# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 19:20:39 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-deoxy-2-({[(1,1-dioxido-1-benzothiophen-2-yl)methoxy]carbonyl}amino)-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[C@H](NC(=O)OCC2=Cc3ccccc3[S]2(=O)=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
 4V3  4V3  2-deoxy-2-({[(1,1-dioxido-1-benzothiophen-2-yl)methoxy]carbonyl}amino)-beta-D-glucopyranose  ligand  46  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4V3
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
 4V3  C10  C  CH2   0  -0.161   7.2043   0.1378   0.6609
 4V3  C13  C  C     0   0.776   0.6962   0.6029  -0.7263
 4V3  C01  C  CH1   0   0.039   3.8276  -1.1300  -0.7156
 4V3  C02  C  CH1   0  -0.166   3.0483   0.1086  -0.2884
 4V3  C03  C  CH1   0   0.309   3.5983   0.6228   1.0442
 4V3  O04  O  O2    0  -0.495   4.9730   0.8883   0.9163
 4V3  C05  C  CH1   0  -0.022   5.7453  -0.2621   0.6417
 4V3  C06  C  CH1   0  -0.003   5.3254  -0.8380  -0.7153
 4V3  N07  N  NH1   0  -0.661   1.6428  -0.1814  -0.1904
 4V3  O08  O  OH1   0  -0.672   5.9805  -2.0540  -0.9992
 4V3  O09  O  OH1   0  -0.661   3.3705  -1.5207  -1.9814
 4V3  O12  O  OH1   0  -0.668   7.5485   0.5529   1.9600
 4V3  O14  O  O2    0  -0.488  -0.5278   0.1415  -0.4112
 4V3  O15  O  O     0  -0.509   0.8792   1.5874  -1.4086
 4V3  C16  C  CH2   0  -0.180  -1.6258   0.8511  -0.9449
 4V3  C17  C  CR5   0  -0.229  -2.8588   0.2305  -0.3975
 4V3  C18  C  CR15  0  -0.187  -3.0427  -0.8110   0.4105
 4V3  C19  C  CR56  0   0.229  -4.4471  -1.1010   0.7260
 4V3  C20  C  CR56  0  -0.222  -5.3392  -0.2241   0.1189
 4V3  S21  S  S     0   1.240  -4.4300   0.9477  -0.8457
 4V3  C22  C  CR16  0  -0.311  -4.9446  -2.1112   1.5302
 4V3  C23  C  CR16  0  -0.226  -6.3234  -2.2135   1.7032
 4V3  C24  C  CR16  0  -0.261  -7.1936  -1.3239   1.0871
 4V3  C25  C  CR16  0  -0.265  -6.7034  -0.3029   0.2741
 4V3  O26  O  OS    0  -0.645  -4.5420   2.2924  -0.2959
 4V3  O27  O  OS    0  -0.645  -4.6780   0.7669  -2.2702
 4V3  H1   H  HCH2  0   0.203   7.8026  -0.7241   0.3423
 4V3  H2   H  HCH2  0   0.201   7.3658   0.9326  -0.0806
 4V3  H3   H  HCH1  0   0.211   3.6470  -1.9252   0.0291
 4V3  H4   H  HCH1  0   0.277   3.1859   0.8913  -1.0392
 4V3  H5   H  HCH1  0   0.188   3.4489  -0.1506   1.8191
 4V3  H6   H  HCH1  0   0.223   5.5737  -1.0299   1.4146
 4V3  H7   H  HCH1  0   0.228   5.5289  -0.0866  -1.4923
 4V3  H8   H  HNH1  0   0.404   1.3543  -0.9764   0.3601
 4V3  H9   H  HOH1  0   0.464   6.7976  -1.8697  -1.4699
 4V3  H10  H  HOH1  0   0.452   3.8740  -2.2969  -2.2498
 4V3  H12  H  HOH1  0   0.457   8.4769   0.8017   1.9557
 4V3  H13  H  HCH2  0   0.271  -1.5902   1.9102  -0.6706
 4V3  H14  H  HCH2  0   0.272  -1.6375   0.7996  -2.0387
 4V3  H15  H  HCR5  0   0.294  -2.2396  -1.4106   0.8166
 4V3  H16  H  HCR6  0   0.276  -4.2758  -2.8092   2.0163
 4V3  H17  H  HCR6  0   0.279  -6.7226  -3.0005   2.3288
 4V3  H18  H  HCR6  0   0.279  -8.2600  -1.4210   1.2374
 4V3  H19  H  HCR6  0   0.290  -7.3737   0.3950  -0.2100
 4V3  O11  O  OH1   0  -0.649   2.9506   1.7931   1.3640
 4V3  H11  H  HOH1  0   0.467   3.0479   1.9664   2.3063

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
 4V3  O09  C01  single    1.401  0.020  1.401
 4V3  O14  C16  single    1.412  0.020  1.412
