# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 08:06:11 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (1R,2R,4S,5R)-2-(1-benzothiophen-5-ylmethyl)-1,4,5-trihydroxy-3-oxocyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@](O)([C@@H](Cc2ccc3sccc3c2)C(=O)[C@H]1O)C(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
 BZ5  BZ5  '(1R,2R,4S,5R)-2-(1-benzothiophen-5-ylmethyl)-1,4,5-trihydroxy-3-oxocyclohexanecarboxylic acid'  ligand  38  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BZ5
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
 BZ5  CAK   C  CR15   0  -0.207   4.0039  -1.1083   1.5525
 BZ5  CAT   C  CR56   0   0.214   3.1681  -0.6548   0.4766
 BZ5  CAI   C  CR16   0  -0.385   1.8324  -0.9650   0.2037
 BZ5  CAH   C  CR6    0   0.144   1.1946  -0.4187  -0.8969
 BZ5  CAR   C  CR16   0  -0.324   1.9094   0.4484  -1.7389
 BZ5  CAJ   C  CR16   0  -0.259   3.2319   0.7687  -1.5007
 BZ5  CAU   C  CR56   0  -0.239   3.8556   0.2154  -0.3866
 BZ5  SAO   S  S2     0   0.195   5.4924   0.4545   0.1357
 BZ5  CAS   C  CR15   0  -0.467   5.2527  -0.5976   1.4901
 BZ5  CAQ   C  C      0   0.374  -1.3419   1.2888  -0.2163
 BZ5  CAX   C  CT     0   0.073  -2.6318  -0.8025  -0.2214
 BZ5  CAP   C  C      0   0.434  -2.5555  -2.3427  -0.0247
 BZ5  CA0   C  CH1    0  -0.363  -1.2047  -0.2046  -0.1314
 BZ5  OAC   O  O      0  -0.575  -2.0696  -2.7654   1.0321
 BZ5  OAB   O  OC    -1  -0.597  -3.0132  -3.0052  -0.9823
 BZ5  OAF   O  OH1    0  -0.700  -3.1638  -0.5369  -1.4928
 BZ5  CAM   C  CH2    0  -0.475  -3.5271  -0.1987   0.8660
 BZ5  CAV   C  CH1    0   0.048  -3.6106   1.3132   0.7616
 BZ5  OAD   O  OH1    0  -0.670  -4.4361   1.7908   1.7962
 BZ5  CAW   C  CH1    0  -0.053  -2.2021   1.9216   0.8581
 BZ5  OAE   O  OH1    0  -0.672  -2.2330   3.3157   0.7611
 BZ5  CAA   C  CH2    0  -0.517  -0.2441  -0.7654  -1.1787
 BZ5  HAK   H  HCR5   0   0.268   3.6715  -1.7825   2.3296
 BZ5  HAS   H  HCR5   0   0.299   6.0698  -0.7783   2.1719
 BZ5  HAI   H  HCR6   0   0.246   1.2989  -1.6473   0.8576
 BZ5  HAR   H  HCR6   0   0.248   1.4121   0.8748  -2.6002
 BZ5  HAA1  H  HCH2   0   0.253  -0.5290  -0.4171  -2.1711
 BZ5  HAA2  H  HCH2   0   0.265  -0.3381  -1.8537  -1.1970
 BZ5  HAJ   H  HCR6   0   0.264   3.7651   1.4355  -2.1659
 BZ5  HA0   H  HCH1   0   0.284  -0.8344  -0.4434   0.8726
 BZ5  HAW   H  HCH1   0   0.252  -1.7824   1.6444   1.8356
