# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 07:20:24 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (1R,2S,4S,5R)-1,4,5-trihydroxy-3-oxo-2-(pentafluorobenzyl)cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@](O)([C@H](Cc2c(F)c(F)c(F)c(F)c2F)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
 2HN  2HN  '(1R,2S,4S,5R)-1,4,5-trihydroxy-3-oxo-2-(pentafluorobenzyl)cyclohexanecarboxylic acid'  ligand  35  25  .  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_2HN
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
 2HN  FAK   F  F      0  -0.293   1.0086  -1.8467  -1.5512
 2HN  CAT   C  CR6    0   0.419   1.7243  -0.9228  -0.9082
 2HN  CAR   C  CR6    0   0.286   3.0358  -1.2346  -0.5981
 2HN  FAI   F  F      0  -0.290   3.5446  -2.4159  -0.9315
 2HN  CAP   C  CR6    0   0.275   3.8185  -0.3084   0.0618
 2HN  FAG   F  F      0  -0.286   5.0769  -0.5945   0.3674
 2HN  CAQ   C  CR6    0   0.281   3.2823   0.9190   0.4030
 2HN  FAH   F  F      0  -0.290   4.0318   1.8156   1.0351
 2HN  CAS   C  CR6    0   0.412   1.9692   1.2015   0.0800
 2HN  FAJ   F  F      0  -0.290   1.4882   2.3979   0.4164
 2HN  CAU   C  CR6    0  -0.290   1.1511   0.2945  -0.5786
 2HN  CAL   C  CH2    0  -0.520  -0.2774   0.6375  -0.9040
 2HN  CAX   C  CH1    0  -0.380  -1.1890   0.5592   0.3380
 2HN  CAY   C  CT     0   0.080  -2.6797   0.9164   0.1111
 2HN  OAF   O  OH1    0  -0.698  -3.2798   0.9356   1.3865
 2HN  CAN   C  C      0   0.443  -2.8162   2.3338  -0.5075
 2HN  OAC   O  OC    -1  -0.595  -3.1601   3.2166   0.3087
 2HN  OAA   O  O      0  -0.573  -2.5787   2.4696  -1.7159
 2HN  CAO   C  C      0   0.385  -1.1387  -0.8187   0.9591
 2HN  OAB   O  O      0  -0.381  -0.4991  -1.0635   1.9550
 2HN  CAW   C  CH1    0  -0.070  -1.9026  -1.9152   0.2324
 2HN  OAE   O  OH1    0  -0.665  -1.9377  -3.1099   0.9570
 2HN  CAV   C  CH1    0   0.055  -3.3444  -1.5018  -0.0748
 2HN  OAD   O  OH1    0  -0.670  -3.9546  -2.4300  -0.9420
 2HN  CAM   C  CH2    0  -0.491  -3.3764  -0.1379  -0.7429
 2HN  HAL1  H  HCH2   0   0.296  -0.3175   1.6504  -1.2996
 2HN  HAL2  H  HCH2   0   0.275  -0.6430  -0.0030  -1.7056
 2HN  HAX   H  HCH1   0   0.280  -0.8011   1.2594   1.0831
 2HN  HAF   H  HOH1   0   0.433  -3.4032   1.8921   1.5447
 2HN  HAM1  H  HCH2   0   0.258  -4.4168   0.1556  -0.9070
 2HN  HAM2  H  HCH2   0   0.242  -2.9095  -0.1986  -1.7286
 2HN  HAW   H  HCH1   0   0.235  -1.4034  -2.0506  -0.7421
 2HN  HAE   H  HOH1   0   0.455  -1.0395  -3.3800   1.1746
 2HN  HAV   H  HCH1   0   0.221  -3.8914  -1.4512   0.8761
 2HN  HAD   H  HOH1   0   0.451  -4.0247  -3.2732  -0.4832

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
 2HN  FAK  CAT   single    1.334  0.020  1.334
 2HN  CAT  CAR   aromatic  1.383  0.020  1.383
 2HN  CAT  CAU   aromatic  1.385  0.020  1.385
 2HN  CAR  FAI   single    1.329  0.020  1.329
