# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 18:23:20 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: [(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] (~{E})-3-(4-hydroxyphenyl)prop-2-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OC(=O)\C=C\c2ccc(O)cc2)[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
 VKK  VKK  "p-coumaroyl glucose"  ligand  41  23  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VKK
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
 VKK  O5'  O  O2    0  -0.490  33.1933  21.5321  28.1901
 VKK  C5'  C  CH1   0  -0.018  32.2228  20.9481  27.3366
 VKK  C4'  C  CH1   0   0.025  32.6614  21.0916  25.8705
 VKK  O4'  O  OH1   0  -0.666  31.6757  20.5910  25.0016
 VKK  C3'  C  CH1   0   0.013  32.8722  22.5656  25.5547
 VKK  O3'  O  OH1   0  -0.662  33.3750  22.6794  24.2496
 VKK  C2'  C  CH1   0  -0.039  33.8296  23.1821  26.5707
 VKK  O2'  O  OH1   0  -0.662  33.8980  24.5608  26.3096
 VKK  C1'  C  CH1   0   0.286  33.3160  22.9029  27.9787
 VKK  C8   C  CR6   0   0.357  37.8387  26.3793  34.7024
 VKK  C5   C  CR6   0   0.120  35.9376  25.2129  32.9962
 VKK  C6   C  CR16  0  -0.294  37.2238  25.5291  32.5377
 VKK  C4   C  C1    0  -0.208  34.9162  24.6167  32.1545
 VKK  C6'  C  CH2   0  -0.193  32.0026  19.5166  27.7744
 VKK  O6'  O  OH1   0  -0.666  33.1691  18.7647  27.5478
 VKK  O1'  O  O2    0  -0.500  34.2786  23.3854  28.8775
 VKK  C3   C  C1    0  -0.447  35.0440  24.2532  30.8697
 VKK  C7   C  CR16  0  -0.312  38.1603  26.1017  33.3699
 VKK  C9   C  CR16  0  -0.368  36.5662  26.0711  35.1785
 VKK  C10  C  CR16  0  -0.284  35.6353  25.4988  34.3299
 VKK  O2   O  O     0  -0.438  32.7993  23.5003  30.5661
 VKK  H1   H  HCH1  0   0.231  31.2575  21.4656  27.4587
 VKK  H2   H  HCH1  0   0.227  33.6180  20.5705  25.7317
 VKK  H3   H  HOH1  0   0.457  31.7910  19.6400  24.9184
 VKK  H4   H  HCH1  0   0.210  31.8997  23.0795  25.6480
 VKK  H5   H  HOH1  0   0.448  33.5085  23.6146  24.0623
 VKK  H6   H  HCH1  0   0.232  34.8119  22.7002  26.4585
 VKK  H7   H  HOH1  0   0.459  34.7004  24.9157  26.7044
 VKK  H8   H  HCH1  0   0.216  32.3524  23.4120  28.1347
 VKK  H9   H  HCR6  0   0.260  37.5036  25.3311  31.5111
 VKK  H10  H  H     0   0.269  33.9545  24.4578  32.6336
 VKK  H11  H  HCH2  0   0.209  31.1424  19.1243  27.2189
 VKK  H12  H  HCH2  0   0.222  31.7145  19.5208  28.8336
 VKK  H13  H  HOH1  0   0.458  32.9897  17.8513  27.7878
 VKK  H14  H  H     0   0.276  35.9724  24.3738  30.3262
 VKK  H15  H  HCR6  0   0.270  39.1478  26.3422  32.9968
 VKK  H16  H  HCR6  0   0.277  36.3019  26.2802  36.2086
 VKK  H17  H  HCR6  0   0.266  34.6490  25.2678  34.7149
 VKK  H18  H  HOH1  0   0.478  38.4653  27.0920  36.3591
 VKK  C2   C  C     0   0.597  33.9118  23.6833  30.1382
 VKK  O8   O  OH1   0  -0.615  38.7890  26.9393  35.4632

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
 VKK  O3'  C3'  single    1.403  0.020  1.403
 VKK  O4'  C4'  single    1.406  0.020  1.406
 VKK  C3'  C4'  single    1.522  0.020  1.522
 VKK  C3'  C2'  single    1.526  0.020  1.526
 VKK  C4'  C5'  single    1.537  0.020  1.537
 VKK  O2'  C2'  single    1.405  0.020  1.405
 VKK  C2'  C1'  single    1.525  0.020  1.525
 VKK  O6'  C6'  single    1.406  0.020  1.406
 VKK  C5'  C6'  single    1.513  0.020  1.513
