# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 01:29:34 2020
#   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  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_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   0.011   0.5715   0.0365   1.9409
 I3P  C2   C  CH1    0  -0.018   1.9476   0.0087   1.3042
 I3P  C3   C  CH1    0  -0.029   1.9084  -0.6942  -0.0493
 I3P  C4   C  CH1    0   0.095   0.9086  -0.0463  -1.0058
 I3P  C5   C  CH1    0   0.078  -0.4854  -0.0127  -0.3572
 I3P  C6   C  CH1    0   0.054  -0.4697   0.6748   1.0157
 I3P  O1   O  O2     0  -0.670   0.6630   0.7207   3.1676
 I3P  O2   O  OH1    0  -0.680   2.4363   1.3275   1.1758
 I3P  O3   O  OH1    0  -0.660   3.1948  -0.6575  -0.6375
 I3P  O4   O  O2     0  -0.662   0.8470  -0.7666  -2.1971
 I3P  O5   O  O2     0  -0.663  -1.3640   0.6539  -1.2104
 I3P  O6   O  OH1    0  -0.730  -1.7592   0.6223   1.5641
 I3P  P1   P  P      0   1.240  -0.1325   0.0905   4.5206
 I3P  O11  O  O      0  -0.882   0.4142  -1.3140   4.7225
 I3P  O12  O  OP    -1  -0.877   0.2263   1.1051   5.5913
 I3P  O13  O  OP    -1  -0.885  -1.6203   0.1079   4.1031
 I3P  P4   P  P      0   1.217   1.4848  -0.1953  -3.6623
 I3P  O41  O  O      0  -0.914   2.8115  -0.9336  -3.8386
 I3P  O42  O  OP    -1  -0.906   0.4281  -0.6301  -4.6719
 I3P  O43  O  OP    -1  -0.918   1.6395   1.3173  -3.5055
 I3P  P5   P  P      0   1.219  -2.8395   0.0046  -1.7348
 I3P  O51  O  O      0  -0.919  -2.7308  -1.5108  -1.5675
 I3P  O52  O  OP    -1  -0.915  -3.9092   0.6407  -0.8463
 I3P  O53  O  OP    -1  -0.910  -2.9097   0.4927  -3.1788
 I3P  H1   H  HCH1   0   0.184   0.2850  -1.0160   2.0988
 I3P  H2   H  HCH1   0   0.195   2.6070  -0.5730   1.9715
 I3P  H3   H  HCH1   0   0.186   1.5945  -1.7362   0.1244
 I3P  H4   H  HCH1   0   0.161   1.2282   0.9859  -1.1974
 I3P  H5   H  HCH1   0   0.150  -0.8112  -1.0529  -0.2061
 I3P  H6   H  HCH1   0   0.135  -0.1656   1.7258   0.8571
 I3P  HO2  H  HOH1   0   0.436   3.1786   1.2866   0.5616
 I3P  HO3  H  HOH1   0   0.441   3.7768  -1.2142  -0.1098
 I3P  HO6  H  HOH1   0   0.436  -1.7116   0.4560   2.5485

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  1.516  0.020  1.516
 I3P  C1  C6   single  1.532  0.020  1.532
 I3P  C1  O1   single  1.408  0.020  1.408
 I3P  C1  H1   single  0.970  0.020  1.090
 I3P  C2  C3   single  1.526  0.020  1.526
 I3P  C2  O2   single  1.412  0.020  1.412
 I3P  C2  H2   single  0.970  0.020  1.090
 I3P  C3  C4   single  1.528  0.020  1.528
 I3P  C3  O3   single  1.415  0.020  1.415
 I3P  C3  H3   single  0.970  0.020  1.090
 I3P  C4  C5   single  1.538  0.020  1.538
 I3P  C4  O4   single  1.393  0.020  1.393
 I3P  C4  H4   single  0.970  0.020  1.090
 I3P  C5  C6   single  1.536  0.020  1.536
 I3P  C5  O5   single  1.394  0.020  1.394
 I3P  C5  H5   single  0.970  0.020  1.090
 I3P  C6  O6   single  1.402  0.020  1.402
 I3P  C6  H6   single  0.970  0.020  1.090
