# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 18:09:16 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (1R,2S,4S,5R)-1,4,5-trihydroxy-2-(4-methoxybenzyl)-3-oxocyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C[C@@H]2C(=O)[C@@H](O)[C@H](O)C[C@]2(O)C(O)=O)cc1
#
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
 9ZT  9ZT  '(1R,2S,4S,5R)-1,4,5-trihydroxy-2-(4-methoxybenzyl)-3-oxocyclohexanecarboxylic acid'  ligand  39  22  .  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_9ZT
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
 9ZT  CAA   C  CH3    0  -0.463   6.2472   0.1714   0.5879
 9ZT  OAN   O  O2     0  -0.488   5.3749  -0.6232  -0.1873
 9ZT  CAR   C  C      0   0.476   4.0988  -0.2157  -0.3363
 9ZT  CAK   C  C1     0  -0.368   3.2682  -1.0372  -1.0981
 9ZT  CAI   C  C1     0  -0.269   1.9453  -0.6886  -1.3037
 9ZT  CAJ   C  C1     0  -0.402   3.5775   0.9548   0.2105
 9ZT  CAH   C  C1     0  -0.262   2.2465   1.2834  -0.0081
 9ZT  CAQ   C  C      0   0.056   1.4048   0.4754  -0.7621
 9ZT  CAL   C  CH2    0  -0.551  -0.0413   0.8362  -0.9631
 9ZT  CAP   C  C      0   0.407  -0.6996  -0.7847   0.8349
 9ZT  OAC   O  O      0  -0.371  -0.0775  -1.0609   1.8351
 9ZT  CAT   C  CH1    0  -0.110  -1.3530  -1.8910   0.0281
 9ZT  CAU   C  CH1    0  -0.395  -0.8787   0.6183   0.3145
 9ZT  OAF   O  OH1    0  -0.688  -1.1790  -3.1380   0.6307
 9ZT  CAS   C  CH1    0   0.056  -2.8414  -1.5987  -0.2043
 9ZT  OAE   O  OH1    0  -0.697  -3.3855  -2.4999  -1.1396
 9ZT  CAM   C  CH2    0  -0.521  -3.0524  -0.1863  -0.7264
 9ZT  CAV   C  CT     0   0.106  -2.4076   0.8477   0.1937
 9ZT  CAO   C  C      0   0.328  -2.7096   2.2935  -0.2731
 9ZT  OAB   O  O      0  -0.375  -2.5393   2.5749  -1.4706
 9ZT  OAD   O  OC    -1  -0.708  -3.1041   3.0606   0.6236
 9ZT  OAG   O  OH1    0  -0.707  -2.9404   0.6861   1.4901
 9ZT  HAM1  H  HCH2   0   0.257  -2.6545  -0.1004  -1.7386
 9ZT  HAM2  H  HCH2   0   0.275  -4.1257   0.0082  -0.7964
 9ZT  HAG   H  HOH1   0   0.433  -3.1530   1.5991   1.7526
 9ZT  HAU   H  HCH1   0   0.269  -0.4994   1.3000   1.0825
 9ZT  HAS   H  HCH1   0   0.254  -3.3496  -1.7024   0.7630
 9ZT  HAE   H  HOH1   0   0.414  -3.4439  -3.3655  -0.7250
 9ZT  HAT   H  HCH1   0   0.288  -0.8587  -1.8800  -0.9584
 9ZT  HAF   H  HOH1   0   0.444  -0.7428  -2.9837   1.4813
 9ZT  HAL1  H  HCH2   0   0.275  -0.1243   1.8850  -1.2465
 9ZT  HAL2  H  HCH2   0   0.281  -0.4438   0.2664  -1.8023
 9ZT  HAI   H  H      0   0.249   1.3221  -1.3441  -1.9012
 9ZT  HAH   H  H      0   0.250   1.8681   2.2048   0.4196
 9ZT  HAK   H  H      0   0.252   3.6660  -1.9478  -1.5279
 9ZT  HAJ   H  H      0   0.276   4.1874   1.6220   0.8041
 9ZT  HAA1  H  HCH3   0   0.240   6.3789   1.1712   0.1651
 9ZT  HAA2  H  HCH3   0   0.213   5.9018   0.2699   1.6204
 9ZT  HAA3  H  HCH3   0   0.274   7.2093  -0.3346   0.5899

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
 9ZT  OAB  CAO   deloc     1.242  0.020  1.242
 9ZT  CAO  OAD   deloc     1.244  0.020  1.244
 9ZT  CAO  CAV   single    1.549  0.020  1.549
