# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 17:32:54 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-[(E)-2-(4-phenylphenyl)prop-1-enyl]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C(=C/[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O)c2ccc(cc2)c3ccccc3
#
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
 VNY  VNY  (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-[(E)-2-(4-phenylphenyl)prop-1-enyl]oxane-3,4,5-triol  ligand  50  26  .  2021-08-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VNY
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
 VNY  O6    O  OH1   0  -0.672  -3.6078  -2.9618   1.7101
 VNY  C6    C  CH2   0  -0.155  -4.3584  -1.7732   1.7932
 VNY  C5    C  CH1   0  -0.010  -3.6233  -0.6766   1.0504
 VNY  O5    O  O2    0  -0.485  -3.5605  -1.0535  -0.3084
 VNY  C4    C  CH1   0   0.033  -4.3285   0.6737   1.1980
 VNY  O4    O  OH1   0  -0.676  -4.2817   1.0396   2.5573
 VNY  C3    C  CH1   0  -0.007  -3.6300   1.7129   0.3281
 VNY  O3    O  OH1   0  -0.673  -4.3438   2.9202   0.4534
 VNY  C2    C  CH1   0   0.023  -3.5299   1.2354  -1.1173
 VNY  O2    O  OH1   0  -0.670  -4.8317   1.2009  -1.6494
 VNY  C1    C  CH1   0  -0.107  -2.8739  -0.1532  -1.1623
 VNY  C7    C  C1    0  -0.288  -1.4041  -0.0924  -0.8674
 VNY  C8    C  C     0   0.057  -0.4085  -0.5742  -1.6230
 VNY  C21   C  CH3   0  -0.745  -0.5904  -1.3027  -2.9232
 VNY  C9    C  CR6   0   0.086   0.9916  -0.4033  -1.1657
 VNY  C10   C  CR16  0  -0.294   1.9452  -1.4034  -1.3664
 VNY  C11   C  CR16  0  -0.293   3.2450  -1.2575  -0.9104
 VNY  C12   C  CR6   0   0.076   3.6517  -0.0989  -0.2481
 VNY  C13   C  CR16  0  -0.295   2.7062   0.9119  -0.0678
 VNY  C14   C  CR16  0  -0.295   1.4064   0.7636  -0.5198
 VNY  C15   C  CR6   0   0.090   5.0347   0.0548   0.2438
 VNY  C20   C  CR16  0  -0.311   5.2923   0.7007   1.4548
 VNY  C19   C  CR16  0  -0.240   6.5904   0.8422   1.9229
 VNY  C18   C  CR16  0  -0.267   7.6571   0.3403   1.1888
 VNY  C17   C  CR16  0  -0.239   7.4143  -0.3028  -0.0180
 VNY  C16   C  CR16  0  -0.311   6.1159  -0.4444  -0.4854
 VNY  H6    H  HOH1  0   0.456  -4.0276  -3.6170   2.2741
 VNY  H61C  H  HCH2  0   0.193  -5.3595  -1.8924   1.3549
 VNY  H62C  H  HCH2  0   0.212  -4.4968  -1.4541   2.8312
 VNY  H5    H  HCH1  0   0.217  -2.6129  -0.5871   1.4792
 VNY  H4    H  HCH1  0   0.211  -5.3688   0.5631   0.8572
 VNY  H1    H  HCH1  0   0.259  -3.0310  -0.5501  -2.1680
 VNY  HA    H  HOH1  0   0.452  -4.6908   1.9070   2.6427
 VNY  H3    H  HCH1  0   0.225  -2.6081   1.8373   0.7143
 VNY  HB    H  HOH1  0   0.457  -3.7746   3.6451   0.1777
 VNY  H2    H  HCH1  0   0.229  -2.8902   1.9304  -1.6821
 VNY  HC    H  HOH1  0   0.453  -4.7708   0.9872  -2.5855
 VNY  H7    H  H     0   0.253  -1.1225   0.3704   0.0732
 VNY  H211  H  HCH3  0   0.251   0.0227  -0.8530  -3.7056
 VNY  H212  H  HCH3  0   0.252  -0.2765  -2.3443  -2.8342
 VNY  H213  H  HCH3  0   0.256  -1.6201  -1.3087  -3.2700
