# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:14:55 2021
#   Inital geometry file: a 59 line input string
#   Ligand name: (1~{S},5~{R})-8-methyl-8-azabicyclo[3.2.1]octan-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H]2CC[C@@H]1C[C@H](N)C2
#
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
 SVJ  SVJ  (1~{S},5~{R})-8-methyl-8-azabicyclo[3.2.1]octan-3-amine  ligand  26  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SVJ
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
 SVJ  N1   N  NH2   0  -0.785  30.9329  112.6894  23.5774
 SVJ  C4   C  CH1   0  -0.123  27.8699  112.5953  24.6920
 SVJ  C5   C  CH2   0  -0.413  28.9083  111.5286  24.3505
 SVJ  C6   C  CH1   0  -0.094  29.7889  111.8894  23.1465
 SVJ  C7   C  CH2   0  -0.413  28.9823  112.6449  22.0815
 SVJ  N    N  NT    0  -0.401  27.0414  112.8003  23.5030
 SVJ  C    C  CH3   0  -0.526  25.7905  113.4727  23.7883
 SVJ  C1   C  CH1   0  -0.124  27.9373  113.5952  22.6623
 SVJ  C2   C  CH2   0  -0.446  28.5389  114.6580  23.6101
 SVJ  C3   C  CH2   0  -0.447  28.4941  113.9772  24.9905
 SVJ  H1   H  HNH2  0   0.337  31.4866  112.1492  24.2322
 SVJ  H2   H  HNH2  0   0.337  31.5383  112.8566  22.7822
 SVJ  H4   H  HCH1  0   0.226  27.2540  112.2329  25.5195
 SVJ  H5   H  HCH2  0   0.220  28.3731  110.6008  24.1320
 SVJ  H6   H  HCH2  0   0.221  29.5393  111.3249  25.2214
 SVJ  H7   H  HCH1  0   0.204  30.1204  110.9446  22.6912
 SVJ  H8   H  HCH2  0   0.220  28.4566  111.9179  21.4564
 SVJ  H9   H  HCH2  0   0.221  29.6640  113.1871  21.4188
 SVJ  H11  H  HCH3  0   0.229  25.1831  112.8524  24.4494
 SVJ  H12  H  HCH3  0   0.196  25.8895  114.4603  24.2614
 SVJ  H13  H  HCH3  0   0.229  25.2314  113.6117  22.8615
 SVJ  H14  H  HCH1  0   0.226  27.3762  114.0471  21.8402
 SVJ  H15  H  HCH2  0   0.230  29.5496  114.9355  23.3175
 SVJ  H16  H  HCH2  0   0.223  27.9309  115.5649  23.5993
 SVJ  H17  H  HCH2  0   0.232  29.4815  113.8889  25.4401
 SVJ  H18  H  HCH2  0   0.223  27.8648  114.5352  25.6862

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
 SVJ  C7  C1   single  1.527  0.020  1.527
 SVJ  C7  C6   single  1.535  0.020  1.535
 SVJ  C1  N    single  1.463  0.020  1.463
 SVJ  C1  C2   single  1.546  0.020  1.546
 SVJ  C6  N1   single  1.461  0.020  1.461
 SVJ  C6  C5   single  1.535  0.020  1.535
 SVJ  N   C    single  1.449  0.020  1.449
 SVJ  N   C4   single  1.464  0.020  1.464
 SVJ  C2  C3   single  1.540  0.020  1.540
 SVJ  C5  C4   single  1.527  0.020  1.527
 SVJ  C4  C3   single  1.545  0.020  1.545
 SVJ  N1  H1   single  0.890  0.020  1.040
 SVJ  N1  H2   single  0.890  0.020  1.040
 SVJ  C4  H4   single  0.970  0.020  1.090
 SVJ  C5  H5   single  0.970  0.020  1.090