 4V3  O14  C13  single    1.345  0.020  1.345
 4V3  O08  C06  single    1.410  0.020  1.410
 4V3  C01  C06  single    1.526  0.020  1.526
 4V3  C01  C02  single    1.525  0.020  1.525
 4V3  N07  C13  single    1.341  0.020  1.341
 4V3  N07  C02  single    1.439  0.020  1.439
 4V3  C16  C17  single    1.485  0.020  1.485
 4V3  C13  O15  double    1.212  0.020  1.212
 4V3  C06  C05  single    1.533  0.020  1.533
 4V3  C02  C03  single    1.531  0.020  1.531
 4V3  O27  S21  double    1.457  0.020  1.457
 4V3  C17  C18  double    1.331  0.020  1.331
 4V3  C17  S21  single    1.784  0.020  1.784
 4V3  C18  C19  single    1.468  0.020  1.468
 4V3  C05  O04  single    1.413  0.020  1.413
 4V3  C05  C10  single    1.513  0.020  1.513
 4V3  C03  O04  single    1.406  0.020  1.406
 4V3  C03  O11  single    1.375  0.020  1.375
 4V3  S21  O26  double    1.457  0.020  1.457
 4V3  S21  C20  single    1.769  0.020  1.769
 4V3  C10  O12  single    1.407  0.020  1.407
 4V3  C19  C20  aromatic  1.391  0.020  1.391
 4V3  C19  C22  aromatic  1.384  0.020  1.384
 4V3  C20  C25  aromatic  1.375  0.020  1.375
 4V3  C22  C23  aromatic  1.393  0.020  1.393
 4V3  C25  C24  aromatic  1.394  0.020  1.394
 4V3  C23  C24  aromatic  1.389  0.020  1.389
 4V3  C10  H1   single    0.970  0.020  1.090
 4V3  C10  H2   single    0.970  0.020  1.090
 4V3  C01  H3   single    0.970  0.020  1.090
 4V3  C02  H4   single    0.970  0.020  1.090
 4V3  C03  H5   single    0.970  0.020  1.090
 4V3  C05  H6   single    0.970  0.020  1.090
 4V3  C06  H7   single    0.970  0.020  1.090
 4V3  N07  H8   single    0.860  0.020  1.020
 4V3  O08  H9   single    0.850  0.020  0.980
 4V3  O09  H10  single    0.850  0.020  0.980
 4V3  O11  H11  single    0.850  0.020  0.980
 4V3  O12  H12  single    0.850  0.020  0.980
 4V3  C16  H13  single    0.970  0.020  1.090
 4V3  C16  H14  single    0.970  0.020  1.090
 4V3  C18  H15  single    0.930  0.020  1.080
 4V3  C22  H16  single    0.930  0.020  1.080
 4V3  C23  H17  single    0.930  0.020  1.080
 4V3  C24  H18  single    0.930  0.020  1.080
 4V3  C25  H19  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
 4V3  H2   C10  H1   106.99  3.000
 4V3  H2   C10  O12  111.95  3.000
 4V3  H1   C10  O12  111.52  3.000
 4V3  H2   C10  C05  108.93  3.000
 4V3  H1   C10  C05  108.35  3.000
 4V3  O12  C10  C05  109.01  3.000
 4V3  O15  C13  O14  123.23  3.000
 4V3  O15  C13  N07  126.41  3.000
 4V3  O14  C13  N07  110.36  3.000
 4V3  H3   C01  O09  110.80  3.000
 4V3  H3   C01  C06  107.35  3.000
 4V3  O09  C01  C06  111.94  3.000
 4V3  H3   C01  C02  108.21  3.000
 4V3  C06  C01  C02  110.26  3.000
 4V3  O09  C01  C02  108.23  3.000
 4V3  H4   C02  N07  108.31  3.000
 4V3  H4   C02  C03  108.20  3.000
 4V3  N07  C02  C03  111.07  3.000
 4V3  H4   C02  C01  108.95  3.000
 4V3  C03  C02  C01  109.47  3.000
 4V3  N07  C02  C01  110.78  3.000
 4V3  H5   C03  O11  111.65  3.000
 4V3  H5   C03  O04  109.16  3.000
 4V3  O11  C03  O04  108.72  3.000
 4V3  H5   C03  C02  109.08  3.000
 4V3  O11  C03  C02  108.60  3.000
 4V3  O04  C03  C02  109.61  3.000
 4V3  C05  O04  C03  113.48  3.000
 4V3  H6   C05  C06  108.44  3.000
 4V3  H6   C05  O04  110.22  3.000
 4V3  C06  C05  O04  109.17  3.000
 4V3  H6   C05  C10  108.98  3.000
 4V3  O04  C05  C10  108.03  3.000
 4V3  C06  C05  C10  112.01  3.000
