# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 23:34:16 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (1R,4S,5R)-1,4,5-trihydroxy-3-[(5-methyl-1-benzothiophen-2-yl)methoxy]cyclohex-2-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2sc(COC3=C[C@](O)(C[C@@H](O)[C@@H]3O)C(O)=O)cc2c1
#
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
 CB6  CB6  '(1R,4S,5R)-1,4,5-trihydroxy-3-[(5-methyl-1-benzothiophen-2-yl)methoxy]cyclohex-2-ene-1-carboxylic acid'  ligand  41  24  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CB6
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
 CB6  CAK   C  CR15   0  -0.243  -2.6766  -1.1096  -0.7713
 CB6  CAT   C  CR56   0   0.239  -3.9797  -0.5373  -0.5947
 CB6  CAI   C  CR16   0  -0.381  -5.2071  -0.9646  -1.1147
 CB6  CAH   C  CR6    0   0.102  -6.3671  -0.2656  -0.8346
 CB6  CAR   C  CR16   0  -0.307  -6.2920   0.8838  -0.0268
 CB6  CAJ   C  CR16   0  -0.263  -5.0956   1.3319   0.4961
 CB6  CAU   C  CR56   0  -0.246  -3.9391   0.6108   0.2110
 CB6  SAO   S  S2     0   0.217  -2.3214   0.9601   0.7318
 CB6  CAS   C  CR5    0  -0.188  -1.7081  -0.4254  -0.1231
 CB6  CAL   C  CH2    0  -0.232  -0.2631  -0.7630  -0.0328
 CB6  OAN   O  O2     0  -0.479   0.4739   0.4206  -0.2501
 CB6  CAQ   C  C      0   0.325   1.8203   0.3656  -0.1171
 CB6  CAG   C  C1     0  -0.327   2.5375  -0.7388   0.0845
 CB6  CAX   C  CT     0   0.034   4.0342  -0.7223   0.2303
 CB6  CAP   C  C      0   0.413   4.6549  -1.9085  -0.5639
 CB6  OAC   O  O      0  -0.577   4.3837  -2.0025  -1.7677
 CB6  OAB   O  OC    -1  -0.604   5.3907  -2.6606   0.1161
 CB6  OAF   O  OH1    0  -0.702   4.3713  -0.8901   1.5919
 CB6  CAM   C  CH2    0  -0.487   4.6069   0.5917  -0.3096
 CB6  CAV   C  CH1    0   0.053   3.8454   1.7760   0.2479
 CB6  OAD   O  OH1    0  -0.676   4.5043   2.9647  -0.1268
 CB6  CAW   C  CH1    0  -0.058   2.4183   1.7448  -0.2797
 CB6  OAE   O  OH1    0  -0.669   1.6827   2.7234   0.4203
 CB6  CAA   C  CH3    0  -0.723  -7.6965  -0.7227  -1.3620
 CB6  HAK   H  HCR5   0   0.269  -2.4860  -1.9974  -1.3594
 CB6  HAI   H  HCR6   0   0.250  -5.2402  -1.8484  -1.7415
 CB6  HAR   H  HCR6   0   0.252  -7.1993   1.4348   0.1905
 CB6  HAA1  H  HCH3   0   0.248  -8.3063  -1.1531  -0.5654
 CB6  HAA2  H  HCH3   0   0.244  -8.2637   0.1061  -1.7868
 CB6  HAA3  H  HCH3   0   0.244  -7.5811  -1.4818  -2.1344
 CB6  HAJ   H  HCR6   0   0.266  -5.0631   2.2214   1.1119
 CB6  HAL1  H  HCH2   0   0.251  -0.0243  -1.1772   0.9544
 CB6  HAL2  H  HCH2   0   0.251  -0.0230  -1.5297  -0.7775
