# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:57:27 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (1S,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@@H](O)[C@H](O[P](O)(O)=O)[C@@H](O)[C@H]1O
#
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
 I4D  I4D  '(1S,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl dihydrogen phosphate'  ligand  29  16  .  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_I4D
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
 I4D  O5   O  OH1   0  -0.663   0.1821   2.3755  -0.1979
 I4D  C5   C  CH1   0   0.030   0.7672   1.2379   0.3758
 I4D  C6   C  CH1   0   0.018   2.1902   1.0220  -0.1301
 I4D  O6   O  OH1   0  -0.677   2.9342   2.1438   0.2848
 I4D  C4   C  CH1   0  -0.018  -0.1179   0.0485   0.0376
 I4D  O4   O  O2    0  -0.604  -1.3876   0.2677   0.6563
 I4D  P4   P  P     0   1.427  -2.7588  -0.0027  -0.1398
 I4D  O43  O  OH1   0  -0.730  -3.8382   0.2673   1.0025
 I4D  O42  O  O     0  -0.709  -2.9340   0.7751  -1.3828
 I4D  O41  O  OH1   0  -0.778  -2.8322  -1.5763  -0.3123
 I4D  C3   C  CH1   0   0.052   0.4799  -1.2406   0.5904
 I4D  O3   O  OH1   0  -0.693  -0.3772  -2.3176   0.2481
 I4D  C2   C  CH1   0  -0.037   1.8875  -1.4693   0.0563
 I4D  O2   O  OH1   0  -0.666   1.8118  -1.6568  -1.3342
 I4D  C1   C  CH1   0  -0.022   2.7738  -0.2751   0.4165
 I4D  O1   O  OH1   0  -0.671   4.0602  -0.4185  -0.1453
 I4D  H5   H  HOH1  0   0.453   0.7456   3.1307   0.0023
 I4D  HA   H  HCH1  0   0.220   0.8075   1.3291   1.4740
 I4D  H6   H  HCH1  0   0.221   2.1616   0.9605  -1.2275
 I4D  H4   H  HCH1  0   0.266  -0.2246  -0.0204  -1.0517
 I4D  HB   H  HOH1  0   0.457   3.7925   2.1181  -0.1495
 I4D  H1   H  HCH1  0   0.230   2.8302  -0.2033   1.5119
 I4D  H3   H  HCH1  0   0.257   0.5425  -1.1449   1.6815
 I4D  H43  H  HOH1  0   0.500  -4.2255   1.1519   0.9685
 I4D  H41  H  HOH1  0   0.497  -1.9735  -2.0173  -0.0791
 I4D  HC   H  HOH1  0   0.483  -0.2323  -3.0482   0.8598
 I4D  H2   H  HCH1  0   0.242   2.2977  -2.3632   0.5530
 I4D  HD   H  HOH1  0   0.452   2.7131  -1.6686  -1.6763
 I4D  HE   H  HOH1  0   0.462   4.5614  -1.0522   0.3780

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
 I4D  O5   C5   single  1.402  0.020  1.402
 I4D  C5   C6   single  1.526  0.020  1.526
 I4D  C5   C4   single  1.521  0.020  1.521
 I4D  C6   O6   single  1.409  0.020  1.409
 I4D  C6   C1   single  1.524  0.020  1.524
 I4D  C4   O4   single  1.429  0.020  1.429
 I4D  C4   C3   single  1.525  0.020  1.525
 I4D  O4   P4   single  1.608  0.020  1.608
 I4D  P4   O43  single  1.595  0.020  1.595
 I4D  P4   O42  double  1.477  0.020  1.477
 I4D  P4   O41  single  1.585  0.020  1.585
 I4D  C3   O3   single  1.418  0.020  1.418
 I4D  C3   C2   single  1.523  0.020  1.523
 I4D  C2   O2   single  1.405  0.020  1.405