 9ZT  CAV  CAM   single    1.527  0.020  1.527
 9ZT  CAV  OAG   single    1.411  0.020  1.411
 9ZT  CAV  CAU   single    1.551  0.020  1.551
 9ZT  CAM  CAS   single    1.520  0.020  1.520
 9ZT  CAS  OAE   single    1.408  0.020  1.408
 9ZT  CAS  CAT   single    1.534  0.020  1.534
 9ZT  CAT  OAF   single    1.396  0.020  1.396
 9ZT  CAT  CAP   single    1.517  0.020  1.517
 9ZT  CAP  OAC   double    1.210  0.020  1.210
 9ZT  CAP  CAU   single    1.507  0.020  1.507
 9ZT  CAU  CAL   single    1.543  0.020  1.543
 9ZT  CAL  CAQ   single    1.504  0.020  1.504
 9ZT  CAQ  CAI   aromatic  1.393  0.020  1.393
 9ZT  CAQ  CAH   aromatic  1.389  0.020  1.389
 9ZT  CAI  CAK   aromatic  1.383  0.020  1.383
 9ZT  CAK  CAR   aromatic  1.395  0.020  1.395
 9ZT  CAH  CAJ   aromatic  1.388  0.020  1.388
 9ZT  CAJ  CAR   aromatic  1.393  0.020  1.393
 9ZT  CAR  OAN   single    1.348  0.020  1.348
 9ZT  OAN  CAA   single    1.412  0.020  1.412
 9ZT  CAM  HAM1  single    0.970  0.020  1.090
 9ZT  CAM  HAM2  single    0.970  0.020  1.090
 9ZT  OAG  HAG   single    0.850  0.020  0.980
 9ZT  CAU  HAU   single    0.970  0.020  1.090
 9ZT  CAS  HAS   single    0.970  0.020  1.090
 9ZT  OAE  HAE   single    0.850  0.020  0.980
 9ZT  CAT  HAT   single    0.970  0.020  1.090
 9ZT  OAF  HAF   single    0.850  0.020  0.980
 9ZT  CAL  HAL1  single    0.970  0.020  1.090
 9ZT  CAL  HAL2  single    0.970  0.020  1.090
 9ZT  CAI  HAI   single    0.930  0.020  1.080
 9ZT  CAH  HAH   single    0.930  0.020  1.080
 9ZT  CAK  HAK   single    0.930  0.020  1.080
 9ZT  CAJ  HAJ   single    0.930  0.020  1.080
 9ZT  CAA  HAA1  single    0.970  0.020  1.090
 9ZT  CAA  HAA2  single    0.970  0.020  1.090
 9ZT  CAA  HAA3  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
 9ZT  HAA3  CAA  HAA2  108.65  3.000
 9ZT  HAA3  CAA  HAA1  108.65  3.000
 9ZT  HAA2  CAA  HAA1  108.72  3.000
 9ZT  HAA3  CAA  OAN   106.61  3.000
 9ZT  HAA2  CAA  OAN   111.97  3.000
 9ZT  HAA1  CAA  OAN   112.13  3.000
 9ZT  CAR   OAN  CAA   118.39  3.000
 9ZT  CAJ   CAR  CAK   119.10  3.000
 9ZT  CAJ   CAR  OAN   124.40  3.000
 9ZT  CAK   CAR  OAN   116.50  3.000
 9ZT  HAK   CAK  CAI   120.28  3.000
 9ZT  HAK   CAK  CAR   119.56  3.000
 9ZT  CAI   CAK  CAR   120.15  3.000
 9ZT  HAI   CAI  CAQ   119.77  3.000
 9ZT  HAI   CAI  CAK   118.64  3.000
 9ZT  CAQ   CAI  CAK   121.59  3.000
 9ZT  HAJ   CAJ  CAH   118.76  3.000
 9ZT  HAJ   CAJ  CAR   121.51  3.000
 9ZT  CAH   CAJ  CAR   119.73  3.000
 9ZT  HAH   CAH  CAQ   119.80  3.000
 9ZT  HAH   CAH  CAJ   118.28  3.000
 9ZT  CAQ   CAH  CAJ   121.92  3.000
 9ZT  CAL   CAQ  CAH   121.04  3.000
 9ZT  CAH   CAQ  CAI   117.51  3.000
 9ZT  CAL   CAQ  CAI   121.44  3.000
 9ZT  HAL2  CAL  HAL1  105.94  3.000
 9ZT  HAL2  CAL  CAU   111.27  3.000
 9ZT  HAL1  CAL  CAU   108.06  3.000
 9ZT  HAL2  CAL  CAQ   109.40  3.000
 9ZT  HAL1  CAL  CAQ   109.81  3.000
 9ZT  CAU   CAL  CAQ   112.17  3.000
 9ZT  CAU   CAP  CAT   116.36  3.000
 9ZT  CAU   CAP  OAC   124.00  3.000
 9ZT  CAT   CAP  OAC   119.64  3.000
