# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 10:40:27 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[3-[(~{E})-2-(4-hydroxyphenyl)ethenyl]-5-oxidanyl-phenoxy]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2cc(O)cc(\C=C\c3ccc(O)cc3)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
 7KP  7KP  (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[3-[(~{E})-2-(4-hydroxyphenyl)ethenyl]-5-oxidanyl-phenoxy]oxane-3,4,5-triol  ligand  50  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7KP
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
 7KP  C1   C  CH1   0   0.207  -3.2833  -0.1592  -0.9813
 7KP  C2   C  CH1   0  -0.012  -4.1018   1.0854  -1.3323
 7KP  C3   C  CH1   0  -0.008  -4.3920   1.8894  -0.0721
 7KP  C4   C  CH1   0   0.029  -5.0481   0.9946   0.9728
 7KP  C5   C  CH1   0  -0.016  -4.1954  -0.2503   1.2189
 7KP  C6   C  CH2   0  -0.161  -4.9078  -1.2448   2.1115
 7KP  CAG  C  CR6   0   0.424  -0.9678  -0.5699  -0.5302
 7KP  CAH  C  CR16  0  -0.471  -1.0817  -1.9499  -0.6098
 7KP  CAI  C  CR6   0   0.425   0.0835  -2.7207  -0.5799
 7KP  CAJ  C  CR16  0  -0.518   1.3322  -2.1341  -0.4514
 7KP  CAK  C  CR6   0   0.210   1.4386  -0.7422  -0.3554
 7KP  CAL  C  CR16  0  -0.463   0.2828   0.0312  -0.3999
 7KP  CAM  C  C1    0  -0.323   2.7183  -0.0483  -0.2209
 7KP  CAN  C  C1    0  -0.303   3.9267  -0.6207  -0.1330
 7KP  CAO  C  CR16  0  -0.321   5.3396   1.4570   0.0664
 7KP  CAP  C  CR16  0  -0.359   6.5788   2.0585   0.1808
 7KP  CAQ  C  CR6   0   0.346   7.7367   1.2808   0.2295
 7KP  CAR  C  CR16  0  -0.327   7.6280  -0.1058   0.1651
 7KP  CAS  C  CR16  0  -0.300   6.3805  -0.6927   0.0505
 7KP  CAT  C  CR6   0   0.149   5.2074   0.0664  -0.0041
 7KP  O1   O  O2    0  -0.499  -2.0172   0.2835  -0.5653
 7KP  O2   O  OH1   0  -0.664  -3.4415   1.9160  -2.2498
 7KP  O3   O  OH1   0  -0.674  -5.2806   2.9522  -0.3268
 7KP  O4   O  OH1   0  -0.672  -5.1993   1.6626   2.2009
 7KP  O5   O  O2    0  -0.494  -3.9310  -0.9125  -0.0099
 7KP  O6   O  OH1   0  -0.666  -4.0467  -2.3282   2.3642
 7KP  OBA  O  OH1   0  -0.634  -0.0788  -4.0554  -0.6718
 7KP  H1   H  HCH1  0   0.263  -3.1869  -0.8145  -1.8554
 7KP  H2   H  HCH1  0   0.238  -5.0571   0.7255  -1.7388
 7KP  H3   H  HCH1  0   0.222  -3.4450   2.2675   0.3406
 7KP  H4   H  HCH1  0   0.213  -6.0252   0.6711   0.5776
 7KP  H5   H  HCH1  0   0.234  -3.2561   0.0510   1.7033
 7KP  H6   H  HCH2  0   0.213  -5.1967  -0.7317   3.0346
 7KP  H7   H  HCH2  0   0.196  -5.8356  -1.5631   1.6157
 7KP  H8   H  HCR6  0   0.288  -2.0371  -2.4519  -0.6720
 7KP  H9   H  HCR6  0   0.266   2.2153  -2.7616  -0.4278
 7KP  H10  H  HCR6  0   0.256   0.3487   1.1107  -0.3408
 7KP  H11  H  H     0   0.249   2.6398   1.0342  -0.1937
 7KP  H13  H  H     0   0.252   4.0022  -1.7040  -0.1579
 7KP  H15  H  HCR6  0   0.258   4.4655   2.0944   0.0321
 7KP  H16  H  HCR6  0   0.274   6.6460   3.1396   0.2310