 CB6  HAG   H  H      0   0.265   2.0541  -1.7043   0.1909
 CB6  HAW   H  HCH1   0   0.229   2.4484   1.9809  -1.3555
 CB6  HAF   H  HOH1   0   0.426   4.9669  -1.6654   1.5549
 CB6  HAM1  H  HCH2   0   0.243   5.6647   0.6639  -0.0428
 CB6  HAM2  H  HCH2   0   0.233   4.5444   0.6000  -1.4015
 CB6  HAV   H  HCH1   0   0.206   3.8028   1.6886   1.3437
 CB6  HAD   H  HOH1   0   0.447   4.0371   3.7055   0.2734
 CB6  HAE   H  HOH1   0   0.454   0.8320   2.8436  -0.0124

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
 CB6  CAK  CAT   aromatic  1.434  0.020  1.434
 CB6  CAK  CAS   aromatic  1.351  0.020  1.351
 CB6  CAT  CAI   aromatic  1.400  0.020  1.400
 CB6  CAT  CAU   aromatic  1.403  0.020  1.403
 CB6  CAI  CAH   aromatic  1.383  0.020  1.383
 CB6  CAH  CAR   aromatic  1.407  0.020  1.407
 CB6  CAH  CAA   single    1.501  0.020  1.501
 CB6  CAR  CAJ   aromatic  1.380  0.020  1.380
 CB6  CAJ  CAU   aromatic  1.392  0.020  1.392
 CB6  CAU  SAO   aromatic  1.735  0.020  1.735
 CB6  SAO  CAS   aromatic  1.740  0.020  1.740
 CB6  CAS  CAL   single    1.487  0.020  1.487
 CB6  CAL  OAN   single    1.411  0.020  1.411
 CB6  OAN  CAQ   single    1.354  0.020  1.354
 CB6  CAQ  CAG   double    1.332  0.020  1.332
 CB6  CAQ  CAW   single    1.512  0.020  1.512
 CB6  CAG  CAX   single    1.504  0.020  1.504
 CB6  CAX  CAP   single    1.557  0.020  1.557
 CB6  CAX  OAF   single    1.413  0.020  1.413
 CB6  CAX  CAM   single    1.532  0.020  1.532
 CB6  CAP  OAC   deloc     1.238  0.020  1.238
 CB6  CAP  OAB   deloc     1.253  0.020  1.253
 CB6  CAM  CAV   single    1.514  0.020  1.514
 CB6  CAV  OAD   single    1.410  0.020  1.410
 CB6  CAV  CAW   single    1.522  0.020  1.522
 CB6  CAW  OAE   single    1.410  0.020  1.410
 CB6  CAK  HAK   single    0.930  0.020  1.080
 CB6  CAI  HAI   single    0.930  0.020  1.080
 CB6  CAR  HAR   single    0.930  0.020  1.080
 CB6  CAA  HAA1  single    0.970  0.020  1.090
 CB6  CAA  HAA2  single    0.970  0.020  1.090
 CB6  CAA  HAA3  single    0.970  0.020  1.090
 CB6  CAJ  HAJ   single    0.930  0.020  1.080
 CB6  CAL  HAL1  single    0.970  0.020  1.090
 CB6  CAL  HAL2  single    0.970  0.020  1.090
 CB6  CAG  HAG   single    0.930  0.020  1.080
 CB6  CAW  HAW   single    0.970  0.020  1.090
 CB6  OAF  HAF   single    0.850  0.020  0.980
 CB6  CAM  HAM1  single    0.970  0.020  1.090
 CB6  CAM  HAM2  single    0.970  0.020  1.090
 CB6  CAV  HAV   single    0.970  0.020  1.090
 CB6  OAD  HAD   single    0.850  0.020  0.980
 CB6  OAE  HAE   single    0.850  0.020  0.980

