# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 20:58:50 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (5Z)-7-{(1R,4S,5R,6R)-6-[(1E)-oct-1-en-1-yl]-2,3-diazabicyclo[2.2.1]hept-2-en-5-yl}hept-5-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC\C=C\[C@H]1[C@H]2C[C@H](N=N2)[C@@H]1C\C=C/CCCC(O)=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
 U51  U51  '(5Z)-7-{(1R,4S,5R,6R)-6-[(1E)-oct-1-en-1-yl]-2,3-diazabicyclo[2.2.1]hept-2-en-5-yl}hept-5-enoic acid'  ligand  56  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U51
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
 U51  OAW  O  O     0  -0.445  -5.6572  -3.4385   1.0065
 U51  CAV  C  C     0   0.549  -4.8260  -3.7175   0.1784
 U51  OAX  O  OH1   0  -0.598  -4.4928  -4.9713  -0.1171
 U51  CAR  C  CH2   0  -0.580  -4.0464  -2.7239  -0.6373
 U51  CAQ  C  CH2   0  -0.417  -4.3861  -1.2762  -0.3218
 U51  CAP  C  CH2   0  -0.494  -3.5542  -0.3068  -1.1630
 U51  CAO  C  C1    0  -0.213  -3.9281   1.1189  -0.8981
 U51  CAN  C  C1    0  -0.211  -3.2245   2.0098  -0.2012
 U51  CAF  C  CH2   0  -0.501  -1.8930   1.7834   0.4468
 U51  CAD  C  CH1   0  -0.223  -0.7364   2.3972  -0.3389
 U51  CAC  C  CH1   0  -0.190  -0.7975   3.9294  -0.5744
 U51  CAB  C  CH2   0  -0.445   0.6391   4.2309  -0.9795
 U51  NAT  N  N     0  -0.164  -0.8442   4.5231   0.7768
 U51  NAS  N  N     0  -0.162   0.2662   4.3936   1.3011
 U51  CAA  C  CH1   0  -0.183   1.1616   3.7024   0.3488
 U51  CAE  C  CH1   0  -0.312   0.6413   2.2360   0.3657
 U51  CAG  C  C1    0  -0.179   1.5591   1.2814  -0.3244
 U51  CAH  C  C1    0  -0.209   2.0122   0.1554   0.2194
 U51  CAI  C  CH2   0  -0.483   2.9336  -0.8120  -0.4516
 U51  CAJ  C  CH2   0  -0.415   4.2262  -1.0267   0.3364
 U51  CAK  C  CH2   0  -0.413   5.1862  -1.9908  -0.3489
 U51  CAL  C  CH2   0  -0.407   6.4598  -2.2331   0.4513
 U51  CAM  C  CH2   0  -0.419   7.4524  -3.1491  -0.2544
 U51  CAU  C  CH3   0  -0.662   8.7132  -3.3924   0.5638
 U51  H1   H  HOH1  0   0.478  -5.0072  -5.5863   0.4271
 U51  H2   H  HCH2  0   0.277  -2.9802  -2.9114  -0.4749
 U51  H3   H  HCH2  0   0.278  -4.2228  -2.9382  -1.6963
 U51  H4   H  HCH2  0   0.233  -5.4489  -1.0959  -0.5005
 U51  H5   H  HCH2  0   0.233  -4.2063  -1.0734   0.7363
 U51  H6   H  HCH2  0   0.231  -2.4920  -0.4752  -0.9716
 U51  H7   H  HCH2  0   0.237  -3.7133  -0.5244  -2.2241
 U51  H8   H  H     0   0.234  -4.8862   1.4329  -1.3029
 U51  H10  H  H     0   0.234  -3.6356   3.0095  -0.0927
 U51  H12  H  HCH2  0   0.242  -1.9094   2.1988   1.4586
 U51  H13  H  HCH2  0   0.246  -1.6894   0.7166   0.5643
 U51  H14  H  HCH1  0   0.266  -0.7063   1.9250  -1.3248
 U51  H15  H  HCH1  0   0.262  -1.6122   4.2811  -1.2026
 U51  H16  H  HCH2  0   0.263   0.9748   3.6661  -1.8483
 U51  H17  H  HCH2  0   0.269   0.8409   5.2913  -1.1378
 U51  H20  H  HCH1  0   0.263   2.2087   3.8352   0.6085
 U51  H21  H  HCH1  0   0.265   0.5061   1.9047   1.4002
