# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 06:21:20 2021
#   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  39  24  .  2021-08-11  2022-11-17
;
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  OH1   0  -0.739  25.2039   -9.5764  13.5563
 I3S  P3   P  P     0   1.446  24.9919  -10.2200  12.1138
 I3S  O12  O  OH1   0  -0.759  23.6358  -10.9881  12.4262
 I3S  O10  O  O     0  -0.692  26.1140  -10.9819  11.5384
 I3S  O3   O  O2    0  -0.598  24.6114   -9.0195  11.1144
 I3S  C3   C  CH1   0  -0.010  23.6033   -8.0588  11.3992
 I3S  C2   C  CH1   0  -0.023  24.2450   -6.7133  11.7100
 I3S  O2   O  OH1   0  -0.658  25.0648   -6.3622  10.6306
 I3S  C1   C  CH1   0  -0.012  23.1396   -5.6841  11.9538
 I3S  O1   O  O2    0  -0.611  23.7893   -4.4419  12.2117
 I3S  P1   P  P     0   1.431  23.1402   -3.3163  13.1694
 I3S  OP2  O  O     0  -0.708  22.5116   -3.8707  14.3855
 I3S  OP3  O  OH1   0  -0.758  22.2269   -2.4374  12.2135
 I3S  OP1  O  OH1   0  -0.724  24.3549   -2.3125  13.3717
 I3S  C6   C  CH1   0   0.051  22.2202   -5.5608  10.7472
 I3S  O6   O  OH1   0  -0.693  21.1981   -4.6335  11.0611
 I3S  C5   C  CH1   0  -0.005  21.6047   -6.9172  10.4151
 I3S  O5   O  OH1   0  -0.665  20.8158   -6.7497   9.2661
 I3S  C4   C  CH1   0   0.016  22.6923   -7.9609  10.1858
 I3S  O4   O  O2    0  -0.604  22.0339   -9.2117   9.9892
 I3S  P4   P  P     0   1.464  22.4345  -10.2553   8.8499
 I3S  OP5  O  OH1   0  -0.759  22.8637  -11.4925   9.7782
 I3S  OP6  O  OH1   0  -0.722  21.0295  -10.7606   8.2975
 I3S  OP4  O  O     0  -0.693  23.4110   -9.7905   7.8501
 I3S  H11  H  HOH1  0   0.504  26.1177   -9.3194  13.7379
 I3S  H12  H  HOH1  0   0.504  23.2195  -11.3587  11.6260
 I3S  H3   H  HCH1  0   0.279  23.0043   -8.3570  12.2676
 I3S  H2   H  HCH1  0   0.267  24.8209   -6.8090  12.6405
 I3S  HO2  H  HOH1  0   0.464  25.5355   -5.5513  10.8500
 I3S  H1   H  HCH1  0   0.270  22.5596   -5.9966  12.8303
 I3S  HP3  H  HOH1  0   0.496  21.6792   -3.0288  11.6478
 I3S  HP1  H  HOH1  0   0.505  24.8361   -2.4422  14.1996
 I3S  H6   H  HCH1  0   0.249  22.8017   -5.2090   9.8856
 I3S  HO6  H  HOH1  0   0.476  20.6211   -4.5434  10.2921
 I3S  H5   H  HCH1  0   0.250  20.9927   -7.2337  11.2714
 I3S  HO5  H  HOH1  0   0.466  20.0724   -7.3585   9.2994
 I3S  H4   H  HCH1  0   0.275  23.2743   -7.6977   9.2979
 I3S  HP5  H  HOH1  0   0.516  23.2105  -12.2626   9.3045
 I3S  HP6  H  HOH1  0   0.505  20.7384  -10.3215   7.4868

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   single  1.594  0.020  1.594
 I3S  O11  H11  single  0.850  0.020  0.980
 I3S  P3   O12  single  1.590  0.020  1.590
 I3S  P3   O10  double  1.473  0.020  1.473
 I3S  P3   O3   single  1.608  0.020  1.608
 I3S  O12  H12  single  0.850  0.020  0.980
 I3S  O3   C3   single  1.421  0.020  1.421
 I3S  C3   C2   single  1.523  0.020  1.523
 I3S  C3   C4   single  1.520  0.020  1.520
 I3S  C3   H3   single  0.970  0.020  1.090
 I3S  C2   O2   single  1.400  0.020  1.400
 I3S  C2   C1   single  1.530  0.020  1.530
 I3S  C2   H2   single  0.970  0.020  1.090
 I3S  O2   HO2  single  0.850  0.020  0.980
 I3S  C1   O1   single  1.425  0.020  1.425
 I3S  C1   C6   single  1.522  0.020  1.522
 I3S  C1   H1   single  0.970  0.020  1.090
 I3S  O1   P1   single  1.614  0.020  1.614
 I3S  P1   OP2  double  1.477  0.020  1.477
