# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 09:16:41 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (1~{R},2~{S},3~{S},6~{S})-6-[3,5-bis(fluoranyl)phenoxy]-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1=C[C@H](Oc2cc(F)cc(F)c2)[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
 F9W  F9W  (1~{R},2~{S},3~{S},6~{S})-6-[3,5-bis(fluoranyl)phenoxy]-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol  ligand  34  20  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F9W
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
 F9W  CAJ  C  CR16  0  -0.549   1.9316   0.6009   0.7059
 F9W  CAK  C  CR6   0   0.569   3.2234   1.0817   0.8209
 F9W  FAH  F  F     0  -0.308   3.4152   2.1956   1.5372
 F9W  CAF  C  CR16  0  -0.588   4.3201   0.4826   0.2383
 F9W  CAQ  C  CR6   0   0.555   4.0665  -0.6636  -0.4951
 F9W  FAA  F  F     0  -0.307   5.0992  -1.2805  -1.0804
 F9W  CAP  C  CR16  0  -0.522   2.8087  -1.1996  -0.6522
 F9W  CAI  C  CR6   0   0.433   1.7285  -0.5585  -0.0407
 F9W  OAG  O  O2    0  -0.495   0.5336  -1.1362  -0.2282
 F9W  CAB  C  CH1   0  -0.001  -0.6441  -0.5921   0.3692
 F9W  CAL  C  C1    0  -0.312  -1.1447   0.5863  -0.4084
 F9W  CAC  C  CH1   0  -0.025  -1.6550  -1.7370   0.4095
 F9W  OAR  O  OH1   0  -0.665  -1.8157  -2.3507  -0.8427
 F9W  CAD  C  CH1   0  -0.021  -3.0149  -1.1775   0.8006
 F9W  OAT  O  OH1   0  -0.672  -2.8778  -0.5745   2.0613
 F9W  CAE  C  CH1   0  -0.030  -3.5026  -0.1685  -0.2435
 F9W  OAS  O  OH1   0  -0.670  -4.6043   0.5561   0.2772
 F9W  CAM  C  C     0   0.036  -2.4332   0.8094  -0.6507
 F9W  CAN  C  CH2   0  -0.174  -2.9197   2.0022  -1.4201
 F9W  OAO  O  OH1   0  -0.666  -1.8398   2.7002  -1.9830
 F9W  H1   H  HCR6  0   0.305   1.1275   1.1369   1.1893
 F9W  H2   H  HCR6  0   0.301   5.3176   0.8851   0.3468
 F9W  H3   H  HCR6  0   0.292   2.6568  -2.0989  -1.2342
 F9W  H4   H  HCH1  0   0.261  -0.4241  -0.3009   1.4022
 F9W  H5   H  H     0   0.264  -0.4029   1.2950  -0.7592
 F9W  H6   H  HCH1  0   0.244  -1.3297  -2.4655   1.1658
 F9W  H7   H  HOH1  0   0.456  -0.9750  -2.7362  -1.1071
 F9W  H8   H  HCH1  0   0.235  -3.7380  -2.0071   0.8410
 F9W  H9   H  HOH1  0   0.449  -3.6288   0.0192   2.1785
 F9W  H10  H  HCH1  0   0.251  -3.8079  -0.7167  -1.1442
 F9W  H11  H  HOH1  0   0.463  -5.3974   0.0207   0.1744
 F9W  H12  H  HCH2  0   0.209  -3.6205   1.6520  -2.1933
 F9W  H13  H  HCH2  0   0.223  -3.5061   2.6426  -0.7502
 F9W  H14  H  HOH1  0   0.461  -2.1700   3.5331  -2.3294

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
 F9W  OAS  CAE  single    1.418  0.020  1.418