 U51  H22  H  H     0   0.238   1.8519   1.5333  -1.3423
 U51  H23  H  H     0   0.232   1.7124  -0.0923   1.2364
 U51  H24  H  HCH2  0   0.228   2.4294  -1.7783  -0.5665
 U51  H25  H  HCH2  0   0.228   3.1677  -0.4620  -1.4613
 U51  H26  H  HCH2  0   0.216   4.7240  -0.0631   0.4848
 U51  H27  H  HCH2  0   0.214   3.9827  -1.4015   1.3363
 U51  H28  H  HCH2  0   0.209   4.6802  -2.9463  -0.5267
 U51  H29  H  HCH2  0   0.209   5.4461  -1.5970  -1.3377
 U51  H30  H  HCH2  0   0.206   6.9440  -1.2733   0.6641
 U51  H31  H  HCH2  0   0.207   6.2008  -2.6628   1.4254
 U51  H32  H  HCH2  0   0.210   6.9681  -4.1048  -0.4778
 U51  H33  H  HCH2  0   0.210   7.7195  -2.7118  -1.2214
 U51  H34  H  HCH3  0   0.226   9.4176  -4.0381   0.0379
 U51  H35  H  HCH3  0   0.215   9.2256  -2.4537   0.7841
 U51  H36  H  HCH3  0   0.216   8.4776  -3.8685   1.5176

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
 U51  CAU  CAM  single  1.523  0.020  1.523
 U51  CAM  CAL  single  1.524  0.020  1.524
 U51  CAL  CAK  single  1.524  0.020  1.524
 U51  CAK  CAJ  single  1.523  0.020  1.523
 U51  CAJ  CAI  single  1.529  0.020  1.529
 U51  OAW  CAV  double  1.206  0.020  1.206
 U51  CAI  CAH  single  1.495  0.020  1.495
 U51  CAQ  CAP  single  1.530  0.020  1.530
 U51  CAQ  CAR  single  1.520  0.020  1.520
 U51  CAP  CAO  single  1.498  0.020  1.498
 U51  CAV  CAR  single  1.503  0.020  1.503
 U51  CAV  OAX  single  1.330  0.020  1.330
 U51  CAH  CAG  double  1.330  0.020  1.330
 U51  CAG  CAE  single  1.493  0.020  1.493
 U51  CAO  CAN  double  1.332  0.020  1.332
 U51  CAD  CAE  single  1.556  0.020  1.556
 U51  CAD  CAF  single  1.527  0.020  1.527
 U51  CAD  CAC  single  1.551  0.020  1.551
 U51  CAB  CAC  single  1.523  0.020  1.523
 U51  CAB  CAA  single  1.522  0.020  1.522
 U51  CAE  CAA  single  1.556  0.020  1.556
 U51  CAN  CAF  single  1.498  0.020  1.498
 U51  CAC  NAT  single  1.477  0.020  1.477
 U51  CAA  NAS  single  1.479  0.020  1.479
 U51  NAT  NAS  double  1.235  0.020  1.235
 U51  OAX  H1   single  0.850  0.020  0.980
 U51  CAR  H2   single  0.970  0.020  1.090
 U51  CAR  H3   single  0.970  0.020  1.090
 U51  CAQ  H4   single  0.970  0.020  1.090
 U51  CAQ  H5   single  0.970  0.020  1.090
 U51  CAP  H6   single  0.970  0.020  1.090
 U51  CAP  H7   single  0.970  0.020  1.090
 U51  CAO  H8   single  0.930  0.020  1.080
 U51  CAN  H10  single  0.930  0.020  1.080
 U51  CAF  H12  single  0.970  0.020  1.090
 U51  CAF  H13  single  0.970  0.020  1.090
 U51  CAD  H14  single  0.970  0.020  1.090
 U51  CAC  H15  single  0.970  0.020  1.090
 U51  CAB  H16  single  0.970  0.020  1.090
 U51  CAB  H17  single  0.970  0.020  1.090
 U51  CAA  H20  single  0.970  0.020  1.090
 U51  CAE  H21  single  0.970  0.020  1.090
 U51  CAG  H22  single  0.930  0.020  1.080
 U51  CAH  H23  single  0.930  0.020  1.080
 U51  CAI  H24  single  0.970  0.020  1.090
