# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:07:33 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2R,3aR,5R,6S,7S,7aR)-5-(hydroxymethyl)tetrahydro-3aH-[1,3,2]dioxaphospholo[4,5-b]pyran-2,6,7-triol 2-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H]2O[P](O)(=O)O[C@@H]2[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
 1S3  1S3  '(2R,3aR,5R,6S,7S,7aR)-5-(hydroxymethyl)tetrahydro-3aH-[1,3,2]dioxaphospholo[4,5-b]pyran-2,6,7-triol 2-oxide'  D-saccharide  26  15  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1S3
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
 1S3  C1   C  CH1   0   0.260  72.6029  44.5757  66.5187
 1S3  O1   O  O2    0  -0.603  72.7430  44.5540  67.9550
 1S3  P    P  P     0   1.452  73.7779  45.6798  68.4477
 1S3  O2P  O  OH1   0  -0.723  72.8957  46.5525  69.4441
 1S3  O3P  O  O     0  -0.663  75.0838  45.2495  68.9686
 1S3  O5   O  O2    0  -0.471  71.4066  44.0599  66.1346
 1S3  C5   C  CH1   0  -0.030  70.2523  44.8742  66.3350
 1S3  C6   C  CH2   0  -0.200  69.0523  44.0652  65.8977
 1S3  O6   O  OH1   0  -0.665  69.0921  43.8790  64.5047
 1S3  C4   C  CH1   0   0.013  70.4245  46.1981  65.5793
 1S3  O4   O  OH1   0  -0.661  69.2857  47.0048  65.7181
 1S3  C3   C  CH1   0   0.027  71.6054  46.9358  66.1923
 1S3  O3   O  OH1   0  -0.656  71.8268  48.1310  65.4944
 1S3  C2   C  CH1   0  -0.101  72.8473  46.0433  66.1351
 1S3  O2   O  O2    0  -0.587  73.8406  46.4992  67.0594
 1S3  H1   H  HCH1  0   0.282  73.3749  43.9290  66.0926
 1S3  H2A  H  HOH1  0   0.503  73.3520  46.8022  70.2601
 1S3  H5   H  HCH1  0   0.248  70.1195  45.0862  67.4051
 1S3  H61  H  HCH2  0   0.215  68.1514  44.5993  66.2207
 1S3  H62  H  HCH2  0   0.226  69.0625  43.1128  66.4435
 1S3  HO6  H  HOH1  0   0.459  68.2908  43.4205  64.2370
 1S3  H4   H  HCH1  0   0.236  70.6430  45.9847  64.5244
 1S3  HO4  H  HOH1  0   0.459  68.6437  46.7501  65.0485
 1S3  H3   H  HCH1  0   0.231  71.3509  47.1375  67.2432
 1S3  HO3  H  HOH1  0   0.456  72.3948  48.6984  66.0256
 1S3  H2   H  HCH1  0   0.294  73.2753  46.0931  65.1320

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
 1S3  O6   C6   single  1.406  0.020  1.406
 1S3  O3   C3   single  1.402  0.020  1.402
 1S3  C4   O4   single  1.402  0.020  1.402
 1S3  C4   C3   single  1.521  0.020  1.521
 1S3  C4   C5   single  1.534  0.020  1.534
 1S3  C6   C5   single  1.512  0.020  1.512
 1S3  O5   C5   single  1.427  0.020  1.427
 1S3  O5   C1   single  1.358  0.020  1.358
 1S3  C2   C3   single  1.530  0.020  1.530
 1S3  C2   C1   single  1.537  0.020  1.537
 1S3  C2   O2   single  1.431  0.020  1.431
 1S3  C1   O1   single  1.443  0.020  1.443
 1S3  O2   P    single  1.613  0.020  1.613
 1S3  O1   P    single  1.607  0.020  1.607
 1S3  P    O3P  double  1.470  0.020  1.470
 1S3  P    O2P  single  1.591  0.020  1.591
 1S3  C1   H1   single  0.970  0.020  1.090
 1S3  O2P  H2A  single  0.850  0.020  0.980
 1S3  C5   H5   single  0.970  0.020  1.090
 1S3  C6   H61  single  0.970  0.020  1.090
 1S3  C6   H62  single  0.970  0.020  1.090
 1S3  O6   HO6  single  0.850  0.020  0.980
 1S3  C4   H4   single  0.970  0.020  1.090
 1S3  O4   HO4  single  0.850  0.020  0.980
 1S3  C3   H3   single  0.970  0.020  1.090
 1S3  O3   HO3  single  0.850  0.020  0.980
 1S3  C2   H2   single  0.970  0.020  1.090

