# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 12:36:47 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (5R,6R,7S,8R,8aS)-6,7,8-trihydroxy-5-(hydroxymethyl)hexahydroimidazo[1,2-a]pyridine-2,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@H](O)[C@H]2NC(=O)C(=O)N12
#
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
 KIF  KIF  (5R,6R,7S,8R,8aS)-6,7,8-trihydroxy-5-(hydroxymethyl)hexahydroimidazo[1,2-a]pyridine-2,3-dione  ligand  28  16  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KIF
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
 KIF  C4   C  CH1   0   0.030   0.4343  -1.0776  -1.7846
 KIF  O4   O  OH1   0  -0.665   0.1795  -2.3695  -1.2833
 KIF  C3   C  CH1   0  -0.048  -0.8930  -0.3646  -2.0728
 KIF  O3   O  OH1   0  -0.664  -0.6156   0.8249  -2.7675
 KIF  C2   C  CH1   0   0.023  -1.6657  -0.0852  -0.7793
 KIF  O2   O  OH1   0  -0.666  -2.8112   0.6937  -1.0232
 KIF  C1   C  CR15  0   0.152  -0.7912   0.7053   0.1862
 KIF  N9   N  NR15  0  -0.654  -1.3304   0.7818   1.5162
 KIF  C8   C  CR5   0   0.439  -0.5545   0.2073   2.4425
 KIF  O8   O  O     0  -0.451  -0.7258   0.1139   3.6384
 KIF  C7   C  CR5   0   0.423   0.6472  -0.3416   1.6779
 KIF  O7   O  O     0  -0.459   1.5642  -0.9631   2.1693
 KIF  N    N  NR5   0  -0.485   0.4496  -0.0012   0.3972
 KIF  C5   C  CH1   0  -0.166   1.2840  -0.3681  -0.7261
 KIF  C6   C  CH2   0  -0.138   2.0790   0.8199  -1.2512
 KIF  O6   O  OH1   0  -0.664   2.9064   1.2660  -0.2048
 KIF  H4   H  HCH1  0   0.248   1.0138  -1.1208  -2.7164
 KIF  HO4  H  HOH1  0   0.459  -0.2759  -2.8783  -1.9620
 KIF  H3   H  HCH1  0   0.246  -1.5059  -1.0376  -2.6942
 KIF  HO3  H  HOH1  0   0.454  -1.4376   1.3235  -2.8408
 KIF  H2   H  HCH1  0   0.241  -1.9153  -1.0394  -0.3017
 KIF  HO2  H  HOH1  0   0.467  -3.5210   0.1178  -1.3248
 KIF  H1   H  HCR5  0   0.284  -0.6094   1.7120  -0.2065
 KIF  H9   H  HNR5  0   0.420  -2.1952   1.2612   1.7160
 KIF  H5   H  HCH1  0   0.288   2.0089  -1.0969  -0.3547
 KIF  H61  H  HCH2  0   0.217   1.4175   1.6119  -1.6115
 KIF  H62  H  HCH2  0   0.210   2.6603   0.4720  -2.1148
 KIF  HO6  H  HOH1  0   0.459   3.2885   2.1085  -0.4651

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
 KIF  C4  O4   single  1.409  0.020  1.409
 KIF  C4  C3   single  1.534  0.020  1.534
 KIF  C4  C5   single  1.532  0.020  1.532
 KIF  C4  H4   single  0.970  0.020  1.090
 KIF  O4  HO4  single  0.850  0.020  0.980
 KIF  C3  O3   single  1.405  0.020  1.405
 KIF  C3  C2   single  1.532  0.020  1.532
 KIF  C3  H3   single  0.970  0.020  1.090
 KIF  O3  HO3  single  0.850  0.020  0.980
 KIF  C2  O2   single  1.407  0.020  1.407
 KIF  C2  C1   single  1.524  0.020  1.524
 KIF  C2  H2   single  0.970  0.020  1.090
 KIF  O2  HO2  single  0.850  0.020  0.980
 KIF  C1  N9   single  1.437  0.020  1.437
 KIF  C1  N    single  1.443  0.020  1.443
 KIF  C1  H1   single  0.970  0.020  1.090
 KIF  N9  C8   single  1.338  0.020  1.338
 KIF  N9  H9   single  0.860  0.020  1.020
 KIF  C8  O8   double  1.212  0.020  1.212
 KIF  C8  C7   single  1.526  0.020  1.526