 I4D  C2   C1   single  1.530  0.020  1.530
 I4D  C1   O1   single  1.411  0.020  1.411
 I4D  O5   H5   single  0.850  0.020  0.980
 I4D  C5   HA   single  0.970  0.020  1.090
 I4D  C6   H6   single  0.970  0.020  1.090
 I4D  C4   H4   single  0.970  0.020  1.090
 I4D  O6   HB   single  0.850  0.020  0.980
 I4D  C1   H1   single  0.970  0.020  1.090
 I4D  C3   H3   single  0.970  0.020  1.090
 I4D  O43  H43  single  0.850  0.020  0.980
 I4D  O41  H41  single  0.850  0.020  0.980
 I4D  O3   HC   single  0.850  0.020  0.980
 I4D  C2   H2   single  0.970  0.020  1.090
 I4D  O2   HD   single  0.850  0.020  0.980
 I4D  O1   HE   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
 I4D  H5   O5   C5   107.88  3.000
 I4D  HA   C5   C4   107.91  3.000
 I4D  HA   C5   C6   107.93  3.000
 I4D  C4   C5   C6   111.01  3.000
 I4D  HA   C5   O5   110.83  3.000
 I4D  C4   C5   O5   107.50  3.000
 I4D  C6   C5   O5   111.61  3.000
 I4D  H6   C6   C1   108.68  3.000
 I4D  H6   C6   O6   110.63  3.000
 I4D  C1   C6   O6   111.71  3.000
 I4D  H6   C6   C5   108.34  3.000
 I4D  C1   C6   C5   111.02  3.000
 I4D  O6   C6   C5   106.40  3.000
 I4D  HB   O6   C6   108.48  3.000
 I4D  H4   C4   C3   110.19  3.000
 I4D  H4   C4   O4   110.68  3.000
 I4D  C3   C4   O4   108.73  3.000
 I4D  H4   C4   C5   109.07  3.000
 I4D  C3   C4   C5   110.64  3.000
 I4D  O4   C4   C5   107.50  3.000
 I4D  P4   O4   C4   121.15  3.000
 I4D  O41  P4   O42  115.20  3.000
 I4D  O41  P4   O43  102.40  3.000
 I4D  O42  P4   O43  115.69  3.000
 I4D  O41  P4   O4   105.09  3.000
 I4D  O42  P4   O4   115.42  3.000
 I4D  O43  P4   O4   101.19  3.000
 I4D  H43  O43  P4   113.64  3.000
 I4D  H41  O41  P4   112.05  3.000
 I4D  H3   C3   C2   108.01  3.000
 I4D  H3   C3   O3   109.92  3.000
 I4D  C2   C3   O3   111.09  3.000
 I4D  H3   C3   C4   108.01  3.000
 I4D  C2   C3   C4   111.24  3.000
 I4D  O3   C3   C4   108.52  3.000
 I4D  HC   O3   C3   109.37  3.000
 I4D  H2   C2   C1   108.14  3.000
 I4D  H2   C2   O2   110.97  3.000
 I4D  C1   C2   O2   111.61  3.000
 I4D  H2   C2   C3   107.93  3.000
 I4D  C1   C2   C3   109.61  3.000
 I4D  O2   C2   C3   108.51  3.000
 I4D  HD   O2   C2   107.60  3.000
 I4D  H1   C1   O1   110.89  3.000
 I4D  H1   C1   C2   108.38  3.000
 I4D  O1   C1   C2   110.80  3.000
 I4D  H1   C1   C6   108.75  3.000
 I4D  O1   C1   C6   107.03  3.000
 I4D  C2   C1   C6   110.98  3.000
 I4D  HE   O1   C1   108.98  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
 I4D  Var_01  O43  P4  O4  C4  175.50  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
 I4D  chir_01  C5  O5  C6  C4  positiv
 I4D  chir_02  C6  O6  C5  C1  positiv
 I4D  chir_03  C4  O4  C3  C5  positiv
 I4D  chir_04  C3  O3  C4  C2  positiv
 I4D  chir_05  C2  O2  C3  C1  positiv
 I4D  chir_06  C1  O1  C2  C6  positiv

