# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:34:48 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-[3-chloranyl-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-phenyl]-2,3,5,6-tetrakis(fluoranyl)benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccc(cc2Cl)c3c(F)c(F)c(C#N)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
 EJK  EJK  4-[3-chloranyl-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-phenyl]-2,3,5,6-tetrakis(fluoranyl)benzenecarbonitrile  ligand  45  31  .  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_EJK
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
 EJK  C4   C   CH1   0   0.030  -5.5120   0.7688  -0.3728
 EJK  C5   C   CH1   0  -0.018  -4.1334   1.4169  -0.2336
 EJK  C6   C   CH2   0  -0.158  -4.2131   2.9271  -0.2922
 EJK  C3   C   CH1   0   0.001  -5.4040  -0.7329  -0.1302
 EJK  C1   C   CH1   0   0.199  -3.4094  -0.2651   1.2888
 EJK  C2   C   CH1   0  -0.025  -4.7451  -1.0111   1.2189
 EJK  CAA  C   CR6   0   0.481  -1.2417  -0.6346   0.3480
 EJK  CAB  C   CR16  0  -0.359  -0.5929   0.2698   1.1835
 EJK  CAC  C   CR16  0  -0.255   0.7797   0.4384   1.0991
 EJK  CAD  C   CR6   0   0.072   1.5324  -0.2797   0.1783
 EJK  CAE  C   CR16  0  -0.223   0.8884  -1.1718  -0.6743
 EJK  CAF  C   CR6   0  -0.158  -0.4791  -1.3374  -0.5902
 EJK  CAG  C   CR6   0  -0.376   2.9955  -0.1107   0.1016
 EJK  CAH  C   CR6   0   0.436   3.8509  -1.1830   0.3230
 EJK  CAI  C   CR6   0   0.471   5.2201  -1.0378   0.2530
 EJK  CAJ  C   CR6   0  -0.388   5.7788   0.1998  -0.0387
 EJK  CAK  C   CR6   0   0.471   4.9345   1.2798  -0.2608
 EJK  CAL  C   CR6   0   0.437   3.5664   1.1198  -0.1927
 EJK  CBE  C   CSP   0   0.104   7.1876   0.3581  -0.1070
 EJK  FAH  F   F     0  -0.278   3.3494  -2.3754   0.6237
 EJK  FAI  F   F     0  -0.267   6.0147  -2.0722   0.4725
 EJK  FAK  F   F     0  -0.267   5.4565   2.4608  -0.5480
 EJK  FAL  F   F     0  -0.277   2.7885   2.1698  -0.4274
 EJK  NBF  N   NS    0  -0.212   8.3297   0.4859  -0.1608
 EJK  O1   O   O2    0  -0.483  -2.5536  -0.9077   0.3639
 EJK  O2   O   OH1   0  -0.664  -5.5936  -0.5484   2.2351
 EJK  O3   O   OH1   0  -0.671  -6.7013  -1.2711  -0.2132
 EJK  O4   O   OH1   0  -0.674  -5.9749   1.0397  -1.6737
 EJK  O5   O   O2    0  -0.484  -3.5465   1.0824   1.0180
 EJK  O6   O   OH1   0  -0.667  -2.9075   3.4513  -0.2717
 EJK  CL1  CL  CL    0  -0.097  -1.2751  -2.4385  -1.6547
 EJK  H41  H   HCH1  0   0.216  -6.1848   1.2052   0.3808
 EJK  H5   H   HCH1  0   0.234  -3.4981   1.0643  -1.0585
 EJK  H61  H   HCH2  0   0.213  -4.7479   3.2076  -1.2057
 EJK  H62  H   HCH2  0   0.197  -4.8128   3.2845   0.5568
 EJK  H31  H   HCH1  0   0.233  -4.7597  -1.1552  -0.9133
 EJK  H1   H   HCH1  0   0.272  -2.9901  -0.3364   2.2994