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
 CB6  HAK   CAK  CAS   123.36  3.000
 CB6  HAK   CAK  CAT   123.68  3.000
 CB6  CAS   CAK  CAT   112.96  3.000
 CB6  CAU   CAT  CAI   119.24  3.000
 CB6  CAU   CAT  CAK   111.78  3.000
 CB6  CAI   CAT  CAK   128.98  3.000
 CB6  HAI   CAI  CAH   120.24  3.000
 CB6  HAI   CAI  CAT   119.37  3.000
 CB6  CAH   CAI  CAT   120.39  3.000
 CB6  CAA   CAH  CAR   119.85  3.000
 CB6  CAA   CAH  CAI   121.17  3.000
 CB6  CAR   CAH  CAI   118.97  3.000
 CB6  HAR   CAR  CAJ   118.99  3.000
 CB6  HAR   CAR  CAH   119.07  3.000
 CB6  CAJ   CAR  CAH   121.94  3.000
 CB6  HAJ   CAJ  CAU   121.14  3.000
 CB6  HAJ   CAJ  CAR   120.55  3.000
 CB6  CAU   CAJ  CAR   118.30  3.000
 CB6  SAO   CAU  CAJ   127.49  3.000
 CB6  SAO   CAU  CAT   111.35  3.000
 CB6  CAJ   CAU  CAT   121.15  3.000
 CB6  CAS   SAO  CAU    91.19  3.000
 CB6  CAL   CAS  SAO   119.58  3.000
 CB6  CAL   CAS  CAK   127.65  3.000
 CB6  SAO   CAS  CAK   112.72  3.000
 CB6  HAL2  CAL  HAL1  107.44  3.000
 CB6  HAL2  CAL  OAN   111.59  3.000
 CB6  HAL1  CAL  OAN   109.97  3.000
 CB6  HAL2  CAL  CAS   109.31  3.000
 CB6  HAL1  CAL  CAS   110.61  3.000
 CB6  OAN   CAL  CAS   107.93  3.000
 CB6  CAQ   OAN  CAL   118.04  3.000
 CB6  CAW   CAQ  CAG   124.03  3.000
 CB6  CAW   CAQ  OAN   110.22  3.000
 CB6  CAG   CAQ  OAN   125.72  3.000
 CB6  HAG   CAG  CAX   116.34  3.000
 CB6  HAG   CAG  CAQ   120.85  3.000
 CB6  CAX   CAG  CAQ   122.77  3.000
 CB6  CAM   CAX  OAF   110.64  3.000
 CB6  CAM   CAX  CAP   108.96  3.000
 CB6  OAF   CAX  CAP   107.82  3.000
 CB6  CAM   CAX  CAG   110.32  3.000
 CB6  OAF   CAX  CAG   109.24  3.000
 CB6  CAP   CAX  CAG   109.81  3.000
 CB6  OAB   CAP  OAC   127.66  3.000
 CB6  OAB   CAP  CAX   114.50  3.000
 CB6  OAC   CAP  CAX   117.83  3.000
 CB6  HAF   OAF  CAX   101.71  3.000
 CB6  HAM2  CAM  HAM1  107.36  3.000
 CB6  HAM2  CAM  CAV   109.44  3.000
 CB6  HAM1  CAM  CAV   110.19  3.000
 CB6  HAM2  CAM  CAX   109.70  3.000
 CB6  HAM1  CAM  CAX   109.41  3.000
 CB6  CAV   CAM  CAX   110.68  3.000
 CB6  HAV   CAV  CAW   107.91  3.000
 CB6  HAV   CAV  OAD   110.48  3.000
 CB6  CAW   CAV  OAD   111.31  3.000
 CB6  HAV   CAV  CAM   108.91  3.000
 CB6  CAW   CAV  CAM   109.14  3.000
 CB6  OAD   CAV  CAM   109.06  3.000
 CB6  HAD   OAD  CAV   108.14  3.000
 CB6  HAW   CAW  OAE   110.51  3.000
 CB6  HAW   CAW  CAV   107.97  3.000
 CB6  OAE   CAW  CAV   107.63  3.000
 CB6  HAW   CAW  CAQ   108.13  3.000
 CB6  OAE   CAW  CAQ   111.92  3.000
 CB6  CAV   CAW  CAQ   110.63  3.000
