# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 09:38:18 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-[(Z)-3-(4-phenylphenyl)prop-2-enyl]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C\C=C/c2ccc(cc2)c3ccccc3)[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
 8L8  8L8  (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-[(Z)-3-(4-phenylphenyl)prop-2-enyl]oxane-3,4,5-triol  ligand  50  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8L8
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
 8L8  C1   C  CH1   0  -0.017   2.4785  -0.0268  -0.9816
 8L8  C2   C  CH1   0   0.031   2.7824  -1.5088  -1.1893
 8L8  O2   O  OH1   0  -0.674   3.4485  -1.6385  -2.4233
 8L8  C3   C  CH1   0  -0.006   3.6381  -2.0429  -0.0431
 8L8  O3   O  OH1   0  -0.676   3.9777  -3.3741  -0.3522
 8L8  C4   C  CH1   0   0.007   4.8689  -1.1695   0.1625
 8L8  O4   O  OH1   0  -0.675   5.5560  -1.6799   1.2860
 8L8  C5   C  CH1   0  -0.015   4.4186   0.2810   0.3704
 8L8  O5   O  O2    0  -0.490   3.6619   0.7038  -0.7442
 8L8  C6   C  CH2   0  -0.159   5.5885   1.2300   0.5099
 8L8  O6   O  OH1   0  -0.666   5.0993   2.5185   0.7947
 8L8  C7   C  CH2   0  -0.584   1.3991   0.2019   0.0845
 8L8  C8   C  C1    0  -0.170   1.1415   1.6581   0.3083
 8L8  C9   C  C1    0  -0.297  -0.0377   2.2782   0.4106
 8L8  C10  C  CR6   0   0.086  -1.3813   1.6885   0.3763
 8L8  C11  C  CR16  0  -0.302  -1.6933   0.4561   0.9545
 8L8  C12  C  CR16  0  -0.297  -2.9774  -0.0600   0.8878
 8L8  C13  C  CR6   0   0.077  -4.0044   0.6364   0.2494
 8L8  C14  C  CR16  0  -0.298  -3.7004   1.8818  -0.3047
 8L8  C15  C  CR16  0  -0.288  -2.4189   2.3983  -0.2345
 8L8  C16  C  CR6   0   0.093  -5.3695   0.0804   0.1693
 8L8  C17  C  CR16  0  -0.313  -6.1618   0.2922  -0.9612
 8L8  C18  C  CR16  0  -0.239  -7.4437  -0.2320  -1.0401
 8L8  C19  C  CR16  0  -0.267  -7.9592  -0.9809   0.0096
 8L8  C20  C  CR16  0  -0.240  -7.1819  -1.1990   1.1395
 8L8  C21  C  CR16  0  -0.314  -5.9009  -0.6727   1.2187
 8L8  H1   H  HCH1  0   0.259   2.0878   0.3672  -1.9251
 8L8  H2   H  HCH1  0   0.227   1.8302  -2.0606  -1.2011
 8L8  H3   H  HCH1  0   0.217   3.0400  -2.0048   0.8805
 8L8  H4   H  HCH1  0   0.223   5.4971  -1.2185  -0.7372
 8L8  H5   H  HCH1  0   0.218   3.8228   0.3289   1.2960
 8L8  H8   H  H     0   0.252   2.0253   2.2854   0.3616
 8L8  H9   H  H     0   0.248  -0.0166   3.3604   0.4965
 8L8  H11  H  HCR6  0   0.265  -0.9332  -0.1031   1.4840
 8L8  H12  H  HCR6  0   0.254  -3.1760  -1.0277   1.3313
 8L8  H14  H  HCR6  0   0.254  -4.4778   2.4675  -0.7792
 8L8  H15  H  HCR6  0   0.254  -2.2154   3.3718  -0.6647
 8L8  H17  H  HCR6  0   0.254  -5.7679   0.8553  -1.7985
 8L8  H18  H  HCR6  0   0.258  -8.0387  -0.0606  -1.9279
 8L8  H19  H  HCR6  0   0.257  -8.9585  -1.3913  -0.0533
 8L8  H20  H  HCR6  0   0.258  -7.5755  -1.7753   1.9668
 8L8  H21  H  HCR6  0   0.254  -5.3166  -0.8354   2.1160