 7KP  H17  H  HCR6  0   0.265   8.5184  -0.7206   0.2038
 7KP  H18  H  HCR6  0   0.256   6.3145  -1.7732   0.0016
 7KP  H19  H  HOH1  0   0.461  -3.5761   1.5696  -3.1368
 7KP  H20  H  HOH1  0   0.456  -4.8348   3.5948  -0.8875
 7KP  H21  H  HOH1  0   0.455  -5.7444   2.4423   2.0526
 7KP  H22  H  HOH1  0   0.456  -4.4946  -2.9255   2.9696
 7KP  H23  H  HOH1  0   0.475   0.7761  -4.4993  -0.6420
 7KP  H24  H  HOH1  0   0.476   8.9176   2.7771   0.3577
 7KP  OBB  O  OH1   0  -0.627   8.9669   1.8148   0.3368

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
 7KP  O2   C2   single    1.403  0.020  1.403
 7KP  C2   C1   single    1.530  0.020  1.530
 7KP  C2   C3   single    1.523  0.020  1.523
 7KP  O3   C3   single    1.409  0.020  1.409
 7KP  C1   O5   single    1.389  0.020  1.389
 7KP  C1   O1   single    1.404  0.020  1.404
 7KP  OBA  CAI  single    1.348  0.020  1.348
 7KP  C3   C4   single    1.524  0.020  1.524
 7KP  O5   C5   single    1.421  0.020  1.421
 7KP  CAH  CAI  aromatic  1.397  0.020  1.397
 7KP  CAH  CAG  aromatic  1.387  0.020  1.387
 7KP  CAI  CAJ  aromatic  1.386  0.020  1.386
 7KP  C4   C5   single    1.529  0.020  1.529
 7KP  C4   O4   single    1.406  0.020  1.406
 7KP  O1   CAG  single    1.353  0.020  1.353
 7KP  O6   C6   single    1.407  0.020  1.407
 7KP  CAG  CAL  aromatic  1.394  0.020  1.394
 7KP  C5   C6   single    1.514  0.020  1.514
 7KP  CAJ  CAK  aromatic  1.399  0.020  1.399
 7KP  CAL  CAK  aromatic  1.391  0.020  1.391
 7KP  CAK  CAM  single    1.462  0.020  1.462
 7KP  CAM  CAN  double    1.340  0.020  1.340
 7KP  CAN  CAT  single    1.459  0.020  1.459
 7KP  CAS  CAT  aromatic  1.398  0.020  1.398
 7KP  CAS  CAR  aromatic  1.383  0.020  1.383
 7KP  CAT  CAO  aromatic  1.399  0.020  1.399
 7KP  CAR  CAQ  aromatic  1.392  0.020  1.392
 7KP  CAO  CAP  aromatic  1.382  0.020  1.382
 7KP  CAQ  CAP  aromatic  1.396  0.020  1.396
 7KP  CAQ  OBB  single    1.345  0.020  1.345
 7KP  C1   H1   single    0.970  0.020  1.090
 7KP  C2   H2   single    0.970  0.020  1.090
 7KP  C3   H3   single    0.970  0.020  1.090
 7KP  C4   H4   single    0.970  0.020  1.090
 7KP  C5   H5   single    0.970  0.020  1.090
 7KP  C6   H6   single    0.970  0.020  1.090
 7KP  C6   H7   single    0.970  0.020  1.090
 7KP  CAH  H8   single    0.930  0.020  1.080
 7KP  CAJ  H9   single    0.930  0.020  1.080
 7KP  CAL  H10  single    0.930  0.020  1.080
 7KP  CAM  H11  single    0.930  0.020  1.080
 7KP  CAN  H13  single    0.930  0.020  1.080
 7KP  CAO  H15  single    0.930  0.020  1.080
 7KP  CAP  H16  single    0.930  0.020  1.080
 7KP  CAR  H17  single    0.930  0.020  1.080
 7KP  CAS  H18  single    0.930  0.020  1.080
 7KP  O2   H19  single    0.850  0.020  0.980
 7KP  O3   H20  single    0.850  0.020  0.980
 7KP  O4   H21  single    0.850  0.020  0.980
 7KP  O6   H22  single    0.850  0.020  0.980
 7KP  OBA  H23  single    0.850  0.020  0.980
 7KP  OBB  H24  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