 CB6  HAE   OAE  CAW   108.95  3.000
 CB6  HAA3  CAA  HAA2  107.98  3.000
 CB6  HAA3  CAA  HAA1  107.57  3.000
 CB6  HAA2  CAA  HAA1  107.06  3.000
 CB6  HAA3  CAA  CAH   111.56  3.000
 CB6  HAA2  CAA  CAH   111.47  3.000
 CB6  HAA1  CAA  CAH   110.99  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
 CB6  CONST_01  CAH   CAI  CAT  CAK  180.00   0.0  0
 CB6  CONST_02  CAJ   CAU  CAT  CAK  180.00   0.0  0
 CB6  CONST_03  SAO   CAU  CAT  CAK    0.00   0.0  0
 CB6  CONST_04  CAU   SAO  CAS  CAK    0.00   0.0  0
 CB6  CONST_05  SAO   CAS  CAK  CAT    0.00   0.0  0
 CB6  CONST_06  CAR   CAH  CAI  CAT    0.00   0.0  0
 CB6  CONST_07  CAR   CAJ  CAU  CAT    0.00   0.0  0
 CB6  CONST_08  CAS   SAO  CAU  CAT    0.00   0.0  0
 CB6  CONST_09  CAS   CAK  CAT  CAI  180.00   0.0  0
 CB6  CONST_10  CAJ   CAU  CAT  CAI    0.00   0.0  0
 CB6  CONST_11  SAO   CAU  CAT  CAI  180.00   0.0  0
 CB6  CONST_12  CAJ   CAR  CAH  CAI    0.00   0.0  0
 CB6  CONST_13  CAU   CAT  CAI  CAH    0.00   0.0  0
 CB6  CONST_14  CAU   CAJ  CAR  CAH    0.00   0.0  0
 CB6  CONST_15  SAO   CAU  CAJ  CAR  180.00   0.0  0
 CB6  CONST_16  CAS   SAO  CAU  CAJ  180.00   0.0  0
 CB6  CONST_17  CAS   CAK  CAT  CAU    0.00   0.0  0
 CB6  CONST_18  CAL   CAS  CAK  CAT  180.00   0.0  0
 CB6  CONST_19  CAA   CAH  CAI  CAT  180.00   0.0  0
 CB6  CONST_20  CAA   CAH  CAR  CAJ  180.00   0.0  0
 CB6  CONST_21  CAL   CAS  SAO  CAU  180.00   0.0  0
 CB6  CONST_22  HAI   CAI  CAT  CAK    0.00   0.0  0
 CB6  CONST_23  HAJ   CAJ  CAU  CAT  180.00   0.0  0
 CB6  CONST_24  HAK   CAK  CAT  CAI    0.00   0.0  0
 CB6  CONST_25  HAR   CAR  CAH  CAI  180.00   0.0  0
 CB6  Var_01    CAW   CAQ  CAG  CAX    2.64  30.0  1
 CB6  Var_02    OAN   CAL  CAS  CAK  135.48  30.0  2
 CB6  Var_03    CAG   CAQ  OAN  CAL    6.49  30.0  3
 CB6  Var_04    HAA1  CAA  CAH  CAI  106.86  30.0  2

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
 CB6  chir_01  CAX  CAG  OAF  CAM  positiv
 CB6  chir_02  CAV  OAD  CAM  CAW  positiv
 CB6  chir_03  CAW  OAE  CAV  CAQ  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
 CB6  plan-1  CAK  0.020
 CB6  plan-1  CAT  0.020
 CB6  plan-1  CAI  0.020
 CB6  plan-1  CAH  0.020
 CB6  plan-1  CAR  0.020
 CB6  plan-1  CAJ  0.020
 CB6  plan-1  CAU  0.020
 CB6  plan-1  SAO  0.020
 CB6  plan-1  CAS  0.020
 CB6  plan-1  CAL  0.020
 CB6  plan-1  CAA  0.020
 CB6  plan-1  HAK  0.020
 CB6  plan-1  HAI  0.020
 CB6  plan-1  HAR  0.020
 CB6  plan-1  HAJ  0.020
 CB6  plan-2  CAX  0.020
 CB6  plan-2  CAP  0.020
 CB6  plan-2  OAC  0.020
 CB6  plan-2  OAB  0.020

