# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:37:08 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-2-(2-methoxy-2-oxoethyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Cc1[nH]c2[C@H](O)[C@@H](O)[C@H](O)[C@@H](CO)[n+]2c1
#
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
 GI2  GI2  (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-2-(2-methoxy-2-oxoethyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  36  19  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GI2
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
 GI2  C1    C  CH2   0  -0.703  -0.7848   5.4220  -0.0510
 GI2  C2    C  C     0   0.616   0.6385   5.6971  -0.4877
 GI2  C4    C  CH3   0  -0.426   2.0615   7.3469  -1.3736
 GI2  C1B   C  CR56  0   0.650  -1.0066   1.8806   0.6710
 GI2  C2B   C  CR16  0  -0.056  -0.9822   0.4411   0.2877
 GI2  C3B   C  CR16  0   0.028  -1.5737  -0.3750   1.4307
 GI2  C4B   C  CR16  0  -0.026  -0.9361   0.0655   2.7520
 GI2  C5B   C  CR16  0  -0.119  -1.3236   1.5107   3.0912
 GI2  C6B   C  CH2   0  -0.225  -0.5595   2.0787   4.2835
 GI2  O2B   O  OH1   0  -0.653  -1.6787   0.3190  -0.9172
 GI2  O3B   O  OH1   0  -0.662  -1.3074  -1.7167   1.1483
 GI2  O4B   O  OH1   0  -0.662  -1.4104  -0.7782   3.7672
 GI2  N1B   N  N     1  -0.472  -1.1172   2.3500   1.9048
 GI2  O6B   O  OH1   0  -0.655   0.8030   2.2706   4.0171
 GI2  N2B   N  NR15  0  -0.634  -0.8870   2.9122  -0.1484
 GI2  C7B   C  CR5   0   0.321  -0.9205   4.0828   0.5654
 GI2  C8B   C  CR15  0  -0.109  -1.0663   3.7236   1.8628
 GI2  O1    O  O2    0  -0.446   0.7693   6.9383  -0.9146
 GI2  O5    O  O     0  -0.436   1.5255   4.8845  -0.4608
 GI2  H1C1  H  HCH2  0   0.327  -1.1071   6.1840   0.6598
 GI2  H1C2  H  HCH2  0   0.328  -1.4414   5.5160  -0.9209
 GI2  H4C1  H  HCH3  0   0.257   1.9597   8.3896  -1.6575
 GI2  H4C2  H  HCH3  0   0.244   2.3750   6.7640  -2.2388
 GI2  H4C3  H  HCH3  0   0.244   2.8075   7.2555  -0.5854
 GI2  H2B   H  HCR6  0   0.291   0.0728   0.1537   0.1700
 GI2  HA    H  HNR5  0   0.453  -0.7927   2.8298  -1.1521
 GI2  H3B   H  HCR6  0   0.241  -2.6567  -0.1793   1.4798
 GI2  HB    H  HOH1  0   0.476  -1.3272  -0.4344  -1.4017
 GI2  H4B   H  HCR6  0   0.253   0.1549  -0.0120   2.6461
 GI2  HC    H  HOH1  0   0.459  -1.6803  -2.2542   1.8557
 GI2  H5B   H  HCR6  0   0.308  -2.3914   1.5391   3.3262
 GI2  HD    H  HOH1  0   0.472  -0.6850  -1.0360   4.3421
 GI2  H6B1  H  HCH2  0   0.257  -0.7400   1.4182   5.1375
 GI2  H6B2  H  HCH2  0   0.260  -0.9836   3.0463   4.5562
 GI2  H6B   H  HOH1  0   0.461   1.2769   1.4446   4.1477
 GI2  H8B   H  HCR5  0   0.338  -1.1413   4.3423   2.7394

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
 GI2  C1   C2    single    1.514  0.020  1.514
