# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:53:15 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCC[NH+]2CC[C@@H](C[C@]12C)C(C)=C
#
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
 JF1  JF1  (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium  ligand  41  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JF1
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
 JF1  CAJ  C  CH2   0  -0.429   0.7377   0.7185   0.1311
 JF1  CAO  C  CT    0   0.078  -0.6788   0.3280  -0.3055
 JF1  CAD  C  CH3   0  -0.698  -0.8272   0.3995  -1.8200
 JF1  CAM  C  CH1   0  -0.236  -1.7262   1.2008   0.4260
 JF1  CAC  C  CH3   0  -0.670  -1.6176   2.6780   0.0613
 JF1  CAF  C  CH2   0  -0.433  -3.1530   0.7044   0.1981
 JF1  CAE  C  CH2   0  -0.468  -3.3104  -0.7559   0.5888
 JF1  CAH  C  CH2   0  -0.311  -2.2789  -1.6270  -0.0923
 JF1  NAN  N  NT1   1  -0.544  -0.9037  -1.1098   0.1770
 JF1  CAI  C  CH2   0  -0.315   0.1300  -2.0782  -0.2981
 JF1  CAG  C  CH2   0  -0.454   1.5168  -1.6443   0.1214
 JF1  CAL  C  CH1   0  -0.343   1.8305  -0.2304  -0.3651
 JF1  CAK  C  C     0   0.209   3.2057   0.2294   0.0581
 JF1  CAB  C  C2    0  -0.597   4.1421   0.4753  -0.8559
 JF1  CAA  C  CH3   0  -0.739   3.4740   0.3995   1.5252
 JF1  H1   H  HCH2  0   0.276   0.9370   1.7255  -0.2361
 JF1  H2   H  HCH2  0   0.255   0.7636   0.7764   1.2250
 JF1  H3   H  HCH3  0   0.264  -0.1783  -0.2969  -2.3469
 JF1  H4   H  HCH3  0   0.264  -1.8461   0.2279  -2.1616
 JF1  H5   H  HCH3  0   0.272  -0.5402   1.3967  -2.1496
 JF1  H6   H  HCH1  0   0.247  -1.5116   1.1101   1.5000
 JF1  H7   H  HCH3  0   0.232  -1.8486   2.8514  -0.9901
 JF1  H8   H  HCH3  0   0.248  -2.3378   3.2466   0.6496
 JF1  H9   H  HCH3  0   0.245  -0.6327   3.0945   0.2676
 JF1  H10  H  HCH2  0   0.258  -3.8347   1.3162   0.7914
 JF1  H11  H  HCH2  0   0.235  -3.4434   0.8488  -0.8466
 JF1  H12  H  HCH2  0   0.249  -3.2154  -0.8678   1.6730
 JF1  H13  H  HCH2  0   0.273  -4.2996  -1.1293   0.3213
 JF1  H14  H  HCH2  0   0.302  -2.3082  -2.6478   0.2850
 JF1  H15  H  HCH2  0   0.292  -2.4129  -1.6663  -1.1719
 JF1  H16  H  HNT1  0   0.448  -0.8098  -1.0787   1.1966
 JF1  H17  H  HCH2  0   0.307  -0.1272  -3.0410   0.1398
 JF1  H18  H  HCH2  0   0.292   0.0325  -2.1680  -1.3788
 JF1  H19  H  HCH2  0   0.251   1.5931  -1.7009   1.2113
 JF1  H20  H  HCH2  0   0.277   2.2307  -2.3625  -0.2845
 JF1  H21  H  HCH1  0   0.259   1.8167  -0.2383  -1.4593
 JF1  H22  H  H     0   0.233   5.1368   0.8019  -0.5778
 JF1  H23  H  H     0   0.234   3.9459   0.3612  -1.9154
 JF1  H24  H  HCH3  0   0.242   3.2690  -0.5144   2.0865
 JF1  H25  H  HCH3  0   0.249   4.5116   0.6755   1.7067
 JF1  H26  H  HCH3  0   0.244   2.8447   1.1790   1.9602

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
