# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:47:55 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (3R,5S,6R,9aR)-6,9a-dimethyl-3-(prop-1-en-2-yl)octahydro-2H-quinolizinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCC[C@]2(C)CC[C@@H](C[NH+]12)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
 JF4  JF4  (3R,5S,6R,9aR)-6,9a-dimethyl-3-(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 OK
;

data_comp_JF4
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
 JF4  CAA  C  C2    0  -0.589   4.0282  -0.5813   0.8635
 JF4  CAK  C  C     0   0.198   3.0491  -0.3173   0.0015
 JF4  CAB  C  CH3   0  -0.740   3.2233  -0.5014  -1.4776
 JF4  CAL  C  CH1   0  -0.351   1.7180   0.1955   0.4996
 JF4  CAG  C  CH2   0  -0.439   1.4030   1.6108   0.0267
 JF4  CAI  C  CH2   0  -0.434   0.0547   2.0420   0.5765
 JF4  CAO  C  CT    0   0.051  -1.1121   1.1124   0.2330
 JF4  CAD  C  CH3   0  -0.681  -2.3161   1.5502   1.0642
 JF4  NAN  N  NT1   1  -0.553  -0.7256  -0.3134   0.6368
 JF4  CAJ  C  CH2   0  -0.309   0.5971  -0.7504   0.0896
 JF4  CAH  C  CH2   0  -0.434  -1.4331   1.1136  -1.2624
 JF4  CAE  C  CH2   0  -0.453  -2.5097   0.1041  -1.6466
 JF4  CAF  C  CH2   0  -0.443  -2.1655  -1.2925  -1.1445
 JF4  CAM  C  CH1   0  -0.118  -1.8340  -1.3071   0.3389
 JF4  CAC  C  CH3   0  -0.692  -1.4984  -2.6895   0.8661
 JF4  H1   H  H     0   0.239   3.8959  -0.4530   1.9310
 JF4  H2   H  H     0   0.237   4.9969  -0.9340   0.5312
 JF4  H3   H  HCH3  0   0.244   2.5532  -1.2691  -1.8717
 JF4  H4   H  HCH3  0   0.245   3.0060   0.4151  -2.0296
 JF4  H5   H  HCH3  0   0.254   4.2414  -0.8026  -1.7188
 JF4  H6   H  HCH1  0   0.267   1.7579   0.2064   1.5953
 JF4  H7   H  HCH2  0   0.265   2.1733   2.2973   0.3817
 JF4  H8   H  HCH2  0   0.240   1.4149   1.6671  -1.0643
 JF4  H9   H  HCH2  0   0.255   0.1243   2.1288   1.6660
 JF4  H10  H  HCH2  0   0.271  -0.2094   3.0351   0.2081
 JF4  H11  H  HCH3  0   0.269  -2.4410   2.6252   0.9370
 JF4  H12  H  HCH3  0   0.260  -3.2522   1.0814   0.7710
 JF4  H13  H  HCH3  0   0.257  -2.1586   1.3643   2.1282
 JF4  H15  H  HCH2  0   0.287   0.5029  -0.8233  -0.9915
 JF4  H16  H  HCH2  0   0.317   0.7932  -1.7462   0.4801
 JF4  H17  H  HCH2  0   0.271  -1.7511   2.1256  -1.5201
 JF4  H18  H  HCH2  0   0.255  -0.5306   0.9236  -1.8481
 JF4  H19  H  HCH2  0   0.239  -3.4780   0.4089  -1.2443
 JF4  H20  H  HCH2  0   0.261  -2.6207   0.0897  -2.7313
 JF4  H21  H  HCH2  0   0.273  -3.0117  -1.9660  -1.2893
 JF4  H22  H  HCH2  0   0.248  -1.3402  -1.7183  -1.7214
 JF4  H23  H  HCH1  0   0.305  -2.6893  -0.9361   0.9038
 JF4  H24  H  HCH3  0   0.258  -1.1337  -2.6566   1.8935
 JF4  H25  H  HCH3  0   0.272  -2.4132  -3.2801   0.8642
 JF4  H26  H  HCH3  0   0.248  -0.7699  -3.2124   0.2482
 JF4  H14  H  HNT1  0   0.451  -0.6208  -0.3050   1.6546

