# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:11:55 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
 3DQ  3DQ  '(1R,2S,4S,5R)-1,4,5-trihydroxy-2-(4-methoxybenzyl)-3-oxocyclohexanecarboxylic acid'  ligand  39  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3DQ
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
 3DQ  CAA   C  CH3    0  -0.436  -6.2242   0.0769  -0.6461
 3DQ  OAN   O  O2     0  -0.473  -5.3483  -0.6908   0.1534
 3DQ  CAR   C  CR6    0   0.364  -4.0803  -0.2596   0.3117
 3DQ  CAK   C  CR16   0  -0.325  -3.2450  -1.0572   1.0933
 3DQ  CAI   C  CR16   0  -0.302  -1.9286  -0.6863   1.3054
 3DQ  CAJ   C  CR16   0  -0.367  -3.5720   0.9126  -0.2442
 3DQ  CAH   C  CR16   0  -0.294  -2.2472   1.2644  -0.0182
 3DQ  CAQ   C  CR6    0   0.121  -1.3993   0.4790   0.7533
 3DQ  CAL   C  CH2    0  -0.535   0.0433   0.8594   0.9541
 3DQ  CAU   C  CH1    0  -0.361   0.8732   0.6356  -0.3249
 3DQ  CAP   C  C      0   0.378   0.6947  -0.7658  -0.8494
 3DQ  OAC   O  O      0  -0.391   0.1508  -1.0317  -1.8976
 3DQ  CAT   C  CH1    0  -0.064   1.3088  -1.8669  -0.0077
 3DQ  OAF   O  OH1    0  -0.671   1.0630  -3.1374  -0.5369
 3DQ  CAS   C  CH1    0   0.051   2.8141  -1.5980   0.1578
 3DQ  OAE   O  OH1    0  -0.671   3.3841  -2.5152   1.0622
 3DQ  CAM   C  CH2    0  -0.485   3.0532  -0.1922   0.6832
 3DQ  CAV   C  CT     0   0.076   2.4063   0.8626  -0.2103
 3DQ  CAO   C  C      0   0.443   2.7043   2.3000   0.2973
 3DQ  OAB   O  O      0  -0.573   2.5689   2.5375   1.5051
 3DQ  OAD   O  OC    -1  -0.599   3.0613   3.0934  -0.6024
 3DQ  OAG   O  OH1    0  -0.700   2.9345   0.7456  -1.5120
 3DQ  HAA1  H  HCH3   0   0.227  -5.8650   0.1680  -1.6747
 3DQ  HAA2  H  HCH3   0   0.258  -7.1764  -0.4481  -0.6552
 3DQ  HAA3  H  HCH3   0   0.227  -6.3804   1.0794  -0.2385
 3DQ  HAK   H  HCR6   0   0.259  -3.6336  -1.9669   1.5345
 3DQ  HAJ   H  HCR6   0   0.277  -4.1870   1.5623  -0.8521
 3DQ  HAI   H  HCR6   0   0.248  -1.3013  -1.3200   1.9217
 3DQ  HAH   H  HCR6   0   0.251  -1.8765   2.1834  -0.4582
 3DQ  HAL1  H  HCH2   0   0.270   0.1171   1.9128   1.2224
 3DQ  HAL2  H  HCH2   0   0.249   0.4539   0.3027   1.7986
 3DQ  HAU   H  HCH1   0   0.269   0.4972   1.3206  -1.0917
 3DQ  HAT   H  HCH1   0   0.246   0.8614  -1.8237   0.9946
 3DQ  HAF   H  HOH1   0   0.445   0.8593  -3.0336  -1.4755
 3DQ  HAS   H  HCH1   0   0.213   3.2807  -1.6998  -0.8320
 3DQ  HAE   H  HOH1   0   0.450   3.3125  -3.3961   0.6801
 3DQ  HAM1  H  HCH2   0   0.241   2.6689  -0.1065   1.7019
 3DQ  HAM2  H  HCH2   0   0.253   4.1298  -0.0085   0.7381
 3DQ  HAG   H  HOH1   0   0.431   3.1276   1.6772  -1.7381

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
 3DQ  CAA  OAN   single    1.413  0.020  1.413
 3DQ  OAN  CAR   single    1.349  0.020  1.349
 3DQ  CAR  CAK   aromatic  1.395  0.020  1.395
 3DQ  CAR  CAJ   aromatic  1.393  0.020  1.393
 3DQ  CAK  CAI   aromatic  1.384  0.020  1.384
 3DQ  CAI  CAQ   aromatic  1.394  0.020  1.394