 VNY  H10   H  HCR6  0   0.253   1.6708  -2.3268  -1.8595
 VNY  H14   H  HCR6  0   0.253   0.7110   1.5836  -0.3920
 VNY  H11   H  HCR6  0   0.255   3.9444  -2.0716  -1.0534
 VNY  H13   H  HCR6  0   0.255   2.9940   1.8420   0.4063
 VNY  H20   H  HCR6  0   0.254   4.4698   1.0797   2.0492
 VNY  H16   H  HCR6  0   0.254   5.9454  -0.9316  -1.4374
 VNY  H19   H  HCR6  0   0.258   6.7682   1.3400   2.8673
 VNY  H18   H  HCR6  0   0.258   8.6697   0.4499   1.5543
 VNY  H17   H  HCR6  0   0.258   8.2392  -0.6899  -0.6024

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
 VNY  O6   C6    single    1.408  0.020  1.408
 VNY  C6   C5    single    1.515  0.020  1.515
 VNY  C5   O5    single    1.412  0.020  1.412
 VNY  C5   C4    single    1.531  0.020  1.531
 VNY  O5   C1    single    1.418  0.020  1.418
 VNY  C4   O4    single    1.408  0.020  1.408
 VNY  C4   C3    single    1.525  0.020  1.525
 VNY  C3   O3    single    1.408  0.020  1.408
 VNY  C3   C2    single    1.526  0.020  1.526
 VNY  C2   O2    single    1.407  0.020  1.407
 VNY  C2   C1    single    1.536  0.020  1.536
 VNY  C1   C7    single    1.500  0.020  1.500
 VNY  C7   C8    double    1.339  0.020  1.339
 VNY  C8   C21   single    1.501  0.020  1.501
 VNY  C8   C9    single    1.483  0.020  1.483
 VNY  C9   C10   aromatic  1.396  0.020  1.396
 VNY  C9   C14   aromatic  1.397  0.020  1.397
 VNY  C10  C11   aromatic  1.385  0.020  1.385
 VNY  C11  C12   aromatic  1.395  0.020  1.395
 VNY  C12  C13   aromatic  1.396  0.020  1.396
 VNY  C12  C15   single    1.476  0.020  1.476
 VNY  C13  C14   aromatic  1.384  0.020  1.384
 VNY  C15  C20   aromatic  1.397  0.020  1.397
 VNY  C15  C16   aromatic  1.396  0.020  1.396
 VNY  C20  C19   aromatic  1.387  0.020  1.387
 VNY  C19  C18   aromatic  1.389  0.020  1.389
 VNY  C18  C17   aromatic  1.389  0.020  1.389
 VNY  C17  C16   aromatic  1.387  0.020  1.387
 VNY  O6   H6    single    0.850  0.020  0.980
 VNY  C6   H61C  single    0.970  0.020  1.090
 VNY  C6   H62C  single    0.970  0.020  1.090
 VNY  C5   H5    single    0.970  0.020  1.090
 VNY  C4   H4    single    0.970  0.020  1.090
 VNY  C1   H1    single    0.970  0.020  1.090
 VNY  O4   HA    single    0.850  0.020  0.980
 VNY  C3   H3    single    0.970  0.020  1.090
 VNY  O3   HB    single    0.850  0.020  0.980
 VNY  C2   H2    single    0.970  0.020  1.090
 VNY  O2   HC    single    0.850  0.020  0.980
 VNY  C7   H7    single    0.930  0.020  1.080
 VNY  C21  H211  single    0.970  0.020  1.090
 VNY  C21  H212  single    0.970  0.020  1.090
 VNY  C21  H213  single    0.970  0.020  1.090
 VNY  C10  H10   single    0.930  0.020  1.080
 VNY  C14  H14   single    0.930  0.020  1.080
 VNY  C11  H11   single    0.930  0.020  1.080
 VNY  C13  H13   single    0.930  0.020  1.080
 VNY  C20  H20   single    0.930  0.020  1.080
 VNY  C16  H16   single    0.930  0.020  1.080
 VNY  C19  H19   single    0.930  0.020  1.080
 VNY  C18  H18   single    0.930  0.020  1.080
 VNY  C17  H17   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