 BZ5  HAF   H  HOH1   0   0.433  -3.3332  -1.4364  -1.8380
 BZ5  HAM1  H  HCH2   0   0.252  -4.5307  -0.6246   0.7809
 BZ5  HAM2  H  HCH2   0   0.239  -3.1396  -0.4753   1.8499
 BZ5  HAV   H  HCH1   0   0.212  -4.0271   1.5879  -0.2188
 BZ5  HAD   H  HOH1   0   0.450  -4.5473   2.7397   1.6759
 BZ5  HAE   H  HOH1   0   0.446  -1.9478   3.5569  -0.1303
 BZ5  OAN   O  O      0  -0.390  -0.8729   1.9723  -1.0987

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
 BZ5  CAK  CAT   aromatic  1.436  0.020  1.436
 BZ5  CAK  CAS   aromatic  1.351  0.020  1.351
 BZ5  CAT  CAI   aromatic  1.398  0.020  1.398
 BZ5  CAT  CAU   aromatic  1.405  0.020  1.405
 BZ5  CAI  CAH   aromatic  1.384  0.020  1.384
 BZ5  CAH  CAR   aromatic  1.404  0.020  1.404
 BZ5  CAH  CAA   single    1.506  0.020  1.506
 BZ5  CAR  CAJ   aromatic  1.381  0.020  1.381
 BZ5  CAJ  CAU   aromatic  1.392  0.020  1.392
 BZ5  CAU  SAO   aromatic  1.735  0.020  1.735
 BZ5  SAO  CAS   aromatic  1.732  0.020  1.732
 BZ5  OAN  CAQ   double    1.211  0.020  1.211
 BZ5  CAQ  CA0   single    1.502  0.020  1.502
 BZ5  CAQ  CAW   single    1.515  0.020  1.515
 BZ5  CAX  CAP   single    1.555  0.020  1.555
 BZ5  CAX  CA0   single    1.550  0.020  1.550
 BZ5  CAX  OAF   single    1.404  0.020  1.404
 BZ5  CAX  CAM   single    1.533  0.020  1.533
 BZ5  CAP  OAC   deloc     1.238  0.020  1.238
 BZ5  CAP  OAB   deloc     1.251  0.020  1.251
 BZ5  CA0  CAA   single    1.528  0.020  1.528
 BZ5  CAM  CAV   single    1.518  0.020  1.518
 BZ5  CAV  OAD   single    1.407  0.020  1.407
 BZ5  CAV  CAW   single    1.537  0.020  1.537
 BZ5  CAW  OAE   single    1.398  0.020  1.398
 BZ5  CAK  HAK   single    0.930  0.020  1.080
 BZ5  CAS  HAS   single    0.930  0.020  1.080
 BZ5  CAI  HAI   single    0.930  0.020  1.080
 BZ5  CAR  HAR   single    0.930  0.020  1.080
 BZ5  CAA  HAA1  single    0.970  0.020  1.090
 BZ5  CAA  HAA2  single    0.970  0.020  1.090
 BZ5  CAJ  HAJ   single    0.930  0.020  1.080
 BZ5  CA0  HA0   single    0.970  0.020  1.090
 BZ5  CAW  HAW   single    0.970  0.020  1.090
 BZ5  OAF  HAF   single    0.850  0.020  0.980
 BZ5  CAM  HAM1  single    0.970  0.020  1.090
 BZ5  CAM  HAM2  single    0.970  0.020  1.090
 BZ5  CAV  HAV   single    0.970  0.020  1.090
 BZ5  OAD  HAD   single    0.850  0.020  0.980
 BZ5  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
