# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:13:03 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (1S,2S,3S,4S,5R,6R)-3,5,6-trihydroxycyclohexane-1,2,4-triyl tris[dihydrogen (phosphate)]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@H](O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@@H](O)[C@H]1O[P](O)(O)=O
#
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
 I3S  I3S  '(1S,2S,3S,4S,5R,6R)-3,5,6-trihydroxycyclohexane-1,2,4-triyl tris[dihydrogen (phosphate)]'  ligand  33  24  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I3S
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
 I3S  O11  O  OP    -1  -0.913   2.6111  -3.5274   0.4461
 I3S  P3   P  P      0   1.228   1.4499  -2.9221  -0.3357
 I3S  O12  O  OP    -1  -0.935   0.1079  -3.6153  -0.0907
 I3S  O10  O  O      0  -0.945   1.7376  -2.6670  -1.8136
 I3S  O3   O  O2     0  -0.628   1.3199  -1.3964   0.3914
 I3S  C3   C  CH1    0   0.057   0.4691  -0.4387  -0.1611
 I3S  C2   C  CH1    0  -0.050  -0.9427  -0.5586   0.4089
 I3S  O2   O  OH1    0  -0.648  -0.8962  -0.4690   1.8212
 I3S  C1   C  CH1    0   0.004  -1.8804   0.5112  -0.1603
 I3S  O1   O  O2     0  -0.613  -3.1185   0.5480   0.4958
 I3S  P1   P  P      0   1.163  -4.2901  -0.6621   0.2428
 I3S  OP2  O  O      0  -0.812  -3.7760  -1.8764   1.0148
 I3S  OP3  O  OP    -1  -1.013  -5.5138   0.0012   0.8631
 I3S  OP1  O  OP    -1  -0.921  -4.3582  -0.8594  -1.2678
 I3S  C6   C  CH1    0   0.056  -1.2687   1.8959  -0.0182
 I3S  O6   O  OH1    0  -0.636  -2.0659   2.8774  -0.6651
 I3S  C5   C  CH1    0  -0.039   0.1300   1.9744  -0.6158
 I3S  O5   O  OH1    0  -0.645   0.6472   3.2754  -0.4585
 I3S  C4   C  CH1    0   0.053   1.0682   0.9605   0.0358
 I3S  O4   O  O2     0  -0.489   2.3278   1.0145  -0.5569
 I3S  P4   P  P      0   1.151   3.7029   1.5707   0.2713
 I3S  OP5  O  OP    -1  -1.012   4.8084   0.7474  -0.3841
 I3S  OP6  O  OP    -1  -1.008   3.7961   3.0633  -0.0387
 I3S  OP4  O  O      0  -0.877   3.4666   1.2709   1.7493
 I3S  H3   H  HCH1   0   0.203   0.3718  -0.5898  -1.2498
 I3S  H2   H  HCH1   0   0.208  -1.3251  -1.5424   0.1223
 I3S  HO2  H  HOH1   0   0.425  -1.8078  -0.6087   2.1035
 I3S  H1   H  HCH1   0   0.270  -2.0123   0.2911  -1.2319
 I3S  H6   H  HCH1   0   0.213  -1.1874   2.1231   1.0543
 I3S  HO6  H  HOH1   0   0.427  -2.6638   3.2607  -0.0192
 I3S  H5   H  HCH1   0   0.138   0.0529   1.7226  -1.6902
 I3S  HO5  H  HOH1   0   0.407  -0.0554   3.8747  -0.7358
 I3S  H4   H  HCH1   0   0.184   1.1324   1.1765   1.1113

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
 I3S  O11  P3   deloc   1.525  0.020  1.525
 I3S  P3   O12  deloc   1.530  0.020  1.530
 I3S  P3   O10  deloc   1.527  0.020  1.527
 I3S  P3   O3   single  1.695  0.020  1.695
 I3S  O3   C3   single  1.395  0.020  1.395
 I3S  C3   C2   single  1.527  0.020  1.527
 I3S  C3   C4   single  1.535  0.020  1.535
 I3S  C3   H3   single  0.970  0.020  1.090
 I3S  C2   O2   single  1.416  0.020  1.416
 I3S  C2   C1   single  1.532  0.020  1.532
 I3S  C2   H2   single  0.970  0.020  1.090
 I3S  O2   HO2  single  0.850  0.020  0.980
 I3S  C1   O1   single  1.402  0.020  1.402
 I3S  C1   C6   single  1.520  0.020  1.520
 I3S  C1   H1   single  0.970  0.020  1.090
 I3S  O1   P1   single  1.703  0.020  1.703
