# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 11:40:30 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{S},6~{R})-2-(hydroxymethyl)-6-[4-[2,3,4,5,6-pentakis(fluoranyl)phenyl]phenoxy]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccc(cc2)c3c(F)c(F)c(F)c(F)c3F)[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 EJN  EJN  (2~{R},3~{S},4~{S},5~{S},6~{R})-2-(hydroxymethyl)-6-[4-[2,3,4,5,6-pentakis(fluoranyl)phenyl]phenoxy]oxane-3,4,5-triol  ligand  44  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EJN
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
 EJN  O3   O  OH1   0  -0.671   6.5625   1.4686  -0.8247
 EJN  C4   C  CH1   0   0.027   5.5431  -0.6243  -0.3815
 EJN  C5   C  CH1   0  -0.014   4.2103  -1.3170  -0.0886
 EJN  O4   O  OH1   0  -0.674   6.0912  -1.2330  -1.5259
 EJN  C6   C  CH2   0  -0.160   4.4085  -2.7610   0.3217
 EJN  O5   O  O2    0  -0.488   3.5322  -0.6713   0.9796
 EJN  O6   O  OH1   0  -0.667   3.1485  -3.3711   0.4662
 EJN  C1   C  CH1   0   0.200   3.2790   0.6816   0.8214
 EJN  C2   C  CH1   0  -0.021   4.5641   1.4781   0.5722
 EJN  C3   C  CH1   0   0.002   5.3095   0.8653  -0.6108
 EJN  CAA  C  CR6   0   0.387   1.0989   0.7201  -0.1707
 EJN  CAB  C  CR16  0  -0.339   0.3089   1.3055  -1.1589
 EJN  CAC  C  CR16  0  -0.260  -1.0638   1.1529  -1.1341
 EJN  CAD  C  CR6   0   0.092  -1.6783   0.4138  -0.1249
 EJN  CAE  C  CR16  0  -0.264  -0.8816  -0.1793   0.8465
 EJN  CAF  C  CR16  0  -0.349   0.4993  -0.0403   0.8294
 EJN  CAG  C  CR6   0  -0.420  -3.1480   0.2729  -0.0890
 EJN  CAH  C  CR6   0   0.437  -3.7653  -0.9612  -0.2273
 EJN  CAI  C  CR6   0   0.276  -5.1404  -1.0981  -0.1963
 EJN  CAJ  C  CR6   0   0.282  -5.9335   0.0211  -0.0271
 EJN  CAK  C  CR6   0   0.277  -5.3480   1.2654   0.1120
 EJN  CAL  C  CR6   0   0.437  -3.9711   1.3765   0.0811
 EJN  FAH  F  F     0  -0.282  -3.0274  -2.0523  -0.4096
 EJN  FAI  F  F     0  -0.290  -5.7050  -2.2926  -0.3370
 EJN  FAJ  F  F     0  -0.285  -7.2536  -0.0992   0.0037
 EJN  FAK  F  F     0  -0.290  -6.1095   2.3406   0.2828
 EJN  FAL  F  F     0  -0.282  -3.4329   2.5834   0.2324
 EJN  O1   O  O2    0  -0.501   2.4276   0.9488  -0.2700
 EJN  O2   O  OH1   0  -0.665   5.3915   1.4114   1.7034
 EJN  H32  H  HOH1  0   0.458   6.4330   2.2830  -1.3194
 EJN  H41  H  HCH1  0   0.216   6.2067  -0.7527   0.4862
 EJN  H5   H  HCH1  0   0.231   3.5985  -1.2907  -1.0014
 EJN  H42  H  HOH1  0   0.453   6.9130  -0.7781  -1.7381
 EJN  H61  H  HCH2  0   0.213   5.0126  -3.2561  -0.4457
 EJN  H62  H  HCH2  0   0.196   4.9872  -2.7888   1.2558
 EJN  H63  H  HOH1  0   0.456   3.2923  -4.3012   0.6622
 EJN  H1   H  HCH1  0   0.266   2.8046   1.0105   1.7544
