN8  H4   H  HCH1  0   0.283  166.8035  -7.8336  35.3110
 QN8  H5   H  HCH1  0   0.264  166.7686  -7.9523  31.2600
 QN8  H6   H  HCH2  0   0.249  169.1863  -7.4185  31.7421
 QN8  H7   H  HCH2  0   0.253  168.3182  -6.0070  31.1688
 QN8  H8   H  HCH2  0   0.250  169.7222  -6.2423  33.6872
 QN8  H9   H  HCH2  0   0.247  168.7483  -4.8887  33.1719
 QN8  H10  H  HCH2  0   0.245  166.5222  -4.6609  33.8084
 QN8  H11  H  HCH2  0   0.245  165.7151  -5.9290  34.7106
 QN8  H12  H  HCH2  0   0.250  165.8924  -5.6637  31.7942
 QN8  H13  H  HCH2  0   0.250  165.0201  -6.8838  32.6992

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
 QN8  C5  C4   single  1.537  0.020  1.537
 QN8  C5  C6   single  1.547  0.020  1.547
 QN8  C4  C8   single  1.536  0.020  1.536
 QN8  C4  C3   single  1.505  0.020  1.505
 QN8  C8  C7   single  1.549  0.020  1.549
 QN8  O1  C3   double  1.210  0.020  1.210
 QN8  C3  C2   single  1.526  0.020  1.526
 QN8  C6  N1   single  1.461  0.020  1.461
 QN8  C7  N1   single  1.459  0.020  1.459
 QN8  N1  C2   single  1.461  0.020  1.461
 QN8  C2  C1   single  1.524  0.020  1.524
 QN8  C1  H1   single  0.970  0.020  1.090
 QN8  C1  H2   single  0.970  0.020  1.090
 QN8  C1  H3   single  0.970  0.020  1.090
 QN8  C2  H4   single  0.970  0.020  1.090
 QN8  C4  H5   single  0.970  0.020  1.090
 QN8  C5  H6   single  0.970  0.020  1.090
 QN8  C5  H7   single  0.970  0.020  1.090
 QN8  C6  H8   single  0.970  0.020  1.090
 QN8  C6  H9   single  0.970  0.020  1.090
 QN8  C7  H10  single  0.970  0.020  1.090
 QN8  C7  H11  single  0.970  0.020  1.090
 QN8  C8  H12  single  0.970  0.020  1.090
 QN8  C8  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
 QN8  H3   C1  H2   107.62  3.000
 QN8  H3   C1  H1   108.28  3.000
 QN8  H2   C1  H1   108.09  3.000
 QN8  H3   C1  C2   112.69  3.000
 QN8  H2   C1  C2   110.08  3.000
 QN8  H1   C1  C2   109.95  3.000
 QN8  H4   C2  N1   107.02  3.000
 QN8  H4   C2  C3   107.00  3.000
 QN8  N1   C2  C3   109.90  3.000
 QN8  H4   C2  C1   107.35  3.000
 QN8  N1   C2  C1   113.48  3.000
 QN8  C3   C2  C1   111.74  3.000
 QN8  O1   C3  C4   125.19  3.000
 QN8  O1   C3  C2   123.37  3.000
 QN8  C4   C3  C2   111.44  3.000
 QN8  H5   C4  C8   111.42  3.000
 QN8  H5   C4  C5   111.35  3.000
 QN8  C8   C4  C5   108.66  3.000
 QN8  H5   C4  C3   110.66  3.000
 QN8  C8   C4  C3   107.77  3.000
 QN8  C5   C4  C3   106.79  3.000
 QN8  H7   C5  H6   106.84  3.000
 QN8  H7   C5  C6   111.34  3.000
 QN8  H6   C5  C6   111.23  3.000
 QN8  H7   C5  C4   108.63  3.000
 QN8  H6   C5  C4   110.34  3.000
 QN8  C6   C5  C4   108.44  3.000
 QN8  H9   C6  H8   106.25  3.000
 QN8  H9   C6  N1   107.61  3.000
 QN8  H8   C6  N1   109.43  3.000
 QN8  H9   C6  C5   110.85  3.000
 QN8  H8   C6  C5   111.01  3.000
 QN8  N1   C6  C5   111.51  3.000
 QN8  H11  C7  H10  106.81  3.000
 QN8  H11  C7  N1   108.35  3.000
 QN8  H10  C7  N1   108.28  3.000
 QN8  H11  C7  C8   110.82  3.000
 QN8  H10  C7  C8   110.90  3.000
 QN8  N1   C7  C8   111.51  3.000
 QN8  H13  C8  H12  106.68  3.000
 QN8  H13  C8  C7   111.22  3.000
 QN8  H12  C8  C7   111.35  3.000
 QN8  H13  C8  C4   110.49  3.000
 QN8  H12  C8  C4   108.59  3.000
 QN8  C7   C8  C4   108.48  3.000
 QN8  C7   N1  C6   108.75  3.000
 QN8  C7   N1  C2   108.93  3.000
 QN8  C6   N1  C2   111.14  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
 QN8  Var_01  C5   C6  N1  C2    56.69  30.0  3
 QN8  Var_02  C8   C7  N1  C2   -61.55  30.0  1
 QN8  Var_03  N1   C6  C5  C4     4.22  30.0  3
 QN8  Var_04  N1   C7  C8  C4     1.55  30.0  1
 QN8  Var_05  C7   N1  C6  C5   -63.22  30.0  3
 QN8  Var_06  C8   C7  N1  C6    59.73  30.0  1
 QN8  Var_07  H8   C6  N1  C2   -66.51  30.0  3
 QN8  Var_08  H9   C6  N1  C2   178.45  30.0  3
 QN8  Var_09  H10  C7  N1  C2   176.18  30.0  1
 QN8  Var_10  H11  C7  N1  C2    60.68  30.0  1
 QN8  Var_11  H8   C6  C5  C4   126.52  30.0  3
 QN8  Var_12  H9   C6  C5  C4  -115.64  30.0  3
 QN8  Var_13  H10  C7  C8  C4   122.31  30.0  1
 QN8  Var_14  H11  C7  C8  C4  -119.25  30.0  1
 QN8  Var_15  H10  C7  N1  C6   -62.55  30.0  1
 QN8  Var_16  H11  C7  N1  C6  -178.05  30.0  1
 QN8  Var_17  H8   C6  N1  C7   173.58  30.0  3
 QN8  Var_18  H9   C6  N1  C7    58.54  30.0  3
 QN8  Var_19  H6   C5  C6  N1  -117.28  30.0  3
 QN8  Var_20  H7   C5  C6  N1   123.69  30.0  3
 QN8  Var_21  H12  C8  C7  N1  -117.90  30.0  1
 QN8  Var_22  H13  C8  C7  N1   123.26  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
 QN8  chir_01  C2  C3  N1  C1  positiv
 QN8  chir_02  C4  C3  C8  C5  negativ

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
 QN8  plan-1  C2  0.020
 QN8  plan-1  C3  0.020
 QN8  plan-1  C4  0.020
 QN8  plan-1  O1  0.020