 2HN  CAR  CAP   aromatic  1.380  0.020  1.380
 2HN  CAP  FAG   single    1.326  0.020  1.326
 2HN  CAP  CAQ   aromatic  1.382  0.020  1.382
 2HN  CAQ  FAH   single    1.329  0.020  1.329
 2HN  CAQ  CAS   aromatic  1.381  0.020  1.381
 2HN  CAS  FAJ   single    1.333  0.020  1.333
 2HN  CAS  CAU   aromatic  1.388  0.020  1.388
 2HN  CAU  CAL   single    1.505  0.020  1.505
 2HN  CAL  CAX   single    1.543  0.020  1.543
 2HN  CAX  CAY   single    1.550  0.020  1.550
 2HN  CAX  CAO   single    1.512  0.020  1.512
 2HN  CAY  OAF   single    1.410  0.020  1.410
 2HN  CAY  CAN   single    1.553  0.020  1.553
 2HN  CAY  CAM   single    1.525  0.020  1.525
 2HN  CAN  OAC   deloc     1.251  0.020  1.251
 2HN  CAN  OAA   deloc     1.239  0.020  1.239
 2HN  CAO  OAB   double    1.209  0.020  1.209
 2HN  CAO  CAW   single    1.521  0.020  1.521
 2HN  CAW  OAE   single    1.398  0.020  1.398
 2HN  CAW  CAV   single    1.531  0.020  1.531
 2HN  CAV  OAD   single    1.409  0.020  1.409
 2HN  CAV  CAM   single    1.519  0.020  1.519
 2HN  CAL  HAL1  single    0.970  0.020  1.090
 2HN  CAL  HAL2  single    0.970  0.020  1.090
 2HN  CAX  HAX   single    0.970  0.020  1.090
 2HN  OAF  HAF   single    0.850  0.020  0.980
 2HN  CAM  HAM1  single    0.970  0.020  1.090
 2HN  CAM  HAM2  single    0.970  0.020  1.090
 2HN  CAW  HAW   single    0.970  0.020  1.090
 2HN  OAE  HAE   single    0.850  0.020  0.980
 2HN  CAV  HAV   single    0.970  0.020  1.090
 2HN  OAD  HAD   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
 2HN  CAU   CAT  CAR   122.48  3.000
 2HN  CAU   CAT  FAK   120.08  3.000
 2HN  CAR   CAT  FAK   117.44  3.000
 2HN  CAP   CAR  FAI   119.96  3.000
 2HN  CAP   CAR  CAT   119.57  3.000
 2HN  FAI   CAR  CAT   120.47  3.000
 2HN  CAQ   CAP  FAG   120.18  3.000
 2HN  CAQ   CAP  CAR   119.59  3.000
 2HN  FAG   CAP  CAR   120.23  3.000
 2HN  CAS   CAQ  FAH   120.63  3.000
 2HN  CAS   CAQ  CAP   119.51  3.000
 2HN  FAH   CAQ  CAP   119.86  3.000
 2HN  CAU   CAS  FAJ   119.59  3.000
 2HN  CAU   CAS  CAQ   122.53  3.000
 2HN  FAJ   CAS  CAQ   117.88  3.000
 2HN  CAL   CAU  CAS   120.89  3.000
 2HN  CAL   CAU  CAT   122.80  3.000
 2HN  CAS   CAU  CAT   116.32  3.000
 2HN  HAL2  CAL  HAL1  105.51  3.000
 2HN  HAL2  CAL  CAX   111.36  3.000
 2HN  HAL1  CAL  CAX   108.55  3.000
 2HN  HAL2  CAL  CAU   110.11  3.000
 2HN  HAL1  CAL  CAU   109.01  3.000
 2HN  CAX   CAL  CAU   112.05  3.000
 2HN  HAX   CAX  CAO   106.96  3.000
 2HN  HAX   CAX  CAY   107.06  3.000
 2HN  CAO   CAX  CAY   107.59  3.000
 2HN  HAX   CAX  CAL   107.84  3.000
 2HN  CAO   CAX  CAL   110.93  3.000
 2HN  CAY   CAX  CAL   116.04  3.000
 2HN  CAM   CAY  CAN   111.58  3.000
 2HN  CAM   CAY  OAF   108.76  3.000
 2HN  CAN   CAY  OAF   108.10  3.000
 2HN  CAM   CAY  CAX   111.23  3.000
 2HN  CAN   CAY  CAX   110.69  3.000
