# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 20:39:53 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  27  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  -0.666   0.1462   2.2868  -0.0963
 I4D  C5   C  CH1    0   0.016   0.7869   1.1482   0.4262
 I4D  C6   C  CH1    0   0.019   2.1959   1.0170  -0.1388
 I4D  O6   O  OH1    0  -0.684   2.9062   2.1789   0.2386
 I4D  C4   C  CH1    0   0.087  -0.0775  -0.0749   0.1150
 I4D  O4   O  O2     0  -0.671  -1.3046   0.0649   0.7522
 I4D  P4   P  P      0   1.213  -2.7921   0.1006  -0.0901
 I4D  O43  O  OP    -1  -0.906  -3.4926   1.2903   0.5585
 I4D  O42  O  O      0  -0.903  -2.4388   0.2873  -1.5623
 I4D  O41  O  OP    -1  -0.901  -3.4408  -1.2406   0.2342
 I4D  C3   C  CH1    0   0.028   0.6305  -1.3354   0.6191
 I4D  O3   O  OH1    0  -0.661  -0.1726  -2.4461   0.3087
 I4D  C2   C  CH1    0  -0.044   2.0373  -1.4791   0.0455
 I4D  O2   O  OH1    0  -0.669   1.9553  -1.6773  -1.3466
 I4D  C1   C  CH1    0  -0.024   2.8680  -0.2433   0.3841
 I4D  O1   O  OH1    0  -0.676   4.1514  -0.3131  -0.2065
 I4D  H5   H  HOH1   0   0.440   0.7192   3.0417   0.0737
 I4D  HA   H  HCH1   0   0.182   0.8751   1.2291   1.5242
 I4D  H6   H  HCH1   0   0.206   2.1266   0.9508  -1.2344
 I4D  H4   H  HCH1   0   0.191  -0.2041  -0.1448  -0.9723
 I4D  HB   H  HOH1   0   0.452   3.7557   2.1733  -0.2130
 I4D  H1   H  HCH1   0   0.218   2.9486  -0.1701   1.4785
 I4D  H3   H  HCH1   0   0.191   0.7499  -1.2367   1.7111
 I4D  HC   H  HOH1   0   0.443   0.2361  -3.2262   0.6965
 I4D  H2   H  HCH1   0   0.218   2.5151  -2.3497   0.5283
 I4D  HD   H  HOH1   0   0.444   2.8520  -1.6228  -1.6958
 I4D  HE   H  HOH1   0   0.458   4.6880  -0.9378   0.2916

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  1.407  0.020  1.407
 I4D  C5  C6   single  1.524  0.020  1.524
 I4D  C5  C4   single  1.530  0.020  1.530
 I4D  C6  O6   single  1.413  0.020  1.413
 I4D  C6  C1   single  1.521  0.020  1.521
 I4D  C4  O4   single  1.390  0.020  1.390
 I4D  C4  C3   single  1.531  0.020  1.531
 I4D  O4  P4   single  1.710  0.020  1.710
 I4D  P4  O43  deloc   1.525  0.020  1.525
 I4D  P4  O42  deloc   1.525  0.020  1.525
 I4D  P4  O41  deloc   1.525  0.020  1.525
 I4D  C3  O3   single  1.405  0.020  1.405
 I4D  C3  C2   single  1.526  0.020  1.526
 I4D  C2  O2   single  1.409  0.020  1.409
 I4D  C2  C1   single  1.527  0.020  1.527
 I4D  C1  O1   single  1.414  0.020  1.414
 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  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   107.33  3.000
 I4D  HA   C5  C4   107.81  3.000
 I4D  HA   C5  C6   107.53  3.000
 I4D  C4   C5  C6   112.22  3.000
 I4D  HA   C5  O5   110.25  3.000
 I4D  C4   C5  O5   108.31  3.000
 I4D  C6   C5  O5   110.68  3.000
 I4D  H6   C6  C1   108.69  3.000
 I4D  H6   C6  O6   110.31  3.000
 I4D  C1   C6  O6   111.55  3.000
 I4D  H6   C6  C5   108.44  3.000
 I4D  C1   C6  C5   110.64  3.000
 I4D  O6   C6  C5   107.15  3.000
 I4D  HB   O6  C6   108.28  3.000
 I4D  H4   C4  C3   109.10  3.000
 I4D  H4   C4  O4   111.04  3.000
 I4D  C3   C4  O4   109.89  3.000
 I4D  H4   C4  C5   108.53  3.000
 I4D  C3   C4  C5   109.27  3.000
 I4D  O4   C4  C5   108.98  3.000
 I4D  P4   O4  C4   122.98  3.000
 I4D  O41  P4  O42  114.30  3.000
 I4D  O41  P4  O43  113.59  3.000
 I4D  O42  P4  O43  114.92  3.000
 I4D  O41  P4  O4   104.30  3.000
 I4D  O42  P4  O4   106.05  3.000
 I4D  O43  P4  O4   101.91  3.000
 I4D  H3   C3  C2   106.30  3.000
 I4D  H3   C3  O3   110.56  3.000
 I4D  C2   C3  O3   111.68  3.000
 I4D  H3   C3  C4   107.60  3.000
 I4D  C2   C3  C4   112.34  3.000
 I4D  O3   C3  C4   108.28  3.000
 I4D  HC   O3  C3   107.99  3.000
 I4D  H2   C2  C1   107.80  3.000
 I4D  H2   C2  O2   110.26  3.000
 I4D  C1   C2  O2   111.39  3.000
 I4D  H2   C2  C3   107.99  3.000
 I4D  C1   C2  C3   109.99  3.000
 I4D  O2   C2  C3   109.34  3.000
 I4D  HD   O2  C2   107.22  3.000
 I4D  H1   C1  O1   110.63  3.000
 I4D  H1   C1  C2   108.32  3.000
 I4D  O1   C1  C2   111.17  3.000
 I4D  H1   C1  C6   108.62  3.000
 I4D  O1   C1  C6   107.35  3.000
 I4D  C2   C1  C6   110.73  3.000
 I4D  HE   O1  C1   108.77  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  -133.66  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