 GI2  C1   C7B   single    1.480  0.020  1.480
 GI2  C1   H1C1  single    0.970  0.020  1.090
 GI2  C1   H1C2  single    0.970  0.020  1.090
 GI2  C2   O1    single    1.319  0.020  1.319
 GI2  C2   O5    double    1.203  0.020  1.203
 GI2  C4   O1    single    1.431  0.020  1.431
 GI2  C4   H4C1  single    0.970  0.020  1.090
 GI2  C4   H4C2  single    0.970  0.020  1.090
 GI2  C4   H4C3  single    0.970  0.020  1.090
 GI2  C1B  C2B   single    1.490  0.020  1.490
 GI2  C1B  N1B   aromatic  1.325  0.020  1.325
 GI2  C1B  N2B   aromatic  1.323  0.020  1.323
 GI2  C2B  C3B   single    1.524  0.020  1.524
 GI2  C2B  O2B   single    1.397  0.020  1.397
 GI2  C2B  H2B   single    0.970  0.020  1.090
 GI2  C3B  C4B   single    1.532  0.020  1.532
 GI2  C3B  O3B   single    1.397  0.020  1.397
 GI2  C3B  H3B   single    0.970  0.020  1.090
 GI2  C4B  C5B   single    1.534  0.020  1.534
 GI2  C4B  O4B   single    1.403  0.020  1.403
 GI2  C4B  H4B   single    0.970  0.020  1.090
 GI2  C5B  C6B   single    1.526  0.020  1.526
 GI2  C5B  N1B   single    1.468  0.020  1.468
 GI2  C5B  H5B   single    0.970  0.020  1.090
 GI2  C6B  O6B   single    1.401  0.020  1.401
 GI2  C6B  H6B1  single    0.970  0.020  1.090
 GI2  C6B  H6B2  single    0.970  0.020  1.090
 GI2  O2B  HB    single    0.850  0.020  0.980
 GI2  O3B  HC    single    0.850  0.020  0.980
 GI2  O4B  HD    single    0.850  0.020  0.980
 GI2  N1B  C8B   aromatic  1.375  0.020  1.375
 GI2  O6B  H6B   single    0.850  0.020  0.980
 GI2  N2B  C7B   aromatic  1.372  0.020  1.372
 GI2  N2B  HA    single    0.860  0.020  1.020
 GI2  C7B  C8B   aromatic  1.354  0.020  1.354
 GI2  C8B  H8B   single    0.930  0.020  1.080

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
 GI2  H1C2  C1   H1C1  106.31  3.000
 GI2  H1C2  C1   C7B   110.72  3.000
 GI2  H1C1  C1   C7B   109.48  3.000
 GI2  H1C2  C1   C2    108.62  3.000
 GI2  H1C1  C1   C2    109.80  3.000
 GI2  C7B   C1   C2    111.76  3.000
 GI2  O5    C2   O1    124.72  3.000
 GI2  O5    C2   C1    124.32  3.000
 GI2  O1    C2   C1    110.95  3.000
 GI2  H4C3  C4   H4C2  109.43  3.000
 GI2  H4C3  C4   H4C1  109.52  3.000
 GI2  H4C2  C4   H4C1  109.46  3.000
 GI2  H4C3  C4   O1    111.25  3.000
 GI2  H4C2  C4   O1    111.22  3.000
 GI2  H4C1  C4   O1    105.87  3.000
 GI2  N2B   C1B  N1B   107.95  3.000
 GI2  N2B   C1B  C2B   126.34  3.000
 GI2  N1B   C1B  C2B   125.69  3.000
 GI2  H2B   C2B  O2B   111.29  3.000
 GI2  H2B   C2B  C3B   108.22  3.000
 GI2  O2B   C2B  C3B   113.99  3.000
 GI2  H2B   C2B  C1B   107.20  3.000
 GI2  O2B   C2B  C1B   107.35  3.000
 GI2  C3B   C2B  C1B   108.55  3.000
 GI2  H3B   C3B  O3B   111.54  3.000
 GI2  H3B   C3B  C4B   108.64  3.000
 GI2  O3B   C3B  C4B   111.80  3.000