 F9W  CAN  OAO  single    1.404  0.020  1.404
 F9W  CAN  CAM  single    1.500  0.020  1.500
 F9W  CAM  CAE  single    1.505  0.020  1.505
 F9W  CAM  CAL  double    1.330  0.020  1.330
 F9W  CAE  CAD  single    1.532  0.020  1.532
 F9W  CAL  CAB  single    1.498  0.020  1.498
 F9W  OAT  CAD  single    1.404  0.020  1.404
 F9W  CAC  CAD  single    1.522  0.020  1.522
 F9W  CAC  CAB  single    1.528  0.020  1.528
 F9W  CAC  OAR  single    1.404  0.020  1.404
 F9W  CAB  OAG  single    1.428  0.020  1.428
 F9W  OAG  CAI  single    1.340  0.020  1.340
 F9W  CAJ  CAI  aromatic  1.394  0.020  1.394
 F9W  CAJ  CAK  aromatic  1.383  0.020  1.383
 F9W  CAI  CAP  aromatic  1.397  0.020  1.397
 F9W  FAH  CAK  single    1.338  0.020  1.338
 F9W  CAK  CAF  aromatic  1.379  0.020  1.379
 F9W  CAP  CAQ  aromatic  1.376  0.020  1.376
 F9W  CAF  CAQ  aromatic  1.384  0.020  1.384
 F9W  CAQ  FAA  single    1.338  0.020  1.338
 F9W  CAJ  H1   single    0.930  0.020  1.080
 F9W  CAF  H2   single    0.930  0.020  1.080
 F9W  CAP  H3   single    0.930  0.020  1.080
 F9W  CAB  H4   single    0.970  0.020  1.090
 F9W  CAL  H5   single    0.930  0.020  1.080
 F9W  CAC  H6   single    0.970  0.020  1.090
 F9W  OAR  H7   single    0.850  0.020  0.980
 F9W  CAD  H8   single    0.970  0.020  1.090
 F9W  OAT  H9   single    0.850  0.020  0.980
 F9W  CAE  H10  single    0.970  0.020  1.090
 F9W  OAS  H11  single    0.850  0.020  0.980
 F9W  CAN  H12  single    0.970  0.020  1.090
 F9W  CAN  H13  single    0.970  0.020  1.090
 F9W  OAO  H14  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
 F9W  H1   CAJ  CAI  122.95  3.000
 F9W  H1   CAJ  CAK  119.04  3.000
 F9W  CAI  CAJ  CAK  118.02  3.000
 F9W  CAF  CAK  FAH  118.28  3.000
 F9W  CAF  CAK  CAJ  123.83  3.000
 F9W  FAH  CAK  CAJ  117.89  3.000
 F9W  H2   CAF  CAQ  122.04  3.000
 F9W  H2   CAF  CAK  121.99  3.000
 F9W  CAQ  CAF  CAK  115.97  3.000
 F9W  CAP  CAQ  FAA  118.42  3.000
 F9W  FAA  CAQ  CAF  118.18  3.000
 F9W  CAP  CAQ  CAF  123.39  3.000
 F9W  H3   CAP  CAI  120.55  3.000
 F9W  H3   CAP  CAQ  120.90  3.000
 F9W  CAI  CAP  CAQ  118.56  3.000
 F9W  OAG  CAI  CAP  115.48  3.000
 F9W  CAP  CAI  CAJ  120.23  3.000
 F9W  OAG  CAI  CAJ  124.29  3.000
 F9W  CAB  OAG  CAI  120.82  3.000
 F9W  H4   CAB  CAC  107.89  3.000
 F9W  H4   CAB  CAL  110.34  3.000
 F9W  CAC  CAB  CAL  112.47  3.000
 F9W  H4   CAB  OAG  109.27  3.000
 F9W  CAC  CAB  OAG  105.73  3.000
 F9W  CAL  CAB  OAG  110.98  3.000
 F9W  H5   CAL  CAM  119.62  3.000
 F9W  H5   CAL  CAB  116.97  3.000
 F9W  CAM  CAL  CAB  123.39  3.000