 EJK  H21  H   HCH1  0   0.245  -4.5498  -2.0875   1.3170
 EJK  HAB  H   HCR6  0   0.300  -1.1402   0.8553   1.9073
 EJK  HAC  H   HCR6  0   0.275   1.2610   1.1321   1.7757
 EJK  HAE  H   HCR6  0   0.287   1.4460  -1.7261  -1.4175
 EJK  H22  H   HOH1  0   0.460  -5.3046  -0.9210   3.0738
 EJK  H32  H   HOH1  0   0.459  -6.6354  -2.2061  -0.4279
 EJK  H42  H   HOH1  0   0.453  -6.8200   0.5914  -1.7838
 EJK  H63  H   HOH1  0   0.456  -2.9720   4.4072  -0.3490

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
 EJK  O4   C4   single    1.407  0.020  1.407
 EJK  O3   C3   single    1.407  0.020  1.407
 EJK  C4   C3   single    1.525  0.020  1.525
 EJK  C4   C5   single    1.530  0.020  1.530
 EJK  C3   C2   single    1.527  0.020  1.527
 EJK  C6   O6   single    1.407  0.020  1.407
 EJK  C6   C5   single    1.513  0.020  1.513
 EJK  C5   O5   single    1.422  0.020  1.422
 EJK  CL1  CAF  single    1.726  0.020  1.726
 EJK  C2   O2   single    1.402  0.020  1.402
 EJK  C2   C1   single    1.531  0.020  1.531
 EJK  O5   C1   single    1.381  0.020  1.381
 EJK  FAL  CAL  single    1.328  0.020  1.328
 EJK  O1   C1   single    1.415  0.020  1.415
 EJK  O1   CAA  single    1.340  0.020  1.340
 EJK  CAF  CAA  aromatic  1.398  0.020  1.398
 EJK  CAF  CAE  aromatic  1.380  0.020  1.380
 EJK  CAA  CAB  aromatic  1.392  0.020  1.392
 EJK  CAE  CAD  aromatic  1.392  0.020  1.392
 EJK  FAK  CAK  single    1.323  0.020  1.323
 EJK  CAL  CAK  aromatic  1.379  0.020  1.379
 EJK  CAL  CAG  aromatic  1.388  0.020  1.388
 EJK  CAB  CAC  aromatic  1.385  0.020  1.385
 EJK  CAD  CAC  aromatic  1.389  0.020  1.389
 EJK  CAD  CAG  single    1.475  0.020  1.475
 EJK  CAK  CAJ  aromatic  1.389  0.020  1.389
 EJK  CAG  CAH  aromatic  1.389  0.020  1.389
 EJK  CAJ  CBE  single    1.419  0.020  1.419
 EJK  CAJ  CAI  aromatic  1.389  0.020  1.389
 EJK  CAH  CAI  aromatic  1.379  0.020  1.379
 EJK  CAH  FAH  single    1.328  0.020  1.328
 EJK  CBE  NBF  triple    1.150  0.020  1.150
 EJK  CAI  FAI  single    1.323  0.020  1.323
 EJK  C4   H41  single    0.970  0.020  1.090
 EJK  C5   H5   single    0.970  0.020  1.090
 EJK  C6   H61  single    0.970  0.020  1.090
 EJK  C6   H62  single    0.970  0.020  1.090
 EJK  C3   H31  single    0.970  0.020  1.090
 EJK  C1   H1   single    0.970  0.020  1.090
 EJK  C2   H21  single    0.970  0.020  1.090
 EJK  CAB  HAB  single    0.930  0.020  1.080
 EJK  CAC  HAC  single    0.930  0.020  1.080
 EJK  CAE  HAE  single    0.930  0.020  1.080
 EJK  O2   H22  single    0.850  0.020  0.980
 EJK  O3   H32  single    0.850  0.020  0.980
 EJK  O4   H42  single    0.850  0.020  0.980
 EJK  O6   H63  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
 EJK  H41  C4   O4   110.83  3.000
 EJK  H41  C4   C3   108.95  3.000