 EJN  H21  H  HCH1  0   0.241   4.2905   2.5152   0.3358
 EJN  H31  H  HCH1  0   0.232   4.6726   0.9693  -1.4995
 EJN  HAB  H  HCR6  0   0.271   0.7783   1.8871  -1.9420
 EJN  HAC  H  HCR6  0   0.263  -1.6587   1.6107  -1.9141
 EJN  HAE  H  HCR6  0   0.265  -1.3362  -0.7548   1.6427
 EJN  HAF  H  HCR6  0   0.288   1.0810  -0.5368   1.5923
 EJN  H22  H  HOH1  0   0.458   5.0110   1.9590   2.3969

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
 EJN  O3   C3   single    1.407  0.020  1.407
 EJN  C3   C2   single    1.527  0.020  1.527
 EJN  C3   C4   single    1.525  0.020  1.525
 EJN  CAF  CAE  aromatic  1.388  0.020  1.388
 EJN  CAF  CAA  aromatic  1.392  0.020  1.392
 EJN  O4   C4   single    1.407  0.020  1.407
 EJN  CAE  CAD  aromatic  1.389  0.020  1.389
 EJN  O1   CAA  single    1.352  0.020  1.352
 EJN  O1   C1   single    1.410  0.020  1.410
 EJN  C2   C1   single    1.532  0.020  1.532
 EJN  C2   O2   single    1.403  0.020  1.403
 EJN  CAA  CAB  aromatic  1.394  0.020  1.394
 EJN  C4   C5   single    1.530  0.020  1.530
 EJN  FAL  CAL  single    1.330  0.020  1.330
 EJN  C1   O5   single    1.385  0.020  1.385
 EJN  CAD  CAG  single    1.477  0.020  1.477
 EJN  CAD  CAC  aromatic  1.394  0.020  1.394
 EJN  C5   O5   single    1.420  0.020  1.420
 EJN  C5   C6   single    1.514  0.020  1.514
 EJN  CAL  CAG  aromatic  1.387  0.020  1.387
 EJN  CAL  CAK  aromatic  1.382  0.020  1.382
 EJN  FAK  CAK  single    1.329  0.020  1.329
 EJN  CAG  CAH  aromatic  1.387  0.020  1.387
 EJN  CAB  CAC  aromatic  1.381  0.020  1.381
 EJN  CAK  CAJ  aromatic  1.382  0.020  1.382
 EJN  CAH  FAH  single    1.330  0.020  1.330
 EJN  CAH  CAI  aromatic  1.382  0.020  1.382
 EJN  C6   O6   single    1.407  0.020  1.407
 EJN  CAJ  CAI  aromatic  1.382  0.020  1.382
 EJN  CAJ  FAJ  single    1.326  0.020  1.326
 EJN  CAI  FAI  single    1.329  0.020  1.329
 EJN  O3   H32  single    0.850  0.020  0.980
 EJN  C4   H41  single    0.970  0.020  1.090
 EJN  C5   H5   single    0.970  0.020  1.090
 EJN  O4   H42  single    0.850  0.020  0.980
 EJN  C6   H61  single    0.970  0.020  1.090
 EJN  C6   H62  single    0.970  0.020  1.090
 EJN  O6   H63  single    0.850  0.020  0.980
 EJN  C1   H1   single    0.970  0.020  1.090
 EJN  C2   H21  single    0.970  0.020  1.090
 EJN  C3   H31  single    0.970  0.020  1.090
 EJN  CAB  HAB  single    0.930  0.020  1.080
 EJN  CAC  HAC  single    0.930  0.020  1.080
 EJN  CAE  HAE  single    0.930  0.020  1.080
 EJN  CAF  HAF  single    0.930  0.020  1.080
 EJN  O2   H22  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
 EJN  H32  O3   C3   108.74  3.000
 EJN  H41  C4   C3   108.97  3.000
 EJN  H41  C4   O4   110.85  3.000