 JF1  CAC  CAM  single  1.525  0.020  1.525
 JF1  CAF  CAM  single  1.528  0.020  1.528
 JF1  CAF  CAE  single  1.520  0.020  1.520
 JF1  CAM  CAO  single  1.547  0.020  1.547
 JF1  CAE  CAH  single  1.512  0.020  1.512
 JF1  CAO  CAD  single  1.524  0.020  1.524
 JF1  CAO  CAJ  single  1.533  0.020  1.533
 JF1  CAO  NAN  single  1.533  0.020  1.533
 JF1  CAH  NAN  single  1.494  0.020  1.494
 JF1  CAJ  CAL  single  1.530  0.020  1.530
 JF1  NAN  CAI  single  1.494  0.020  1.494
 JF1  CAB  CAK  double  1.331  0.020  1.331
 JF1  CAL  CAK  single  1.510  0.020  1.510
 JF1  CAL  CAG  single  1.528  0.020  1.528
 JF1  CAI  CAG  single  1.512  0.020  1.512
 JF1  CAK  CAA  single  1.501  0.020  1.501
 JF1  CAJ  H1   single  0.970  0.020  1.090
 JF1  CAJ  H2   single  0.970  0.020  1.090
 JF1  CAD  H3   single  0.970  0.020  1.090
 JF1  CAD  H4   single  0.970  0.020  1.090
 JF1  CAD  H5   single  0.970  0.020  1.090
 JF1  CAM  H6   single  0.970  0.020  1.090
 JF1  CAC  H7   single  0.970  0.020  1.090
 JF1  CAC  H8   single  0.970  0.020  1.090
 JF1  CAC  H9   single  0.970  0.020  1.090
 JF1  CAF  H10  single  0.970  0.020  1.090
 JF1  CAF  H11  single  0.970  0.020  1.090
 JF1  CAE  H12  single  0.970  0.020  1.090
 JF1  CAE  H13  single  0.970  0.020  1.090
 JF1  CAH  H14  single  0.970  0.020  1.090
 JF1  CAH  H15  single  0.970  0.020  1.090
 JF1  NAN  H16  single  0.890  0.020  1.040
 JF1  CAI  H17  single  0.970  0.020  1.090
 JF1  CAI  H18  single  0.970  0.020  1.090
 JF1  CAG  H19  single  0.970  0.020  1.090
 JF1  CAG  H20  single  0.970  0.020  1.090
 JF1  CAL  H21  single  0.970  0.020  1.090
 JF1  CAB  H22  single  0.930  0.020  1.080
 JF1  CAB  H23  single  0.930  0.020  1.080
 JF1  CAA  H24  single  0.970  0.020  1.090
 JF1  CAA  H25  single  0.970  0.020  1.090
 JF1  CAA  H26  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
 JF1  H2   CAJ  H1   106.44  3.000
 JF1  H2   CAJ  CAL  109.86  3.000
 JF1  H1   CAJ  CAL  109.45  3.000
 JF1  H2   CAJ  CAO  108.64  3.000
 JF1  H1   CAJ  CAO  107.96  3.000
 JF1  CAL  CAJ  CAO  114.19  3.000
 JF1  NAN  CAO  CAM  106.32  3.000
 JF1  NAN  CAO  CAD  110.03  3.000
 JF1  CAM  CAO  CAD  112.18  3.000
 JF1  NAN  CAO  CAJ  106.55  3.000
 JF1  CAD  CAO  CAJ  111.17  3.000
 JF1  CAM  CAO  CAJ  110.31  3.000
 JF1  H5   CAD  H4   107.23  3.000
 JF1  H5   CAD  H3   106.40  3.000
 JF1  H4   CAD  H3   107.79  3.000
 JF1  H5   CAD  CAO  108.55  3.000
 JF1  H4   CAD  CAO  113.32  3.000
 JF1  H3   CAD  CAO  113.16  3.000
 JF1  H6   CAM  CAF  107.54  3.000
 JF1  H6   CAM  CAC  107.44  3.000
 JF1  CAF  CAM  CAC  110.21  3.000
 JF1  H6   CAM  CAO  106.46  3.000
 JF1  CAF  CAM  CAO  112.23  3.000
 JF1  CAC  CAM  CAO  112.65  3.000
 JF1  H9   CAC  H8   107.21  3.000