 VNY  H6    O6   C6    107.94  3.000
 VNY  H62C  C6   H61C  107.13  3.000
 VNY  H62C  C6   C5    108.38  3.000
 VNY  H61C  C6   C5    108.96  3.000
 VNY  H62C  C6   O6    111.68  3.000
 VNY  H61C  C6   O6    111.74  3.000
 VNY  C5    C6   O6    108.87  3.000
 VNY  H5    C5   C4    108.27  3.000
 VNY  H5    C5   O5    110.84  3.000
 VNY  C4    C5   O5    110.42  3.000
 VNY  H5    C5   C6    108.25  3.000
 VNY  C4    C5   C6    111.58  3.000
 VNY  O5    C5   C6    107.48  3.000
 VNY  C1    O5   C5    115.57  3.000
 VNY  H4    C4   C3    108.97  3.000
 VNY  H4    C4   O4    110.89  3.000
 VNY  C3    C4   O4    111.00  3.000
 VNY  H4    C4   C5    108.49  3.000
 VNY  C3    C4   C5    109.58  3.000
 VNY  O4    C4   C5    107.87  3.000
 VNY  HA    O4   C4    107.79  3.000
 VNY  H3    C3   C2    107.89  3.000
 VNY  H3    C3   O3    110.05  3.000
 VNY  C2    C3   O3    112.70  3.000
 VNY  H3    C3   C4    107.61  3.000
 VNY  C2    C3   C4    110.93  3.000
 VNY  O3    C3   C4    107.54  3.000
 VNY  HB    O3   C3    108.70  3.000
 VNY  H2    C2   C1    107.91  3.000
 VNY  H2    C2   O2    111.05  3.000
 VNY  C1    C2   O2    111.22  3.000
 VNY  H2    C2   C3    109.07  3.000
 VNY  C1    C2   C3    109.80  3.000
 VNY  O2    C2   C3    107.78  3.000
 VNY  HC    O2   C2    108.35  3.000
 VNY  H1    C1   C7    109.66  3.000
 VNY  H1    C1   C2    107.09  3.000
 VNY  C7    C1   C2    112.08  3.000
 VNY  H1    C1   O5    104.72  3.000
 VNY  C7    C1   O5    112.44  3.000
 VNY  C2    C1   O5    110.45  3.000
 VNY  H7    C7   C8    116.71  3.000
 VNY  H7    C7   C1    116.21  3.000
 VNY  C8    C7   C1    127.06  3.000
 VNY  C9    C8   C21   115.93  3.000
 VNY  C9    C8   C7    119.10  3.000
 VNY  C21   C8   C7    124.96  3.000
 VNY  H213  C21  H212  107.06  3.000
 VNY  H213  C21  H211  107.82  3.000
 VNY  H212  C21  H211  106.87  3.000
 VNY  H213  C21  C8    113.19  3.000
 VNY  H212  C21  C8    110.95  3.000
 VNY  H211  C21  C8    110.67  3.000
 VNY  C14   C9   C10   117.52  3.000
 VNY  C14   C9   C8    121.28  3.000
 VNY  C10   C9   C8    121.19  3.000
 VNY  H10   C10  C11   118.54  3.000
 VNY  H10   C10  C9    120.23  3.000
 VNY  C11   C10  C9    121.20  3.000
 VNY  H11   C11  C12   119.92  3.000
 VNY  H11   C11  C10   118.91  3.000
 VNY  C12   C11  C10   121.15  3.000
 VNY  C15   C12  C13   121.08  3.000
 VNY  C15   C12  C11   121.19  3.000
 VNY  C13   C12  C11   117.73  3.000
 VNY  H13   C13  C14   118.98  3.000
 VNY  H13   C13  C12   119.90  3.000
 VNY  C14   C13  C12   121.09  3.000
 VNY  H14   C14  C13   118.91  3.000
 VNY  H14   C14  C9    119.77  3.000
 VNY  C13   C14  C9    121.29  3.000
 VNY  C16   C15  C20   118.38  3.000
 VNY  C16   C15  C12   120.95  3.000
 VNY  C20   C15  C12   120.67  3.000
 VNY  H20   C20  C19   119.32  3.000
 VNY  H20   C20  C15   119.84  3.000
 VNY  C19   C20  C15   120.83  3.000
 VNY  H19   C19  C18   120.08  3.000
 VNY  H19   C19  C20   119.68  3.000
 VNY  C18   C19  C20   120.24  3.000