 EJN  C3   C4   O4   111.09  3.000
 EJN  H41  C4   C5   108.76  3.000
 EJN  O4   C4   C5   107.40  3.000
 EJN  C3   C4   C5   109.73  3.000
 EJN  H5   C5   O5   110.36  3.000
 EJN  H5   C5   C6   108.70  3.000
 EJN  O5   C5   C6   106.99  3.000
 EJN  H5   C5   C4   108.36  3.000
 EJN  C6   C5   C4   111.69  3.000
 EJN  O5   C5   C4   110.73  3.000
 EJN  H42  O4   C4   107.89  3.000
 EJN  H62  C6   H61  107.08  3.000
 EJN  H62  C6   O6   111.91  3.000
 EJN  H61  C6   O6   111.71  3.000
 EJN  H62  C6   C5   108.86  3.000
 EJN  H61  C6   C5   108.27  3.000
 EJN  O6   C6   C5   108.91  3.000
 EJN  C1   O5   C5   116.44  3.000
 EJN  H63  O6   C6   107.85  3.000
 EJN  H1   C1   O1   109.89  3.000
 EJN  H1   C1   C2   110.19  3.000
 EJN  O1   C1   C2   106.39  3.000
 EJN  H1   C1   O5   105.94  3.000
 EJN  C2   C1   O5   111.90  3.000
 EJN  O1   C1   O5   112.57  3.000
 EJN  H21  C2   O2   111.43  3.000
 EJN  H21  C2   C3   109.50  3.000
 EJN  O2   C2   C3   108.52  3.000
 EJN  H21  C2   C1   108.47  3.000
 EJN  O2   C2   C1   109.80  3.000
 EJN  C3   C2   C1   109.08  3.000
 EJN  H31  C3   C2   107.81  3.000
 EJN  H31  C3   C4   107.64  3.000
 EJN  C2   C3   C4   110.50  3.000
 EJN  H31  C3   O3   110.66  3.000
 EJN  C4   C3   O3   107.77  3.000
 EJN  C2   C3   O3   112.37  3.000
 EJN  O1   CAA  CAF  124.64  3.000
 EJN  O1   CAA  CAB  115.72  3.000
 EJN  CAF  CAA  CAB  119.64  3.000
 EJN  HAB  CAB  CAC  120.22  3.000
 EJN  HAB  CAB  CAA  119.51  3.000
 EJN  CAC  CAB  CAA  120.27  3.000
 EJN  HAC  CAC  CAD  120.24  3.000
 EJN  HAC  CAC  CAB  119.11  3.000
 EJN  CAD  CAC  CAB  120.65  3.000
 EJN  CAG  CAD  CAE  120.86  3.000
 EJN  CAG  CAD  CAC  120.46  3.000
 EJN  CAE  CAD  CAC  118.67  3.000
 EJN  HAE  CAE  CAF  118.70  3.000
 EJN  HAE  CAE  CAD  120.02  3.000
 EJN  CAF  CAE  CAD  121.28  3.000
 EJN  HAF  CAF  CAE  118.75  3.000
 EJN  HAF  CAF  CAA  121.77  3.000
 EJN  CAE  CAF  CAA  119.48  3.000
 EJN  CAL  CAG  CAH  117.13  3.000
 EJN  CAH  CAG  CAD  121.70  3.000
 EJN  CAL  CAG  CAD  121.17  3.000
 EJN  FAH  CAH  CAI  118.29  3.000
 EJN  CAI  CAH  CAG  121.92  3.000
 EJN  FAH  CAH  CAG  119.79  3.000
 EJN  FAI  CAI  CAJ  119.81  3.000
 EJN  FAI  CAI  CAH  120.62  3.000
 EJN  CAJ  CAI  CAH  119.57  3.000
 EJN  FAJ  CAJ  CAK  120.07  3.000
 EJN  FAJ  CAJ  CAI  120.05  3.000
 EJN  CAK  CAJ  CAI  119.88  3.000
 EJN  FAK  CAK  CAL  120.59  3.000
 EJN  FAK  CAK  CAJ  119.91  3.000
 EJN  CAL  CAK  CAJ  119.50  3.000
 EJN  FAL  CAL  CAK  118.27  3.000
 EJN  CAK  CAL  CAG  122.01  3.000
 EJN  FAL  CAL  CAG  119.72  3.000
 EJN  CAA  O1   C1   120.31  3.000
 EJN  H22  O2   C2   108.71  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
