# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 19:36:12 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (2R)-2-(pyridin-3-yl)-1-azabicyclo[2.2.2]octane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN2CCC1C[C@@H]2c3cccnc3
#
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
 4VU  4VU  (2R)-2-(pyridin-3-yl)-1-azabicyclo[2.2.2]octane  ligand  30  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4VU
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
 4VU  C1   C  CR16  0  -0.317   3.2731  -1.1456  -0.2571
 4VU  N1   N  NT    0  -0.405  -1.0680   1.0203  -0.1993
 4VU  C2   C  CR16  0  -0.081   3.8174   0.1190  -0.0956
 4VU  N2   N  N     0  -0.403   3.0824   1.2242  -0.0936
 4VU  C4   C  CR16  0  -0.093   1.7690   1.1023  -0.2541
 4VU  C5   C  CR6   0  -0.003   1.1108  -0.1150  -0.4142
 4VU  C6   C  CR16  0  -0.195   1.9013  -1.2600  -0.4164
 4VU  C7   C  CH1   0  -0.129  -0.3807  -0.1911  -0.6412
 4VU  C9   C  CH2   0  -0.330  -2.3880   1.0620  -0.8225
 4VU  C10  C  CH2   0  -0.459  -1.0450  -1.4460  -0.0186
 4VU  C11  C  CH2   0  -0.457  -3.1660  -0.2509  -0.5698
 4VU  C12  C  CH1   0  -0.257  -2.4177  -1.0290   0.5148
 4VU  C14  C  CH2   0  -0.451  -2.1951  -0.1016   1.7100
 4VU  H1   H  HCR6  0   0.268   3.9109  -2.0189  -0.2552
 4VU  H3   H  HCR6  0   0.260   4.8869   0.2437   0.0346
 4VU  H4   H  HCR6  0   0.256   1.1931   2.0208  -0.2542
 4VU  H5   H  HCR6  0   0.268   1.4556  -2.2388  -0.5459
 4VU  H6   H  HCH1  0   0.268  -0.5206  -0.2378  -1.7280
 4VU  H17  H  HCH2  0   0.236  -2.9229   1.9210  -0.4110
 4VU  H16  H  HCH2  0   0.240  -2.2688   1.2478  -1.8924
 4VU  H8   H  HCH2  0   0.244  -1.1354  -2.2428  -0.7598
 4VU  H7   H  HCH2  0   0.231  -0.4437  -1.8434   0.8043
 4VU  H10  H  HCH2  0   0.235  -4.1904  -0.0432  -0.2528
 4VU  H11  H  HCH2  0   0.230  -3.2302  -0.8485  -1.4829
 4VU  H9   H  HCH1  0   0.236  -2.9864  -1.9113   0.8145
 4VU  H12  H  HCH2  0   0.237  -0.2403   0.8809   1.7054
 4VU  H13  H  HCH2  0   0.240  -1.5818   1.9967   1.5670
 4VU  H15  H  HCH2  0   0.229  -3.1486   0.3176   2.0422
 4VU  H14  H  HCH2  0   0.234  -1.7806  -0.6560   2.5551
 4VU  C13  C  CH2   0  -0.333  -1.2258   1.0130   1.2541

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
 4VU  C14  C12  single    1.529  0.020  1.529
 4VU  C14  C13  single    1.546  0.020  1.546
 4VU  C11  C12  single    1.530  0.020  1.530
 4VU  C11  C9   single    1.547  0.020  1.547
 4VU  C12  C10  single    1.531  0.020  1.531
 4VU  C9   N1   single    1.460  0.020  1.460
 4VU  C13  N1   single    1.462  0.020  1.462
 4VU  N1   C7   single    1.461  0.020  1.461
 4VU  C10  C7   single    1.550  0.020  1.550
 4VU  C7   C5   single    1.511  0.020  1.511
 4VU  C5   C6   aromatic  1.391  0.020  1.391
 4VU  C5   C4   aromatic  1.393  0.020  1.393
 4VU  C6   C1   aromatic  1.386  0.020  1.386
 4VU  C4   N2   aromatic  1.329  0.020  1.329
 4VU  C1   C2   aromatic  1.386  0.020  1.386
 4VU  N2   C2   aromatic  1.327  0.020  1.327
 4VU  C1   H1   single    0.930  0.020  1.080
 4VU  C2   H3   single    0.930  0.020  1.080
 4VU  C4   H4   single    0.930  0.020  1.080
 4VU  C6   H5   single    0.930  0.020  1.080
 4VU  C7   H6   single    0.970  0.020  1.090
 4VU  C9   H17  single    0.970  0.020  1.090
 4VU  C9   H16  single    0.970  0.020  1.090
 4VU  C10  H8   single    0.970  0.020  1.090
 4VU  C10  H7   single    0.970  0.020  1.090
 4VU  C11  H10  single    0.970  0.020  1.090
 4VU  C11  H11  single    0.970  0.020  1.090
 4VU  C12  H9   single    0.970  0.020  1.090
 4VU  C13  H12  single    0.970  0.020  1.090