 9ZT  HAT   CAT  CAS   107.29  3.000
 9ZT  HAT   CAT  OAF   109.82  3.000
 9ZT  CAS   CAT  OAF   110.88  3.000
 9ZT  HAT   CAT  CAP   105.97  3.000
 9ZT  OAF   CAT  CAP   111.60  3.000
 9ZT  CAS   CAT  CAP   111.06  3.000
 9ZT  HAU   CAU  CAV   107.70  3.000
 9ZT  HAU   CAU  CAP   107.23  3.000
 9ZT  CAV   CAU  CAP   106.37  3.000
 9ZT  HAU   CAU  CAL   107.76  3.000
 9ZT  CAP   CAU  CAL   110.67  3.000
 9ZT  CAV   CAU  CAL   116.72  3.000
 9ZT  HAF   OAF  CAT   107.05  3.000
 9ZT  HAS   CAS  CAM   109.04  3.000
 9ZT  HAS   CAS  OAE   110.24  3.000
 9ZT  CAM   CAS  OAE   108.22  3.000
 9ZT  HAS   CAS  CAT   107.32  3.000
 9ZT  OAE   CAS  CAT   110.70  3.000
 9ZT  CAM   CAS  CAT   111.32  3.000
 9ZT  HAE   OAE  CAS   108.25  3.000
 9ZT  HAM2  CAM  HAM1  106.54  3.000
 9ZT  HAM2  CAM  CAV   109.43  3.000
 9ZT  HAM1  CAM  CAV   110.59  3.000
 9ZT  HAM2  CAM  CAS   108.88  3.000
 9ZT  HAM1  CAM  CAS   109.95  3.000
 9ZT  CAV   CAM  CAS   111.31  3.000
 9ZT  OAG   CAV  CAO   108.07  3.000
 9ZT  OAG   CAV  CAM   108.46  3.000
 9ZT  CAO   CAV  CAM   111.60  3.000
 9ZT  OAG   CAV  CAU   106.49  3.000
 9ZT  CAM   CAV  CAU   111.29  3.000
 9ZT  CAO   CAV  CAU   110.72  3.000
 9ZT  OAD   CAO  OAB   126.78  3.000
 9ZT  OAD   CAO  CAV   114.84  3.000
 9ZT  OAB   CAO  CAV   118.38  3.000
 9ZT  HAG   OAG  CAV   102.88  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
 9ZT  CONST_01  CAQ   CAI  CAK  CAR     0.00   0.0  0
 9ZT  CONST_02  CAQ   CAH  CAJ  CAR     0.00   0.0  0
 9ZT  CONST_03  CAH   CAQ  CAI  CAK     0.00   0.0  0
 9ZT  CONST_04  CAH   CAJ  CAR  CAK     0.00   0.0  0
 9ZT  CONST_05  CAJ   CAH  CAQ  CAI     0.00   0.0  0
 9ZT  CONST_06  CAJ   CAR  CAK  CAI     0.00   0.0  0
 9ZT  CONST_07  CAI   CAK  CAR  OAN   180.00   0.0  0
 9ZT  CONST_08  CAH   CAJ  CAR  OAN   180.00   0.0  0
 9ZT  CONST_09  CAL   CAQ  CAI  CAK   180.00   0.0  0
 9ZT  CONST_10  CAL   CAQ  CAH  CAJ   180.00   0.0  0
 9ZT  CONST_11  HAI   CAI  CAK  CAR   180.00   0.0  0
 9ZT  CONST_12  HAH   CAH  CAJ  CAR   180.00   0.0  0
 9ZT  CONST_13  HAJ   CAJ  CAR  CAK   180.00   0.0  0
 9ZT  CONST_14  HAK   CAK  CAR  CAJ   180.00   0.0  0
 9ZT  Var_01    CAU   CAL  CAQ  CAI   106.00  30.0  2
 9ZT  Var_02    CAK   CAR  OAN  CAA  -179.36  30.0  2
 9ZT  Var_03    HAA1  CAA  OAN  CAR   -61.87  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
 9ZT  chir_01  CAT  CAS  OAF  CAP  positiv
 9ZT  chir_02  CAU  CAL  CAP  CAV  positiv
 9ZT  chir_03  CAS  OAE  CAM  CAT  positiv
 9ZT  chir_04  CAV  CAO  CAM  CAU  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
 9ZT  plan-1  OAN  0.020
 9ZT  plan-1  CAR  0.020
 9ZT  plan-1  CAK  0.020
 9ZT  plan-1  CAI  0.020
 9ZT  plan-1  CAJ  0.020
 9ZT  plan-1  CAH  0.020
 9ZT  plan-1  CAQ  0.020
 9ZT  plan-1  CAL  0.020
 9ZT  plan-1  HAI  0.020
 9ZT  plan-1  HAH  0.020
 9ZT  plan-1  HAK  0.020
 9ZT  plan-1  HAJ  0.020
 9ZT  plan-2  CAP  0.020
 9ZT  plan-2  OAC  0.020
 9ZT  plan-2  CAT  0.020
 9ZT  plan-2  CAU  0.020
 9ZT  plan-3  CAV  0.020
 9ZT  plan-3  CAO  0.020
 9ZT  plan-3  OAB  0.020
 9ZT  plan-3  OAD  0.020