 U51  CAI  H25  single  0.970  0.020  1.090
 U51  CAJ  H26  single  0.970  0.020  1.090
 U51  CAJ  H27  single  0.970  0.020  1.090
 U51  CAK  H28  single  0.970  0.020  1.090
 U51  CAK  H29  single  0.970  0.020  1.090
 U51  CAL  H30  single  0.970  0.020  1.090
 U51  CAL  H31  single  0.970  0.020  1.090
 U51  CAM  H32  single  0.970  0.020  1.090
 U51  CAM  H33  single  0.970  0.020  1.090
 U51  CAU  H34  single  0.970  0.020  1.090
 U51  CAU  H35  single  0.970  0.020  1.090
 U51  CAU  H36  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
 U51  CAR  CAV  OAX  111.87  3.000
 U51  OAX  CAV  OAW  122.90  3.000
 U51  CAR  CAV  OAW  125.24  3.000
 U51  H1   OAX  CAV  109.91  3.000
 U51  H3   CAR  H2   105.48  3.000
 U51  H3   CAR  CAQ  110.56  3.000
 U51  H2   CAR  CAQ  110.49  3.000
 U51  H3   CAR  CAV  108.17  3.000
 U51  H2   CAR  CAV  108.13  3.000
 U51  CAQ  CAR  CAV  113.64  3.000
 U51  H5   CAQ  H4   106.73  3.000
 U51  H5   CAQ  CAP  109.00  3.000
 U51  H4   CAQ  CAP  109.54  3.000
 U51  H5   CAQ  CAR  109.95  3.000
 U51  H4   CAQ  CAR  109.91  3.000
 U51  CAP  CAQ  CAR  111.59  3.000
 U51  H7   CAP  H6   106.29  3.000
 U51  H7   CAP  CAO  108.93  3.000
 U51  H6   CAP  CAO  111.01  3.000
 U51  H7   CAP  CAQ  109.15  3.000
 U51  H6   CAP  CAQ  109.56  3.000
 U51  CAO  CAP  CAQ  111.74  3.000
 U51  H8   CAO  CAN  117.87  3.000
 U51  H8   CAO  CAP  115.43  3.000
 U51  CAN  CAO  CAP  126.68  3.000
 U51  H10  CAN  CAF  115.61  3.000
 U51  H10  CAN  CAO  117.89  3.000
 U51  CAF  CAN  CAO  126.50  3.000
 U51  H13  CAF  H12  105.92  3.000
 U51  H13  CAF  CAD  107.86  3.000
 U51  H12  CAF  CAD  109.55  3.000
 U51  H13  CAF  CAN  111.08  3.000
 U51  H12  CAF  CAN  109.23  3.000
 U51  CAD  CAF  CAN  112.95  3.000
 U51  H14  CAD  CAE  109.83  3.000
 U51  H14  CAD  CAC  106.90  3.000
 U51  CAE  CAD  CAC  101.88  3.000
 U51  H14  CAD  CAF  108.13  3.000
 U51  CAC  CAD  CAF  116.44  3.000
 U51  CAE  CAD  CAF  113.33  3.000
 U51  H15  CAC  NAT  112.02  3.000
 U51  H15  CAC  CAB  119.29  3.000
 U51  NAT  CAC  CAB  101.17  3.000
 U51  H15  CAC  CAD  115.90  3.000
 U51  NAT  CAC  CAD  105.03  3.000
 U51  CAB  CAC  CAD  101.47  3.000
 U51  H17  CAB  H16  109.34  3.000
 U51  H17  CAB  CAA  113.62  3.000
 U51  H16  CAB  CAA  114.22  3.000
 U51  H17  CAB  CAC  113.93  3.000
 U51  H16  CAB  CAC  113.59  3.000
 U51  CAA  CAB  CAC   91.32  3.000
 U51  NAS  NAT  CAC  108.53  3.000
 U51  CAA  NAS  NAT  108.67  3.000
 U51  H20  CAA  CAE  115.76  3.000
 U51  H20  CAA  NAS  111.86  3.000
 U51  CAE  CAA  NAS  103.36  3.000
 U51  H20  CAA  CAB  119.79  3.000
 U51  NAS  CAA  CAB  101.06  3.000
 U51  CAE  CAA  CAB  102.82  3.000
 U51  H21  CAE  CAG  108.61  3.000
 U51  H21  CAE  CAA  109.69  3.000
 U51  CAG  CAE  CAA  113.07  3.000
 U51  H21  CAE  CAD  110.49  3.000
 U51  CAA  CAE  CAD  101.16  3.000
 U51  CAG  CAE  CAD  113.65  3.000
 U51  H22  CAG  CAH  119.11  3.000