 KIF  C7  O7   double  1.212  0.020  1.212
 KIF  C7  N    single  1.340  0.020  1.340
 KIF  N   C5   single  1.447  0.020  1.447
 KIF  C5  C6   single  1.523  0.020  1.523
 KIF  C5  H5   single  0.970  0.020  1.090
 KIF  C6  O6   single  1.407  0.020  1.407
 KIF  C6  H61  single  0.970  0.020  1.090
 KIF  C6  H62  single  0.970  0.020  1.090
 KIF  O6  HO6  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
 KIF  H4   C4  C5   108.17  3.000
 KIF  H4   C4  C3   108.39  3.000
 KIF  C5   C4  C3   113.24  3.000
 KIF  H4   C4  O4   111.18  3.000
 KIF  C5   C4  O4   106.21  3.000
 KIF  C3   C4  O4   109.67  3.000
 KIF  HO4  O4  C4   108.62  3.000
 KIF  H3   C3  C2   107.86  3.000
 KIF  H3   C3  O3   110.37  3.000
 KIF  C2   C3  O3   111.26  3.000
 KIF  H3   C3  C4   107.65  3.000
 KIF  C2   C3  C4   111.25  3.000
 KIF  O3   C3  C4   108.39  3.000
 KIF  HO3  O3  C3   107.88  3.000
 KIF  H2   C2  C1   107.84  3.000
 KIF  H2   C2  O2   111.85  3.000
 KIF  C1   C2  O2   106.85  3.000
 KIF  H2   C2  C3   108.91  3.000
 KIF  C1   C2  C3   109.88  3.000
 KIF  O2   C2  C3   111.42  3.000
 KIF  HO2  O2  C2   108.88  3.000
 KIF  H1   C1  N    111.07  3.000
 KIF  H1   C1  N9   110.18  3.000
 KIF  N    C1  N9   102.32  3.000
 KIF  H1   C1  C2   110.16  3.000
 KIF  N    C1  C2   109.39  3.000
 KIF  N9   C1  C2   113.50  3.000
 KIF  H9   N9  C8   124.34  3.000
 KIF  H9   N9  C1   122.02  3.000
 KIF  C8   N9  C1   113.59  3.000
 KIF  C7   C8  O8   125.31  3.000
 KIF  C7   C8  N9   105.32  3.000
 KIF  O8   C8  N9   129.38  3.000
 KIF  N    C7  O7   129.01  3.000
 KIF  N    C7  C8   105.75  3.000
 KIF  O7   C7  C8   125.24  3.000
 KIF  C5   N   C7   126.36  3.000
 KIF  C5   N   C1   120.43  3.000
 KIF  C7   N   C1   113.01  3.000
 KIF  H5   C5  C6   106.92  3.000
 KIF  H5   C5  N    106.72  3.000
 KIF  C6   C5  N    111.78  3.000
 KIF  H5   C5  C4   107.10  3.000
 KIF  C6   C5  C4   114.38  3.000
 KIF  N    C5  C4   109.53  3.000
 KIF  H62  C6  H61  106.91  3.000
 KIF  H62  C6  O6   111.98  3.000
 KIF  H61  C6  O6   111.81  3.000
 KIF  H62  C6  C5   107.49  3.000
 KIF  H61  C6  C5   111.28  3.000
 KIF  O6   C6  C5   107.33  3.000
 KIF  HO6  O6  C6   108.08  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
 KIF  CONST_01  C7  C8  N9  C1    0.00  0.0  0
 KIF  CONST_02  C8  C7  N   C1    0.00  0.0  0
 KIF  CONST_03  C5  N   C7  C8  180.00  0.0  0
 KIF  CONST_04  O8  C8  N9  C1  180.00  0.0  0
 KIF  CONST_05  O7  C7  N   C1  180.00  0.0  0
 KIF  CONST_06  C5  N   C7  O7    0.00  0.0  0
 KIF  CONST_07  H9  N9  C8  C7  180.00  0.0  0

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
 KIF  chir_01  C4  O4  C3  C5  negativ
 KIF  chir_02  C3  O3  C4  C2  negativ
 KIF  chir_03  C2  O2  C3  C1  negativ
 KIF  chir_04  C1  N9  N   C2  negativ
 KIF  chir_05  C5  N   C6  C4  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 KIF  plan-1  C1  0.020
 KIF  plan-1  N9  0.020
 KIF  plan-1  C8  0.020
 KIF  plan-1  O8  0.020
 KIF  plan-1  C7  0.020
 KIF  plan-1  O7  0.020
 KIF  plan-1  N   0.020
 KIF  plan-1  C5  0.020
 KIF  plan-1  H9  0.020

