# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:06:00 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (1R,4R,5R)-1,4,5-trihydroxy-3-[(1R)-1-hydroxy-2-phenylethyl]cyclohex-2-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@](O)(C=C([C@H](O)Cc2ccccc2)[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
 NDY  NDY  '(1R,4R,5R)-1,4,5-trihydroxy-3-[(1R)-1-hydroxy-2-phenylethyl]cyclohex-2-ene-1-carboxylic acid'  ligand  38  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NDY
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
 NDY  CAK   C  CR16   0  -0.305  -4.0451   0.9432   0.0074
 NDY  CAI   C  CR16   0  -0.241  -5.4016   0.7897   0.2588
 NDY  CAH   C  CR16   0  -0.274  -6.0163  -0.4370   0.0398
 NDY  CAJ   C  CR16   0  -0.242  -5.2630  -1.5044  -0.4306
 NDY  CAL   C  CR16   0  -0.320  -3.9052  -1.3455  -0.6766
 NDY  CAQ   C  CR6    0   0.160  -3.2782  -0.1207  -0.4644
 NDY  CAM   C  CH2    0  -0.578  -1.8065   0.0564  -0.6997
 NDY  CAR   C  CH1    0   0.018  -0.9955  -0.0836   0.6002
 NDY  OAC   O  OH1    0  -0.650  -1.2236  -1.3311   1.2047
 NDY  CAP   C  CR6    0   0.012   0.4740   0.2041   0.3601
 NDY  CAG   C  CR16   0  -0.236   1.4222  -0.6934   0.6201
 NDY  CAU   C  CR6    0   0.035   2.8956  -0.4780   0.4024
 NDY  CAO   C  C      0   0.413   3.5180  -1.7395  -0.2589
 NDY  OAB   O  OC    -1  -0.603   4.4815  -2.2345   0.3701
 NDY  OAA   O  O      0  -0.577   3.0278  -2.1351  -1.3247
 NDY  OAF   O  OH1    0  -0.703   3.5142  -0.2948   1.6586
 NDY  CAN   C  C      0  -0.493   3.1262   0.7369  -0.4979
 NDY  CAS   C  CR16   0   0.045   2.2714   1.9024  -0.0356
 NDY  OAD   O  OH1    0  -0.684   2.5094   3.0849  -0.7743
 NDY  CAT   C  CR16   0  -0.011   0.8038   1.5550  -0.2290
 NDY  OAE   O  OH1    0  -0.674  -0.0419   2.5185   0.3645
 NDY  HAK   H  HCR6   0   0.244  -3.5737   1.9051   0.1774
 NDY  HAI   H  HCR6   0   0.252  -5.9797   1.6305   0.6208
 NDY  HAH   H  HCR6   0   0.252  -7.0748  -0.5589   0.2305
 NDY  HAJ   H  HCR6   0   0.252  -5.7324  -2.4640  -0.6072
 NDY  HAL   H  HCR6   0   0.242  -3.3305  -2.1849  -1.0503
 NDY  HAM1  H  HCH2   0   0.254  -1.4440  -0.6768  -1.4278
 NDY  HAM2  H  HCH2   0   0.266  -1.6234   1.0422  -1.1285
 NDY  HAR   H  HCH1   0   0.250  -1.3803   0.6520   1.3127
 NDY  HAC   H  HOH1   0   0.443  -1.0154  -2.0264   0.5705
 NDY  HAG   H  HCR6   0   0.234   1.1455  -1.6460   1.0601
 NDY  HAT   H  HCR6   0   0.218   0.6216   1.5095  -1.3164
 NDY  HAF   H  HOH1   0   0.426   4.2033  -0.9891   1.6440
 NDY  HAN1  H  H      0   0.238   4.1873   1.0053  -0.4843
 NDY  HAN2  H  H      0   0.229   2.8665   0.4873  -1.5310
 NDY  HAS   H  HCR6   0   0.204   2.4447   2.0760   1.0360
 NDY  HAD   H  HOH1   0   0.452   3.3900   3.4061  -0.5581
 NDY  HAE   H  HOH1   0   0.452   0.0987   3.3538  -0.0924

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
 NDY  CAK  CAI   aromatic  1.388  0.020  1.388