 VNY  H18   C18  C17   120.26  3.000
 VNY  H18   C18  C19   120.24  3.000
 VNY  C17   C18  C19   119.50  3.000
 VNY  H17   C17  C16   119.66  3.000
 VNY  H17   C17  C18   120.10  3.000
 VNY  C16   C17  C18   120.24  3.000
 VNY  H16   C16  C17   119.31  3.000
 VNY  H16   C16  C15   119.86  3.000
 VNY  C17   C16  C15   120.82  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
 VNY  CONST_01  C12   C11  C10  C9     0.00   0.0  0
 VNY  CONST_02  C12   C13  C14  C9     0.00   0.0  0
 VNY  CONST_03  C13   C14  C9   C10    0.00   0.0  0
 VNY  CONST_04  C13   C12  C11  C10    0.00   0.0  0
 VNY  CONST_05  C15   C12  C11  C10  180.00   0.0  0
 VNY  CONST_06  C14   C9   C10  C11    0.00   0.0  0
 VNY  CONST_07  C14   C13  C12  C11    0.00   0.0  0
 VNY  CONST_10  C19   C20  C15  C12  180.00   0.0  0
 VNY  CONST_11  C17   C16  C15  C12  180.00   0.0  0
 VNY  CONST_14  C15   C12  C13  C14  180.00   0.0  0
 VNY  CONST_15  C18   C19  C20  C15    0.00   0.0  0
 VNY  CONST_16  C18   C17  C16  C15    0.00   0.0  0
 VNY  CONST_17  C17   C16  C15  C20    0.00   0.0  0
 VNY  CONST_18  C17   C18  C19  C20    0.00   0.0  0
 VNY  CONST_19  C16   C15  C20  C19    0.00   0.0  0
 VNY  CONST_20  C16   C17  C18  C19    0.00   0.0  0
 VNY  CONST_21  C11   C10  C9   C8   180.00   0.0  0
 VNY  CONST_22  C13   C14  C9   C8   180.00   0.0  0
 VNY  CONST_23  H11   C11  C10  C9   180.00   0.0  0
 VNY  CONST_24  H13   C13  C14  C9   180.00   0.0  0
 VNY  CONST_25  H14   C14  C9   C10  180.00   0.0  0
 VNY  CONST_26  H10   C10  C11  C12  180.00   0.0  0
 VNY  CONST_27  H20   C20  C15  C12    0.00   0.0  0
 VNY  CONST_28  H16   C16  C15  C12    0.00   0.0  0
 VNY  CONST_29  H19   C19  C20  C15  180.00   0.0  0
 VNY  CONST_30  H17   C17  C16  C15  180.00   0.0  0
 VNY  CONST_31  H18   C18  C19  C20  180.00   0.0  0
 VNY  Var_01    C9    C8   C7   C1   179.36   0.0  2
 VNY  Var_02    C10   C9   C8   C7   142.68  30.0  2
 VNY  Var_03    H211  C21  C8   C9   -52.57  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
 VNY  chir_01  C5  C6  O5  C4  negativ
 VNY  chir_02  C4  O4  C5  C3  positiv
 VNY  chir_03  C3  O3  C4  C2  negativ
 VNY  chir_04  C2  O2  C3  C1  negativ
 VNY  chir_05  C1  O5  C7  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
 VNY  plan-1  C8   0.020
 VNY  plan-1  C9   0.020
 VNY  plan-1  C10  0.020
 VNY  plan-1  C11  0.020
 VNY  plan-1  C12  0.020
 VNY  plan-1  C13  0.020
 VNY  plan-1  C14  0.020
 VNY  plan-1  C15  0.020
 VNY  plan-1  H10  0.020
 VNY  plan-1  H14  0.020
 VNY  plan-1  H11  0.020
 VNY  plan-1  H13  0.020
 VNY  plan-2  C1   0.020
 VNY  plan-2  C7   0.020
 VNY  plan-2  C8   0.020
 VNY  plan-2  C21  0.020
 VNY  plan-2  C9   0.020
 VNY  plan-2  H7   0.020
 VNY  plan-3  C12  0.020
 VNY  plan-3  C15  0.020
 VNY  plan-3  C20  0.020
 VNY  plan-3  C19  0.020
 VNY  plan-3  C18  0.020
 VNY  plan-3  C17  0.020
 VNY  plan-3  C16  0.020
 VNY  plan-3  H20  0.020
 VNY  plan-3  H16  0.020
 VNY  plan-3  H19  0.020
 VNY  plan-3  H18  0.020
 VNY  plan-3  H17  0.020