 2HN  OAF   CAY  CAX   106.27  3.000
 2HN  HAF   OAF  CAY   102.33  3.000
 2HN  OAA   CAN  OAC   127.72  3.000
 2HN  OAA   CAN  CAY   118.16  3.000
 2HN  OAC   CAN  CAY   114.12  3.000
 2HN  CAW   CAO  OAB   120.89  3.000
 2HN  CAW   CAO  CAX   116.35  3.000
 2HN  OAB   CAO  CAX   122.72  3.000
 2HN  HAW   CAW  CAV   106.38  3.000
 2HN  HAW   CAW  OAE   111.37  3.000
 2HN  CAV   CAW  OAE   108.12  3.000
 2HN  HAW   CAW  CAO   106.45  3.000
 2HN  CAV   CAW  CAO   111.97  3.000
 2HN  OAE   CAW  CAO   112.40  3.000
 2HN  HAE   OAE  CAW   109.47  3.000
 2HN  HAV   CAV  CAM   109.20  3.000
 2HN  HAV   CAV  OAD   110.33  3.000
 2HN  CAM   CAV  OAD   108.16  3.000
 2HN  HAV   CAV  CAW   107.93  3.000
 2HN  CAM   CAV  CAW   110.52  3.000
 2HN  OAD   CAV  CAW   110.70  3.000
 2HN  HAD   OAD  CAV   108.37  3.000
 2HN  HAM2  CAM  HAM1  106.63  3.000
 2HN  HAM2  CAM  CAV   109.75  3.000
 2HN  HAM1  CAM  CAV   109.09  3.000
 2HN  HAM2  CAM  CAY   110.39  3.000
 2HN  HAM1  CAM  CAY   109.46  3.000
 2HN  CAV   CAM  CAY   111.39  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
 2HN  CONST_01  CAQ  CAP  CAR  CAT    0.00   0.0  0
 2HN  CONST_02  CAQ  CAS  CAU  CAT    0.00   0.0  0
 2HN  CONST_03  CAS  CAU  CAT  CAR    0.00   0.0  0
 2HN  CONST_04  CAS  CAQ  CAP  CAR    0.00   0.0  0
 2HN  CONST_05  CAU  CAT  CAR  CAP    0.00   0.0  0
 2HN  CONST_06  CAU  CAS  CAQ  CAP    0.00   0.0  0
 2HN  CONST_07  CAP  CAR  CAT  FAK  180.00   0.0  0
 2HN  CONST_08  CAS  CAU  CAT  FAK  180.00   0.0  0
 2HN  CONST_09  FAG  CAP  CAR  CAT  180.00   0.0  0
 2HN  CONST_10  FAJ  CAS  CAU  CAT  180.00   0.0  0
 2HN  CONST_11  CAL  CAU  CAT  CAR  180.00   0.0  0
 2HN  CONST_12  FAH  CAQ  CAP  CAR  180.00   0.0  0
 2HN  CONST_13  CAU  CAT  CAR  FAI  180.00   0.0  0
 2HN  CONST_14  CAQ  CAP  CAR  FAI  180.00   0.0  0
 2HN  CONST_15  FAJ  CAS  CAQ  CAP  180.00   0.0  0
 2HN  CONST_16  CAS  CAQ  CAP  FAG  180.00   0.0  0
 2HN  CONST_17  CAL  CAU  CAS  CAQ  180.00   0.0  0
 2HN  CONST_18  CAU  CAS  CAQ  FAH  180.00   0.0  0
 2HN  Var_01    CAX  CAL  CAU  CAT  103.97  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
 2HN  chir_01  CAX  CAL  CAY  CAO  negativ
 2HN  chir_02  CAY  CAM  CAN  CAX  positiv
 2HN  chir_03  CAW  OAE  CAO  CAV  positiv
 2HN  chir_04  CAV  OAD  CAW  CAM  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
 2HN  plan-1  FAK  0.020
 2HN  plan-1  CAT  0.020
 2HN  plan-1  CAR  0.020
 2HN  plan-1  FAI  0.020
 2HN  plan-1  CAP  0.020
 2HN  plan-1  FAG  0.020
 2HN  plan-1  CAQ  0.020
 2HN  plan-1  FAH  0.020
 2HN  plan-1  CAS  0.020
 2HN  plan-1  FAJ  0.020
 2HN  plan-1  CAU  0.020
 2HN  plan-1  CAL  0.020
 2HN  plan-2  CAX  0.020
 2HN  plan-2  CAO  0.020
 2HN  plan-2  OAB  0.020
 2HN  plan-2  CAW  0.020
 2HN  plan-3  CAY  0.020
 2HN  plan-3  CAN  0.020
 2HN  plan-3  OAC  0.020
 2HN  plan-3  OAA  0.020