 8L8  H6   H  HCH2  0   0.202   6.2390   0.8629   1.3121
 8L8  H6A  H  HCH2  0   0.197   6.1776   1.2089  -0.4179
 8L8  H7   H  HCH2  0   0.268   0.4955  -0.3090  -0.2529
 8L8  H7A  H  HCH2  0   0.256   1.6738  -0.2724   1.0332
 8L8  HO2  H  HOH1  0   0.448   3.8114  -2.5299  -2.4702
 8L8  HO3  H  HOH1  0   0.454   4.6553  -3.6626   0.2692
 8L8  HO4  H  HOH1  0   0.462   6.4920  -1.4782   1.2013
 8L8  HO6  H  HOH1  0   0.456   5.8533   3.0950   0.9476

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
 8L8  C1   C2   single    1.527  0.020  1.527
 8L8  C1   O5   single    1.411  0.020  1.411
 8L8  C1   C7   single    1.534  0.020  1.534
 8L8  C1   H1   single    0.970  0.020  1.090
 8L8  C2   O2   single    1.408  0.020  1.408
 8L8  C2   C3   single    1.527  0.020  1.527
 8L8  C2   H2   single    0.970  0.020  1.090
 8L8  O2   HO2  single    0.850  0.020  0.980
 8L8  C3   O3   single    1.408  0.020  1.408
 8L8  C3   C4   single    1.523  0.020  1.523
 8L8  C3   H3   single    0.970  0.020  1.090
 8L8  O3   HO3  single    0.850  0.020  0.980
 8L8  C4   O4   single    1.412  0.020  1.412
 8L8  C4   C5   single    1.533  0.020  1.533
 8L8  C4   H4   single    0.970  0.020  1.090
 8L8  O4   HO4  single    0.850  0.020  0.980
 8L8  C5   O5   single    1.412  0.020  1.412
 8L8  C5   C6   single    1.513  0.020  1.513
 8L8  C5   H5   single    0.970  0.020  1.090
 8L8  C6   O6   single    1.407  0.020  1.407
 8L8  C6   H6   single    0.970  0.020  1.090
 8L8  C6   H6A  single    0.970  0.020  1.090
 8L8  O6   HO6  single    0.850  0.020  0.980
 8L8  C7   C8   single    1.496  0.020  1.496
 8L8  C7   H7   single    0.970  0.020  1.090
 8L8  C7   H7A  single    0.970  0.020  1.090
 8L8  C8   C9   double    1.336  0.020  1.336
 8L8  C8   H8   single    0.930  0.020  1.080
 8L8  C9   C10  single    1.468  0.020  1.468
 8L8  C9   H9   single    0.930  0.020  1.080
 8L8  C10  C11  aromatic  1.397  0.020  1.397
 8L8  C10  C15  aromatic  1.398  0.020  1.398
 8L8  C11  C12  aromatic  1.386  0.020  1.386
 8L8  C11  H11  single    0.930  0.020  1.080
 8L8  C12  C13  aromatic  1.395  0.020  1.395
 8L8  C12  H12  single    0.930  0.020  1.080
 8L8  C13  C14  aromatic  1.397  0.020  1.397
 8L8  C13  C16  single    1.476  0.020  1.476
 8L8  C14  C15  aromatic  1.383  0.020  1.383
 8L8  C14  H14  single    0.930  0.020  1.080
 8L8  C15  H15  single    0.930  0.020  1.080
 8L8  C16  C17  aromatic  1.397  0.020  1.397
 8L8  C16  C21  aromatic  1.397  0.020  1.397
 8L8  C17  C18  aromatic  1.387  0.020  1.387
 8L8  C17  H17  single    0.930  0.020  1.080
 8L8  C18  C19  aromatic  1.389  0.020  1.389
 8L8  C18  H18  single    0.930  0.020  1.080
 8L8  C19  C20  aromatic  1.389  0.020  1.389
 8L8  C19  H19  single    0.930  0.020  1.080
 8L8  C20  C21  aromatic  1.387  0.020  1.387
 8L8  C20  H20  single    0.930  0.020  1.080
 8L8  C21  H21  single    0.930  0.020  1.080