 3DQ  CAJ  CAH   aromatic  1.389  0.020  1.389
 3DQ  CAH  CAQ   aromatic  1.390  0.020  1.390
 3DQ  CAQ  CAL   single    1.505  0.020  1.505
 3DQ  CAL  CAU   single    1.541  0.020  1.541
 3DQ  CAU  CAP   single    1.507  0.020  1.507
 3DQ  CAU  CAV   single    1.554  0.020  1.554
 3DQ  CAP  OAC   double    1.210  0.020  1.210
 3DQ  CAP  CAT   single    1.516  0.020  1.516
 3DQ  CAT  OAF   single    1.398  0.020  1.398
 3DQ  CAT  CAS   single    1.538  0.020  1.538
 3DQ  CAS  OAE   single    1.409  0.020  1.409
 3DQ  CAS  CAM   single    1.520  0.020  1.520
 3DQ  CAM  CAV   single    1.526  0.020  1.526
 3DQ  CAV  CAO   single    1.553  0.020  1.553
 3DQ  CAV  OAG   single    1.410  0.020  1.410
 3DQ  CAO  OAD   deloc     1.252  0.020  1.252
 3DQ  CAO  OAB   deloc     1.238  0.020  1.238
 3DQ  CAA  HAA1  single    0.970  0.020  1.090
 3DQ  CAA  HAA2  single    0.970  0.020  1.090
 3DQ  CAA  HAA3  single    0.970  0.020  1.090
 3DQ  CAK  HAK   single    0.930  0.020  1.080
 3DQ  CAJ  HAJ   single    0.930  0.020  1.080
 3DQ  CAI  HAI   single    0.930  0.020  1.080
 3DQ  CAH  HAH   single    0.930  0.020  1.080
 3DQ  CAL  HAL1  single    0.970  0.020  1.090
 3DQ  CAL  HAL2  single    0.970  0.020  1.090
 3DQ  CAU  HAU   single    0.970  0.020  1.090
 3DQ  CAT  HAT   single    0.970  0.020  1.090
 3DQ  OAF  HAF   single    0.850  0.020  0.980
 3DQ  CAS  HAS   single    0.970  0.020  1.090
 3DQ  OAE  HAE   single    0.850  0.020  0.980
 3DQ  CAM  HAM1  single    0.970  0.020  1.090
 3DQ  CAM  HAM2  single    0.970  0.020  1.090
 3DQ  OAG  HAG   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
 3DQ  HAA3  CAA  HAA2  108.71  3.000
 3DQ  HAA3  CAA  HAA1  108.74  3.000
 3DQ  HAA2  CAA  HAA1  108.67  3.000
 3DQ  HAA3  CAA  OAN   112.07  3.000
 3DQ  HAA2  CAA  OAN   106.57  3.000
 3DQ  HAA1  CAA  OAN   111.97  3.000
 3DQ  CAR   OAN  CAA   118.40  3.000
 3DQ  CAJ   CAR  CAK   119.09  3.000
 3DQ  CAJ   CAR  OAN   124.42  3.000
 3DQ  CAK   CAR  OAN   116.49  3.000
 3DQ  HAK   CAK  CAI   120.26  3.000
 3DQ  HAK   CAK  CAR   119.58  3.000
 3DQ  CAI   CAK  CAR   120.15  3.000
 3DQ  HAI   CAI  CAQ   119.62  3.000
 3DQ  HAI   CAI  CAK   118.74  3.000
 3DQ  CAQ   CAI  CAK   121.64  3.000
 3DQ  HAJ   CAJ  CAH   118.78  3.000
 3DQ  HAJ   CAJ  CAR   121.47  3.000
 3DQ  CAH   CAJ  CAR   119.74  3.000
 3DQ  HAH   CAH  CAQ   119.72  3.000
 3DQ  HAH   CAH  CAJ   118.34  3.000
 3DQ  CAQ   CAH  CAJ   121.94  3.000
 3DQ  CAL   CAQ  CAH   121.06  3.000
 3DQ  CAL   CAQ  CAI   121.49  3.000
 3DQ  CAH   CAQ  CAI   117.44  3.000
 3DQ  HAL2  CAL  HAL1  106.08  3.000
 3DQ  HAL2  CAL  CAU   111.44  3.000
 3DQ  HAL1  CAL  CAU   107.96  3.000
 3DQ  HAL2  CAL  CAQ   109.55  3.000
 3DQ  HAL1  CAL  CAQ   110.00  3.000
 3DQ  CAU   CAL  CAQ   111.64  3.000
 3DQ  HAU   CAU  CAV   107.41  3.000
 3DQ  HAU   CAU  CAP   107.31  3.000
 3DQ  CAV   CAU  CAP   106.16  3.000
 3DQ  HAU   CAU  CAL   107.79  3.000
 3DQ  CAV   CAU  CAL   116.67  3.000