 NDY  CAK  CAQ   aromatic  1.394  0.020  1.394
 NDY  CAI  CAH   aromatic  1.389  0.020  1.389
 NDY  CAH  CAJ   aromatic  1.389  0.020  1.389
 NDY  CAJ  CAL   aromatic  1.389  0.020  1.389
 NDY  CAL  CAQ   aromatic  1.392  0.020  1.392
 NDY  CAQ  CAM   single    1.501  0.020  1.501
 NDY  CAM  CAR   single    1.539  0.020  1.539
 NDY  CAR  OAC   single    1.405  0.020  1.405
 NDY  CAR  CAP   single    1.516  0.020  1.516
 NDY  CAP  CAG   double    1.331  0.020  1.331
 NDY  CAP  CAT   single    1.510  0.020  1.510
 NDY  CAG  CAU   single    1.505  0.020  1.505
 NDY  CAU  CAO   single    1.554  0.020  1.554
 NDY  CAU  OAF   single    1.412  0.020  1.412
 NDY  CAU  CAN   single    1.530  0.020  1.530
 NDY  CAO  OAB   deloc     1.253  0.020  1.253
 NDY  CAO  OAA   deloc     1.238  0.020  1.238
 NDY  CAN  CAS   single    1.517  0.020  1.517
 NDY  CAS  OAD   single    1.414  0.020  1.414
 NDY  CAS  CAT   single    1.521  0.020  1.521
 NDY  CAT  OAE   single    1.413  0.020  1.413
 NDY  CAK  HAK   single    0.930  0.020  1.080
 NDY  CAI  HAI   single    0.930  0.020  1.080
 NDY  CAH  HAH   single    0.930  0.020  1.080
 NDY  CAJ  HAJ   single    0.930  0.020  1.080
 NDY  CAL  HAL   single    0.930  0.020  1.080
 NDY  CAM  HAM1  single    0.970  0.020  1.090
 NDY  CAM  HAM2  single    0.970  0.020  1.090
 NDY  CAR  HAR   single    0.970  0.020  1.090
 NDY  OAC  HAC   single    0.850  0.020  0.980
 NDY  CAG  HAG   single    0.930  0.020  1.080
 NDY  CAT  HAT   single    0.970  0.020  1.090
 NDY  OAF  HAF   single    0.850  0.020  0.980
 NDY  CAN  HAN1  single    0.970  0.020  1.090
 NDY  CAN  HAN2  single    0.970  0.020  1.090
 NDY  CAS  HAS   single    0.970  0.020  1.090
 NDY  OAD  HAD   single    0.850  0.020  0.980
 NDY  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
 NDY  HAK   CAK  CAQ   119.40  3.000
 NDY  HAK   CAK  CAI   119.63  3.000
 NDY  CAQ   CAK  CAI   120.97  3.000
 NDY  HAI   CAI  CAH   120.14  3.000
 NDY  HAI   CAI  CAK   119.77  3.000
 NDY  CAH   CAI  CAK   120.09  3.000
 NDY  HAH   CAH  CAJ   120.24  3.000
 NDY  HAH   CAH  CAI   120.29  3.000
 NDY  CAJ   CAH  CAI   119.48  3.000
 NDY  HAJ   CAJ  CAL   119.75  3.000
 NDY  HAJ   CAJ  CAH   120.09  3.000
 NDY  CAL   CAJ  CAH   120.16  3.000
 NDY  HAL   CAL  CAQ   119.68  3.000
 NDY  HAL   CAL  CAJ   119.39  3.000
 NDY  CAQ   CAL  CAJ   120.92  3.000
 NDY  CAM   CAQ  CAL   121.43  3.000
 NDY  CAM   CAQ  CAK   120.17  3.000
 NDY  CAL   CAQ  CAK   118.38  3.000
 NDY  HAM2  CAM  HAM1  106.76  3.000
 NDY  HAM2  CAM  CAR   109.02  3.000
 NDY  HAM1  CAM  CAR   109.05  3.000
 NDY  HAM2  CAM  CAQ   109.45  3.000
 NDY  HAM1  CAM  CAQ   110.48  3.000
 NDY  CAR   CAM  CAQ   111.94  3.000
 NDY  HAR   CAR  CAP   108.45  3.000
 NDY  HAR   CAR  OAC   105.05  3.000
 NDY  CAP   CAR  OAC   113.20  3.000
 NDY  HAR   CAR  CAM   107.68  3.000
 NDY  CAP   CAR  CAM   111.08  3.000
