# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 14:18:41 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: (1R,2R,3S,4R,5R,6S)-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
 I3P  I3P  '(1R,2R,3S,4R,5R,6S)-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_I3P
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
 I3P  C1    C  CH1   0   0.102   3.0266  57.2360  28.7797
 I3P  C2    C  CH1   0  -0.046   2.3300  58.4966  28.2857
 I3P  C3    C  CH1   0   0.053   1.3575  58.1321  27.1650
 I3P  C4    C  CH1   0  -0.030   0.3389  57.1138  27.6694
 I3P  C5    C  CH1   0  -0.042   1.0421  55.8693  28.1814
 I3P  C6    C  CH1   0  -0.022   2.0404  56.1934  29.2937
 I3P  O1    O  O2    0  -0.546   3.9028  57.5606  29.8538
 I3P  O2    O  OH1   0  -0.605   1.6748  59.0862  29.3779
 I3P  O3    O  OH1   0  -0.573   0.7350  59.3186  26.7492
 I3P  O4    O  O2    0  -0.508  -0.5023  56.7210  26.5901
 I3P  O5    O  O2    0  -0.331   0.0795  54.9663  28.7290
 I3P  O6    O  OH1   0  -0.684   2.7619  55.0506  29.6561
 I3P  P1    P  P     0   1.164   5.4582  57.7885  29.5995
 I3P  O11   O  O     0  -0.647   5.8477  58.8410  28.6393
 I3P  O12   O  OH1   0  -0.607   5.9562  56.3196  29.2077
 I3P  O13   O  OH1   0  -0.575   5.8740  58.0163  31.1203
 I3P  P4    P  P     0   1.086  -2.0703  57.0774  26.5132
 I3P  O41   O  O     0  -0.810  -2.6861  57.4713  27.7978
 I3P  O42   O  OH1   0  -0.558  -2.1088  58.1878  25.3666
 I3P  O43   O  OH1   0  -0.578  -2.6426  55.8024  25.7775
 I3P  P5    P  P     0   1.090  -0.5013  53.6708  28.0131
 I3P  O51   O  O     0  -0.820  -1.7262  53.8410  27.1881
 I3P  O52   O  OH1   0  -0.590   0.7324  53.0449  27.2274
 I3P  O53   O  OH1   0  -0.595  -0.7069  52.7936  29.3171
 I3P  H1    H  HCH1  0   0.218   3.5821  56.8024  27.9383
 I3P  H2    H  HCH1  0   0.253   3.0903  59.1673  27.8627
 I3P  H3    H  HCH1  0   0.188   1.9361  57.6786  26.3475
 I3P  H4    H  HCH1  0   0.294  -0.2553  57.5620  28.4717
 I3P  H5    H  HCH1  0   0.311   1.5832  55.3913  27.3575
 I3P  H6    H  HCH1  0   0.265   1.4928  56.6095  30.1488
 I3P  HO2   H  HOH1  0   0.434   1.2582  59.9026  29.0822
 I3P  HO3   H  HOH1  0   0.473   0.2791  59.1703  25.9150
 I3P  HO6   H  HOH1  0   0.439   2.2681  54.5680  30.3249
 I3P  HO12  H  HOH1  0   0.447   6.7277  56.3119  28.6260
 I3P  HO13  H  HOH1  0   0.494   6.6742  58.5466  31.2290
 I3P  HO42  H  HOH1  0   0.475  -2.7985  58.8540  25.4918
 I3P  HO43  H  HOH1  0   0.474  -2.3844  54.9653  26.2535
 I3P  HO52  H  HOH1  0   0.465   0.5539  52.8247  26.3029
 I3P  HO53  H  HOH1  0   0.442  -1.3242  52.0568  29.2086

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
 I3P  C1   C2    single  1.523  0.020  1.523
 I3P  C1   C6    single  1.524  0.020  1.524
 I3P  C1   O1    single  1.424  0.020  1.424
 I3P  C1   H1    single  0.970  0.020  1.090
 I3P  C2   C3    single  1.528  0.020  1.528
 I3P  C2   O2    single  1.403  0.020  1.403
 I3P  C2   H2    single  0.970  0.020  1.090
 I3P  C3   C4    single  1.526  0.020  1.526
 I3P  C3   O3    single  1.403  0.020  1.403
 I3P  C3   H3    single  0.970  0.020  1.090
 I3P  C4   C5    single  1.518  0.020  1.518
 I3P  C4   O4    single  1.424  0.020  1.424
 I3P  C4   H4    single  0.970  0.020  1.090
 I3P  C5   C6    single  1.529  0.020  1.529
 I3P  C5   O5    single  1.429  0.020  1.429
 I3P  C5   H5    single  0.970  0.020  1.090
 I3P  C6   O6    single  1.399  0.020  1.399
 I3P  C6   H6    single  0.970  0.020  1.090
 I3P  O1   P1    single  1.592  0.020  1.592
 I3P  O2   HO2   single  0.850  0.020  0.980
 I3P  O3   HO3   single  0.850  0.020  0.980
 I3P  O4   P4    single  1.610  0.020  1.610