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
 JF4  CAA  CAK  double  1.331  0.020  1.331
 JF4  CAB  CAK  single  1.501  0.020  1.501
 JF4  CAK  CAL  single  1.511  0.020  1.511
 JF4  CAG  CAL  single  1.525  0.020  1.525
 JF4  CAG  CAI  single  1.519  0.020  1.519
 JF4  CAL  CAJ  single  1.523  0.020  1.523
 JF4  CAI  CAO  single  1.531  0.020  1.531
 JF4  CAJ  NAN  single  1.497  0.020  1.497
 JF4  CAO  NAN  single  1.532  0.020  1.532
 JF4  CAO  CAH  single  1.529  0.020  1.529
 JF4  CAO  CAD  single  1.527  0.020  1.527
 JF4  NAN  CAM  single  1.518  0.020  1.518
 JF4  CAH  CAE  single  1.525  0.020  1.525
 JF4  CAM  CAC  single  1.517  0.020  1.517
 JF4  CAM  CAF  single  1.520  0.020  1.520
 JF4  CAE  CAF  single  1.523  0.020  1.523
 JF4  CAA  H1   single  0.930  0.020  1.080
 JF4  CAA  H2   single  0.930  0.020  1.080
 JF4  CAB  H3   single  0.970  0.020  1.090
 JF4  CAB  H4   single  0.970  0.020  1.090
 JF4  CAB  H5   single  0.970  0.020  1.090
 JF4  CAL  H6   single  0.970  0.020  1.090
 JF4  CAG  H7   single  0.970  0.020  1.090
 JF4  CAG  H8   single  0.970  0.020  1.090
 JF4  CAI  H9   single  0.970  0.020  1.090
 JF4  CAI  H10  single  0.970  0.020  1.090
 JF4  CAD  H11  single  0.970  0.020  1.090
 JF4  CAD  H12  single  0.970  0.020  1.090
 JF4  CAD  H13  single  0.970  0.020  1.090
 JF4  CAJ  H15  single  0.970  0.020  1.090
 JF4  CAJ  H16  single  0.970  0.020  1.090
 JF4  CAH  H17  single  0.970  0.020  1.090
 JF4  CAH  H18  single  0.970  0.020  1.090
 JF4  CAE  H19  single  0.970  0.020  1.090
 JF4  CAE  H20  single  0.970  0.020  1.090
 JF4  CAF  H21  single  0.970  0.020  1.090
 JF4  CAF  H22  single  0.970  0.020  1.090
 JF4  CAM  H23  single  0.970  0.020  1.090
 JF4  CAC  H24  single  0.970  0.020  1.090
 JF4  CAC  H25  single  0.970  0.020  1.090
 JF4  CAC  H26  single  0.970  0.020  1.090
 JF4  NAN  H14  single  0.890  0.020  1.040

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
 JF4  H2   CAA  H1   116.75  3.000
 JF4  H2   CAA  CAK  121.59  3.000
 JF4  H1   CAA  CAK  121.66  3.000
 JF4  CAL  CAK  CAB  117.96  3.000
 JF4  CAL  CAK  CAA  120.13  3.000
 JF4  CAB  CAK  CAA  121.91  3.000
 JF4  H5   CAB  H4   107.84  3.000
 JF4  H5   CAB  H3   107.41  3.000
 JF4  H4   CAB  H3   106.58  3.000
 JF4  H5   CAB  CAK  111.15  3.000
 JF4  H4   CAB  CAK  111.85  3.000
 JF4  H3   CAB  CAK  111.75  3.000
 JF4  H6   CAL  CAJ  107.58  3.000
 JF4  H6   CAL  CAG  107.95  3.000
 JF4  CAJ  CAL  CAG  109.93  3.000
 JF4  H6   CAL  CAK  107.50  3.000
 JF4  CAJ  CAL  CAK  110.42  3.000
 JF4  CAG  CAL  CAK  113.25  3.000
 JF4  H8   CAG  H7   106.55  3.000
 JF4  H8   CAG  CAI  110.89  3.000
 JF4  H7   CAG  CAI  109.29  3.000
 JF4  H8   CAG  CAL  110.81  3.000
 JF4  H7   CAG  CAL  109.70  3.000
 JF4  CAI  CAG  CAL  109.55  3.000
