# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 15:30:09 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: [(2~{S},3~{S},4~{S},5~{R},6~{S})-6-methoxy-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 DO7  DO7  "[(2S,3S,4S,5R,6S)-6-methoxy-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid"  ligand  29  16  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DO7
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
 DO7  C4   C  CH2    0  -0.669   7.8841  -20.6122   94.9765
 DO7  C5   C  CH1    0   0.045   7.0658  -18.4719   96.0521
 DO7  C6   C  CH1    0  -0.009   7.0945  -17.6839   97.3573
 DO7  C7   C  CH1    0  -0.014   8.5326  -17.4997   97.8241
 DO7  C1   C  CH3    0  -0.411   9.4149  -20.7839   99.2246
 DO7  C2   C  CH1    0   0.248   9.2487  -18.8527   97.8964
 DO7  C3   C  CH1    0   0.022   7.8161  -19.7905   96.2482
 DO7  O1   O  O2     0  -0.489   8.7201  -19.5855   98.9485
 DO7  O2   O  O2     0  -0.495   9.1418  -19.5134   96.6661
 DO7  S1   S  S      0   1.401   8.2921  -22.3593   95.2351
 DO7  O3   O  OS     0  -0.759   8.1492  -22.9626   93.8953
 DO7  O4   O  OS     0  -0.762   7.2953  -22.8509   96.2087
 DO7  O5   O  OS    -1  -0.756   9.6736  -22.4185   95.7472
 DO7  O6   O  OH1    0  -0.667   5.7501  -18.7698   95.6599
 DO7  O7   O  OH1    0  -0.671   6.4608  -16.4491   97.1159
 DO7  O8   O  OH1    0  -0.664   8.5067  -16.8322   99.0602
 DO7  H7   H  HCH2   0   0.262   8.6101  -20.1899   94.2775
 DO7  H6   H  HCH2   0   0.276   6.9103  -20.6079   94.4858
 DO7  H9   H  HCH1   0   0.205   7.5874  -17.8844   95.2785
 DO7  H11  H  HCH1   0   0.214   6.5435  -18.2613   98.1150
 DO7  H13  H  HCH1   0   0.225   9.0612  -16.9055   97.0647
 DO7  H1   H  HCH3   0   0.233   8.9990  -21.1964  100.1422
 DO7  H2   H  HCH3   0   0.215   9.3056  -21.5248   98.4290
 DO7  H3   H  HCH3   0   0.208  10.4844  -20.6015   99.3797
 DO7  H4   H  HCH1   0   0.225  10.3294  -18.7010   98.0384
 DO7  H5   H  HCH1   0   0.230   7.2794  -20.3709   97.0098
 DO7  H10  H  HOH1   0   0.452   5.2638  -17.9421   95.5848
 DO7  H12  H  HOH1   0   0.452   6.3651  -15.9864   97.9545
 DO7  H14  H  HOH1   0   0.456   9.3752  -16.4537   99.2275

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
 DO7  O3  S1   deloc   1.476  0.020  1.476
 DO7  C4  S1   single  1.813  0.020  1.813
 DO7  C4  C3   single  1.516  0.020  1.516
 DO7  S1  O5   deloc   1.475  0.020  1.475
 DO7  S1  O4   deloc   1.478  0.020  1.478
 DO7  O6  C5   single  1.405  0.020  1.405
 DO7  C5  C3   single  1.530  0.020  1.530
 DO7  C5  C6   single  1.525  0.020  1.525
 DO7  C3  O2   single  1.417  0.020  1.417
 DO7  O2  C2   single  1.401  0.020  1.401
 DO7  O7  C6   single  1.409  0.020  1.409
 DO7  C6  C7   single  1.523  0.020  1.523
 DO7  C7  C2   single  1.533  0.020  1.533
 DO7  C7  O8   single  1.405  0.020  1.405
 DO7  C2  O1   single  1.387  0.020  1.387
 DO7  O1  C1   single  1.412  0.020  1.412
 DO7  C4  H7   single  0.970  0.020  1.090
 DO7  C4  H6   single  0.970  0.020  1.090
 DO7  C5  H9   single  0.970  0.020  1.090