 I3P  O1  P1   single  1.691  0.020  1.691
 I3P  O2  HO2  single  0.850  0.020  0.980
 I3P  O3  HO3  single  0.850  0.020  0.980
 I3P  O4  P4   single  1.697  0.020  1.697
 I3P  O5  P5   single  1.695  0.020  1.695
 I3P  O6  HO6  single  0.850  0.020  0.980
 I3P  P1  O11  deloc   1.521  0.020  1.521
 I3P  P1  O12  deloc   1.518  0.020  1.518
 I3P  P1  O13  deloc   1.545  0.020  1.545
 I3P  P4  O41  deloc   1.528  0.020  1.528
 I3P  P4  O42  deloc   1.525  0.020  1.525
 I3P  P4  O43  deloc   1.528  0.020  1.528
 I3P  P5  O51  deloc   1.528  0.020  1.528
 I3P  P5  O52  deloc   1.529  0.020  1.529
 I3P  P5  O53  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
 I3P  H1   C1  O1   110.87  3.000
 I3P  H1   C1  C6   107.92  3.000
 I3P  O1   C1  C6   111.59  3.000
 I3P  H1   C1  C2   106.18  3.000
 I3P  O1   C1  C2   108.41  3.000
 I3P  C6   C1  C2   111.76  3.000
 I3P  H2   C2  O2   109.89  3.000
 I3P  H2   C2  C3   107.99  3.000
 I3P  O2   C2  C3   111.00  3.000
 I3P  H2   C2  C1   107.33  3.000
 I3P  O2   C2  C1   109.58  3.000
 I3P  C3   C2  C1   110.96  3.000
 I3P  H3   C3  O3   110.43  3.000
 I3P  H3   C3  C4   108.25  3.000
 I3P  O3   C3  C4   108.89  3.000
 I3P  H3   C3  C2   107.64  3.000
 I3P  O3   C3  C2   109.48  3.000
 I3P  C4   C3  C2   112.14  3.000
 I3P  H4   C4  O4   110.48  3.000
 I3P  H4   C4  C5   108.48  3.000
 I3P  O4   C4  C5   109.38  3.000
 I3P  H4   C4  C3   108.51  3.000
 I3P  O4   C4  C3   110.18  3.000
 I3P  C5   C4  C3   109.78  3.000
 I3P  H5   C5  O5   110.45  3.000
 I3P  H5   C5  C6   107.67  3.000
 I3P  O5   C5  C6   109.85  3.000
 I3P  H5   C5  C4   107.79  3.000
 I3P  O5   C5  C4   108.88  3.000
 I3P  C6   C5  C4   112.19  3.000
 I3P  H6   C6  O6   110.16  3.000
 I3P  H6   C6  C5   107.47  3.000
 I3P  O6   C6  C5   108.88  3.000
 I3P  H6   C6  C1   107.20  3.000
 I3P  O6   C6  C1   111.91  3.000
 I3P  C5   C6  C1   111.12  3.000
 I3P  P1   O1  C1   119.04  3.000
 I3P  HO2  O2  C2   106.54  3.000
 I3P  HO3  O3  C3   107.86  3.000
 I3P  P4   O4  C4   123.20  3.000
 I3P  P5   O5  C5   123.68  3.000
 I3P  HO6  O6  C6   110.34  3.000
 I3P  O13  P1  O12  114.24  3.000
 I3P  O13  P1  O11  113.11  3.000
 I3P  O12  P1  O11  116.02  3.000
 I3P  O13  P1  O1   103.45  3.000
 I3P  O12  P1  O1   101.77  3.000
 I3P  O11  P1  O1   106.33  3.000
 I3P  O43  P4  O42  114.85  3.000
 I3P  O43  P4  O41  113.70  3.000
 I3P  O42  P4  O41  112.79  3.000
 I3P  O43  P4  O4   106.41  3.000
 I3P  O42  P4  O4   102.43  3.000
 I3P  O41  P4  O4   105.26  3.000
 I3P  O53  P5  O52  112.62  3.000
 I3P  O53  P5  O51  115.09  3.000
 I3P  O52  P5  O51  113.49  3.000
 I3P  O53  P5  O5   102.13  3.000
 I3P  O52  P5  O5   105.65  3.000
 I3P  O51  P5  O5   106.50  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   57.85  30.0  3
 I3P  Var_02  O41  P4  O4  C4  101.85  30.0  3
 I3P  Var_03  O51  P5  O5  C5  -21.31  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