 JF4  H10  CAI  H9   106.19  3.000
 JF4  H10  CAI  CAO  107.00  3.000
 JF4  H9   CAI  CAO  108.65  3.000
 JF4  H10  CAI  CAG  110.54  3.000
 JF4  H9   CAI  CAG  109.04  3.000
 JF4  CAO  CAI  CAG  115.03  3.000
 JF4  CAH  CAO  NAN  108.15  3.000
 JF4  CAH  CAO  CAD  111.50  3.000
 JF4  NAN  CAO  CAD  108.80  3.000
 JF4  CAD  CAO  CAI  107.74  3.000
 JF4  CAH  CAO  CAI  112.26  3.000
 JF4  NAN  CAO  CAI  108.29  3.000
 JF4  H13  CAD  H12  108.28  3.000
 JF4  H13  CAD  H11  107.36  3.000
 JF4  H12  CAD  H11  107.17  3.000
 JF4  H13  CAD  CAO  111.59  3.000
 JF4  H12  CAD  CAO  114.10  3.000
 JF4  H11  CAD  CAO  108.04  3.000
 JF4  H14  NAN  CAM  105.98  3.000
 JF4  H14  NAN  CAJ  105.99  3.000
 JF4  CAM  NAN  CAJ  112.48  3.000
 JF4  H14  NAN  CAO  106.29  3.000
 JF4  CAM  NAN  CAO  111.92  3.000
 JF4  CAJ  NAN  CAO  113.48  3.000
 JF4  H16  CAJ  H15  108.13  3.000
 JF4  H16  CAJ  NAN  107.19  3.000
 JF4  H15  CAJ  NAN  107.85  3.000
 JF4  H16  CAJ  CAL  109.84  3.000
 JF4  H15  CAJ  CAL  111.90  3.000
 JF4  NAN  CAJ  CAL  111.76  3.000
 JF4  H18  CAH  H17  105.98  3.000
 JF4  H18  CAH  CAE  109.45  3.000
 JF4  H17  CAH  CAE  110.40  3.000
 JF4  H18  CAH  CAO  110.53  3.000
 JF4  H17  CAH  CAO  107.01  3.000
 JF4  CAE  CAH  CAO  113.20  3.000
 JF4  H20  CAE  H19  106.25  3.000
 JF4  H20  CAE  CAF  109.80  3.000
 JF4  H19  CAE  CAF  109.56  3.000
 JF4  H20  CAE  CAH  109.34  3.000
 JF4  H19  CAE  CAH  110.39  3.000
 JF4  CAF  CAE  CAH  111.37  3.000
 JF4  H22  CAF  H21  105.96  3.000
 JF4  H22  CAF  CAM  110.28  3.000
 JF4  H21  CAF  CAM  107.02  3.000
 JF4  H22  CAF  CAE  110.71  3.000
 JF4  H21  CAF  CAE  110.30  3.000
 JF4  CAM  CAF  CAE  112.32  3.000
 JF4  H23  CAM  CAC  107.67  3.000
 JF4  H23  CAM  CAF  109.35  3.000
 JF4  CAC  CAM  CAF  113.34  3.000
 JF4  H23  CAM  NAN  104.38  3.000
 JF4  CAF  CAM  NAN  110.15  3.000
 JF4  CAC  CAM  NAN  111.51  3.000
 JF4  H26  CAC  H25  107.49  3.000
 JF4  H26  CAC  H24  108.98  3.000
 JF4  H25  CAC  H24  107.39  3.000
 JF4  H26  CAC  CAM  112.85  3.000
 JF4  H25  CAC  CAM  107.93  3.000
 JF4  H24  CAC  CAM  111.95  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
 JF4  Var_01  CAO  CAI  CAG  CAL  -55.95  30.0  1
 JF4  Var_02  CAF  CAE  CAH  CAO  -53.11  30.0  1
 JF4  Var_03  CAM  CAF  CAE  CAH   51.89  30.0  1
 JF4  Var_04  H1   CAA  CAK  CAL    0.97   0.0  2
 JF4  Var_05  H3   CAB  CAK  CAL  -64.23  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
 JF4  chir_01  CAL  CAK  CAG  CAJ  negativ
 JF4  chir_02  CAO  NAN  CAH  CAI  positiv
 JF4  chir_03  NAN  CAM  CAO  CAJ  positiv
 JF4  chir_04  CAM  NAN  CAF  CAC  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
 JF4  plan-1  CAA  0.020
 JF4  plan-1  CAK  0.020
 JF4  plan-1  CAB  0.020
 JF4  plan-1  CAL  0.020
 JF4  plan-1  H1   0.020
 JF4  plan-1  H2   0.020

