# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:45:05 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (5R,6R,7S,8S)-2-(carboxymethyl)-6,7,8-trihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)c2[nH]c(CC(O)=O)c[n+]12
#
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
 GI4  GI4  (5R,6R,7S,8S)-2-(carboxymethyl)-6,7,8-trihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  33  18  .  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_GI4
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
 GI4  C1    C  CH2   0  -0.703  -0.7805   5.2660  -0.3030
 GI4  C1B   C  CR56  0   0.651  -1.0119   1.7717   0.6222
 GI4  C2B   C  CR16  0  -0.057  -1.0756   0.3137   0.3229
 GI4  C3B   C  CR16  0   0.028  -1.7468  -0.3753   1.5052
 GI4  C4B   C  CR16  0  -0.017  -1.0425   0.0576   2.7941
 GI4  C5B   C  CR16  0  -0.128  -1.2467   1.5513   3.0759
 GI4  C6B   C  CH2   0  -0.216  -0.3087   2.0689   4.1629
 GI4  O2B   O  OH1   0  -0.654  -1.7585   0.1708  -0.8865
 GI4  O3B   O  OH1   0  -0.663  -1.6315  -1.7512   1.2934
 GI4  O4B   O  OH1   0  -0.664  -1.5798  -0.6636   3.8724
 GI4  N1B   N  N     1  -0.480  -1.0631   2.3102   1.8317
 GI4  O6B   O  OH1   0  -0.651   1.0457   1.9102   3.8375
 GI4  N2B   N  NR15  0  -0.633  -0.9042   2.7544  -0.2566
 GI4  C7B   C  CR5   0   0.334  -0.8838   3.9631   0.3918
 GI4  C8B   C  CR15  0  -0.134  -0.9869   3.6795   1.7119
 GI4  C2    C  C     0   0.569   0.5797   5.4741  -0.9295
 GI4  O1    O  O     0  -0.427   1.4569   4.6508  -0.9362
 GI4  O5    O  OH1   0  -0.584   0.6746   6.6744  -1.4754
 GI4  H1C1  H  HCH2  0   0.331  -0.9799   6.0702   0.4076
 GI4  H1C2  H  HCH2  0   0.331  -1.5436   5.3521  -1.0823
 GI4  H2B   H  HCR6  0   0.293  -0.0422  -0.0553   0.2476
 GI4  HA    H  HNR5  0   0.454  -0.8526   2.6148  -1.2575
 GI4  H3B   H  HCR6  0   0.239  -2.8011  -0.0587   1.5474
 GI4  HB    H  HOH1  0   0.477  -1.4641  -0.6397  -1.3137
 GI4  H4B   H  HCR6  0   0.259   0.0303  -0.1400   2.6804
 GI4  HC    H  HOH1  0   0.458  -2.0527  -2.2061   2.0311
 GI4  H5B   H  HCR6  0   0.311  -2.2780   1.7161   3.4001
 GI4  HD    H  HOH1  0   0.472  -0.8697  -1.1025   4.3481
 GI4  H6B1  H  HCH2  0   0.265  -0.5110   1.4877   5.0638
 GI4  H6B2  H  HCH2  0   0.249  -0.5576   3.1069   4.4084
 GI4  H6B   H  HOH1  0   0.458   1.3159   2.6144   3.2408
 GI4  H8B   H  HCR5  0   0.345  -1.0292   4.3440   2.5573
 GI4  H5    H  HOH1  0   0.488   1.5457   6.7898  -1.8850

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
 GI4  C1   C7B   single    1.480  0.020  1.480
 GI4  C1   C2    single    1.512  0.020  1.512
 GI4  C1   H1C1  single    0.970  0.020  1.090
 GI4  C1   H1C2  single    0.970  0.020  1.090
 GI4  C1B  C2B   single    1.490  0.020  1.490
 GI4  C1B  N1B   aromatic  1.325  0.020  1.325
 GI4  C1B  N2B   aromatic  1.323  0.020  1.323
 GI4  C2B  C3B   single    1.524  0.020  1.524
 GI4  C2B  O2B   single    1.396  0.020  1.396
 GI4  C2B  H2B   single    0.970  0.020  1.090
 GI4  C3B  C4B   single    1.531  0.020  1.531
 GI4  C3B  O3B   single    1.397  0.020  1.397
 GI4  C3B  H3B   single    0.970  0.020  1.090
 GI4  C4B  C5B   single    1.534  0.020  1.534
 GI4  C4B  O4B   single    1.404  0.020  1.404
 GI4  C4B  H4B   single    0.970  0.020  1.090
 GI4  C5B  C6B   single    1.526  0.020  1.526
 GI4  C5B  N1B   single    1.469  0.020  1.469
 GI4  C5B  H5B   single    0.970  0.020  1.090
 GI4  C6B  O6B   single    1.402  0.020  1.402
 GI4  C6B  H6B1  single    0.970  0.020  1.090
 GI4  C6B  H6B2  single    0.970  0.020  1.090
 GI4  O2B  HB    single    0.850  0.020  0.980
 GI4  O3B  HC    single    0.850  0.020  0.980
 GI4  O4B  HD    single    0.850  0.020  0.980
 GI4  N1B  C8B   aromatic  1.377  0.020  1.377
 GI4  O6B  H6B   single    0.850  0.020  0.980
 GI4  N2B  C7B   aromatic  1.372  0.020  1.372