 F9W  H6   CAC  CAD  109.35  3.000
 F9W  H6   CAC  OAR  110.97  3.000
 F9W  CAD  CAC  OAR  106.72  3.000
 F9W  H6   CAC  CAB  108.60  3.000
 F9W  OAR  CAC  CAB  112.32  3.000
 F9W  CAD  CAC  CAB  108.82  3.000
 F9W  H7   OAR  CAC  108.69  3.000
 F9W  H8   CAD  CAE  108.19  3.000
 F9W  H8   CAD  OAT  110.77  3.000
 F9W  CAE  CAD  OAT  111.12  3.000
 F9W  H8   CAD  CAC  108.62  3.000
 F9W  OAT  CAD  CAC  107.54  3.000
 F9W  CAE  CAD  CAC  110.58  3.000
 F9W  H9   OAT  CAD  107.31  3.000
 F9W  H10  CAE  CAM  107.47  3.000
 F9W  H10  CAE  OAS  109.91  3.000
 F9W  CAM  CAE  OAS  108.62  3.000
 F9W  H10  CAE  CAD  108.60  3.000
 F9W  CAM  CAE  CAD  112.72  3.000
 F9W  OAS  CAE  CAD  109.49  3.000
 F9W  H11  OAS  CAE  108.46  3.000
 F9W  CAN  CAM  CAE  115.14  3.000
 F9W  CAE  CAM  CAL  122.01  3.000
 F9W  CAN  CAM  CAL  122.74  3.000
 F9W  H13  CAN  H12  105.93  3.000
 F9W  H13  CAN  OAO  111.46  3.000
 F9W  H12  CAN  OAO  111.49  3.000
 F9W  H13  CAN  CAM  108.92  3.000
 F9W  H12  CAN  CAM  108.29  3.000
 F9W  OAO  CAN  CAM  110.58  3.000
 F9W  H14  OAO  CAN  108.13  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
 F9W  CONST_01  CAQ  CAP  CAI  CAJ    0.00   0.0  0
 F9W  CONST_02  CAQ  CAF  CAK  CAJ    0.00   0.0  0
 F9W  CONST_03  CAP  CAI  CAJ  CAK    0.00   0.0  0
 F9W  CONST_04  CAP  CAQ  CAF  CAK    0.00   0.0  0
 F9W  CONST_05  CAI  CAJ  CAK  CAF    0.00   0.0  0
 F9W  CONST_06  CAI  CAP  CAQ  CAF    0.00   0.0  0
 F9W  CONST_07  OAG  CAI  CAJ  CAK  180.00   0.0  0
 F9W  CONST_08  FAA  CAQ  CAF  CAK  180.00   0.0  0
 F9W  CONST_09  CAI  CAJ  CAK  FAH  180.00   0.0  0
 F9W  CONST_10  CAQ  CAF  CAK  FAH  180.00   0.0  0
 F9W  CONST_11  OAG  CAI  CAP  CAQ  180.00   0.0  0
 F9W  CONST_12  CAI  CAP  CAQ  FAA  180.00   0.0  0
 F9W  CONST_13  H3   CAP  CAI  CAJ  180.00   0.0  0
 F9W  CONST_14  H2   CAF  CAK  CAJ  180.00   0.0  0
 F9W  CONST_15  H1   CAJ  CAK  CAF  180.00   0.0  0
 F9W  Var_01    CAE  CAM  CAL  CAB   -4.56  30.0  1
 F9W  Var_02    OAO  CAN  CAM  CAL    8.36  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
 F9W  chir_01  CAB  CAL  CAC  OAG  negativ
 F9W  chir_02  CAC  OAR  CAB  CAD  negativ
 F9W  chir_03  CAD  OAT  CAC  CAE  positiv
 F9W  chir_04  CAE  OAS  CAD  CAM  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
 F9W  plan-1  CAJ  0.020
 F9W  plan-1  CAK  0.020
 F9W  plan-1  FAH  0.020
 F9W  plan-1  CAF  0.020
 F9W  plan-1  CAQ  0.020
 F9W  plan-1  FAA  0.020
 F9W  plan-1  CAP  0.020
 F9W  plan-1  CAI  0.020
 F9W  plan-1  OAG  0.020
 F9W  plan-1  H1   0.020
 F9W  plan-1  H2   0.020
 F9W  plan-1  H3   0.020