 DO7  C6  H11  single  0.970  0.020  1.090
 DO7  C7  H13  single  0.970  0.020  1.090
 DO7  C1  H1   single  0.970  0.020  1.090
 DO7  C1  H2   single  0.970  0.020  1.090
 DO7  C1  H3   single  0.970  0.020  1.090
 DO7  C2  H4   single  0.970  0.020  1.090
 DO7  C3  H5   single  0.970  0.020  1.090
 DO7  O6  H10  single  0.850  0.020  0.980
 DO7  O7  H12  single  0.850  0.020  0.980
 DO7  O8  H14  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
 DO7  H6   C4  H7  107.69  3.000
 DO7  H6   C4  S1  105.60  3.000
 DO7  H7   C4  S1  108.32  3.000
 DO7  H6   C4  C3  109.60  3.000
 DO7  H7   C4  C3  110.92  3.000
 DO7  S1   C4  C3  114.39  3.000
 DO7  H9   C5  O6  111.11  3.000
 DO7  H9   C5  C3  108.49  3.000
 DO7  O6   C5  C3  108.20  3.000
 DO7  H9   C5  C6  108.44  3.000
 DO7  C3   C5  C6  109.05  3.000
 DO7  O6   C5  C6  111.48  3.000
 DO7  H11  C6  O7  110.65  3.000
 DO7  H11  C6  C7  108.98  3.000
 DO7  O7   C6  C7  111.79  3.000
 DO7  H11  C6  C5  107.98  3.000
 DO7  C7   C6  C5  110.04  3.000
 DO7  O7   C6  C5  107.33  3.000
 DO7  H13  C7  O8  111.08  3.000
 DO7  H13  C7  C2  106.56  3.000
 DO7  O8   C7  C2  112.73  3.000
 DO7  H13  C7  C6  107.92  3.000
 DO7  O8   C7  C6  108.04  3.000
 DO7  C2   C7  C6  110.42  3.000
 DO7  H3   C1  H2  108.28  3.000
 DO7  H3   C1  H1  108.45  3.000
 DO7  H2   C1  H1  108.58  3.000
 DO7  H3   C1  O1  111.50  3.000
 DO7  H2   C1  O1  112.57  3.000
 DO7  H1   C1  O1  107.35  3.000
 DO7  H4   C2  O2  104.67  3.000
 DO7  H4   C2  O1  110.44  3.000
 DO7  O2   C2  O1  112.83  3.000
 DO7  H4   C2  C7  110.08  3.000
 DO7  O1   C2  C7  108.92  3.000
 DO7  O2   C2  C7  109.84  3.000
 DO7  H5   C3  O2  110.87  3.000
 DO7  H5   C3  C5  107.75  3.000
 DO7  O2   C3  C5  109.15  3.000
 DO7  H5   C3  C4  108.51  3.000
 DO7  O2   C3  C4  108.15  3.000
 DO7  C5   C3  C4  112.44  3.000
 DO7  C2   O1  C1  114.15  3.000
 DO7  C3   O2  C2  115.00  3.000
 DO7  O5   S1  O4  112.94  3.000
 DO7  O4   S1  O3  113.37  3.000
 DO7  O5   S1  O3  112.92  3.000
 DO7  O4   S1  C4  105.24  3.000
 DO7  O5   S1  C4  107.40  3.000
 DO7  O3   S1  C4  104.05  3.000
 DO7  H10  O6  C5  108.20  3.000
 DO7  H12  O7  C6  108.47  3.000
 DO7  H14  O8  C7  108.86  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
 DO7  Var_01  O3  S1  C4  C3  173.89  30.0  3
 DO7  Var_02  O5  S1  C4  C3  -66.17  30.0  3
 DO7  Var_03  O4  S1  C4  C3   54.42  30.0  3
 DO7  Var_04  H1  C1  O1  C2  172.37  30.0  3
 DO7  Var_05  H2  C1  O1  C2  -68.20  30.0  3
 DO7  Var_06  H3  C1  O1  C2   53.72  30.0  3
 DO7  Var_07  H7  C4  S1  O3  -61.84  30.0  3
 DO7  Var_08  H6  C4  S1  O3   53.29  30.0  3
 DO7  Var_09  H7  C4  S1  O4  178.68  30.0  3
 DO7  Var_10  H6  C4  S1  O4  -66.18  30.0  3
 DO7  Var_11  H7  C4  S1  O5   58.10  30.0  3
 DO7  Var_12  H6  C4  S1  O5  173.24  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
 DO7  chir_01  C5  O6  C3  C6  positiv
 DO7  chir_02  C6  O7  C5  C7  negativ
 DO7  chir_03  C7  O8  C6  C2  positiv
 DO7  chir_04  C2  O1  O2  C7  negativ
 DO7  chir_05  C3  O2  C4  C5  positiv