 3DQ  CAP   CAU  CAL   111.11  3.000
 3DQ  CAT   CAP  OAC   120.22  3.000
 3DQ  CAT   CAP  CAU   115.74  3.000
 3DQ  OAC   CAP  CAU   123.97  3.000
 3DQ  HAT   CAT  CAS   107.07  3.000
 3DQ  HAT   CAT  OAF   108.03  3.000
 3DQ  CAS   CAT  OAF   111.82  3.000
 3DQ  HAT   CAT  CAP   108.24  3.000
 3DQ  CAS   CAT  CAP   109.22  3.000
 3DQ  OAF   CAT  CAP   112.25  3.000
 3DQ  HAF   OAF  CAT   107.89  3.000
 3DQ  HAS   CAS  CAM   109.28  3.000
 3DQ  HAS   CAS  OAE   110.25  3.000
 3DQ  CAM   CAS  OAE   108.46  3.000
 3DQ  HAS   CAS  CAT   107.61  3.000
 3DQ  CAM   CAS  CAT   110.67  3.000
 3DQ  OAE   CAS  CAT   110.57  3.000
 3DQ  HAE   OAE  CAS   108.11  3.000
 3DQ  HAM2  CAM  HAM1  106.65  3.000
 3DQ  HAM2  CAM  CAV   109.30  3.000
 3DQ  HAM1  CAM  CAV   110.04  3.000
 3DQ  HAM2  CAM  CAS   109.13  3.000
 3DQ  HAM1  CAM  CAS   109.86  3.000
 3DQ  CAV   CAM  CAS   111.73  3.000
 3DQ  OAG   CAV  CAO   107.86  3.000
 3DQ  OAG   CAV  CAM   108.93  3.000
 3DQ  CAO   CAV  CAM   111.53  3.000
 3DQ  OAG   CAV  CAU   106.82  3.000
 3DQ  CAO   CAV  CAU   110.40  3.000
 3DQ  CAM   CAV  CAU   111.13  3.000
 3DQ  OAD   CAO  OAB   127.64  3.000
 3DQ  OAB   CAO  CAV   118.37  3.000
 3DQ  OAD   CAO  CAV   113.98  3.000
 3DQ  HAG   OAG  CAV   102.03  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
 3DQ  CONST_01  CAQ   CAI  CAK  CAR     0.00   0.0  0
 3DQ  CONST_02  CAQ   CAH  CAJ  CAR     0.00   0.0  0
 3DQ  CONST_03  CAH   CAJ  CAR  CAK     0.00   0.0  0
 3DQ  CONST_04  CAH   CAQ  CAI  CAK     0.00   0.0  0
 3DQ  CONST_05  CAJ   CAR  CAK  CAI     0.00   0.0  0
 3DQ  CONST_06  CAJ   CAH  CAQ  CAI     0.00   0.0  0
 3DQ  CONST_07  CAI   CAK  CAR  OAN   180.00   0.0  0
 3DQ  CONST_08  CAH   CAJ  CAR  OAN   180.00   0.0  0
 3DQ  CONST_09  CAL   CAQ  CAI  CAK   180.00   0.0  0
 3DQ  CONST_10  CAL   CAQ  CAH  CAJ   180.00   0.0  0
 3DQ  CONST_11  HAI   CAI  CAK  CAR   180.00   0.0  0
 3DQ  CONST_12  HAH   CAH  CAJ  CAR   180.00   0.0  0
 3DQ  CONST_13  HAJ   CAJ  CAR  CAK   180.00   0.0  0
 3DQ  CONST_14  HAK   CAK  CAR  CAJ   180.00   0.0  0
 3DQ  Var_01    CAU   CAL  CAQ  CAI   106.05  30.0  2
 3DQ  Var_02    CAK   CAR  OAN  CAA  -179.14  30.0  2
 3DQ  Var_03    HAA1  CAA  OAN  CAR    60.39  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
 3DQ  chir_01  CAU  CAL  CAP  CAV  positiv
 3DQ  chir_02  CAT  OAF  CAP  CAS  positiv
 3DQ  chir_03  CAS  OAE  CAT  CAM  negativ
 3DQ  chir_04  CAV  CAU  CAM  CAO  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
 3DQ  plan-1  OAN  0.020
 3DQ  plan-1  CAR  0.020
 3DQ  plan-1  CAK  0.020
 3DQ  plan-1  CAI  0.020
 3DQ  plan-1  CAJ  0.020
 3DQ  plan-1  CAH  0.020
 3DQ  plan-1  CAQ  0.020
 3DQ  plan-1  CAL  0.020
 3DQ  plan-1  HAK  0.020
 3DQ  plan-1  HAJ  0.020
 3DQ  plan-1  HAI  0.020
 3DQ  plan-1  HAH  0.020
 3DQ  plan-2  CAU  0.020
 3DQ  plan-2  CAP  0.020
 3DQ  plan-2  OAC  0.020
 3DQ  plan-2  CAT  0.020
 3DQ  plan-3  CAV  0.020
 3DQ  plan-3  CAO  0.020
 3DQ  plan-3  OAB  0.020
 3DQ  plan-3  OAD  0.020