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
 8L8  H1   C1   C7   107.11  3.000
 8L8  H1   C1   O5   104.95  3.000
 8L8  C7   C1   O5   113.33  3.000
 8L8  H1   C1   C2   107.65  3.000
 8L8  C7   C1   C2   112.28  3.000
 8L8  O5   C1   C2   111.01  3.000
 8L8  H2   C2   C3   108.51  3.000
 8L8  H2   C2   O2   110.71  3.000
 8L8  C3   C2   O2   111.13  3.000
 8L8  H2   C2   C1   108.41  3.000
 8L8  C3   C2   C1   110.42  3.000
 8L8  O2   C2   C1   107.62  3.000
 8L8  HO2  O2   C2   107.82  3.000
 8L8  H3   C3   C4   107.81  3.000
 8L8  H3   C3   O3   110.36  3.000
 8L8  C4   C3   O3   112.14  3.000
 8L8  H3   C3   C2   108.25  3.000
 8L8  C4   C3   C2   110.71  3.000
 8L8  O3   C3   C2   107.52  3.000
 8L8  HO3  O3   C3   108.12  3.000
 8L8  H4   C4   C5   108.74  3.000
 8L8  H4   C4   O4   110.92  3.000
 8L8  C5   C4   O4   112.14  3.000
 8L8  H4   C4   C3   109.03  3.000
 8L8  C5   C4   C3   108.88  3.000
 8L8  O4   C4   C3   107.05  3.000
 8L8  HO4  O4   C4   109.14  3.000
 8L8  H5   C5   C6   108.27  3.000
 8L8  H5   C5   O5   111.12  3.000
 8L8  C6   C5   O5   107.42  3.000
 8L8  H5   C5   C4   108.29  3.000
 8L8  C6   C5   C4   112.27  3.000
 8L8  O5   C5   C4   109.49  3.000
 8L8  C5   O5   C1   115.29  3.000
 8L8  H6A  C6   H6   107.05  3.000
 8L8  H6A  C6   O6   112.00  3.000
 8L8  H6   C6   O6   111.40  3.000
 8L8  H6A  C6   C5   108.94  3.000
 8L8  H6   C6   C5   108.44  3.000
 8L8  O6   C6   C5   108.92  3.000
 8L8  HO6  O6   C6   107.97  3.000
 8L8  H7A  C7   H7   105.82  3.000
 8L8  H7A  C7   C8   109.58  3.000
 8L8  H7   C7   C8   111.06  3.000
 8L8  H7A  C7   C1   111.14  3.000
 8L8  H7   C7   C1   107.33  3.000
 8L8  C8   C7   C1   111.73  3.000
 8L8  H8   C8   C9   116.53  3.000
 8L8  H8   C8   C7   115.46  3.000
 8L8  C9   C8   C7   127.97  3.000
 8L8  H9   C9   C10  114.84  3.000
 8L8  H9   C9   C8   116.84  3.000
 8L8  C10  C9   C8   128.29  3.000
 8L8  C15  C10  C11  117.59  3.000
 8L8  C15  C10  C9   119.06  3.000
 8L8  C11  C10  C9   123.33  3.000
 8L8  H11  C11  C12  118.82  3.000
 8L8  H11  C11  C10  120.11  3.000
 8L8  C12  C11  C10  121.05  3.000
 8L8  H12  C12  C13  119.89  3.000
 8L8  H12  C12  C11  118.89  3.000
 8L8  C13  C12  C11  121.21  3.000
 8L8  C16  C13  C14  121.04  3.000
 8L8  C16  C13  C12  121.16  3.000
 8L8  C14  C13  C12  117.80  3.000
 8L8  H14  C14  C15  119.03  3.000
 8L8  H14  C14  C13  120.00  3.000
 8L8  C15  C14  C13  120.96  3.000
 8L8  H15  C15  C14  119.29  3.000
 8L8  H15  C15  C10  119.36  3.000
 8L8  C14  C15  C10  121.35  3.000
 8L8  C21  C16  C17  118.30  3.000
 8L8  C21  C16  C13  120.94  3.000
 8L8  C17  C16  C13  120.76  3.000
 8L8  H17  C17  C18  119.24  3.000
 8L8  H17  C17  C16  119.89  3.000
 8L8  C18  C17  C16  120.86  3.000
 8L8  H18  C18  C19  120.08  3.000
 8L8  H18  C18  C17  119.66  3.000
 8L8  C19  C18  C17  120.26  3.000
 8L8  H19  C19  C20  120.31  3.000