 GI4  N2B  HA    single    0.860  0.020  1.020
 GI4  C7B  C8B   aromatic  1.354  0.020  1.354
 GI4  C8B  H8B   single    0.930  0.020  1.080
 GI4  C2   O1    double    1.203  0.020  1.203
 GI4  C2   O5    single    1.322  0.020  1.322
 GI4  O5   H5    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
 GI4  H1C2  C1   H1C1  106.16  3.000
 GI4  H1C2  C1   C2    108.75  3.000
 GI4  H1C1  C1   C2    109.44  3.000
 GI4  H1C2  C1   C7B   110.78  3.000
 GI4  H1C1  C1   C7B   109.28  3.000
 GI4  C2    C1   C7B   112.24  3.000
 GI4  N2B   C1B  N1B   107.92  3.000
 GI4  N2B   C1B  C2B   126.66  3.000
 GI4  N1B   C1B  C2B   125.41  3.000
 GI4  H2B   C2B  O2B   111.46  3.000
 GI4  H2B   C2B  C3B   108.37  3.000
 GI4  O2B   C2B  C3B   114.22  3.000
 GI4  H2B   C2B  C1B   107.57  3.000
 GI4  O2B   C2B  C1B   107.16  3.000
 GI4  C3B   C2B  C1B   107.78  3.000
 GI4  H3B   C3B  O3B   111.59  3.000
 GI4  H3B   C3B  C4B   109.07  3.000
 GI4  O3B   C3B  C4B   111.60  3.000
 GI4  H3B   C3B  C2B   108.74  3.000
 GI4  O3B   C3B  C2B   106.93  3.000
 GI4  C4B   C3B  C2B   108.82  3.000
 GI4  H4B   C4B  O4B   111.18  3.000
 GI4  H4B   C4B  C5B   108.95  3.000
 GI4  O4B   C4B  C5B   107.95  3.000
 GI4  H4B   C4B  C3B   108.16  3.000
 GI4  O4B   C4B  C3B   108.98  3.000
 GI4  C5B   C4B  C3B   111.64  3.000
 GI4  H5B   C5B  N1B   106.93  3.000
 GI4  H5B   C5B  C6B   108.50  3.000
 GI4  N1B   C5B  C6B   110.56  3.000
 GI4  H5B   C5B  C4B   109.07  3.000
 GI4  N1B   C5B  C4B   109.32  3.000
 GI4  C6B   C5B  C4B   112.29  3.000
 GI4  H6B2  C6B  H6B1  106.12  3.000
 GI4  H6B2  C6B  O6B   112.26  3.000
 GI4  H6B1  C6B  O6B   108.09  3.000
 GI4  H6B2  C6B  C5B   109.96  3.000
 GI4  H6B1  C6B  C5B   107.07  3.000
 GI4  O6B   C6B  C5B   112.96  3.000
 GI4  HB    O2B  C2B   108.73  3.000
 GI4  HC    O3B  C3B   108.23  3.000
 GI4  HD    O4B  C4B   109.40  3.000
 GI4  C8B   N1B  C5B   126.48  3.000
 GI4  C8B   N1B  C1B   108.82  3.000
 GI4  C5B   N1B  C1B   124.62  3.000
 GI4  H6B   O6B  C6B   109.42  3.000
 GI4  HA    N2B  C7B   126.04  3.000
 GI4  HA    N2B  C1B   123.98  3.000
 GI4  C7B   N2B  C1B   109.98  3.000
 GI4  C8B   C7B  N2B   105.97  3.000
 GI4  C8B   C7B  C1    130.33  3.000
 GI4  N2B   C7B  C1    123.70  3.000
 GI4  H8B   C8B  C7B   129.75  3.000
 GI4  H8B   C8B  N1B   122.93  3.000
 GI4  C7B   C8B  N1B   107.30  3.000
 GI4  O5    C2   O1    124.53  3.000
 GI4  O5    C2   C1    111.14  3.000
 GI4  O1    C2   C1    124.34  3.000
 GI4  H5    O5   C2    110.30  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
 GI4  CONST_01  C7B  C8B  N1B  C1B    0.00   0.0  0
 GI4  CONST_02  C8B  C7B  N2B  C1B    0.00   0.0  0
 GI4  CONST_03  C7B  N2B  C1B  N1B    0.00   0.0  0
 GI4  CONST_04  N2B  C7B  C8B  N1B    0.00   0.0  0
 GI4  CONST_05  C8B  N1B  C1B  N2B    0.00   0.0  0
 GI4  CONST_06  C1B  N2B  C7B  C1   180.00   0.0  0
 GI4  CONST_07  N1B  C8B  C7B  C1   180.00   0.0  0
 GI4  CONST_08  H8B  C8B  N1B  C1B  180.00   0.0  0
 GI4  CONST_09  HA   N2B  C1B  C2B    0.00   0.0  0
 GI4  CONST_10  H5   O5   C2   C1   180.00   0.0  0
 GI4  Var_01    C2   C1   C7B  N2B  -69.38  30.0  2
 GI4  Var_02    O1   C2   C1   C7B    4.10  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
 GI4  chir_01  C2B  C1B  C3B  O2B  negativ
 GI4  chir_02  C3B  O3B  C2B  C4B  positiv
 GI4  chir_03  C4B  O4B  C3B  C5B  negativ
 GI4  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
 GI4  plan-1  C1   0.020
 GI4  plan-1  C2   0.020
 GI4  plan-1  O1   0.020
 GI4  plan-1  O5   0.020
 GI4  plan-1  H5   0.020
 GI4  plan-2  C1   0.020
 GI4  plan-2  C1B  0.020
 GI4  plan-2  C2B  0.020
 GI4  plan-2  C5B  0.020
 GI4  plan-2  N1B  0.020
 GI4  plan-2  N2B  0.020
 GI4  plan-2  C7B  0.020
 GI4  plan-2  C8B  0.020
 GI4  plan-2  HA   0.020
 GI4  plan-2  H8B  0.020

