# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:31:16 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-iodophenyl 1,4-dithio-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Sc2ccc(I)cc2)[C@H](O)[C@@H](O)[C@@H]1S
#
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
 V3P  V3P  '4-iodophenyl 1,4-dithio-beta-D-glucopyranoside'  D-saccharide  34  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V3P
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
 V3P  C4   C  CH1   0  -0.461  62.3382  79.0096  58.1553
 V3P  C1   C  CH1   0  -0.143  62.7762  80.1298  55.5672
 V3P  C2   C  CH1   0   0.051  61.8566  78.9165  55.6785
 V3P  O2   O  OH1   0  -0.659  60.8738  79.0116  54.6869
 V3P  C3   C  CH1   0   0.057  61.2484  78.9181  57.0822
 V3P  O3   O  OH1   0  -0.662  60.4842  77.7502  57.2043
 V3P  C5   C  CH1   0   0.040  63.2587  80.1937  57.8663
 V3P  O5   O  O2    0  -0.467  63.7670  80.0539  56.5512
 V3P  S1   S  S2    0   0.067  63.5689  80.1496  53.9411
 V3P  C6   C  CH2   0  -0.149  64.4485  80.2709  58.7969
 V3P  O6   O  OH1   0  -0.660  65.1930  81.4193  58.4709
 V3P  S4   S  S2    0  -0.226  61.5054  79.1676  59.7777
 V3P  C11  C  CR16  0  -0.215  64.2032  83.8369  52.4650
 V3P  C21  C  CR16  0  -0.242  63.7798  82.5276  52.6463
 V3P  C31  C  CR6   0  -0.144  64.0841  81.8387  53.8169
 V3P  C41  C  CR16  0  -0.226  64.8205  82.4746  54.8149
 V3P  C51  C  CR16  0  -0.213  65.2243  83.7918  54.6507
 V3P  C61  C  CR6   0  -0.226  64.9191  84.4621  53.4745
 V3P  I6   I  I     0   0.060  65.5533  86.4500  53.2198
 V3P  H4   H  HCH1  0   0.304  62.9187  78.0830  58.1632
 V3P  H1   H  HCH1  0   0.269  62.1888  81.0544  55.6670
 V3P  H2   H  HCH1  0   0.232  62.4675  78.0073  55.5639
 V3P  HO2  H  HOH1  0   0.459  60.3065  78.2357  54.7441
 V3P  H3   H  HCH1  0   0.221  60.6150  79.8174  57.1598
 V3P  HO3  H  HOH1  0   0.451  60.0552  77.7609  58.0689
 V3P  H5   H  HCH1  0   0.230  62.6759  81.1253  57.9453
 V3P  H61  H  HCH2  0   0.210  64.0778  80.3052  59.8270
 V3P  H62  H  HCH2  0   0.203  65.0423  79.3522  58.6954
 V3P  HO6  H  HOH1  0   0.459  65.9540  81.4588  59.0572
 V3P  HS4  H  HSH1  0   0.245  62.2258  78.2644  60.4481
 V3P  H13  H  HCR6  0   0.279  63.2006  82.0481  51.8678
 V3P  H14  H  HCR6  0   0.289  65.0818  81.9595  55.7292
 V3P  H15  H  HCR6  0   0.283  65.7868  84.2737  55.4387
 V3P  H12  H  HCR6  0   0.284  63.9554  84.3520  51.5470

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
 V3P  I6   C61  single    2.102  0.020  2.102
 V3P  C51  C61  aromatic  1.388  0.020  1.388
 V3P  C51  C41  aromatic  1.387  0.020  1.387
 V3P  C61  C11  aromatic  1.387  0.020  1.387
 V3P  C41  C31  aromatic  1.394  0.020  1.394
 V3P  C11  C21  aromatic  1.388  0.020  1.388
 V3P  C31  C21  aromatic  1.392  0.020  1.392
 V3P  C31  S1   single    1.770  0.020  1.770
 V3P  O2   C2   single    1.399  0.020  1.399
 V3P  S1   C1   single    1.809  0.020  1.809
 V3P  C2   C1   single    1.526  0.020  1.526
 V3P  C2   C3   single    1.530  0.020  1.530
 V3P  C1   O5   single    1.398  0.020  1.398
 V3P  O3   C3   single    1.401  0.020  1.401
 V3P  C3   C4   single    1.532  0.020  1.532
 V3P  O5   C5   single    1.417  0.020  1.417
 V3P  C4   C5   single    1.527  0.020  1.527
 V3P  C4   S4   single    1.830  0.020  1.830
 V3P  C5   C6   single    1.512  0.020  1.512
 V3P  C6   O6   single    1.407  0.020  1.407
 V3P  C4   H4   single    0.970  0.020  1.090
 V3P  C1   H1   single    0.970  0.020  1.090
 V3P  C2   H2   single    0.970  0.020  1.090
 V3P  O2   HO2  single    0.850  0.020  0.980
 V3P  C3   H3   single    0.970  0.020  1.090
 V3P  O3   HO3  single    0.850  0.020  0.980
 V3P  C5   H5   single    0.970  0.020  1.090
 V3P  C6   H61  single    0.970  0.020  1.090
 V3P  C6   H62  single    0.970  0.020  1.090
