# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:13:37 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: (5S)-2-[(1E)-N-{[(2E)-3-chloroprop-2-en-1-yl]oxy}propanimidoyl]-3-hydroxy-5-(tetrahydro-2H-pyran-4-yl)cyclohex-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C(=N/OC/C=C/Cl)C1=C(O)C[C@@H](CC1=O)C2CCOCC2
#
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
 B89  B89  (5S)-2-[(1E)-N-{[(2E)-3-chloroprop-2-en-1-yl]oxy}propanimidoyl]-3-hydroxy-5-(tetrahydro-2H-pyran-4-yl)cyclohex-2-en-1-one  ligand  47  23  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B89
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
 B89  CAA   C   CH3   0  -0.662   1.9637  -2.9950  -0.7246
 B89  OAC   O   OH1   0  -0.583   0.0177   0.2820   1.8696
 B89  CLAD  CL  CL    0  -0.108   8.1359   0.0593   0.9797
 B89  CAE   C   C1    0  -0.290   6.5378   0.6743   0.7476
 B89  CAF   C   C1    0  -0.200   5.4606   0.0542   1.2017
 B89  CAG   C   CH2   0  -0.528   1.8351  -1.6602  -1.4645
 B89  CAH   C   CH2   0  -0.189   4.0984   0.6336   1.0236
 B89  CAI   C   C     0  -0.176  -6.8604   0.3094  -0.7346
 B89  CAJ   C   C     0  -0.176  -6.4838   0.9808   1.4649
 B89  CAK   C   C     0  -0.456  -5.3804   0.3419  -1.0794
 B89  CAL   C   C     0  -0.458  -4.9785   1.0549   1.2658
 B89  CAM   C   CH2   0  -0.563  -2.5507  -0.7020  -1.2321
 B89  CAN   C   CH2   0  -0.538  -2.1757   0.0021   1.1061
 B89  NAO   N   N     0  -0.227   2.0223   0.0351   0.2878
 B89  OAP   O   O     0  -0.484  -7.1961   1.2351   0.2747
 B89  OAQ   O   O2    0  -0.391   3.3480  -0.2875   0.2437
 B89  CAR   C   C     0   0.368  -1.0755  -0.5738  -1.5223
 B89  CAS   C   C     0   0.418  -0.7086  -0.0399   0.8263
 B89  CAT   C   C     0   0.331   1.2843  -0.6076  -0.5416
 B89  CAU   C   C     0  -0.292  -0.1709  -0.4095  -0.3864
 B89  CAV   C   CR16  0  -0.221  -4.5173   0.1009   0.1613
 B89  CAW   C   CH1   0  -0.258  -3.0211   0.2465  -0.1367
 B89  HAA   H   HCH3  0   0.232   2.6478  -2.9271   0.1201
 B89  HAAA  H   HCH3  0   0.230   0.9969  -3.3338  -0.3511
 B89  HAAB  H   HCH3  0   0.240   2.3433  -3.7592  -1.4025
 B89  HOAC  H   HOH1  0   0.473   0.9716   0.2997   1.5908
 B89  HAE   H   H     0   0.312   6.5103   1.6101   0.2040
 B89  HAF   H   H     0   0.286   5.5426  -0.8841   1.7392
 B89  HAG   H   HCH2  0   0.257   2.8098  -1.3512  -1.8420
 B89  HAGA  H   HCH2  0   0.269   1.1864  -1.7822  -2.3239
 B89  HAH   H   HCH2  0   0.239   3.6218   0.7699   2.0002
 B89  HAHA  H   HCH2  0   0.236   4.1445   1.6113   0.5334
 B89  HAI   H   H     0   0.234  -7.4632   0.5573  -1.6100
 B89  HAIA  H   H     0   0.194  -7.1362  -0.7089  -0.4211
 B89  HAJ   H   H     0   0.194  -6.7471  -0.0127   1.8591
 B89  HAJA  H   H     0   0.234  -6.8106   1.7200   2.1985
 B89  HAK   H   H     0   0.242  -5.1964  -0.4169  -1.8428
 B89  HAKA  H   H     0   0.222  -5.1238   1.3116  -1.5200
 B89  HAL   H   H     0   0.223  -4.6883   2.0796   1.0077
 B89  HALA  H   H     0   0.242  -4.5015   0.8177   2.2194
 B89  HAM   H   HCH2  0   0.268  -3.0885  -0.5395  -2.1656
 B89  HAMA  H   HCH2  0   0.262  -2.7432  -1.7371  -0.9204
 B89  HAN   H   HCH2  0   0.277  -2.4543  -0.9605   1.5545
 B89  HANA  H   HCH2  0   0.282  -2.3556   0.7650   1.8642
 B89  HAV   H   HCR6  0   0.220  -4.6942  -0.9293   0.5028
 B89  HAW   H   HCH1  0   0.244  -2.8447   1.2766  -0.4720
 B89  OAB   O   O     0  -0.432  -0.6762  -0.6061  -2.6761