 JF1  H9   CAC  H7   108.27  3.000
 JF1  H8   CAC  H7   107.31  3.000
 JF1  H9   CAC  CAM  112.91  3.000
 JF1  H8   CAC  CAM  109.21  3.000
 JF1  H7   CAC  CAM  111.69  3.000
 JF1  H11  CAF  H10  106.22  3.000
 JF1  H11  CAF  CAE  110.17  3.000
 JF1  H10  CAF  CAE  109.53  3.000
 JF1  H11  CAF  CAM  110.34  3.000
 JF1  H10  CAF  CAM  108.67  3.000
 JF1  CAE  CAF  CAM  111.75  3.000
 JF1  H13  CAE  H12  106.66  3.000
 JF1  H13  CAE  CAH  108.12  3.000
 JF1  H12  CAE  CAH  109.16  3.000
 JF1  H13  CAE  CAF  111.09  3.000
 JF1  H12  CAE  CAF  110.12  3.000
 JF1  CAH  CAE  CAF  111.54  3.000
 JF1  H15  CAH  H14  107.85  3.000
 JF1  H15  CAH  NAN  107.74  3.000
 JF1  H14  CAH  NAN  106.68  3.000
 JF1  H15  CAH  CAE  112.55  3.000
 JF1  H14  CAH  CAE  111.45  3.000
 JF1  NAN  CAH  CAE  110.33  3.000
 JF1  H16  NAN  CAI  105.83  3.000
 JF1  H16  NAN  CAH  105.92  3.000
 JF1  CAI  NAN  CAH  110.81  3.000
 JF1  H16  NAN  CAO  105.74  3.000
 JF1  CAI  NAN  CAO  113.97  3.000
 JF1  CAH  NAN  CAO  113.77  3.000
 JF1  H18  CAI  H17  107.76  3.000
 JF1  H18  CAI  CAG  112.40  3.000
 JF1  H17  CAI  CAG  111.03  3.000
 JF1  H18  CAI  NAN  107.89  3.000
 JF1  H17  CAI  NAN  106.37  3.000
 JF1  CAG  CAI  NAN  111.12  3.000
 JF1  H20  CAG  H19  106.92  3.000
 JF1  H20  CAG  CAL  110.88  3.000
 JF1  H19  CAG  CAL  110.53  3.000
 JF1  H20  CAG  CAI  107.94  3.000
 JF1  H19  CAG  CAI  108.99  3.000
 JF1  CAL  CAG  CAI  111.43  3.000
 JF1  H21  CAL  CAK  107.09  3.000
 JF1  H21  CAL  CAG  108.00  3.000
 JF1  CAK  CAL  CAG  112.30  3.000
 JF1  H21  CAL  CAJ  108.65  3.000
 JF1  CAG  CAL  CAJ  108.90  3.000
 JF1  CAK  CAL  CAJ  111.75  3.000
 JF1  CAA  CAK  CAB  121.62  3.000
 JF1  CAA  CAK  CAL  118.10  3.000
 JF1  CAB  CAK  CAL  120.27  3.000
 JF1  H23  CAB  H22  116.68  3.000
 JF1  H23  CAB  CAK  121.63  3.000
 JF1  H22  CAB  CAK  121.69  3.000
 JF1  H26  CAA  H25  107.56  3.000
 JF1  H26  CAA  H24  106.52  3.000
 JF1  H25  CAA  H24  107.78  3.000
 JF1  H26  CAA  CAK  111.54  3.000
 JF1  H25  CAA  CAK  111.22  3.000
 JF1  H24  CAA  CAK  111.96  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
 JF1  Var_01  CAH  CAE  CAF  CAM   -53.10  30.0  1
 JF1  Var_02  NAN  CAH  CAE  CAF    54.28  30.0  1
 JF1  Var_03  CAL  CAG  CAI  NAN   -55.79  30.0  1
 JF1  Var_04  H22  CAB  CAK  CAL  -179.74   0.0  2
 JF1  Var_05  H24  CAA  CAK  CAL    55.97  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
 JF1  chir_01  CAO  CAM  CAJ  NAN  negativ
 JF1  chir_02  CAM  CAO  CAF  CAC  positiv
 JF1  chir_03  NAN  CAI  CAH  CAO  positiv
 JF1  chir_04  CAL  CAJ  CAK  CAG  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
 JF1  plan-1  CAL  0.020
 JF1  plan-1  CAK  0.020
 JF1  plan-1  CAB  0.020
 JF1  plan-1  CAA  0.020
 JF1  plan-1  H22  0.020
 JF1  plan-1  H23  0.020