 BZ5  HAK   CAK  CAS   123.59  3.000
 BZ5  HAK   CAK  CAT   123.82  3.000
 BZ5  CAS   CAK  CAT   112.59  3.000
 BZ5  CAU   CAT  CAI   119.00  3.000
 BZ5  CAU   CAT  CAK   111.78  3.000
 BZ5  CAI   CAT  CAK   129.21  3.000
 BZ5  HAI   CAI  CAH   120.04  3.000
 BZ5  HAI   CAI  CAT   119.44  3.000
 BZ5  CAH   CAI  CAT   120.51  3.000
 BZ5  CAA   CAH  CAR   121.07  3.000
 BZ5  CAA   CAH  CAI   119.86  3.000
 BZ5  CAR   CAH  CAI   119.07  3.000
 BZ5  HAR   CAR  CAJ   119.06  3.000
 BZ5  HAR   CAR  CAH   119.12  3.000
 BZ5  CAJ   CAR  CAH   121.81  3.000
 BZ5  HAJ   CAJ  CAU   121.08  3.000
 BZ5  HAJ   CAJ  CAR   120.57  3.000
 BZ5  CAU   CAJ  CAR   118.35  3.000
 BZ5  SAO   CAU  CAJ   127.53  3.000
 BZ5  SAO   CAU  CAT   111.22  3.000
 BZ5  CAJ   CAU  CAT   121.24  3.000
 BZ5  CAS   SAO  CAU    91.21  3.000
 BZ5  HAS   CAS  SAO   119.40  3.000
 BZ5  HAS   CAS  CAK   127.40  3.000
 BZ5  SAO   CAS  CAK   113.20  3.000
 BZ5  CAW   CAQ  CA0   115.29  3.000
 BZ5  CAW   CAQ  OAN   120.07  3.000
 BZ5  CA0   CAQ  OAN   124.55  3.000
 BZ5  CAM   CAX  OAF   110.29  3.000
 BZ5  CAM   CAX  CA0   110.17  3.000
 BZ5  OAF   CAX  CA0   109.18  3.000
 BZ5  CAM   CAX  CAP   109.22  3.000
 BZ5  OAF   CAX  CAP   108.70  3.000
 BZ5  CA0   CAX  CAP   109.25  3.000
 BZ5  OAB   CAP  OAC   128.05  3.000
 BZ5  OAB   CAP  CAX   114.20  3.000
 BZ5  OAC   CAP  CAX   117.75  3.000
 BZ5  HA0   CA0  CAA   109.60  3.000
 BZ5  HA0   CA0  CAX   106.26  3.000
 BZ5  CAA   CA0  CAX   113.43  3.000
 BZ5  HA0   CA0  CAQ   107.41  3.000
 BZ5  CAA   CA0  CAQ   112.56  3.000
 BZ5  CAX   CA0  CAQ   107.22  3.000
 BZ5  HAF   OAF  CAX   102.20  3.000
 BZ5  HAM2  CAM  HAM1  107.27  3.000
 BZ5  HAM2  CAM  CAV   109.48  3.000
 BZ5  HAM1  CAM  CAV   109.40  3.000
 BZ5  HAM2  CAM  CAX   109.38  3.000
 BZ5  HAM1  CAM  CAX   109.12  3.000
 BZ5  CAV   CAM  CAX   112.07  3.000
 BZ5  HAV   CAV  CAW   107.70  3.000
 BZ5  HAV   CAV  OAD   110.39  3.000
 BZ5  CAW   CAV  OAD   110.92  3.000
 BZ5  HAV   CAV  CAM   109.32  3.000
 BZ5  CAW   CAV  CAM   109.85  3.000
 BZ5  OAD   CAV  CAM   108.65  3.000
 BZ5  HAD   OAD  CAV   108.08  3.000
 BZ5  HAW   CAW  OAE   108.76  3.000
 BZ5  HAW   CAW  CAV   107.80  3.000
 BZ5  OAE   CAW  CAV   111.72  3.000
 BZ5  HAW   CAW  CAQ   107.97  3.000
 BZ5  OAE   CAW  CAQ   112.33  3.000
 BZ5  CAV   CAW  CAQ   108.08  3.000
 BZ5  HAE   OAE  CAW   107.85  3.000
 BZ5  HAA2  CAA  HAA1  106.30  3.000