 I3P  O5   P5    single  1.590  0.020  1.590
 I3P  O6   HO6   single  0.850  0.020  0.980
 I3P  P1   O11   double  1.477  0.020  1.477
 I3P  P1   O12   single  1.600  0.020  1.600
 I3P  P1   O13   single  1.593  0.020  1.593
 I3P  O12  HO12  single  0.850  0.020  0.980
 I3P  O13  HO13  single  0.850  0.020  0.980
 I3P  P4   O41   double  1.478  0.020  1.478
 I3P  P4   O42   single  1.597  0.020  1.597
 I3P  P4   O43   single  1.579  0.020  1.579
 I3P  O42  HO42  single  0.850  0.020  0.980
 I3P  O43  HO43  single  0.850  0.020  0.980
 I3P  P5   O51   double  1.487  0.020  1.487
 I3P  P5   O52   single  1.591  0.020  1.591
 I3P  P5   O53   single  1.585  0.020  1.585
 I3P  O52  HO52  single  0.850  0.020  0.980
 I3P  O53  HO53  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
 I3P  H1    C1   O1   110.91  3.000
 I3P  H1    C1   C6   108.40  3.000
 I3P  O1    C1   C6   107.44  3.000
 I3P  H1    C1   C2   108.06  3.000
 I3P  O1    C1   C2   109.73  3.000
 I3P  C6    C1   C2   112.31  3.000
 I3P  H2    C2   O2   111.48  3.000
 I3P  H2    C2   C3   107.68  3.000
 I3P  O2    C2   C3   111.96  3.000
 I3P  H2    C2   C1   108.28  3.000
 I3P  O2    C2   C1   107.99  3.000
 I3P  C3    C2   C1   109.37  3.000
 I3P  H3    C3   O3   111.23  3.000
 I3P  H3    C3   C4   108.77  3.000
 I3P  O3    C3   C4   111.47  3.000
 I3P  H3    C3   C2   107.99  3.000
 I3P  O3    C3   C2   107.34  3.000
 I3P  C4    C3   C2   109.97  3.000
 I3P  H4    C4   O4   110.36  3.000
 I3P  H4    C4   C5   109.87  3.000
 I3P  O4    C4   C5   107.65  3.000
 I3P  H4    C4   C3   109.36  3.000
 I3P  O4    C4   C3   109.14  3.000
 I3P  C5    C4   C3   110.44  3.000
 I3P  H5    C5   O5   110.19  3.000
 I3P  H5    C5   C6   108.48  3.000
 I3P  O5    C5   C6   107.15  3.000
 I3P  H5    C5   C4   109.44  3.000
 I3P  O5    C5   C4   109.59  3.000
 I3P  C6    C5   C4   111.95  3.000
 I3P  H6    C6   O6   111.42  3.000
 I3P  H6    C6   C5   108.75  3.000
 I3P  O6    C6   C5   110.60  3.000
 I3P  H6    C6   C1   109.04  3.000
 I3P  O6    C6   C1   108.20  3.000
 I3P  C5    C6   C1   108.79  3.000
 I3P  P1    O1   C1   120.88  3.000
 I3P  HO2   O2   C2   108.61  3.000
 I3P  HO3   O3   C3   109.69  3.000
 I3P  P4    O4   C4   123.41  3.000
 I3P  P5    O5   C5   126.04  3.000
 I3P  HO6   O6   C6   108.99  3.000
 I3P  O13   P1   O12  106.49  3.000
 I3P  O13   P1   O11  116.74  3.000
 I3P  O12   P1   O11  114.40  3.000
 I3P  O13   P1   O1    97.06  3.000
 I3P  O12   P1   O1   102.22  3.000
 I3P  O11   P1   O1   117.61  3.000
 I3P  HO12  O12  P1   113.79  3.000
 I3P  HO13  O13  P1   113.70  3.000
 I3P  O43   P4   O42  102.60  3.000
 I3P  O43   P4   O41  117.97  3.000
 I3P  O42   P4   O41  115.39  3.000
 I3P  O43   P4   O4   101.33  3.000
 I3P  O42   P4   O4   102.22  3.000
 I3P  O41   P4   O4   115.05  3.000
 I3P  HO42  O42  P4   113.78  3.000
 I3P  HO43  O43  P4   111.19  3.000
 I3P  O53   P5   O52  106.81  3.000
 I3P  O53   P5   O51  114.40  3.000
 I3P  O52   P5   O51  114.20  3.000
 I3P  O53   P5   O5    97.35  3.000
 I3P  O52   P5   O5   105.05  3.000
 I3P  O51   P5   O5   117.23  3.000
 I3P  HO52  O52  P5   114.75  3.000
 I3P  HO53  O53  P5   114.34  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
 I3P  Var_01  O11  P1  O1  C1   57.95  30.0  3
 I3P  Var_02  O41  P4  O4  C4  -17.98  30.0  3
 I3P  Var_03  O51  P5  O5  C5  -90.06  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
 I3P  chir_01  C1  C2  C6  O1  positiv
 I3P  chir_02  C2  O2  C1  C3  negativ
 I3P  chir_03  C3  O3  C2  C4  negativ
 I3P  chir_04  C4  O4  C5  C3  negativ
 I3P  chir_05  C5  O5  C6  C4  positiv
 I3P  chir_06  C6  O6  C5  C1  positiv