 GI2  H3B   C3B  C2B   108.66  3.000
 GI2  O3B   C3B  C2B   106.79  3.000
 GI2  C4B   C3B  C2B   109.35  3.000
 GI2  H4B   C4B  O4B   111.29  3.000
 GI2  H4B   C4B  C5B   109.79  3.000
 GI2  O4B   C4B  C5B   108.73  3.000
 GI2  H4B   C4B  C3B   108.05  3.000
 GI2  O4B   C4B  C3B   108.09  3.000
 GI2  C5B   C4B  C3B   110.88  3.000
 GI2  H5B   C5B  N1B   107.22  3.000
 GI2  H5B   C5B  C6B   108.14  3.000
 GI2  N1B   C5B  C6B   110.38  3.000
 GI2  H5B   C5B  C4B   108.58  3.000
 GI2  N1B   C5B  C4B   108.93  3.000
 GI2  C6B   C5B  C4B   113.39  3.000
 GI2  H6B2  C6B  H6B1  106.02  3.000
 GI2  H6B2  C6B  O6B   107.69  3.000
 GI2  H6B1  C6B  O6B   113.03  3.000
 GI2  H6B2  C6B  C5B   109.31  3.000
 GI2  H6B1  C6B  C5B   107.61  3.000
 GI2  O6B   C6B  C5B   112.91  3.000
 GI2  HB    O2B  C2B   108.70  3.000
 GI2  HC    O3B  C3B   108.28  3.000
 GI2  HD    O4B  C4B   109.83  3.000
 GI2  C8B   N1B  C5B   126.95  3.000
 GI2  C8B   N1B  C1B   108.81  3.000
 GI2  C5B   N1B  C1B   124.19  3.000
 GI2  H6B   O6B  C6B   109.62  3.000
 GI2  HA    N2B  C7B   126.04  3.000
 GI2  HA    N2B  C1B   124.03  3.000
 GI2  C7B   N2B  C1B   109.94  3.000
 GI2  C8B   C7B  N2B   105.95  3.000
 GI2  C8B   C7B  C1    130.45  3.000
 GI2  N2B   C7B  C1    123.58  3.000
 GI2  H8B   C8B  C7B   129.48  3.000
 GI2  H8B   C8B  N1B   123.17  3.000
 GI2  C7B   C8B  N1B   107.36  3.000
 GI2  C4    O1   C2    117.52  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
 GI2  CONST_01  C7B   C8B  N1B  C1B     0.00   0.0  0
 GI2  CONST_02  C8B   C7B  N2B  C1B     0.00   0.0  0
 GI2  CONST_03  C7B   N2B  C1B  N1B     0.00   0.0  0
 GI2  CONST_04  N2B   C7B  C8B  N1B     0.00   0.0  0
 GI2  CONST_05  C8B   N1B  C1B  N2B     0.00   0.0  0
 GI2  CONST_06  C1B   N2B  C7B  C1    180.00   0.0  0
 GI2  CONST_07  N1B   C8B  C7B  C1    180.00   0.0  0
 GI2  CONST_08  H8B   C8B  N1B  C1B   180.00   0.0  0
 GI2  CONST_09  HA    N2B  C1B  C2B     0.00   0.0  0
 GI2  Var_01    N2B   C7B  C1   C2    -73.25  30.0  2
 GI2  Var_02    O1    C2   C1   C7B  -173.91  30.0  3
 GI2  Var_03    H4C1  C4   O1   C2   -178.95  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
 GI2  chir_01  C2B  C1B  C3B  O2B  negativ
 GI2  chir_02  C3B  O3B  C2B  C4B  positiv
 GI2  chir_03  C4B  O4B  C3B  C5B  negativ
 GI2  chir_04  C5B  N1B  C4B  C6B  negativ

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
 GI2  plan-1  C1   0.020
 GI2  plan-1  C2   0.020
 GI2  plan-1  O1   0.020
 GI2  plan-1  O5   0.020
 GI2  plan-2  C1   0.020
 GI2  plan-2  C1B  0.020
 GI2  plan-2  C2B  0.020
 GI2  plan-2  C5B  0.020
 GI2  plan-2  N1B  0.020
 GI2  plan-2  N2B  0.020
 GI2  plan-2  C7B  0.020
 GI2  plan-2  C8B  0.020
 GI2  plan-2  HA   0.020
 GI2  plan-2  H8B  0.020