 BZ5  HAA2  CAA  CA0   108.85  3.000
 BZ5  HAA1  CAA  CA0   110.03  3.000
 BZ5  HAA2  CAA  CAH   108.34  3.000
 BZ5  HAA1  CAA  CAH   110.27  3.000
 BZ5  CA0   CAA  CAH   112.82  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
 BZ5  CONST_01  CAH  CAI  CAT  CAK  180.00   0.0  0
 BZ5  CONST_02  CAJ  CAU  CAT  CAK  180.00   0.0  0
 BZ5  CONST_03  SAO  CAU  CAT  CAK    0.00   0.0  0
 BZ5  CONST_04  CAU  SAO  CAS  CAK    0.00   0.0  0
 BZ5  CONST_05  SAO  CAS  CAK  CAT    0.00   0.0  0
 BZ5  CONST_06  CAR  CAH  CAI  CAT    0.00   0.0  0
 BZ5  CONST_07  CAR  CAJ  CAU  CAT    0.00   0.0  0
 BZ5  CONST_08  CAS  SAO  CAU  CAT    0.00   0.0  0
 BZ5  CONST_09  CAS  CAK  CAT  CAI  180.00   0.0  0
 BZ5  CONST_10  CAJ  CAU  CAT  CAI    0.00   0.0  0
 BZ5  CONST_11  SAO  CAU  CAT  CAI  180.00   0.0  0
 BZ5  CONST_12  CAJ  CAR  CAH  CAI    0.00   0.0  0
 BZ5  CONST_13  CAU  CAT  CAI  CAH    0.00   0.0  0
 BZ5  CONST_14  CAU  CAJ  CAR  CAH    0.00   0.0  0
 BZ5  CONST_15  SAO  CAU  CAJ  CAR  180.00   0.0  0
 BZ5  CONST_16  CAS  SAO  CAU  CAJ  180.00   0.0  0
 BZ5  CONST_17  CAS  CAK  CAT  CAU    0.00   0.0  0
 BZ5  CONST_18  CAA  CAH  CAI  CAT  180.00   0.0  0
 BZ5  CONST_19  CAA  CAH  CAR  CAJ  180.00   0.0  0
 BZ5  CONST_20  HAI  CAI  CAT  CAK    0.00   0.0  0
 BZ5  CONST_21  HAS  CAS  CAK  CAT  180.00   0.0  0
 BZ5  CONST_22  HAJ  CAJ  CAU  CAT  180.00   0.0  0
 BZ5  CONST_23  HAK  CAK  CAT  CAI    0.00   0.0  0
 BZ5  CONST_24  HAR  CAR  CAH  CAI  180.00   0.0  0
 BZ5  Var_01    CA0  CAA  CAH  CAI   67.69  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
 BZ5  chir_01  CAX  CA0  OAF  CAM  positiv
 BZ5  chir_02  CA0  CAA  CAX  CAQ  positiv
 BZ5  chir_03  CAV  OAD  CAW  CAM  negativ
 BZ5  chir_04  CAW  OAE  CAQ  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
 BZ5  plan-1  CAK  0.020
 BZ5  plan-1  CAT  0.020
 BZ5  plan-1  CAI  0.020
 BZ5  plan-1  CAH  0.020
 BZ5  plan-1  CAR  0.020
 BZ5  plan-1  CAJ  0.020
 BZ5  plan-1  CAU  0.020
 BZ5  plan-1  SAO  0.020
 BZ5  plan-1  CAS  0.020
 BZ5  plan-1  CAA  0.020
 BZ5  plan-1  HAK  0.020
 BZ5  plan-1  HAS  0.020
 BZ5  plan-1  HAI  0.020
 BZ5  plan-1  HAR  0.020
 BZ5  plan-1  HAJ  0.020
 BZ5  plan-2  CAX  0.020
 BZ5  plan-2  CAP  0.020
 BZ5  plan-2  OAC  0.020
 BZ5  plan-2  OAB  0.020
 BZ5  plan-3  CAQ  0.020
 BZ5  plan-3  CA0  0.020
 BZ5  plan-3  CAW  0.020
 BZ5  plan-3  OAN  0.020