 7KP  H1   C1   O5   105.92  3.000
 7KP  H1   C1   O1   110.20  3.000
 7KP  O5   C1   O1   112.58  3.000
 7KP  H1   C1   C2   110.50  3.000
 7KP  O1   C1   C2   107.09  3.000
 7KP  O5   C1   C2   110.61  3.000
 7KP  H2   C2   O2   111.18  3.000
 7KP  H2   C2   C3   108.27  3.000
 7KP  O2   C2   C3   108.56  3.000
 7KP  H2   C2   C1   106.47  3.000
 7KP  C3   C2   C1   109.97  3.000
 7KP  O2   C2   C1   112.32  3.000
 7KP  H3   C3   O3   110.59  3.000
 7KP  H3   C3   C4   108.37  3.000
 7KP  O3   C3   C4   107.18  3.000
 7KP  H3   C3   C2   109.14  3.000
 7KP  C4   C3   C2   109.84  3.000
 7KP  O3   C3   C2   111.65  3.000
 7KP  H4   C4   O4   110.93  3.000
 7KP  H4   C4   C5   108.24  3.000
 7KP  O4   C4   C5   107.84  3.000
 7KP  H4   C4   C3   107.94  3.000
 7KP  O4   C4   C3   111.48  3.000
 7KP  C5   C4   C3   110.38  3.000
 7KP  H5   C5   O5   110.48  3.000
 7KP  H5   C5   C6   108.80  3.000
 7KP  O5   C5   C6   106.93  3.000
 7KP  H5   C5   C4   108.93  3.000
 7KP  C6   C5   C4   111.55  3.000
 7KP  O5   C5   C4   110.14  3.000
 7KP  H7   C6   H6   107.05  3.000
 7KP  H7   C6   O6   112.01  3.000
 7KP  H6   C6   O6   111.78  3.000
 7KP  H7   C6   C5   108.75  3.000
 7KP  H6   C6   C5   108.26  3.000
 7KP  O6   C6   C5   108.89  3.000
 7KP  O1   CAG  CAL  115.23  3.000
 7KP  CAL  CAG  CAH  120.54  3.000
 7KP  O1   CAG  CAH  124.22  3.000
 7KP  H8   CAH  CAI  118.81  3.000
 7KP  H8   CAH  CAG  122.54  3.000
 7KP  CAI  CAH  CAG  118.63  3.000
 7KP  OBA  CAI  CAJ  122.29  3.000
 7KP  CAJ  CAI  CAH  121.32  3.000
 7KP  OBA  CAI  CAH  116.38  3.000
 7KP  H9   CAJ  CAK  120.84  3.000
 7KP  H9   CAJ  CAI  119.42  3.000
 7KP  CAK  CAJ  CAI  119.74  3.000
 7KP  CAM  CAK  CAL  117.80  3.000
 7KP  CAM  CAK  CAJ  123.03  3.000
 7KP  CAL  CAK  CAJ  119.18  3.000
 7KP  H10  CAL  CAK  120.11  3.000
 7KP  H10  CAL  CAG  119.31  3.000
 7KP  CAK  CAL  CAG  120.58  3.000
 7KP  H11  CAM  CAN  119.31  3.000
 7KP  H11  CAM  CAK  114.35  3.000
 7KP  CAN  CAM  CAK  126.35  3.000
 7KP  H13  CAN  CAT  114.24  3.000
 7KP  H13  CAN  CAM  119.16  3.000
 7KP  CAT  CAN  CAM  126.59  3.000
 7KP  H15  CAO  CAT  120.51  3.000
 7KP  H15  CAO  CAP  118.05  3.000
 7KP  CAT  CAO  CAP  121.44  3.000
 7KP  H16  CAP  CAQ  120.16  3.000
 7KP  H16  CAP  CAO  119.56  3.000
 7KP  CAQ  CAP  CAO  120.27  3.000
 7KP  OBB  CAQ  CAR  118.06  3.000
 7KP  OBB  CAQ  CAP  122.70  3.000
 7KP  CAR  CAQ  CAP  119.24  3.000
 7KP  H17  CAR  CAS  120.25  3.000
 7KP  H17  CAR  CAQ  119.97  3.000
 7KP  CAS  CAR  CAQ  119.78  3.000
 7KP  H18  CAS  CAT  119.24  3.000
 7KP  H18  CAS  CAR  118.79  3.000
 7KP  CAT  CAS  CAR  121.97  3.000
 7KP  CAS  CAT  CAO  117.29  3.000
 7KP  CAO  CAT  CAN  123.75  3.000
 7KP  CAS  CAT  CAN  118.96  3.000
 7KP  CAG  O1   C1   120.54  3.000
 7KP  H19  O2   C2   108.91  3.000
 7KP  H20  O3   C3   108.48  3.000
 7KP  H21  O4   C4   108.13  3.000
 7KP  C5   O5   C1   116.02  3.000