 4V3  H7   C06  O08  111.16  3.000
 4V3  H7   C06  C05  108.55  3.000
 4V3  O08  C06  C05  112.02  3.000
 4V3  H7   C06  C01  108.19  3.000
 4V3  C05  C06  C01  109.93  3.000
 4V3  O08  C06  C01  106.91  3.000
 4V3  H8   N07  C02  118.38  3.000
 4V3  H8   N07  C13  118.49  3.000
 4V3  C02  N07  C13  123.00  3.000
 4V3  H9   O08  C06  109.16  3.000
 4V3  H10  O09  C01  107.80  3.000
 4V3  H12  O12  C10  107.98  3.000
 4V3  C16  O14  C13  116.52  3.000
 4V3  H14  C16  H13  107.23  3.000
 4V3  H14  C16  C17  109.86  3.000
 4V3  H13  C16  C17  109.81  3.000
 4V3  H14  C16  O14  111.24  3.000
 4V3  H13  C16  O14  111.48  3.000
 4V3  C17  C16  O14  107.23  3.000
 4V3  S21  C17  C18  110.20  3.000
 4V3  S21  C17  C16  118.07  3.000
 4V3  C18  C17  C16  131.73  3.000
 4V3  H15  C18  C19  121.34  3.000
 4V3  H15  C18  C17  124.00  3.000
 4V3  C19  C18  C17  114.66  3.000
 4V3  C22  C19  C20  118.91  3.000
 4V3  C22  C19  C18  127.81  3.000
 4V3  C20  C19  C18  113.28  3.000
 4V3  C25  C20  S21  127.53  3.000
 4V3  C25  C20  C19  123.44  3.000
 4V3  S21  C20  C19  109.03  3.000
 4V3  O27  S21  O26  118.05  3.000
 4V3  O26  S21  C20  111.47  3.000
 4V3  O27  S21  C20  111.30  3.000
 4V3  C20  S21  C17   92.83  3.000
 4V3  O26  S21  C17  110.11  3.000
 4V3  O27  S21  C17  110.22  3.000
 4V3  H16  C22  C23  120.56  3.000
 4V3  H16  C22  C19  120.65  3.000
 4V3  C23  C22  C19  118.79  3.000
 4V3  H17  C23  C24  119.44  3.000
 4V3  H17  C23  C22  119.37  3.000
 4V3  C24  C23  C22  121.19  3.000
 4V3  H18  C24  C25  119.58  3.000
 4V3  H18  C24  C23  119.92  3.000
 4V3  C25  C24  C23  120.50  3.000
 4V3  H19  C25  C24  121.03  3.000
 4V3  H19  C25  C20  121.81  3.000
 4V3  C24  C25  C20  117.17  3.000
 4V3  H11  O11  C03  109.45  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
 4V3  CONST_01  C24  C25  C20  C19     0.00   0.0  0
 4V3  CONST_02  C24  C23  C22  C19     0.00   0.0  0
 4V3  CONST_03  C23  C22  C19  C20     0.00   0.0  0
 4V3  CONST_04  C23  C24  C25  C20     0.00   0.0  0
 4V3  CONST_05  C25  C20  C19  C22     0.00   0.0  0
 4V3  CONST_06  C25  C24  C23  C22     0.00   0.0  0
 4V3  CONST_07  H16  C22  C19  C18     0.00   0.0  0
 4V3  CONST_08  H19  C25  C20  C19   180.00   0.0  0
 4V3  CONST_09  H17  C23  C22  C19   180.00   0.0  0
 4V3  CONST_10  H18  C24  C25  C20   180.00   0.0  0
 4V3  Var_01    C18  C17  C16  O14    -1.86  30.0  3
 4V3  Var_02    C17  C16  O14  C13  -176.18  30.0  3
 4V3  Var_03    O14  C13  N07  C02  -176.07  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
 4V3  chir_01  C01  O09  C06  C02  negativ
 4V3  chir_02  C02  N07  C01  C03  positiv
 4V3  chir_03  C03  O04  O11  C02  negativ
 4V3  chir_04  C05  O04  C06  C10  negativ
 4V3  chir_05  C06  O08  C05  C01  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
 4V3  plan-1  C13  0.020
 4V3  plan-1  N07  0.020
 4V3  plan-1  O14  0.020
 4V3  plan-1  O15  0.020
 4V3  plan-2  C16  0.020
 4V3  plan-2  C17  0.020
 4V3  plan-2  C18  0.020
 4V3  plan-2  C19  0.020
 4V3  plan-2  C20  0.020
 4V3  plan-2  S21  0.020
 4V3  plan-2  C22  0.020
 4V3  plan-2  C23  0.020
 4V3  plan-2  C24  0.020
 4V3  plan-2  C25  0.020
 4V3  plan-2  O26  0.020
 4V3  plan-2  O27  0.020
 4V3  plan-2  H15  0.020
 4V3  plan-2  H16  0.020
 4V3  plan-2  H17  0.020
 4V3  plan-2  H18  0.020
 4V3  plan-2  H19  0.020