 V3P  O6   HO6  single    0.850  0.020  0.980
 V3P  S4   HS4  single    1.200  0.020  1.300
 V3P  C11  H12  single    0.930  0.020  1.080
 V3P  C21  H13  single    0.930  0.020  1.080
 V3P  C41  H14  single    0.930  0.020  1.080
 V3P  C51  H15  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
 V3P  H4   C4   S4   107.96  3.000
 V3P  H4   C4   C5   109.77  3.000
 V3P  S4   C4   C5   112.03  3.000
 V3P  H4   C4   C3   109.39  3.000
 V3P  S4   C4   C3   107.60  3.000
 V3P  C5   C4   C3   110.03  3.000
 V3P  H1   C1   S1   107.84  3.000
 V3P  H1   C1   O5   111.11  3.000
 V3P  S1   C1   O5   108.82  3.000
 V3P  H1   C1   C2   109.87  3.000
 V3P  O5   C1   C2   109.41  3.000
 V3P  S1   C1   C2   109.77  3.000
 V3P  H2   C2   C3   108.48  3.000
 V3P  H2   C2   O2   111.83  3.000
 V3P  C3   C2   O2   111.77  3.000
 V3P  H2   C2   C1   108.33  3.000
 V3P  C3   C2   C1   107.80  3.000
 V3P  O2   C2   C1   108.50  3.000
 V3P  HO2  O2   C2   108.48  3.000
 V3P  H3   C3   O3   111.12  3.000
 V3P  H3   C3   C2   107.09  3.000
 V3P  O3   C3   C2   107.22  3.000
 V3P  H3   C3   C4   108.09  3.000
 V3P  O3   C3   C4   112.13  3.000
 V3P  C2   C3   C4   111.10  3.000
 V3P  HO3  O3   C3   108.13  3.000
 V3P  H5   C5   C6   109.20  3.000
 V3P  H5   C5   O5   109.86  3.000
 V3P  C6   C5   O5   107.09  3.000
 V3P  H5   C5   C4   108.85  3.000
 V3P  C6   C5   C4   113.41  3.000
 V3P  O5   C5   C4   108.38  3.000
 V3P  C5   O5   C1   113.17  3.000
 V3P  C31  S1   C1   101.60  3.000
 V3P  H62  C6   H61  107.22  3.000
 V3P  H62  C6   O6   112.03  3.000
 V3P  H61  C6   O6   111.80  3.000
 V3P  H62  C6   C5   109.00  3.000
 V3P  H61  C6   C5   108.30  3.000
 V3P  O6   C6   C5   108.39  3.000
 V3P  HO6  O6   C6   108.12  3.000
 V3P  HS4  S4   C4    98.11  3.000
 V3P  H12  C11  C61  121.44  3.000
 V3P  H12  C11  C21  119.36  3.000
 V3P  C61  C11  C21  119.19  3.000
 V3P  H13  C21  C31  120.18  3.000
 V3P  H13  C21  C11  119.15  3.000
 V3P  C31  C21  C11  120.66  3.000
 V3P  C41  C31  C21  119.46  3.000
 V3P  C21  C31  S1   117.87  3.000
 V3P  C41  C31  S1   122.61  3.000
 V3P  H14  C41  C51  118.81  3.000
 V3P  H14  C41  C31  121.04  3.000
 V3P  C51  C41  C31  120.15  3.000
 V3P  H15  C51  C61  121.11  3.000
 V3P  H15  C51  C41  119.22  3.000
 V3P  C61  C51  C41  119.66  3.000
 V3P  I6   C61  C51  119.54  3.000
 V3P  C51  C61  C11  120.85  3.000
 V3P  I6   C61  C11  119.61  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
 V3P  CONST_01  C41  C51  C61  C11    0.00   0.0  0
 V3P  CONST_02  C41  C31  C21  C11    0.00   0.0  0
 V3P  CONST_03  C51  C61  C11  C21    0.00   0.0  0
 V3P  CONST_04  C51  C41  C31  C21    0.00   0.0  0
 V3P  CONST_05  C61  C51  C41  C31    0.00   0.0  0
 V3P  CONST_06  C61  C11  C21  C31    0.00   0.0  0
 V3P  CONST_07  C51  C41  C31  S1   180.00   0.0  0
 V3P  CONST_08  C11  C21  C31  S1   180.00   0.0  0
 V3P  CONST_09  I6   C61  C11  C21  180.00   0.0  0
 V3P  CONST_10  I6   C61  C51  C41  180.00   0.0  0
 V3P  CONST_11  H15  C51  C61  C11  180.00   0.0  0
 V3P  CONST_12  H14  C41  C31  C21  180.00   0.0  0
 V3P  CONST_13  H12  C11  C21  C31  180.00   0.0  0
 V3P  CONST_14  H13  C21  C31  C41  180.00   0.0  0
 V3P  Var_01    C41  C31  S1   C1    51.34  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
 V3P  chir_01  C4  C3  C5  S4  negativ
 V3P  chir_02  C1  S1  O5  C2  positiv
 V3P  chir_03  C2  O2  C1  C3  negativ
 V3P  chir_04  C3  O3  C2  C4  positiv
 V3P  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
 V3P  plan-1  S1   0.020
 V3P  plan-1  C11  0.020
 V3P  plan-1  C21  0.020
 V3P  plan-1  C31  0.020
 V3P  plan-1  C41  0.020
 V3P  plan-1  C51  0.020
 V3P  plan-1  C61  0.020
 V3P  plan-1  I6   0.020
 V3P  plan-1  H13  0.020
 V3P  plan-1  H14  0.020
 V3P  plan-1  H15  0.020
 V3P  plan-1  H12  0.020