 7KP  H22  O6   C6   107.85  3.000
 7KP  H23  OBA  CAI  110.32  3.000
 7KP  H24  OBB  CAQ  110.57  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
 7KP  CONST_01  CAJ  CAI  CAH  CAG     0.00   0.0  0
 7KP  CONST_02  CAJ  CAK  CAL  CAG     0.00   0.0  0
 7KP  CONST_03  CAK  CAJ  CAI  CAH     0.00   0.0  0
 7KP  CONST_04  CAK  CAL  CAG  CAH     0.00   0.0  0
 7KP  CONST_05  CAL  CAG  CAH  CAI     0.00   0.0  0
 7KP  CONST_06  CAL  CAK  CAJ  CAI     0.00   0.0  0
 7KP  CONST_07  CAR  CAS  CAT  CAO     0.00   0.0  0
 7KP  CONST_08  CAR  CAQ  CAP  CAO     0.00   0.0  0
 7KP  CONST_09  CAS  CAT  CAO  CAP     0.00   0.0  0
 7KP  CONST_10  CAS  CAR  CAQ  CAP     0.00   0.0  0
 7KP  CONST_11  CAT  CAS  CAR  CAQ     0.00   0.0  0
 7KP  CONST_12  CAT  CAO  CAP  CAQ     0.00   0.0  0
 7KP  CONST_13  OBA  CAI  CAH  CAG   180.00   0.0  0
 7KP  CONST_14  CAM  CAK  CAL  CAG   180.00   0.0  0
 7KP  CONST_15  O1   CAG  CAH  CAI   180.00   0.0  0
 7KP  CONST_16  CAM  CAK  CAJ  CAI   180.00   0.0  0
 7KP  CONST_17  OBA  CAI  CAJ  CAK   180.00   0.0  0
 7KP  CONST_18  O1   CAG  CAL  CAK   180.00   0.0  0
 7KP  CONST_19  CAR  CAS  CAT  CAN   180.00   0.0  0
 7KP  CONST_20  CAP  CAO  CAT  CAN   180.00   0.0  0
 7KP  CONST_21  OBB  CAQ  CAP  CAO   180.00   0.0  0
 7KP  CONST_22  OBB  CAQ  CAR  CAS   180.00   0.0  0
 7KP  CONST_23  H9   CAJ  CAI  CAH   180.00   0.0  0
 7KP  CONST_24  H10  CAL  CAG  CAH   180.00   0.0  0
 7KP  CONST_25  H8   CAH  CAI  CAJ   180.00   0.0  0
 7KP  CONST_26  H18  CAS  CAT  CAO   180.00   0.0  0
 7KP  CONST_27  H17  CAR  CAQ  CAP   180.00   0.0  0
 7KP  CONST_28  H15  CAO  CAP  CAQ   180.00   0.0  0
 7KP  CONST_29  H16  CAP  CAQ  CAR   180.00   0.0  0
 7KP  Var_01    CAH  CAG  O1   C1    -14.20  30.0  2
 7KP  Var_02    CAT  CAN  CAM  CAK   179.73   0.0  2
 7KP  Var_03    CAN  CAM  CAK  CAJ    -2.06  30.0  2
 7KP  Var_04    CAS  CAT  CAN  CAM  -178.83  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
 7KP  chir_01  C1  C2  O5  O1  positiv
 7KP  chir_02  C2  O2  C1  C3  negativ
 7KP  chir_03  C3  O3  C2  C4  positiv
 7KP  chir_04  C4  O4  C3  C5  negativ
 7KP  chir_05  C5  O5  C4  C6  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
 7KP  plan-1  CAG  0.020
 7KP  plan-1  CAH  0.020
 7KP  plan-1  CAI  0.020
 7KP  plan-1  CAJ  0.020
 7KP  plan-1  CAK  0.020
 7KP  plan-1  CAL  0.020
 7KP  plan-1  CAM  0.020
 7KP  plan-1  O1   0.020
 7KP  plan-1  OBA  0.020
 7KP  plan-1  H8   0.020
 7KP  plan-1  H9   0.020
 7KP  plan-1  H10  0.020
 7KP  plan-2  CAK  0.020
 7KP  plan-2  CAM  0.020
 7KP  plan-2  CAN  0.020
 7KP  plan-2  CAT  0.020
 7KP  plan-2  H11  0.020
 7KP  plan-2  H13  0.020
 7KP  plan-3  CAN  0.020
 7KP  plan-3  CAO  0.020
 7KP  plan-3  CAP  0.020
 7KP  plan-3  CAQ  0.020
 7KP  plan-3  CAR  0.020
 7KP  plan-3  CAS  0.020
 7KP  plan-3  CAT  0.020
 7KP  plan-3  H15  0.020
 7KP  plan-3  H16  0.020
 7KP  plan-3  H17  0.020
 7KP  plan-3  H18  0.020
 7KP  plan-3  OBB  0.020

