# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 16:47:46 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: (1R,2R,3S,4S,5S,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
 I2P  I2P  '(1R,2R,3S,4S,5S,6S)-3,5,6-trihydroxycyclohexane-1,2,4-triyl tris[dihydrogen (phosphate)]'  ligand  39  24  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_I2P
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
 I2P  C1    C  CH1   0   0.070  82.0246  41.7545  -22.4880
 I2P  C2    C  CH1   0  -0.098  81.0646  40.5737  -22.4077
 I2P  C3    C  CH1   0   0.035  81.8333  39.2609  -22.4751
 I2P  C4    C  CH1   0   0.006  82.8937  39.2058  -21.3748
 I2P  C5    C  CH1   0   0.002  83.8307  40.3968  -21.4881
 I2P  C6    C  CH1   0  -0.005  83.0577  41.7020  -21.3631
 I2P  O1    O  OH1   0  -0.694  81.2656  42.9420  -22.4497
 I2P  O2    O  O2    0  -0.599  80.3601  40.6107  -21.1668
 I2P  O3    O  OH1   0  -0.654  80.9148  38.2144  -22.3640
 I2P  O4    O  O2    0  -0.609  83.6295  38.0020  -21.5574
 I2P  O5    O  O2    0  -0.603  84.7848  40.2928  -20.4397
 I2P  O6    O  OH1   0  -0.670  83.9568  42.7788  -21.4804
 I2P  P2    P  P     0   1.453  78.8449  41.1251  -21.0082
 I2P  O21   O  O     0  -0.700  78.4071  40.9663  -19.6096
 I2P  O22   O  OH1   0  -0.741  77.9779  40.3452  -22.1014
 I2P  O23   O  OH1   0  -0.777  78.8095  42.5921  -21.6000
 I2P  P4    P  P     0   1.434  84.2225  37.1512  -20.3304
 I2P  O41   O  O     0  -0.707  83.7421  37.5518  -18.9939
 I2P  O42   O  OH1   0  -0.756  85.8009  37.1485  -20.5378
 I2P  O43   O  OH1   0  -0.727  83.8226  35.7035  -20.8596
 I2P  P5    P  P     0   1.460  86.2872  40.8236  -20.5877
 I2P  O51   O  O     0  -0.693  86.7613  41.0672  -21.9615
 I2P  O52   O  OH1   0  -0.723  86.4395  42.0299  -19.5598
 I2P  O53   O  OH1   0  -0.750  86.9664  39.6203  -19.7691
 I2P  H1    H  HCH1  0   0.255  82.5508  41.6824  -23.4498
 I2P  H2    H  HCH1  0   0.304  80.3723  40.6097  -23.2559
 I2P  H3    H  HCH1  0   0.251  82.3459  39.2449  -23.4479
 I2P  H4    H  HCH1  0   0.274  82.4065  39.2067  -20.3941
 I2P  H5    H  HCH1  0   0.271  84.3405  40.3663  -22.4591
 I2P  H6    H  HCH1  0   0.263  82.5457  41.7274  -20.3941
 I2P  HO1   H  HOH1  0   0.478  81.8484  43.7108  -22.4477
 I2P  HO3   H  HOH1  0   0.460  81.3586  37.3907  -22.5894
 I2P  HO6   H  HOH1  0   0.472  83.8220  43.3841  -20.7458
 I2P  HO22  H  HOH1  0   0.498  77.7007  39.4615  -21.8245
 I2P  HO23  H  HOH1  0   0.500  79.6950  42.9251  -21.8926
 I2P  HO42  H  HOH1  0   0.500  86.2708  37.9088  -20.1467
 I2P  HO43  H  HOH1  0   0.503  84.0550  34.9834  -20.2581
 I2P  HO52  H  HOH1  0   0.502  86.4532  42.9029  -19.9746
 I2P  HO53  H  HOH1  0   0.515  87.9268  39.6883  -19.6647

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
 I2P  C1   C2    single  1.524  0.020  1.524
 I2P  C1   C6    single  1.528  0.020  1.528
 I2P  C1   O1    single  1.410  0.020  1.410
 I2P  C1   H1    single  0.970  0.020  1.090
 I2P  C2   C3    single  1.523  0.020  1.523
 I2P  C2   O2    single  1.427  0.020  1.427
 I2P  C2   H2    single  0.970  0.020  1.090
 I2P  C3   C4    single  1.529  0.020  1.529
 I2P  C3   O3    single  1.397  0.020  1.397
 I2P  C3   H3    single  0.970  0.020  1.090
 I2P  C4   C5    single  1.520  0.020  1.520
 I2P  C4   O4    single  1.423  0.020  1.423
 I2P  C4   H4    single  0.970  0.020  1.090
 I2P  C5   C6    single  1.522  0.020  1.522
 I2P  C5   O5    single  1.421  0.020  1.421
 I2P  C5   H5    single  0.970  0.020  1.090
 I2P  C6   O6    single  1.408  0.020  1.408
 I2P  C6   H6    single  0.970  0.020  1.090
 I2P  O1   HO1   single  0.850  0.020  0.980
 I2P  O2   P2    single  1.608  0.020  1.608