 I3S  P1   OP3  single  1.588  0.020  1.588
 I3S  P1   OP1  single  1.589  0.020  1.589
 I3S  OP3  HP3  single  0.850  0.020  0.980
 I3S  OP1  HP1  single  0.850  0.020  0.980
 I3S  C6   O6   single  1.415  0.020  1.415
 I3S  C6   C5   single  1.526  0.020  1.526
 I3S  C6   H6   single  0.970  0.020  1.090
 I3S  O6   HO6  single  0.850  0.020  0.980
 I3S  C5   O5   single  1.404  0.020  1.404
 I3S  C5   C4   single  1.525  0.020  1.525
 I3S  C5   H5   single  0.970  0.020  1.090
 I3S  O5   HO5  single  0.850  0.020  0.980
 I3S  C4   O4   single  1.427  0.020  1.427
 I3S  C4   H4   single  0.970  0.020  1.090
 I3S  O4   P4   single  1.596  0.020  1.596
 I3S  P4   OP5  single  1.605  0.020  1.605
 I3S  P4   OP6  single  1.592  0.020  1.592
 I3S  P4   OP4  double  1.473  0.020  1.473
 I3S  OP5  HP5  single  0.850  0.020  0.980
 I3S  OP6  HP6  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
 I3S  H11  O11  P3   113.78  3.000
 I3S  O3   P3   O10  108.88  3.000
 I3S  O3   P3   O12  106.33  3.000
 I3S  O10  P3   O12  118.46  3.000
 I3S  O3   P3   O11  107.01  3.000
 I3S  O10  P3   O11  117.45  3.000
 I3S  O12  P3   O11   97.51  3.000
 I3S  H12  O12  P3   112.75  3.000
 I3S  C3   O3   P3   123.23  3.000
 I3S  H3   C3   C4   108.80  3.000
 I3S  H3   C3   C2   107.99  3.000
 I3S  C4   C3   C2   111.01  3.000
 I3S  H3   C3   O3   111.24  3.000
 I3S  C4   C3   O3   107.97  3.000
 I3S  C2   C3   O3   109.83  3.000
 I3S  H2   C2   C1   107.61  3.000
 I3S  H2   C2   O2   111.58  3.000
 I3S  C1   C2   O2   112.16  3.000
 I3S  H2   C2   C3   108.47  3.000
 I3S  C1   C2   C3   108.82  3.000
 I3S  O2   C2   C3   108.12  3.000
 I3S  HO2  O2   C2   108.76  3.000
 I3S  H1   C1   C6   109.71  3.000
 I3S  H1   C1   O1   110.17  3.000
 I3S  C6   C1   O1   110.38  3.000
 I3S  H1   C1   C2   108.53  3.000
 I3S  C6   C1   C2   111.39  3.000
 I3S  O1   C1   C2   106.61  3.000
 I3S  P1   O1   C1   122.12  3.000
 I3S  OP1  P1   OP3   99.60  3.000
 I3S  OP1  P1   OP2  117.24  3.000
 I3S  OP3  P1   OP2  117.30  3.000
 I3S  OP1  P1   O1   102.05  3.000
 I3S  OP3  P1   O1   105.08  3.000
 I3S  OP2  P1   O1   113.45  3.000
 I3S  HP3  OP3  P1   109.47  3.000
 I3S  HP1  OP1  P1   113.89  3.000
 I3S  H6   C6   C5   109.14  3.000
 I3S  H6   C6   O6   110.29  3.000
 I3S  C5   C6   O6   109.84  3.000
 I3S  H6   C6   C1   109.16  3.000
 I3S  C5   C6   C1   110.13  3.000
 I3S  O6   C6   C1   108.27  3.000
 I3S  HO6  O6   C6   108.42  3.000
 I3S  H5   C5   C4   108.50  3.000
 I3S  H5   C5   O5   111.04  3.000
 I3S  C4   C5   O5   111.07  3.000
 I3S  H5   C5   C6   108.12  3.000
 I3S  C4   C5   C6   110.70  3.000
 I3S  O5   C5   C6   107.38  3.000
 I3S  HO5  O5   C5   109.31  3.000
 I3S  H4   C4   O4   110.16  3.000
 I3S  H4   C4   C5   109.69  3.000
 I3S  O4   C4   C5   106.95  3.000
 I3S  H4   C4   C3   110.15  3.000
 I3S  O4   C4   C3   109.26  3.000
 I3S  C5   C4   C3   110.57  3.000
 I3S  P4   O4   C4   123.75  3.000
 I3S  OP4  P4   OP6  116.73  3.000
 I3S  OP4  P4   OP5  117.30  3.000
 I3S  OP6  P4   OP5  101.07  3.000
 I3S  OP4  P4   O4   116.40  3.000
 I3S  OP6  P4   O4   103.51  3.000
 I3S  OP5  P4   O4    99.10  3.000
 I3S  HP5  OP5  P4   115.20  3.000
 I3S  HP6  OP6  P4   114.37  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   41.30  30.0  3
 I3S  Var_02  OP5  P4  O4  C4  117.93  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