 SVJ  C5  H6   single  0.970  0.020  1.090
 SVJ  C6  H7   single  0.970  0.020  1.090
 SVJ  C7  H8   single  0.970  0.020  1.090
 SVJ  C7  H9   single  0.970  0.020  1.090
 SVJ  C   H11  single  0.970  0.020  1.090
 SVJ  C   H12  single  0.970  0.020  1.090
 SVJ  C   H13  single  0.970  0.020  1.090
 SVJ  C1  H14  single  0.970  0.020  1.090
 SVJ  C2  H15  single  0.970  0.020  1.090
 SVJ  C2  H16  single  0.970  0.020  1.090
 SVJ  C3  H17  single  0.970  0.020  1.090
 SVJ  C3  H18  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
 SVJ  H2   N1  H1   105.58  3.000
 SVJ  H2   N1  C6   109.07  3.000
 SVJ  H1   N1  C6   109.06  3.000
 SVJ  H4   C4  C3   112.19  3.000
 SVJ  H4   C4  N    110.03  3.000
 SVJ  C3   C4  N    105.09  3.000
 SVJ  H4   C4  C5   108.70  3.000
 SVJ  C3   C4  C5   113.14  3.000
 SVJ  N    C4  C5   107.52  3.000
 SVJ  H6   C5  H5   106.46  3.000
 SVJ  H6   C5  C6   109.70  3.000
 SVJ  H5   C5  C6   108.88  3.000
 SVJ  H6   C5  C4   110.13  3.000
 SVJ  H5   C5  C4   107.73  3.000
 SVJ  C6   C5  C4   113.66  3.000
 SVJ  H7   C6  C7   107.10  3.000
 SVJ  H7   C6  C5   107.21  3.000
 SVJ  C7   C6  C5   111.01  3.000
 SVJ  H7   C6  N1   110.88  3.000
 SVJ  C5   C6  N1   110.28  3.000
 SVJ  C7   C6  N1   110.28  3.000
 SVJ  H9   C7  H8   106.42  3.000
 SVJ  H9   C7  C1   110.38  3.000
 SVJ  H8   C7  C1   107.59  3.000
 SVJ  H9   C7  C6   109.68  3.000
 SVJ  H8   C7  C6   108.78  3.000
 SVJ  C1   C7  C6   113.70  3.000
 SVJ  C1   N   C    112.93  3.000
 SVJ  C    N   C4   113.19  3.000
 SVJ  C1   N   C4   101.32  3.000
 SVJ  H13  C   H12  107.29  3.000
 SVJ  H13  C   H11  107.56  3.000
 SVJ  H12  C   H11  107.46  3.000
 SVJ  H13  C   N    109.53  3.000
 SVJ  H12  C   N    115.09  3.000
 SVJ  H11  C   N    109.64  3.000
 SVJ  H14  C1  C2   112.13  3.000
 SVJ  H14  C1  N    110.02  3.000
 SVJ  C2   C1  N    105.04  3.000
 SVJ  H14  C1  C7   108.81  3.000
 SVJ  C2   C1  C7   113.24  3.000
 SVJ  N    C1  C7   107.42  3.000
 SVJ  H16  C2  H15  107.62  3.000
 SVJ  H16  C2  C3   111.09  3.000
 SVJ  H15  C2  C3   112.39  3.000
 SVJ  H16  C2  C1   110.38  3.000
 SVJ  H15  C2  C1   111.84  3.000
 SVJ  C3   C2  C1   103.55  3.000
 SVJ  H18  C3  H17  107.53  3.000
 SVJ  H18  C3  C2   111.23  3.000
 SVJ  H17  C3  C2   112.32  3.000
 SVJ  H18  C3  C4   110.33  3.000
 SVJ  H17  C3  C4   111.94  3.000
 SVJ  C2   C3  C4   103.53  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
 SVJ  Var_01  C1   C2  C3  C4   -0.07  30.0  3
 SVJ  Var_02  H11  C   N   C4  -63.30  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
 SVJ  chir_01  C4  N   C5  C3  negativ
 SVJ  chir_02  C6  N1  C7  C5  positiv
 SVJ  chir_03  C1  N   C7  C2  positiv