 4VU  C13  H13  single    0.970  0.020  1.090
 4VU  C14  H15  single    0.970  0.020  1.090
 4VU  C14  H14  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
 4VU  H1   C1   C6   121.16  3.000
 4VU  H1   C1   C2   120.32  3.000
 4VU  C6   C1   C2   118.52  3.000
 4VU  C13  N1   C9   109.08  3.000
 4VU  C13  N1   C7   110.32  3.000
 4VU  C9   N1   C7   108.65  3.000
 4VU  H3   C2   N2   116.76  3.000
 4VU  H3   C2   C1   120.40  3.000
 4VU  N2   C2   C1   122.84  3.000
 4VU  C4   N2   C2   118.09  3.000
 4VU  H4   C4   C5   119.29  3.000
 4VU  H4   C4   N2   116.58  3.000
 4VU  C5   C4   N2   124.13  3.000
 4VU  C7   C5   C6   121.28  3.000
 4VU  C6   C5   C4   116.79  3.000
 4VU  C7   C5   C4   121.86  3.000
 4VU  H5   C6   C5   120.66  3.000
 4VU  H5   C6   C1   119.72  3.000
 4VU  C5   C6   C1   119.62  3.000
 4VU  H6   C7   C10  107.99  3.000
 4VU  H6   C7   C5   106.08  3.000
 4VU  C10  C7   C5   113.80  3.000
 4VU  H6   C7   N1   105.96  3.000
 4VU  C5   C7   N1   112.16  3.000
 4VU  C10  C7   N1   110.37  3.000
 4VU  H16  C9   H17  106.77  3.000
 4VU  H16  C9   C11  111.05  3.000
 4VU  H17  C9   C11  111.08  3.000
 4VU  H16  C9   N1   108.92  3.000
 4VU  H17  C9   N1   107.72  3.000
 4VU  C11  C9   N1   111.14  3.000
 4VU  H7   C10  H8   106.92  3.000
 4VU  H7   C10  C12  109.26  3.000
 4VU  H8   C10  C12  111.17  3.000
 4VU  H7   C10  C7   111.14  3.000
 4VU  H8   C10  C7   110.70  3.000
 4VU  C12  C10  C7   107.68  3.000
 4VU  H11  C11  H10  106.93  3.000
 4VU  H11  C11  C12  110.05  3.000
 4VU  H10  C11  C12  110.46  3.000
 4VU  H11  C11  C9   110.92  3.000
 4VU  H10  C11  C9   110.96  3.000
 4VU  C12  C11  C9   107.54  3.000
 4VU  H9   C12  C14  110.58  3.000
 4VU  H9   C12  C11  110.53  3.000
 4VU  C14  C12  C11  108.47  3.000
 4VU  H9   C12  C10  110.04  3.000
 4VU  C11  C12  C10  109.27  3.000
 4VU  C14  C12  C10  107.89  3.000
 4VU  H14  C14  H15  106.88  3.000
 4VU  H14  C14  C13  110.86  3.000
 4VU  H15  C14  C13  111.10  3.000
 4VU  H14  C14  C12  110.62  3.000
 4VU  H15  C14  C12  110.07  3.000
 4VU  C13  C14  C12  107.34  3.000
 4VU  H13  C13  H12  106.55  3.000
 4VU  H13  C13  C14  111.14  3.000
 4VU  H12  C13  C14  110.91  3.000
 4VU  H13  C13  N1   108.39  3.000
 4VU  H12  C13  N1   108.30  3.000
 4VU  C14  C13  N1   111.37  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
 4VU  CONST_01  C4   C5   C6   C1    0.00   0.0  0
 4VU  CONST_02  C4   N2   C2   C1    0.00   0.0  0
 4VU  CONST_03  C5   C6   C1   C2    0.00   0.0  0
 4VU  CONST_04  C5   C4   N2   C2    0.00   0.0  0
 4VU  CONST_05  C6   C5   C4   N2    0.00   0.0  0
 4VU  CONST_06  C6   C1   C2   N2    0.00   0.0  0
 4VU  CONST_07  C7   C5   C6   C1  180.00   0.0  0
 4VU  CONST_08  C7   C5   C4   N2  180.00   0.0  0
 4VU  CONST_09  H5   C6   C1   C2  180.00   0.0  0
 4VU  CONST_10  H4   C4   N2   C2  180.00   0.0  0
 4VU  CONST_11  H1   C1   C2   N2  180.00   0.0  0
 4VU  CONST_12  H3   C2   N2   C4  180.00   0.0  0
 4VU  Var_01    C12  C11  C9   N1   12.66  30.0  1
 4VU  Var_02    C12  C14  C13  N1   12.76  30.0  3
 4VU  Var_03    C11  C9   N1   C7   52.90  30.0  1
 4VU  Var_04    C14  C13  N1   C7  -67.08  30.0  3

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
 4VU  chir_01  C7   N1   C10  C5   positiv
 4VU  chir_02  C12  C14  C11  C10  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
 4VU  plan-1  C1  0.020
 4VU  plan-1  C2  0.020
 4VU  plan-1  N2  0.020
 4VU  plan-1  C4  0.020
 4VU  plan-1  C5  0.020
 4VU  plan-1  C6  0.020
 4VU  plan-1  C7  0.020
 4VU  plan-1  H1  0.020
 4VU  plan-1  H3  0.020
 4VU  plan-1  H4  0.020
 4VU  plan-1  H5  0.020

