# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:56:56 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (5R,6R,7S,8S)-6,7,8-trihydroxy-2-[(S)-hydroxy(methoxy)methyl]-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: CO[C@H](O)c1[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
 GI1  GI1  (5R,6R,7S,8S)-6,7,8-trihydroxy-2-[(S)-hydroxy(methoxy)methyl]-5-(hydroxymethyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  35  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_GI1
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
 GI1  C1    C  CR56  0   0.657  -1.3250   1.8152   0.6653
 GI1  C2    C  CR16  0  -0.057  -1.4667   0.3738   0.3197
 GI1  O2    O  OH1   0  -0.653  -2.4012   0.2958  -0.7143
 GI1  C3    C  CR16  0   0.021  -1.8649  -0.3718   1.5882
 GI1  O3    O  OH1   0  -0.663  -1.8099  -1.7356   1.2879
 GI1  C4    C  CR16  0  -0.017  -0.8897   0.0011   2.7088
 GI1  C80   C  CR15  0  -0.121  -1.0467   3.6680   1.8157
 GI1  N10   N  N     1  -0.481  -1.1147   2.2951   1.8828
 GI1  O4    O  OH1   0  -0.664  -1.1734  -0.7649   3.8505
 GI1  C5    C  CR16  0  -0.125  -1.0246   1.4775   3.1000
 GI1  C6    C  CH2   0  -0.216   0.1259   1.9528   3.9819
 GI1  O6    O  OH1   0  -0.652   1.3768   1.8311   3.3610
 GI1  N1    N  NR15  0  -0.635  -1.3904   2.8383  -0.1706
 GI1  C7    C  CR5   0   0.207  -1.2175   4.0097   0.5167
 GI1  C8    C  CH1   0   0.263  -1.2854   5.3618  -0.1279
 GI1  O8    O  OH1   0  -0.638  -0.7335   6.3302   0.6940
 GI1  O9    O  O2    0  -0.497  -0.6667   5.2298  -1.3631
 GI1  H2    H  HCR6  0   0.290  -0.4793   0.0081  -0.0009
 GI1  H1    H  HNR5  0   0.453  -1.5337   2.7552  -1.1692
 GI1  HA    H  HOH1  0   0.475  -2.3186  -0.5643  -1.1391
 GI1  H3    H  HCR6  0   0.243  -2.8816  -0.0612   1.8768
 GI1  HB    H  HOH1  0   0.460  -2.1412  -2.2273   2.0469
 GI1  H4    H  HCR6  0   0.258   0.1324  -0.1822   2.3537
 GI1  HC    H  HOH1  0   0.471  -0.4130  -1.3117   4.0639
 GI1  H5    H  HCR6  0   0.311  -1.9613   1.6135   3.6476
 GI1  H80   H  HCR5  0   0.347  -0.9099   4.2866   2.6857
 GI1  H6C1  H  HCH2  0   0.266   0.1268   1.3205   4.8706
 GI1  H6C2  H  HCH2  0   0.249  -0.0680   2.9723   4.3320
 GI1  H6    H  HOH1  0   0.458   1.5224   2.5825   2.7788
 GI1  H8    H  HCH1  0   0.248  -2.3378   5.6519  -0.2513
 GI1  HD    H  HOH1  0   0.460   0.1964   6.1261   0.8588
 GI1  H9C1  H  HCH3  0   0.221  -1.9924   6.4518  -2.4046
 GI1  H9C2  H  HCH3  0   0.247  -0.4730   6.0268  -3.2141
 GI1  H9C3  H  HCH3  0   0.225  -0.4734   7.2346  -1.9191
 GI1  C9    C  CH3   0  -0.413  -0.9187   6.2977  -2.2597

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
 GI1  C1   C2    single    1.489  0.020  1.489
 GI1  C1   N10   aromatic  1.325  0.020  1.325
 GI1  C1   N1    aromatic  1.323  0.020  1.323
 GI1  C2   O2    single    1.396  0.020  1.396
 GI1  C2   C3    single    1.524  0.020  1.524
 GI1  C2   H2    single    0.970  0.020  1.090
 GI1  O2   HA    single    0.850  0.020  0.980
 GI1  C3   O3    single    1.398  0.020  1.398
 GI1  C3   C4    single    1.532  0.020  1.532
 GI1  C3   H3    single    0.970  0.020  1.090
 GI1  O3   HB    single    0.850  0.020  0.980
 GI1  C4   O4    single    1.404  0.020  1.404
 GI1  C4   C5    single    1.533  0.020  1.533
 GI1  C4   H4    single    0.970  0.020  1.090
 GI1  C80  N10   aromatic  1.376  0.020  1.376
 GI1  C80  C7    aromatic  1.354  0.020  1.354
 GI1  C80  H80   single    0.930  0.020  1.080
 GI1  N10  C5    single    1.469  0.020  1.469
 GI1  O4   HC    single    0.850  0.020  0.980
 GI1  C5   C6    single    1.526  0.020  1.526
 GI1  C5   H5    single    0.970  0.020  1.090
 GI1  C6   O6    single    1.402  0.020  1.402
 GI1  C6   H6C1  single    0.970  0.020  1.090
 GI1  C6   H6C2  single    0.970  0.020  1.090
 GI1  O6   H6    single    0.850  0.020  0.980
 GI1  N1   C7    aromatic  1.369  0.020  1.369
 GI1  N1   H1    single    0.860  0.020  1.020