 NDY  OAC   CAR  CAM   111.02  3.000
 NDY  HAC   OAC  CAR   108.81  3.000
 NDY  CAT   CAP  CAG   121.58  3.000
 NDY  CAT   CAP  CAR   116.30  3.000
 NDY  CAG   CAP  CAR   122.10  3.000
 NDY  HAG   CAG  CAU   115.72  3.000
 NDY  HAG   CAG  CAP   119.30  3.000
 NDY  CAU   CAG  CAP   124.93  3.000
 NDY  CAN   CAU  OAF   110.76  3.000
 NDY  CAN   CAU  CAO   109.51  3.000
 NDY  OAF   CAU  CAO   107.96  3.000
 NDY  CAN   CAU  CAG   110.27  3.000
 NDY  OAF   CAU  CAG   108.59  3.000
 NDY  CAO   CAU  CAG   109.72  3.000
 NDY  OAA   CAO  OAB   127.64  3.000
 NDY  OAA   CAO  CAU   117.84  3.000
 NDY  OAB   CAO  CAU   114.53  3.000
 NDY  HAF   OAF  CAU   101.72  3.000
 NDY  HAN2  CAN  HAN1  107.32  3.000
 NDY  HAN2  CAN  CAS   109.22  3.000
 NDY  HAN1  CAN  CAS   110.73  3.000
 NDY  HAN2  CAN  CAU   109.80  3.000
 NDY  HAN1  CAN  CAU   109.49  3.000
 NDY  CAS   CAN  CAU   110.24  3.000
 NDY  HAS   CAS  CAT   108.19  3.000
 NDY  HAS   CAS  OAD   110.52  3.000
 NDY  CAT   CAS  OAD   106.68  3.000
 NDY  HAS   CAS  CAN   109.23  3.000
 NDY  CAT   CAS  CAN   109.24  3.000
 NDY  OAD   CAS  CAN   112.85  3.000
 NDY  HAD   OAD  CAS   108.41  3.000
 NDY  HAT   CAT  OAE   110.08  3.000
 NDY  HAT   CAT  CAS   107.10  3.000
 NDY  OAE   CAT  CAS   111.63  3.000
 NDY  HAT   CAT  CAP   108.14  3.000
 NDY  OAE   CAT  CAP   108.39  3.000
 NDY  CAS   CAT  CAP   111.44  3.000
 NDY  HAE   OAE  CAT   107.76  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
 NDY  CONST_01  CAJ  CAH  CAI  CAK    0.00   0.0  0
 NDY  CONST_02  CAJ  CAL  CAQ  CAK    0.00   0.0  0
 NDY  CONST_03  CAL  CAQ  CAK  CAI    0.00   0.0  0
 NDY  CONST_04  CAL  CAJ  CAH  CAI    0.00   0.0  0
 NDY  CONST_05  CAQ  CAK  CAI  CAH    0.00   0.0  0
 NDY  CONST_06  CAQ  CAL  CAJ  CAH    0.00   0.0  0
 NDY  CONST_07  CAM  CAQ  CAK  CAI  180.00   0.0  0
 NDY  CONST_08  CAM  CAQ  CAL  CAJ  180.00   0.0  0
 NDY  CONST_09  HAH  CAH  CAI  CAK  180.00   0.0  0
 NDY  CONST_10  HAL  CAL  CAQ  CAK  180.00   0.0  0
 NDY  CONST_11  HAJ  CAJ  CAH  CAI  180.00   0.0  0
 NDY  CONST_12  HAK  CAK  CAI  CAH  180.00   0.0  0
 NDY  CONST_13  HAI  CAI  CAH  CAJ  180.00   0.0  0
 NDY  Var_01    CAT  CAP  CAG  CAU    1.54  30.0  1
 NDY  Var_02    CAR  CAM  CAQ  CAK   81.80  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
 NDY  chir_01  CAR  CAM  OAC  CAP  negativ
 NDY  chir_02  CAU  CAN  CAO  CAG  positiv
 NDY  chir_03  CAS  OAD  CAN  CAT  positiv
 NDY  chir_04  CAT  OAE  CAS  CAP  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
 NDY  plan-1  CAK  0.020
 NDY  plan-1  CAI  0.020
 NDY  plan-1  CAH  0.020
 NDY  plan-1  CAJ  0.020
 NDY  plan-1  CAL  0.020
 NDY  plan-1  CAQ  0.020
 NDY  plan-1  CAM  0.020
 NDY  plan-1  HAK  0.020
 NDY  plan-1  HAI  0.020
 NDY  plan-1  HAH  0.020
 NDY  plan-1  HAJ  0.020
 NDY  plan-1  HAL  0.020
 NDY  plan-2  CAU  0.020
 NDY  plan-2  CAO  0.020
 NDY  plan-2  OAB  0.020
 NDY  plan-2  OAA  0.020