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
 1S3  H1   C1   C2   110.82  3.000
 1S3  H1   C1   O5   106.68  3.000
 1S3  C2   C1   O5   115.60  3.000
 1S3  H1   C1   O1   108.09  3.000
 1S3  C2   C1   O1   104.32  3.000
 1S3  O5   C1   O1   111.18  3.000
 1S3  P    O1   C1   110.92  3.000
 1S3  O2   P    O3P  114.77  3.000
 1S3  O3P  P    O2P  115.53  3.000
 1S3  O2   P    O2P  106.37  3.000
 1S3  O2P  P    O1   102.66  3.000
 1S3  O3P  P    O1   118.40  3.000
 1S3  O2   P    O1    96.72  3.000
 1S3  H2A  O2P  P    114.08  3.000
 1S3  C5   O5   C1   117.14  3.000
 1S3  H5   C5   C4   109.07  3.000
 1S3  H5   C5   C6   106.79  3.000
 1S3  C4   C5   C6   114.10  3.000
 1S3  H5   C5   O5   110.16  3.000
 1S3  C6   C5   O5   107.23  3.000
 1S3  C4   C5   O5   109.42  3.000
 1S3  H62  C6   H61  106.50  3.000
 1S3  H62  C6   O6   112.18  3.000
 1S3  H61  C6   O6   112.32  3.000
 1S3  H62  C6   C5   108.25  3.000
 1S3  H61  C6   C5   107.85  3.000
 1S3  O6   C6   C5   109.57  3.000
 1S3  HO6  O6   C6   108.39  3.000
 1S3  H4   C4   C3   109.07  3.000
 1S3  H4   C4   O4   111.62  3.000
 1S3  C3   C4   O4   108.15  3.000
 1S3  H4   C4   C5   109.13  3.000
 1S3  C3   C4   C5   107.89  3.000
 1S3  O4   C4   C5   110.89  3.000
 1S3  HO4  O4   C4   108.71  3.000
 1S3  H3   C3   C2   109.29  3.000
 1S3  H3   C3   O3   110.85  3.000
 1S3  C2   C3   O3   110.52  3.000
 1S3  H3   C3   C4   107.12  3.000
 1S3  C2   C3   C4   109.39  3.000
 1S3  O3   C3   C4   109.60  3.000
 1S3  HO3  O3   C3   108.73  3.000
 1S3  H2   C2   O2   107.86  3.000
 1S3  H2   C2   C3   109.02  3.000
 1S3  O2   C2   C3   110.69  3.000
 1S3  H2   C2   C1   109.59  3.000
 1S3  O2   C2   C1   104.68  3.000
 1S3  C3   C2   C1   114.75  3.000
 1S3  C2   O2   P    111.53  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
 1S3  Var_01  O2  P  O1  C1  13.49  30.0  1

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
 1S3  chir_01  C1  O5  C2   O1   negativ
 1S3  chir_03  C5  C4  C6   O5   negativ
 1S3  chir_04  C4  O4  C5   C3   positiv
 1S3  chir_05  C3  O3  C4   C2   negativ
 1S3  chir_06  C2  O2  C3   C1   positiv
 1S3  chir_07  P   O1  O3P  O2P  both