 GI1  C7   C8    single    1.499  0.020  1.499
 GI1  C8   O8    single    1.385  0.020  1.385
 GI1  C8   O9    single    1.388  0.020  1.388
 GI1  C8   H8    single    0.970  0.020  1.090
 GI1  O8   HD    single    0.850  0.020  0.980
 GI1  C9   O9    single    1.417  0.020  1.417
 GI1  C9   H9C1  single    0.970  0.020  1.090
 GI1  C9   H9C2  single    0.970  0.020  1.090
 GI1  C9   H9C3  single    0.970  0.020  1.090

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
 GI1  N1    C1   N10   107.95  3.000
 GI1  N1    C1   C2    126.69  3.000
 GI1  N10   C1   C2    125.36  3.000
 GI1  H2    C2   C3    108.32  3.000
 GI1  H2    C2   O2    111.49  3.000
 GI1  C3    C2   O2    114.47  3.000
 GI1  H2    C2   C1    107.69  3.000
 GI1  C3    C2   C1    107.77  3.000
 GI1  O2    C2   C1    106.84  3.000
 GI1  HA    O2   C2    108.62  3.000
 GI1  H3    C3   C4    109.11  3.000
 GI1  H3    C3   O3    111.57  3.000
 GI1  C4    C3   O3    111.70  3.000
 GI1  H3    C3   C2    108.74  3.000
 GI1  C4    C3   C2    108.87  3.000
 GI1  O3    C3   C2    106.75  3.000
 GI1  HB    O3   C3    108.38  3.000
 GI1  H4    C4   C5    108.99  3.000
 GI1  H4    C4   O4    111.11  3.000
 GI1  C5    C4   O4    107.46  3.000
 GI1  H4    C4   C3    108.40  3.000
 GI1  C5    C4   C3    111.41  3.000
 GI1  O4    C4   C3    109.48  3.000
 GI1  H80   C80  C7    130.28  3.000
 GI1  H80   C80  N10   122.70  3.000
 GI1  C7    C80  N10   106.99  3.000
 GI1  C5    N10  C80   126.34  3.000
 GI1  C5    N10  C1    124.70  3.000
 GI1  C80   N10  C1    108.92  3.000
 GI1  HC    O4   C4    109.35  3.000
 GI1  H5    C5   C6    108.53  3.000
 GI1  H5    C5   N10   107.05  3.000
 GI1  C6    C5   N10   110.60  3.000
 GI1  H5    C5   C4    108.84  3.000
 GI1  C6    C5   C4    112.40  3.000
 GI1  N10   C5   C4    109.26  3.000
 GI1  H6C2  C6   H6C1  106.22  3.000
 GI1  H6C2  C6   O6    112.36  3.000
 GI1  H6C1  C6   O6    108.05  3.000
 GI1  H6C2  C6   C5    109.96  3.000
 GI1  H6C1  C6   C5    106.92  3.000
 GI1  O6    C6   C5    112.95  3.000
 GI1  H6    O6   C6    109.60  3.000
 GI1  H1    N1   C7    125.69  3.000
 GI1  H1    N1   C1    124.53  3.000
 GI1  C7    N1   C1    109.78  3.000
 GI1  C8    C7   N1    123.37  3.000
 GI1  C8    C7   C80   130.21  3.000
 GI1  N1    C7   C80   106.36  3.000
 GI1  H8    C8   O9    110.62  3.000
 GI1  H8    C8   O8    105.29  3.000
 GI1  O9    C8   O8    114.65  3.000
 GI1  H8    C8   C7    109.26  3.000
 GI1  O9    C8   C7    106.06  3.000
 GI1  O8    C8   C7    110.94  3.000
 GI1  HD    O8   C8    109.70  3.000
 GI1  C9    O9   C8    114.34  3.000
 GI1  H9C3  C9   H9C2  108.68  3.000
 GI1  H9C3  C9   H9C1  108.70  3.000
 GI1  H9C2  C9   H9C1  108.72  3.000
 GI1  H9C3  C9   O9    112.14  3.000
 GI1  H9C2  C9   O9    107.13  3.000
 GI1  H9C1  C9   O9    111.37  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
 GI1  CONST_01  C7    C80  N10  C1     0.00   0.0  0
 GI1  CONST_02  C80   C7   N1   C1     0.00   0.0  0
 GI1  CONST_03  N1    C1   N10  C80    0.00   0.0  0
 GI1  CONST_04  C7    N1   C1   N10    0.00   0.0  0
 GI1  CONST_05  N1    C7   C80  N10    0.00   0.0  0
 GI1  CONST_06  C8    C7   N1   C1   180.00   0.0  0
 GI1  CONST_07  C8    C7   C80  N10  180.00   0.0  0
 GI1  CONST_08  H80   C80  N10  C1   180.00   0.0  0
 GI1  CONST_09  H1    N1   C1   C2     0.00   0.0  0
 GI1  Var_01    H9C1  C9   O9   C8   -55.29  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
 GI1  chir_01  C2  C1   O2  C3  positiv
 GI1  chir_02  C3  O3   C2  C4  positiv
 GI1  chir_03  C4  O4   C5  C3  positiv
 GI1  chir_04  C5  N10  C4  C6  negativ
 GI1  chir_05  C8  O9   O8  C7  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
 GI1  plan-1  C1   0.020
 GI1  plan-1  C2   0.020
 GI1  plan-1  C80  0.020
 GI1  plan-1  N10  0.020
 GI1  plan-1  C5   0.020
 GI1  plan-1  N1   0.020
 GI1  plan-1  C7   0.020
 GI1  plan-1  C8   0.020
 GI1  plan-1  H1   0.020
 GI1  plan-1  H80  0.020

