# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 11:57:34 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: [(2~{S},3~{S},4~{S},5~{R},6~{S})-6-[(2~{R})-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)CO[C@H]1O[C@H](C[S](O)(=O)=O)[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
 VCW  VCW  "[(2S,3S,4S,5R,6S)-6-[(2R)-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid"  ligand  37  20  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VCW
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
 VCW  C4   C  CH2    0  -0.172  19.5076  54.4563  2.8456
 VCW  C5   C  CH1    0  -0.023  18.9657  55.7482  2.2572
 VCW  C6   C  CH2    0  -0.153  17.5881  55.5225  1.6726
 VCW  C7   C  CH1    0  -0.016  22.5380  54.4681  4.9339
 VCW  C8   C  CH1    0  -0.010  23.6445  54.4430  3.8875
 VCW  C1   C  CH2    0  -0.673  22.5655  51.0556  2.3950
 VCW  C2   C  CH1    0   0.029  22.4658  52.5048  2.8276
 VCW  C3   C  CH1    0   0.248  21.2539  53.8811  4.3455
 VCW  C9   C  CH1    0   0.045  23.8083  53.0282  3.3443
 VCW  O1   O  OS     0  -0.759  20.5124  51.3364  0.7796
 VCW  S1   S  S      0   1.405  21.0320  50.3426  1.7438
 VCW  O2   O  OS    -1  -0.756  20.1408  50.1102  2.8931
 VCW  O3   O  OS     0  -0.763  21.4665  49.0861  1.0999
 VCW  O4   O  O2     0  -0.494  21.4926  52.5950  3.8534
 VCW  O5   O  O2     0  -0.506  20.7876  54.7520  3.3703
 VCW  O6   O  OH1    0  -0.667  18.8829  56.7545  3.2401
 VCW  O7   O  OH1    0  -0.665  17.1761  56.6919  1.0059
 VCW  O8   O  OH1    0  -0.663  22.3724  55.7926  5.3712
 VCW  O9   O  OH1    0  -0.671  24.8882  54.8244  4.4293
 VCW  O10  O  OH1    0  -0.669  24.7299  52.9849  2.2846
 VCW  H1   H  HCH2   0   0.211  18.8401  54.0943  3.6399
 VCW  H2   H  HCH2   0   0.218  19.5682  53.6772  2.0788
 VCW  H3   H  HCH1   0   0.206  19.6367  56.0560  1.4391
 VCW  H4   H  HCH2   0   0.197  16.8953  55.2465  2.4794
 VCW  H5   H  HCH2   0   0.199  17.6433  54.6644  0.9903
 VCW  H6   H  HCH1   0   0.227  22.8372  53.8109  5.7630
 VCW  H7   H  HCH1   0   0.216  23.3655  55.1039  3.0536
 VCW  H10  H  HCH1   0   0.230  22.1692  53.1076  1.9598
 VCW  H11  H  HCH1   0   0.235  20.4960  53.7453  5.1308
 VCW  H12  H  HCH1   0   0.207  24.1303  52.3800  4.1760
 VCW  H13  H  HOH1   0   0.442  19.7432  56.8113  3.6703
 VCW  H14  H  HOH1   0   0.452  16.2875  56.5460  0.6697
 VCW  H15  H  HOH1   0   0.457  21.8964  55.7866  6.2074
 VCW  H16  H  HOH1   0   0.453  24.8457  55.7564  4.6650
 VCW  H17  H  HOH1   0   0.452  25.5704  53.3298  2.6037
 VCW  H8   H  HCH2   0   0.260  22.8976  50.4194  3.2193
 VCW  H9   H  HCH2   0   0.274  23.3020  50.9761  1.5952

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
 VCW  O1   S1   deloc   1.479  0.020  1.479
 VCW  S1   O3   deloc   1.477  0.020  1.477
 VCW  S1   O2   deloc   1.473  0.020  1.473
 VCW  S1   C1   single  1.812  0.020  1.812
 VCW  C6   O7   single  1.408  0.020  1.408
 VCW  C6   C5   single  1.513  0.020  1.513
 VCW  C5   C4   single  1.520  0.020  1.520
 VCW  C5   O6   single  1.409  0.020  1.409
 VCW  O10  C9   single  1.405  0.020  1.405
 VCW  C1   C2   single  1.516  0.020  1.516
 VCW  C4   O5   single  1.415  0.020  1.415
 VCW  C2   C9   single  1.531  0.020  1.531
 VCW  C2   O4   single  1.417  0.020  1.417
 VCW  O5   C3   single  1.388  0.020  1.388
 VCW  C9   C8   single  1.524  0.020  1.524
 VCW  C8   O9   single  1.409  0.020  1.409
 VCW  C8   C7   single  1.523  0.020  1.523
 VCW  O4   C3   single  1.398  0.020  1.398
 VCW  C3   C7   single  1.530  0.020  1.530
 VCW  C7   O8   single  1.405  0.020  1.405
 VCW  C4   H1   single  0.970  0.020  1.090
 VCW  C4   H2   single  0.970  0.020  1.090
 VCW  C5   H3   single  0.970  0.020  1.090
 VCW  C6   H4   single  0.970  0.020  1.090
 VCW  C6   H5   single  0.970  0.020  1.090