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
 B89  CAA   CAG   single  1.532  0.020  1.532
 B89  OAB   CAR   double  1.221  0.020  1.221
 B89  OAC   CAS   single  1.311  0.020  1.311
 B89  CLAD  CAE   single  1.728  0.020  1.728
 B89  CAE   CAF   double  1.323  0.020  1.323
 B89  CAF   CAH   single  1.491  0.020  1.491
 B89  CAG   CAT   single  1.504  0.020  1.504
 B89  CAH   OAQ   single  1.421  0.020  1.421
 B89  CAI   CAK   single  1.520  0.020  1.520
 B89  CAI   OAP   single  1.410  0.020  1.410
 B89  CAJ   CAL   single  1.520  0.020  1.520
 B89  CAJ   OAP   single  1.410  0.020  1.410
 B89  CAK   CAV   single  1.530  0.020  1.530
 B89  CAL   CAV   single  1.531  0.020  1.531
 B89  CAM   CAR   single  1.509  0.020  1.509
 B89  CAM   CAW   single  1.523  0.020  1.523
 B89  CAN   CAS   single  1.494  0.020  1.494
 B89  CAN   CAW   single  1.523  0.020  1.523
 B89  NAO   OAQ   single  1.365  0.020  1.365
 B89  NAO   CAT   double  1.283  0.020  1.283
 B89  CAR   CAU   single  1.461  0.020  1.461
 B89  CAS   CAU   double  1.377  0.020  1.377
 B89  CAT   CAU   single  1.477  0.020  1.477
 B89  CAV   CAW   single  1.532  0.020  1.532
 B89  CAA   HAA   single  0.970  0.020  1.090
 B89  CAA   HAAA  single  0.970  0.020  1.090
 B89  CAA   HAAB  single  0.970  0.020  1.090
 B89  OAC   HOAC  single  0.850  0.020  0.980
 B89  CAE   HAE   single  0.930  0.020  1.080
 B89  CAF   HAF   single  0.930  0.020  1.080
 B89  CAG   HAG   single  0.970  0.020  1.090
 B89  CAG   HAGA  single  0.970  0.020  1.090
 B89  CAH   HAH   single  0.970  0.020  1.090
 B89  CAH   HAHA  single  0.970  0.020  1.090
 B89  CAI   HAI   single  0.970  0.020  1.090
 B89  CAI   HAIA  single  0.970  0.020  1.090
 B89  CAJ   HAJ   single  0.970  0.020  1.090
 B89  CAJ   HAJA  single  0.970  0.020  1.090
 B89  CAK   HAK   single  0.970  0.020  1.090
 B89  CAK   HAKA  single  0.970  0.020  1.090
 B89  CAL   HAL   single  0.970  0.020  1.090
 B89  CAL   HALA  single  0.970  0.020  1.090
 B89  CAM   HAM   single  0.970  0.020  1.090
 B89  CAM   HAMA  single  0.970  0.020  1.090
 B89  CAN   HAN   single  0.970  0.020  1.090
 B89  CAN   HANA  single  0.970  0.020  1.090
 B89  CAV   HAV   single  0.970  0.020  1.090
 B89  CAW   HAW   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
 B89  HAAB  CAA  HAAA  107.70  3.000
 B89  HAAB  CAA  HAA   107.90  3.000
 B89  HAAA  CAA  HAA   108.10  3.000
 B89  HAAB  CAA  CAG   109.88  3.000
 B89  HAAA  CAA  CAG   111.21  3.000
 B89  HAA   CAA  CAG   111.91  3.000
 B89  HOAC  OAC  CAS   108.23  3.000
 B89  HAE   CAE  CAF   123.83  3.000
 B89  HAE   CAE  CLAD  113.49  3.000
 B89  CAF   CAE  CLAD  122.68  3.000
 B89  HAF   CAF  CAH   117.68  3.000
 B89  HAF   CAF  CAE   120.93  3.000
 B89  CAH   CAF  CAE   121.37  3.000
 B89  HAGA  CAG  HAG   107.01  3.000
 B89  HAGA  CAG  CAT   110.25  3.000
 B89  HAG   CAG  CAT   109.97  3.000
 B89  HAGA  CAG  CAA   109.59  3.000
 B89  HAG   CAG  CAA   109.84  3.000
 B89  CAT   CAG  CAA   110.13  3.000
 B89  HAHA  CAH  HAH   107.84  3.000
 B89  HAHA  CAH  OAQ   110.81  3.000
 B89  HAH   CAH  OAQ   109.89  3.000
 B89  HAHA  CAH  CAF   111.23  3.000
 B89  HAH   CAH  CAF   109.84  3.000
 B89  OAQ   CAH  CAF   107.23  3.000
 B89  HAIA  CAI  HAI   107.47  3.000
 B89  HAIA  CAI  OAP   110.11  3.000
 B89  HAI   CAI  OAP   107.07  3.000
 B89  HAIA  CAI  CAK   109.17  3.000