 I3S  P1   OP2  deloc   1.528  0.020  1.528
 I3S  P1   OP3  deloc   1.524  0.020  1.524
 I3S  P1   OP1  deloc   1.525  0.020  1.525
 I3S  C6   O6   single  1.420  0.020  1.420
 I3S  C6   C5   single  1.523  0.020  1.523
 I3S  C6   H6   single  0.970  0.020  1.090
 I3S  O6   HO6  single  0.850  0.020  0.980
 I3S  C5   O5   single  1.409  0.020  1.409
 I3S  C5   C4   single  1.527  0.020  1.527
 I3S  C5   H5   single  0.970  0.020  1.090
 I3S  O5   HO5  single  0.850  0.020  0.980
 I3S  C4   O4   single  1.393  0.020  1.393
 I3S  C4   H4   single  0.970  0.020  1.090
 I3S  O4   P4   single  1.699  0.020  1.699
 I3S  P4   OP5  deloc   1.526  0.020  1.526
 I3S  P4   OP6  deloc   1.527  0.020  1.527
 I3S  P4   OP4  deloc   1.526  0.020  1.526

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
 I3S  O3   P3  O10  106.22  3.000
 I3S  O3   P3  O12  105.77  3.000
 I3S  O10  P3  O12  113.32  3.000
 I3S  O3   P3  O11  101.29  3.000
 I3S  O10  P3  O11  114.77  3.000
 I3S  O12  P3  O11  113.94  3.000
 I3S  C3   O3  P3   119.66  3.000
 I3S  H3   C3  C4   106.61  3.000
 I3S  H3   C3  C2   106.02  3.000
 I3S  C4   C3  C2   112.62  3.000
 I3S  H3   C3  O3   110.52  3.000
 I3S  C4   C3  O3   109.69  3.000
 I3S  C2   C3  O3   111.23  3.000
 I3S  H2   C2  C1   108.47  3.000
 I3S  H2   C2  O2   109.25  3.000
 I3S  C1   C2  O2   110.27  3.000
 I3S  H2   C2  C3   107.22  3.000
 I3S  C1   C2  C3   111.86  3.000
 I3S  O2   C2  C3   109.69  3.000
 I3S  HO2  O2  C2   104.58  3.000
 I3S  H1   C1  C6   108.72  3.000
 I3S  H1   C1  O1   110.78  3.000
 I3S  C6   C1  O1   106.73  3.000
 I3S  H1   C1  C2   107.15  3.000
 I3S  C6   C1  C2   110.79  3.000
 I3S  O1   C1  C2   112.64  3.000
 I3S  P1   O1  C1   121.30  3.000
 I3S  OP1  P1  OP3  115.07  3.000
 I3S  OP1  P1  OP2  114.37  3.000
 I3S  OP3  P1  OP2  114.24  3.000
 I3S  OP1  P1  O1   105.65  3.000
 I3S  OP3  P1  O1   100.53  3.000
 I3S  OP2  P1  O1   104.96  3.000
 I3S  H6   C6  C5   107.71  3.000
 I3S  H6   C6  O6   110.06  3.000
 I3S  C5   C6  O6   107.52  3.000
 I3S  H6   C6  C1   108.01  3.000
 I3S  C5   C6  C1   112.32  3.000
 I3S  O6   C6  C1   111.16  3.000
 I3S  HO6  O6  C6   108.61  3.000
 I3S  H5   C5  C4   107.82  3.000
 I3S  H5   C5  O5   110.14  3.000
 I3S  C4   C5  O5   109.87  3.000
 I3S  H5   C5  C6   107.78  3.000
 I3S  C4   C5  C6   111.25  3.000
 I3S  O5   C5  C6   109.93  3.000
 I3S  HO5  O5  C5   105.93  3.000
 I3S  H4   C4  O4   110.85  3.000
 I3S  H4   C4  C5   108.84  3.000
 I3S  O4   C4  C5   110.37  3.000
 I3S  H4   C4  C3   109.12  3.000
 I3S  O4   C4  C3   109.50  3.000
 I3S  C5   C4  C3   108.10  3.000
 I3S  P4   O4  C4   122.49  3.000
 I3S  OP4  P4  OP6  113.45  3.000
 I3S  OP4  P4  OP5  114.96  3.000
 I3S  OP6  P4  OP5  113.32  3.000
 I3S  OP4  P4  O4   106.41  3.000
 I3S  OP6  P4  O4   105.69  3.000
 I3S  OP5  P4  O4   101.56  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
 I3S  Var_01  OP2  P1  O1  C1   74.86  30.0  3
 I3S  Var_02  OP5  P4  O4  C4  149.09  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
 I3S  chir_01  C3  O3  C2  C4  negativ
 I3S  chir_02  C2  O2  C3  C1  positiv
 I3S  chir_03  C1  O1  C6  C2  negativ
 I3S  chir_04  C6  O6  C1  C5  negativ
 I3S  chir_05  C5  O5  C6  C4  positiv
 I3S  chir_06  C4  O4  C3  C5  positiv