 VCW  C7   H6   single  0.970  0.020  1.090
 VCW  C8   H7   single  0.970  0.020  1.090
 VCW  C1   H8   single  0.970  0.020  1.090
 VCW  C1   H9   single  0.970  0.020  1.090
 VCW  C2   H10  single  0.970  0.020  1.090
 VCW  C3   H11  single  0.970  0.020  1.090
 VCW  C9   H12  single  0.970  0.020  1.090
 VCW  O6   H13  single  0.850  0.020  0.980
 VCW  O7   H14  single  0.850  0.020  0.980
 VCW  O8   H15  single  0.850  0.020  0.980
 VCW  O9   H16  single  0.850  0.020  0.980
 VCW  O10  H17  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
 VCW  H2   C4   H1   107.78  3.000
 VCW  H2   C4   O5   111.01  3.000
 VCW  H1   C4   O5   110.52  3.000
 VCW  H2   C4   C5   110.70  3.000
 VCW  H1   C4   C5   110.08  3.000
 VCW  O5   C4   C5   106.77  3.000
 VCW  H3   C5   O6   110.74  3.000
 VCW  H3   C5   C6   108.01  3.000
 VCW  O6   C5   C6   108.81  3.000
 VCW  H3   C5   C4   107.93  3.000
 VCW  O6   C5   C4   110.98  3.000
 VCW  C6   C5   C4   110.32  3.000
 VCW  H5   C6   H4   106.97  3.000
 VCW  H5   C6   O7   111.69  3.000
 VCW  H4   C6   O7   111.84  3.000
 VCW  H5   C6   C5   108.11  3.000
 VCW  H4   C6   C5   109.14  3.000
 VCW  O7   C6   C5   108.99  3.000
 VCW  H6   C7   O8   111.15  3.000
 VCW  H6   C7   C3   106.81  3.000
 VCW  O8   C7   C3   112.50  3.000
 VCW  H6   C7   C8   108.10  3.000
 VCW  O8   C7   C8   108.36  3.000
 VCW  C3   C7   C8   109.83  3.000
 VCW  H7   C8   O9   110.66  3.000
 VCW  H7   C8   C9   108.34  3.000
 VCW  O9   C8   C9   107.06  3.000
 VCW  H7   C8   C7   109.07  3.000
 VCW  O9   C8   C7   111.88  3.000
 VCW  C9   C8   C7   109.76  3.000
 VCW  H9   C1   H8   107.79  3.000
 VCW  H9   C1   S1   106.22  3.000
 VCW  H8   C1   S1   107.41  3.000
 VCW  H9   C1   C2   108.88  3.000
 VCW  H8   C1   C2   111.18  3.000
 VCW  S1   C1   C2   115.03  3.000
 VCW  H10  C2   O4   110.60  3.000
 VCW  H10  C2   C9   108.43  3.000
 VCW  O4   C2   C9   109.65  3.000
 VCW  H10  C2   C1   108.50  3.000
 VCW  O4   C2   C1   108.22  3.000
 VCW  C9   C2   C1   111.44  3.000
 VCW  H11  C3   O5   110.34  3.000
 VCW  H11  C3   O4   104.80  3.000
 VCW  O5   C3   O4   112.79  3.000
 VCW  H11  C3   C7   110.56  3.000
 VCW  O4   C3   C7   110.19  3.000
 VCW  O5   C3   C7   108.15  3.000
 VCW  H12  C9   O10  111.06  3.000
 VCW  H12  C9   C2   108.04  3.000
 VCW  O10  C9   C2   108.07  3.000
 VCW  H12  C9   C8   107.95  3.000
 VCW  C2   C9   C8   110.08  3.000
 VCW  O10  C9   C8   111.58  3.000
 VCW  O3   S1   O2   112.58  3.000
 VCW  O2   S1   O1   113.72  3.000
 VCW  O3   S1   O1   113.00  3.000
 VCW  O2   S1   C1   107.08  3.000
 VCW  O3   S1   C1   104.03  3.000
 VCW  O1   S1   C1   105.49  3.000
 VCW  C3   O4   C2   115.52  3.000
 VCW  C3   O5   C4   115.68  3.000
 VCW  H13  O6   C5   107.52  3.000
 VCW  H14  O7   C6   108.07  3.000
 VCW  H15  O8   C7   108.85  3.000
 VCW  H16  O9   C8   108.50  3.000
 VCW  H17  O10  C9   108.16  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
 VCW  Var_01  C3  O5  C4  C5  158.03  30.0  3
 VCW  Var_02  O1  S1  C1  C2   47.26  30.0  3
 VCW  Var_03  O3  S1  C1  C2  166.42  30.0  3
 VCW  Var_04  O2  S1  C1  C2  -74.19  30.0  3
 VCW  Var_05  H1  C4  O5  C3   38.31  30.0  1
 VCW  Var_06  H2  C4  O5  C3  -81.22  30.0  1
 VCW  Var_07  H8  C1  S1  O1  171.61  30.0  3
 VCW  Var_08  H9  C1  S1  O1  -73.26  30.0  3
 VCW  Var_09  H8  C1  S1  O2   50.16  30.0  3
 VCW  Var_10  H9  C1  S1  O2  165.29  30.0  3
 VCW  Var_11  H8  C1  S1  O3  -69.23  30.0  3
 VCW  Var_12  H9  C1  S1  O3   45.90  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
 VCW  chir_01  C5  C6   C4  O6  positiv
 VCW  chir_02  C7  O8   C8  C3  positiv
 VCW  chir_03  C8  O9   C7  C9  positiv
 VCW  chir_04  C2  O4   C9  C1  negativ
 VCW  chir_05  C3  O4   O5  C7  positiv
 VCW  chir_06  C9  O10  C8  C2  negativ