 B89  HAI   CAI  CAK   110.55  3.000
 B89  OAP   CAI  CAK   112.35  3.000
 B89  HAJA  CAJ  HAJ   107.39  3.000
 B89  HAJA  CAJ  OAP   107.09  3.000
 B89  HAJ   CAJ  OAP   110.13  3.000
 B89  HAJA  CAJ  CAL   110.58  3.000
 B89  HAJ   CAJ  CAL   109.13  3.000
 B89  OAP   CAJ  CAL   112.39  3.000
 B89  HAKA  CAK  HAK   107.12  3.000
 B89  HAKA  CAK  CAV   109.46  3.000
 B89  HAK   CAK  CAV   111.24  3.000
 B89  HAKA  CAK  CAI   109.77  3.000
 B89  HAK   CAK  CAI   107.93  3.000
 B89  CAV   CAK  CAI   111.22  3.000
 B89  HALA  CAL  HAL   107.04  3.000
 B89  HALA  CAL  CAV   111.28  3.000
 B89  HAL   CAL  CAV   109.45  3.000
 B89  HALA  CAL  CAJ   107.91  3.000
 B89  HAL   CAL  CAJ   109.80  3.000
 B89  CAV   CAL  CAJ   111.25  3.000
 B89  HAMA  CAM  HAM   107.29  3.000
 B89  HAMA  CAM  CAW   109.19  3.000
 B89  HAM   CAM  CAW   111.76  3.000
 B89  HAMA  CAM  CAR   107.83  3.000
 B89  HAM   CAM  CAR   107.77  3.000
 B89  CAW   CAM  CAR   112.79  3.000
 B89  HANA  CAN  HAN   106.71  3.000
 B89  HANA  CAN  CAW   111.31  3.000
 B89  HAN   CAN  CAW   109.46  3.000
 B89  HANA  CAN  CAS   108.17  3.000
 B89  HAN   CAN  CAS   107.52  3.000
 B89  CAW   CAN  CAS   113.38  3.000
 B89  CAT   NAO  OAQ   114.80  3.000
 B89  CAJ   OAP  CAI   111.43  3.000
 B89  NAO   OAQ  CAH   109.99  3.000
 B89  CAU   CAR  CAM   117.73  3.000
 B89  CAU   CAR  OAB   122.33  3.000
 B89  CAM   CAR  OAB   119.94  3.000
 B89  CAU   CAS  CAN   123.77  3.000
 B89  CAU   CAS  OAC   123.38  3.000
 B89  CAN   CAS  OAC   112.83  3.000
 B89  CAU   CAT  NAO   115.58  3.000
 B89  CAU   CAT  CAG   121.28  3.000
 B89  NAO   CAT  CAG   122.45  3.000
 B89  CAT   CAU  CAS   120.89  3.000
 B89  CAT   CAU  CAR   120.88  3.000
 B89  CAS   CAU  CAR   118.23  3.000
 B89  HAV   CAV  CAW   107.85  3.000
 B89  HAV   CAV  CAL   108.14  3.000
 B89  CAW   CAV  CAL   112.04  3.000
 B89  HAV   CAV  CAK   107.97  3.000
 B89  CAW   CAV  CAK   112.21  3.000
 B89  CAL   CAV  CAK   108.47  3.000
 B89  HAW   CAW  CAV   107.79  3.000
 B89  HAW   CAW  CAN   108.10  3.000
 B89  CAV   CAW  CAN   111.60  3.000
 B89  HAW   CAW  CAM   108.36  3.000
 B89  CAV   CAW  CAM   112.47  3.000
 B89  CAN   CAW  CAM   108.39  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
 B89  Var_01  CAL  CAJ  OAP  CAI    59.51  30.0  1
 B89  Var_02  CAK  CAI  OAP  CAJ   -59.61  30.0  1
 B89  Var_03  CAS  CAU  CAR  CAM   -16.35  30.0  1
 B89  Var_04  CAR  CAU  CAS  CAN     9.67  30.0  1
 B89  Var_05  CAV  CAK  CAI  OAP    56.16  30.0  1
 B89  Var_06  CAV  CAL  CAJ  OAP   -55.95  30.0  1
 B89  Var_07  CAW  CAM  CAR  CAU    40.78  30.0  1
 B89  Var_08  CAW  CAN  CAS  CAU   -27.08  30.0  1
 B89  Var_09  CAU  CAT  NAO  OAQ   172.05   0.0  2
 B89  Var_10  CAH  CAF  CAE  CLAD  177.98   0.0  2
 B89  Var_11  OAQ  CAH  CAF  CAE   118.65  30.0  3
 B89  Var_12  HAA  CAA  CAG  CAT   -61.33  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
 B89  chir_01  CAV  CAK  CAL  CAW  positiv
 B89  chir_02  CAW  CAM  CAN  CAV  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
 B89  plan-1  CAM   0.020
 B89  plan-1  CAR   0.020
 B89  plan-1  CAU   0.020
 B89  plan-1  OAB   0.020
 B89  plan-2  CLAD  0.020
 B89  plan-2  CAE   0.020
 B89  plan-2  CAF   0.020
 B89  plan-2  CAH   0.020
 B89  plan-2  HAE   0.020
 B89  plan-2  HAF   0.020
 B89  plan-3  CAG   0.020
 B89  plan-3  NAO   0.020
 B89  plan-3  OAQ   0.020
 B89  plan-3  CAT   0.020
 B89  plan-3  CAU   0.020