 U51  H22  CAG  CAE  116.71  3.000
 U51  CAH  CAG  CAE  124.17  3.000
 U51  H23  CAH  CAI  116.22  3.000
 U51  H23  CAH  CAG  118.73  3.000
 U51  CAI  CAH  CAG  125.05  3.000
 U51  H25  CAI  H24  106.48  3.000
 U51  H25  CAI  CAJ  109.86  3.000
 U51  H24  CAI  CAJ  108.61  3.000
 U51  H25  CAI  CAH  109.83  3.000
 U51  H24  CAI  CAH  109.52  3.000
 U51  CAJ  CAI  CAH  112.37  3.000
 U51  H27  CAJ  H26  106.18  3.000
 U51  H27  CAJ  CAK  109.53  3.000
 U51  H26  CAJ  CAK  109.36  3.000
 U51  H27  CAJ  CAI  109.30  3.000
 U51  H26  CAJ  CAI  109.31  3.000
 U51  CAK  CAJ  CAI  112.94  3.000
 U51  H29  CAK  H28  106.05  3.000
 U51  H29  CAK  CAL  109.44  3.000
 U51  H28  CAK  CAL  109.43  3.000
 U51  H29  CAK  CAJ  109.15  3.000
 U51  H28  CAK  CAJ  109.51  3.000
 U51  CAL  CAK  CAJ  113.03  3.000
 U51  H31  CAL  H30  105.98  3.000
 U51  H31  CAL  CAM  109.27  3.000
 U51  H30  CAL  CAM  109.18  3.000
 U51  H31  CAL  CAK  109.37  3.000
 U51  H30  CAL  CAK  109.39  3.000
 U51  CAM  CAL  CAK  113.38  3.000
 U51  H33  CAM  H32  106.06  3.000
 U51  H33  CAM  CAU  109.67  3.000
 U51  H32  CAM  CAU  109.67  3.000
 U51  H33  CAM  CAL  109.15  3.000
 U51  H32  CAM  CAL  109.34  3.000
 U51  CAU  CAM  CAL  112.74  3.000
 U51  H36  CAU  H35  107.45  3.000
 U51  H36  CAU  H34  107.60  3.000
 U51  H35  CAU  H34  107.65  3.000
 U51  H36  CAU  CAM  111.13  3.000
 U51  H35  CAU  CAM  111.08  3.000
 U51  H34  CAU  CAM  111.73  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
 U51  CONST_01  H1   OAX  CAV  OAW     0.00   0.0  0
 U51  Var_01    CAI  CAH  CAG  CAE  -179.83   0.0  2
 U51  Var_02    CAD  CAF  CAN  CAO   103.10  30.0  3
 U51  Var_03    CAF  CAN  CAO  CAP     1.24   0.0  2
 U51  Var_04    CAQ  CAR  CAV  OAW     0.55  30.0  3
 U51  Var_05    CAP  CAQ  CAR  CAV   179.23  30.0  1
 U51  Var_06    CAO  CAP  CAQ  CAR   177.52  30.0  3
 U51  Var_07    CAN  CAO  CAP  CAQ   105.75  30.0  3
 U51  Var_08    CAJ  CAI  CAH  CAG   121.81  30.0  1
 U51  Var_09    CAK  CAJ  CAI  CAH  -178.93  30.0  1
 U51  Var_10    CAL  CAK  CAJ  CAI  -178.57  30.0  1
 U51  Var_11    CAM  CAL  CAK  CAJ  -177.51  30.0  1
 U51  Var_12    CAU  CAM  CAL  CAK  -179.42  30.0  1
 U51  Var_13    H34  CAU  CAM  CAL  -179.20  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
 U51  chir_01  CAD  CAE  CAF  CAC  negativ
 U51  chir_02  CAC  NAT  CAD  CAB  positiv
 U51  chir_03  CAA  NAS  CAE  CAB  negativ
 U51  chir_04  CAE  CAG  CAD  CAA  positiv

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
 U51  plan-1  OAW  0.020
 U51  plan-1  CAV  0.020
 U51  plan-1  OAX  0.020
 U51  plan-1  CAR  0.020
 U51  plan-1  H1   0.020
 U51  plan-2  CAE  0.020
 U51  plan-2  CAG  0.020
 U51  plan-2  CAH  0.020
 U51  plan-2  CAI  0.020
 U51  plan-2  H22  0.020
 U51  plan-2  H23  0.020
 U51  plan-3  CAP  0.020
 U51  plan-3  CAO  0.020
 U51  plan-3  CAN  0.020
 U51  plan-3  CAF  0.020
 U51  plan-3  H8   0.020
 U51  plan-3  H10  0.020