 EJK  O4   C4   C3   111.09  3.000
 EJK  H41  C4   C5   108.70  3.000
 EJK  C3   C4   C5   109.81  3.000
 EJK  O4   C4   C5   107.41  3.000
 EJK  H5   C5   O5   110.27  3.000
 EJK  H5   C5   C6   108.75  3.000
 EJK  O5   C5   C6   106.89  3.000
 EJK  H5   C5   C4   108.46  3.000
 EJK  O5   C5   C4   110.63  3.000
 EJK  C6   C5   C4   111.83  3.000
 EJK  H62  C6   H61  107.13  3.000
 EJK  H62  C6   O6   111.95  3.000
 EJK  H61  C6   O6   111.71  3.000
 EJK  H62  C6   C5   108.86  3.000
 EJK  H61  C6   C5   108.28  3.000
 EJK  O6   C6   C5   108.81  3.000
 EJK  H31  C3   O3   110.59  3.000
 EJK  H31  C3   C2   107.86  3.000
 EJK  O3   C3   C2   112.35  3.000
 EJK  H31  C3   C4   107.86  3.000
 EJK  C2   C3   C4   110.52  3.000
 EJK  O3   C3   C4   107.58  3.000
 EJK  H1   C1   O5   106.39  3.000
 EJK  H1   C1   O1   109.98  3.000
 EJK  O5   C1   O1   112.03  3.000
 EJK  H1   C1   C2   110.12  3.000
 EJK  O1   C1   C2   106.05  3.000
 EJK  O5   C1   C2   112.32  3.000
 EJK  H21  C2   O2   111.48  3.000
 EJK  H21  C2   C1   108.56  3.000
 EJK  O2   C2   C1   109.50  3.000
 EJK  H21  C2   C3   109.52  3.000
 EJK  C1   C2   C3   109.14  3.000
 EJK  O2   C2   C3   108.60  3.000
 EJK  O1   CAA  CAF  116.06  3.000
 EJK  CAF  CAA  CAB  118.37  3.000
 EJK  O1   CAA  CAB  125.57  3.000
 EJK  HAB  CAB  CAC  118.49  3.000
 EJK  HAB  CAB  CAA  121.22  3.000
 EJK  CAC  CAB  CAA  120.29  3.000
 EJK  HAC  CAC  CAD  120.32  3.000
 EJK  HAC  CAC  CAB  118.73  3.000
 EJK  CAD  CAC  CAB  120.94  3.000
 EJK  CAG  CAD  CAE  120.04  3.000
 EJK  CAG  CAD  CAC  120.84  3.000
 EJK  CAE  CAD  CAC  119.12  3.000
 EJK  HAE  CAE  CAF  119.41  3.000
 EJK  HAE  CAE  CAD  120.71  3.000
 EJK  CAF  CAE  CAD  119.87  3.000
 EJK  CL1  CAF  CAE  119.73  3.000
 EJK  CAE  CAF  CAA  121.39  3.000
 EJK  CL1  CAF  CAA  118.88  3.000
 EJK  CAL  CAG  CAH  117.69  3.000
 EJK  CAH  CAG  CAD  120.93  3.000
 EJK  CAL  CAG  CAD  121.38  3.000
 EJK  FAH  CAH  CAI  118.75  3.000
 EJK  FAH  CAH  CAG  119.77  3.000
 EJK  CAI  CAH  CAG  121.47  3.000
 EJK  FAI  CAI  CAJ  119.34  3.000
 EJK  FAI  CAI  CAH  120.39  3.000
 EJK  CAJ  CAI  CAH  120.26  3.000
 EJK  CBE  CAJ  CAK  120.60  3.000
 EJK  CBE  CAJ  CAI  120.58  3.000
 EJK  CAK  CAJ  CAI  118.82  3.000
 EJK  FAK  CAK  CAL  120.38  3.000
 EJK  CAL  CAK  CAJ  120.33  3.000
 EJK  FAK  CAK  CAJ  119.29  3.000
 EJK  FAL  CAL  CAK  118.73  3.000
 EJK  CAK  CAL  CAG  121.43  3.000
 EJK  FAL  CAL  CAG  119.84  3.000
 EJK  NBF  CBE  CAJ  180.00  3.000
 EJK  CAA  O1   C1   120.50  3.000
 EJK  H22  O2   C2   108.79  3.000
 EJK  H32  O3   C3   108.78  3.000
 EJK  H42  O4   C4   107.75  3.000
 EJK  C1   O5   C5   116.29  3.000
 EJK  H63  O6   C6   107.89  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