 I2P  O3   HO3   single  0.850  0.020  0.980
 I2P  O4   P4    single  1.607  0.020  1.607
 I2P  O5   P5    single  1.600  0.020  1.600
 I2P  O6   HO6   single  0.850  0.020  0.980
 I2P  P2   O21   double  1.474  0.020  1.474
 I2P  P2   O22   single  1.598  0.020  1.598
 I2P  P2   O23   single  1.582  0.020  1.582
 I2P  O22  HO22  single  0.850  0.020  0.980
 I2P  O23  HO23  single  0.850  0.020  0.980
 I2P  P4   O41   double  1.476  0.020  1.476
 I2P  P4   O42   single  1.592  0.020  1.592
 I2P  P4   O43   single  1.592  0.020  1.592
 I2P  O42  HO42  single  0.850  0.020  0.980
 I2P  O43  HO43  single  0.850  0.020  0.980
 I2P  P5   O51   double  1.474  0.020  1.474
 I2P  P5   O52   single  1.592  0.020  1.592
 I2P  P5   O53   single  1.606  0.020  1.606
 I2P  O52  HO52  single  0.850  0.020  0.980
 I2P  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
 I2P  H1    C1   O1   109.69  3.000
 I2P  H1    C1   C6   108.56  3.000
 I2P  O1    C1   C6   111.89  3.000
 I2P  H1    C1   C2   107.28  3.000
 I2P  O1    C1   C2   108.18  3.000
 I2P  C6    C1   C2   111.13  3.000
 I2P  H2    C2   O2   111.13  3.000
 I2P  H2    C2   C3   108.24  3.000
 I2P  O2    C2   C3   108.06  3.000
 I2P  H2    C2   C1   109.38  3.000
 I2P  O2    C2   C1   109.67  3.000
 I2P  C3    C2   C1   110.34  3.000
 I2P  H3    C3   O3   111.47  3.000
 I2P  H3    C3   C4   108.22  3.000
 I2P  O3    C3   C4   111.83  3.000
 I2P  H3    C3   C2   106.68  3.000
 I2P  O3    C3   C2   108.08  3.000
 I2P  C4    C3   C2   110.44  3.000
 I2P  H4    C4   O4   110.23  3.000
 I2P  H4    C4   C5   109.91  3.000
 I2P  O4    C4   C5   109.56  3.000
 I2P  H4    C4   C3   109.62  3.000
 I2P  O4    C4   C3   107.26  3.000
 I2P  C5    C4   C3   110.22  3.000
 I2P  H5    C5   O5   109.81  3.000
 I2P  H5    C5   C6   109.42  3.000
 I2P  O5    C5   C6   110.06  3.000
 I2P  H5    C5   C4   109.31  3.000
 I2P  O5    C5   C4   107.55  3.000
 I2P  C6    C5   C4   110.66  3.000
 I2P  H6    C6   O6   110.75  3.000
 I2P  H6    C6   C5   109.25  3.000
 I2P  O6    C6   C5   108.95  3.000
 I2P  H6    C6   C1   109.52  3.000
 I2P  O6    C6   C1   110.13  3.000
 I2P  C5    C6   C1   108.20  3.000
 I2P  HO1   O1   C1   110.25  3.000
 I2P  P2    O2   C2   123.99  3.000
 I2P  HO3   O3   C3   108.63  3.000
 I2P  P4    O4   C4   122.75  3.000
 I2P  P5    O5   C5   122.53  3.000
 I2P  HO6   O6   C6   109.17  3.000
 I2P  O23   P2   O22  100.63  3.000
 I2P  O23   P2   O21  116.62  3.000
 I2P  O22   P2   O21  115.80  3.000
 I2P  O23   P2   O2   106.31  3.000
 I2P  O22   P2   O2   106.71  3.000
 I2P  O21   P2   O2   109.81  3.000
 I2P  HO22  O22  P2   113.93  3.000
 I2P  HO23  O23  P2   113.72  3.000
 I2P  O43   P4   O42  101.78  3.000
 I2P  O43   P4   O41  117.78  3.000
 I2P  O42   P4   O41  116.18  3.000
 I2P  O43   P4   O4    97.75  3.000
 I2P  O42   P4   O4   105.51  3.000
 I2P  O41   P4   O4   115.33  3.000
 I2P  HO42  O42  P4   115.08  3.000
 I2P  HO43  O43  P4   114.21  3.000
 I2P  O53   P5   O52  101.43  3.000
 I2P  O53   P5   O51  117.58  3.000
 I2P  O52   P5   O51  116.48  3.000
 I2P  O53   P5   O5    95.82  3.000
 I2P  O52   P5   O5   106.35  3.000
 I2P  O51   P5   O5   116.30  3.000
 I2P  HO52  O52  P5   114.11  3.000
 I2P  HO53  O53  P5   114.94  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
 I2P  Var_01  O21  P2  O2  C2  177.19  30.0  3
 I2P  Var_02  O41  P4  O4  C4   11.17  30.0  3
 I2P  Var_03  O51  P5  O5  C5  -17.20  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
 I2P  chir_01  C1  C2  C6  O1  positiv
 I2P  chir_02  C2  O2  C3  C1  positiv
 I2P  chir_03  C3  O3  C2  C4  negativ
 I2P  chir_04  C4  O4  C5  C3  negativ
 I2P  chir_05  C5  O5  C6  C4  positiv
 I2P  chir_06  C6  O6  C5  C1  positiv