 VKK  C5'  O5'  single    1.418  0.020  1.418
 VKK  C1'  O5'  single    1.392  0.020  1.392
 VKK  C1'  O1'  single    1.403  0.020  1.403
 VKK  O1'  C2   single    1.346  0.020  1.346
 VKK  C2   O2   double    1.206  0.020  1.206
 VKK  C2   C3   single    1.463  0.020  1.463
 VKK  C3   C4   double    1.341  0.020  1.341
 VKK  C4   C5   single    1.452  0.020  1.452
 VKK  C6   C5   aromatic  1.402  0.020  1.402
 VKK  C6   C7   aromatic  1.377  0.020  1.377
 VKK  C5   C10  aromatic  1.397  0.020  1.397
 VKK  C7   C8   aromatic  1.399  0.020  1.399
 VKK  C10  C9   aromatic  1.384  0.020  1.384
 VKK  C8   C9   aromatic  1.393  0.020  1.393
 VKK  C8   O8   single    1.340  0.020  1.340
 VKK  C5'  H1   single    0.970  0.020  1.090
 VKK  C4'  H2   single    0.970  0.020  1.090
 VKK  O4'  H3   single    0.850  0.020  0.980
 VKK  C3'  H4   single    0.970  0.020  1.090
 VKK  O3'  H5   single    0.850  0.020  0.980
 VKK  C2'  H6   single    0.970  0.020  1.090
 VKK  O2'  H7   single    0.850  0.020  0.980
 VKK  C1'  H8   single    0.970  0.020  1.090
 VKK  C6   H9   single    0.930  0.020  1.080
 VKK  C4   H10  single    0.930  0.020  1.080
 VKK  C6'  H11  single    0.970  0.020  1.090
 VKK  C6'  H12  single    0.970  0.020  1.090
 VKK  O6'  H13  single    0.850  0.020  0.980
 VKK  C3   H14  single    0.930  0.020  1.080
 VKK  C7   H15  single    0.930  0.020  1.080
 VKK  C9   H16  single    0.930  0.020  1.080
 VKK  C10  H17  single    0.930  0.020  1.080
 VKK  O8   H18  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
 VKK  C1'  O5'  C5'  111.98  3.000
 VKK  H1   C5'  C6'  106.54  3.000
 VKK  H1   C5'  C4'  108.17  3.000
 VKK  C6'  C5'  C4'  113.95  3.000
 VKK  H1   C5'  O5'  109.84  3.000
 VKK  C6'  C5'  O5'  108.37  3.000
 VKK  C4'  C5'  O5'  109.90  3.000
 VKK  H2   C4'  C3'  108.22  3.000
 VKK  H2   C4'  O4'  111.33  3.000
 VKK  C3'  C4'  O4'  108.28  3.000
 VKK  H2   C4'  C5'  108.95  3.000
 VKK  C3'  C4'  C5'  109.14  3.000
 VKK  O4'  C4'  C5'  110.86  3.000
 VKK  H3   O4'  C4'  108.75  3.000
 VKK  H4   C3'  C2'  107.96  3.000
 VKK  H4   C3'  O3'  110.89  3.000
 VKK  C2'  C3'  O3'  111.21  3.000
 VKK  H4   C3'  C4'  108.13  3.000
 VKK  C2'  C3'  C4'  109.87  3.000
 VKK  O3'  C3'  C4'  108.73  3.000
 VKK  H5   O3'  C3'  108.01  3.000
 VKK  H6   C2'  C1'  108.35  3.000
 VKK  H6   C2'  O2'  111.56  3.000
 VKK  C1'  C2'  O2'  111.58  3.000
 VKK  H6   C2'  C3'  108.38  3.000
 VKK  C1'  C2'  C3'  109.24  3.000
 VKK  O2'  C2'  C3'  107.65  3.000
 VKK  H7   O2'  C2'  109.05  3.000
 VKK  H8   C1'  O1'  110.54  3.000
 VKK  H8   C1'  C2'  109.94  3.000
 VKK  O1'  C1'  C2'  107.31  3.000
 VKK  H8   C1'  O5'  110.90  3.000
 VKK  O1'  C1'  O5'  107.57  3.000
 VKK  C2'  C1'  O5'  110.50  3.000
 VKK  O8   C8   C9   123.11  3.000
 VKK  O8   C8   C7   117.44  3.000
 VKK  C9   C8   C7   119.45  3.000
 VKK  C10  C5   C4   119.03  3.000
 VKK  C10  C5   C6   117.69  3.000
 VKK  C4   C5   C6   123.28  3.000
 VKK  H9   C6   C7   118.25  3.000
 VKK  H9   C6   C5   120.41  3.000
 VKK  C7   C6   C5   121.34  3.000
 VKK  H10  C4   C3   117.85  3.000
 VKK  H10  C4   C5   115.30  3.000
 VKK  C3   C4   C5   126.84  3.000
 VKK  H12  C6'  H11  106.52  3.000
 VKK  H12  C6'  O6'  112.04  3.000
 VKK  H11  C6'  O6'  112.20  3.000
 VKK  H12  C6'  C5'  108.29  3.000
 VKK  H11  C6'  C5'  107.82  3.000