 EJK  CONST_01  CAD  CAE  CAF  CAA    0.00   0.0  0
 EJK  CONST_02  CAD  CAC  CAB  CAA    0.00   0.0  0
 EJK  CONST_03  CAE  CAF  CAA  CAB    0.00   0.0  0
 EJK  CONST_04  CAE  CAD  CAC  CAB    0.00   0.0  0
 EJK  CONST_05  CAG  CAD  CAC  CAB  180.00   0.0  0
 EJK  CONST_06  CAF  CAA  CAB  CAC    0.00   0.0  0
 EJK  CONST_07  CAF  CAE  CAD  CAC    0.00   0.0  0
 EJK  CONST_10  CAK  CAL  CAG  CAD  180.00   0.0  0
 EJK  CONST_11  CAI  CAH  CAG  CAD  180.00   0.0  0
 EJK  CONST_14  CAG  CAD  CAE  CAF  180.00   0.0  0
 EJK  CONST_15  CAJ  CAK  CAL  CAG    0.00   0.0  0
 EJK  CONST_16  CAJ  CAI  CAH  CAG    0.00   0.0  0
 EJK  CONST_17  CAK  CAL  CAG  CAH    0.00   0.0  0
 EJK  CONST_18  CAK  CAJ  CAI  CAH    0.00   0.0  0
 EJK  CONST_19  CAL  CAK  CAJ  CAI    0.00   0.0  0
 EJK  CONST_20  CAL  CAG  CAH  CAI    0.00   0.0  0
 EJK  CONST_21  CL1  CAF  CAA  CAB  180.00   0.0  0
 EJK  CONST_22  O1   CAA  CAB  CAC  180.00   0.0  0
 EJK  CONST_23  CL1  CAF  CAE  CAD  180.00   0.0  0
 EJK  CONST_24  FAL  CAL  CAG  CAD    0.00   0.0  0
 EJK  CONST_25  FAH  CAH  CAG  CAD    0.00   0.0  0
 EJK  CONST_26  O1   CAA  CAF  CAE  180.00   0.0  0
 EJK  CONST_27  FAK  CAK  CAL  CAG  180.00   0.0  0
 EJK  CONST_28  FAI  CAI  CAH  CAG  180.00   0.0  0
 EJK  CONST_29  FAL  CAL  CAG  CAH  180.00   0.0  0
 EJK  CONST_30  CBE  CAJ  CAI  CAH  180.00   0.0  0
 EJK  CONST_31  FAK  CAK  CAJ  CAI  180.00   0.0  0
 EJK  CONST_32  FAL  CAL  CAK  CAJ  180.00   0.0  0
 EJK  CONST_33  FAH  CAH  CAI  CAJ  180.00   0.0  0
 EJK  CONST_34  FAI  CAI  CAJ  CAK  180.00   0.0  0
 EJK  CONST_35  CBE  CAJ  CAK  CAL  180.00   0.0  0
 EJK  CONST_36  FAH  CAH  CAG  CAL  180.00   0.0  0
 EJK  CONST_37  HAE  CAE  CAF  CAA  180.00   0.0  0
 EJK  CONST_38  HAC  CAC  CAB  CAA  180.00   0.0  0
 EJK  CONST_39  HAB  CAB  CAC  CAD  180.00   0.0  0
 EJK  Var_01    CAF  CAA  O1   C1   179.07  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
 EJK  chir_01  C4  O4  C3  C5  negativ
 EJK  chir_02  C5  O5  C4  C6  negativ
 EJK  chir_03  C3  O3  C4  C2  negativ
 EJK  chir_04  C1  O1  O5  C2  negativ
 EJK  chir_05  C2  O2  C1  C3  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
 EJK  plan-1  CAA  0.020
 EJK  plan-1  CAB  0.020
 EJK  plan-1  CAC  0.020
 EJK  plan-1  CAD  0.020
 EJK  plan-1  CAE  0.020
 EJK  plan-1  CAF  0.020
 EJK  plan-1  CAG  0.020
 EJK  plan-1  O1   0.020
 EJK  plan-1  CL1  0.020
 EJK  plan-1  HAB  0.020
 EJK  plan-1  HAC  0.020
 EJK  plan-1  HAE  0.020
 EJK  plan-2  CAD  0.020
 EJK  plan-2  CAG  0.020
 EJK  plan-2  CAH  0.020
 EJK  plan-2  CAI  0.020
 EJK  plan-2  CAJ  0.020
 EJK  plan-2  CAK  0.020
 EJK  plan-2  CAL  0.020
 EJK  plan-2  CBE  0.020
 EJK  plan-2  FAH  0.020
 EJK  plan-2  FAI  0.020
 EJK  plan-2  FAK  0.020
 EJK  plan-2  FAL  0.020
 EJK  plan-2  NBF  0.020