 EJN  CONST_01  CAD  CAE  CAF  CAA    0.00   0.0  0
 EJN  CONST_02  CAD  CAC  CAB  CAA    0.00   0.0  0
 EJN  CONST_03  CAE  CAF  CAA  CAB    0.00   0.0  0
 EJN  CONST_04  CAE  CAD  CAC  CAB    0.00   0.0  0
 EJN  CONST_05  CAG  CAD  CAC  CAB  180.00   0.0  0
 EJN  CONST_06  CAF  CAE  CAD  CAC    0.00   0.0  0
 EJN  CONST_09  CAF  CAA  CAB  CAC    0.00   0.0  0
 EJN  CONST_10  CAK  CAL  CAG  CAD  180.00   0.0  0
 EJN  CONST_11  CAI  CAH  CAG  CAD  180.00   0.0  0
 EJN  CONST_14  CAG  CAD  CAE  CAF  180.00   0.0  0
 EJN  CONST_15  CAJ  CAK  CAL  CAG    0.00   0.0  0
 EJN  CONST_16  CAJ  CAI  CAH  CAG    0.00   0.0  0
 EJN  CONST_17  CAK  CAL  CAG  CAH    0.00   0.0  0
 EJN  CONST_18  CAK  CAJ  CAI  CAH    0.00   0.0  0
 EJN  CONST_19  CAL  CAG  CAH  CAI    0.00   0.0  0
 EJN  CONST_20  CAL  CAK  CAJ  CAI    0.00   0.0  0
 EJN  CONST_21  O1   CAA  CAB  CAC  180.00   0.0  0
 EJN  CONST_22  FAL  CAL  CAG  CAD    0.00   0.0  0
 EJN  CONST_23  FAH  CAH  CAG  CAD    0.00   0.0  0
 EJN  CONST_24  O1   CAA  CAF  CAE  180.00   0.0  0
 EJN  CONST_25  FAK  CAK  CAL  CAG  180.00   0.0  0
 EJN  CONST_26  FAI  CAI  CAH  CAG  180.00   0.0  0
 EJN  CONST_27  FAL  CAL  CAG  CAH  180.00   0.0  0
 EJN  CONST_28  FAJ  CAJ  CAI  CAH  180.00   0.0  0
 EJN  CONST_29  FAK  CAK  CAJ  CAI  180.00   0.0  0
 EJN  CONST_30  FAL  CAL  CAK  CAJ  180.00   0.0  0
 EJN  CONST_31  FAH  CAH  CAI  CAJ  180.00   0.0  0
 EJN  CONST_32  FAI  CAI  CAJ  CAK  180.00   0.0  0
 EJN  CONST_33  FAH  CAH  CAG  CAL  180.00   0.0  0
 EJN  CONST_34  FAJ  CAJ  CAK  CAL  180.00   0.0  0
 EJN  CONST_35  HAE  CAE  CAF  CAA  180.00   0.0  0
 EJN  CONST_36  HAC  CAC  CAB  CAA  180.00   0.0  0
 EJN  CONST_37  HAF  CAF  CAA  CAB  180.00   0.0  0
 EJN  CONST_38  HAB  CAB  CAC  CAD  180.00   0.0  0
 EJN  Var_01    CAF  CAA  O1   C1   -14.87  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
 EJN  chir_01  C4  C3  O4  C5  positiv
 EJN  chir_02  C5  O5  C4  C6  negativ
 EJN  chir_03  C1  O1  O5  C2  negativ
 EJN  chir_04  C2  O2  C1  C3  positiv
 EJN  chir_05  C3  O3  C2  C4  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
 EJN  plan-1  CAA  0.020
 EJN  plan-1  CAB  0.020
 EJN  plan-1  CAC  0.020
 EJN  plan-1  CAD  0.020
 EJN  plan-1  CAE  0.020
 EJN  plan-1  CAF  0.020
 EJN  plan-1  CAG  0.020
 EJN  plan-1  O1   0.020
 EJN  plan-1  HAB  0.020
 EJN  plan-1  HAC  0.020
 EJN  plan-1  HAE  0.020
 EJN  plan-1  HAF  0.020
 EJN  plan-2  CAD  0.020
 EJN  plan-2  CAG  0.020
 EJN  plan-2  CAH  0.020
 EJN  plan-2  CAI  0.020
 EJN  plan-2  CAJ  0.020
 EJN  plan-2  CAK  0.020
 EJN  plan-2  CAL  0.020
 EJN  plan-2  FAH  0.020
 EJN  plan-2  FAI  0.020
 EJN  plan-2  FAJ  0.020
 EJN  plan-2  FAK  0.020
 EJN  plan-2  FAL  0.020