 VKK  O6'  C6'  C5'  109.78  3.000
 VKK  H13  O6'  C6'  108.24  3.000
 VKK  C2   O1'  C1'  119.28  3.000
 VKK  H14  C3   C4   122.17  3.000
 VKK  H14  C3   C2   117.12  3.000
 VKK  C4   C3   C2   120.70  3.000
 VKK  H15  C7   C6   120.28  3.000
 VKK  H15  C7   C8   119.60  3.000
 VKK  C6   C7   C8   120.12  3.000
 VKK  H16  C9   C10  119.91  3.000
 VKK  H16  C9   C8   120.32  3.000
 VKK  C10  C9   C8   119.77  3.000
 VKK  H17  C10  C9   118.86  3.000
 VKK  H17  C10  C5   119.50  3.000
 VKK  C9   C10  C5   121.64  3.000
 VKK  O2   C2   C3   126.54  3.000
 VKK  C3   C2   O1'  110.09  3.000
 VKK  O2   C2   O1'  123.37  3.000
 VKK  H18  O8   C8   110.82  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
 VKK  CONST_01  C5   C6   C7   C8      0.00   0.0  0
 VKK  CONST_02  C5   C10  C9   C8      0.00   0.0  0
 VKK  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 VKK  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 VKK  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 VKK  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 VKK  CONST_07  O8   C8   C7   C6    180.00   0.0  0
 VKK  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 VKK  CONST_09  C9   C10  C5   C4    180.00   0.0  0
 VKK  CONST_10  O8   C8   C9   C10   180.00   0.0  0
 VKK  CONST_11  H9   C6   C7   C8    180.00   0.0  0
 VKK  CONST_12  H17  C10  C9   C8    180.00   0.0  0
 VKK  CONST_13  H15  C7   C6   C5    180.00   0.0  0
 VKK  CONST_14  H16  C9   C10  C5    180.00   0.0  0
 VKK  CONST_15  H17  C10  C5   C6    180.00   0.0  0
 VKK  CONST_16  H16  C9   C8   C7    180.00   0.0  0
 VKK  CONST_17  H15  C7   C8   C9    180.00   0.0  0
 VKK  CONST_18  H9   C6   C5   C10   180.00   0.0  0
 VKK  Var_01    C3   C4   C5   C6      1.95  30.0  3
 VKK  Var_02    C10  C5   C4   C3   -178.44  30.0  2
 VKK  Var_03    H10  C4   C5   C6   -177.95  30.0  3
 VKK  Var_04    H10  C4   C5   C10     1.65  30.0  3
 VKK  Var_05    C2   C3   C4   C5   -178.86   0.0  2
 VKK  Var_06    O2   C2   O1'  C1'     3.52  30.0  3
 VKK  Var_07    C3   C2   O1'  C1'  -176.08  30.0  3
 VKK  Var_08    H14  C3   C4   C5      0.51   0.0  2
 VKK  Var_09    O1'  C2   C3   C4   -179.42  30.0  1
 VKK  Var_10    O2   C2   C3   C4      0.99  30.0  1
 VKK  Var_11    H10  C4   C3   C2      1.04   0.0  2
 VKK  Var_12    H14  C3   C2   O1'     1.18  30.0  2
 VKK  Var_13    H14  C3   C2   O2   -178.41  30.0  2
 VKK  Var_14    H14  C3   C4   H10  -179.58   0.0  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
 VKK  chir_01  C5'  C4'  C6'  O5'  negativ
 VKK  chir_02  C4'  O4'  C5'  C3'  positiv
 VKK  chir_03  C3'  O3'  C4'  C2'  negativ
 VKK  chir_04  C2'  O2'  C3'  C1'  positiv
 VKK  chir_05  C1'  O1'  O5'  C2'  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
 VKK  plan-1  C8   0.020
 VKK  plan-1  C5   0.020
 VKK  plan-1  C6   0.020
 VKK  plan-1  C4   0.020
 VKK  plan-1  C7   0.020
 VKK  plan-1  C9   0.020
 VKK  plan-1  C10  0.020
 VKK  plan-1  H9   0.020
 VKK  plan-1  H15  0.020
 VKK  plan-1  H16  0.020
 VKK  plan-1  H17  0.020
 VKK  plan-1  O8   0.020
 VKK  plan-2  O1'  0.020
 VKK  plan-2  C3   0.020
 VKK  plan-2  O2   0.020
 VKK  plan-2  C2   0.020
 VKK  plan-3  C5   0.020
 VKK  plan-3  C4   0.020
 VKK  plan-3  C3   0.020
 VKK  plan-3  H10  0.020
 VKK  plan-3  H14  0.020
 VKK  plan-3  C2   0.020