 8L8  H19  C19  C18  120.23  3.000
 8L8  C20  C19  C18  119.46  3.000
 8L8  H20  C20  C21  119.62  3.000
 8L8  H20  C20  C19  120.13  3.000
 8L8  C21  C20  C19  120.25  3.000
 8L8  H21  C21  C20  119.24  3.000
 8L8  H21  C21  C16  119.89  3.000
 8L8  C20  C21  C16  120.86  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
 8L8  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 8L8  CONST_02  C13  C14  C15  C10    0.00   0.0  0
 8L8  CONST_03  C14  C15  C10  C11    0.00   0.0  0
 8L8  CONST_04  C14  C13  C12  C11    0.00   0.0  0
 8L8  CONST_05  C16  C13  C12  C11  180.00   0.0  0
 8L8  CONST_06  C15  C10  C11  C12    0.00   0.0  0
 8L8  CONST_07  C15  C14  C13  C12    0.00   0.0  0
 8L8  CONST_10  C18  C17  C16  C13  180.00   0.0  0
 8L8  CONST_11  C20  C21  C16  C13  180.00   0.0  0
 8L8  CONST_14  C16  C13  C14  C15  180.00   0.0  0
 8L8  CONST_15  C19  C18  C17  C16    0.00   0.0  0
 8L8  CONST_16  C19  C20  C21  C16    0.00   0.0  0
 8L8  CONST_17  C20  C21  C16  C17    0.00   0.0  0
 8L8  CONST_18  C20  C19  C18  C17    0.00   0.0  0
 8L8  CONST_19  C21  C16  C17  C18    0.00   0.0  0
 8L8  CONST_20  C21  C20  C19  C18    0.00   0.0  0
 8L8  CONST_21  C12  C11  C10  C9   180.00   0.0  0
 8L8  CONST_22  C14  C15  C10  C9   180.00   0.0  0
 8L8  CONST_23  H12  C12  C11  C10  180.00   0.0  0
 8L8  CONST_24  H14  C14  C15  C10  180.00   0.0  0
 8L8  CONST_25  H15  C15  C10  C11  180.00   0.0  0
 8L8  CONST_26  H11  C11  C12  C13  180.00   0.0  0
 8L8  CONST_27  H17  C17  C16  C13    0.00   0.0  0
 8L8  CONST_28  H21  C21  C16  C13    0.00   0.0  0
 8L8  CONST_29  H18  C18  C17  C16  180.00   0.0  0
 8L8  CONST_30  H20  C20  C21  C16  180.00   0.0  0
 8L8  CONST_31  H19  C19  C18  C17  180.00   0.0  0
 8L8  Var_01    C11  C10  C9   C8    37.39  30.0  2
 8L8  Var_02    C10  C9   C8   C7     2.31   0.0  2
 8L8  Var_03    C9   C8   C7   C1   134.73  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
 8L8  chir_01  C1  C2  O5  C7  positiv
 8L8  chir_02  C2  O2  C1  C3  positiv
 8L8  chir_03  C3  O3  C2  C4  positiv
 8L8  chir_04  C4  O4  C5  C3  positiv
 8L8  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
 8L8  plan-1  C9   0.020
 8L8  plan-1  C10  0.020
 8L8  plan-1  C11  0.020
 8L8  plan-1  C12  0.020
 8L8  plan-1  C13  0.020
 8L8  plan-1  C14  0.020
 8L8  plan-1  C15  0.020
 8L8  plan-1  C16  0.020
 8L8  plan-1  H11  0.020
 8L8  plan-1  H12  0.020
 8L8  plan-1  H14  0.020
 8L8  plan-1  H15  0.020
 8L8  plan-2  C7   0.020
 8L8  plan-2  C8   0.020
 8L8  plan-2  C9   0.020
 8L8  plan-2  C10  0.020
 8L8  plan-2  H8   0.020
 8L8  plan-2  H9   0.020
 8L8  plan-3  C13  0.020
 8L8  plan-3  C16  0.020
 8L8  plan-3  C17  0.020
 8L8  plan-3  C18  0.020
 8L8  plan-3  C19  0.020
 8L8  plan-3  C20  0.020
 8L8  plan-3  C21  0.020
 8L8  plan-3  H17  0.020
 8L8  plan-3  H18  0.020
 8L8  plan-3  H19  0.020
 8L8  plan-3  H20  0.020
 8L8  plan-3  H21  0.020

