# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:24:01 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (5R,6R,7S,8S)-2-carboxy-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(c[n+]12)C(O)=O
#
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
 GI3  GI3  (5R,6R,7S,8S)-2-carboxy-6,7,8-trihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  29  17  .  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_GI3
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
 GI3  C1    C  CR5    0   0.659   2.9619  2.3724  -2.2507
 GI3  C2    C  CH1    0  -0.099   3.6329  3.1987  -3.2910
 GI3  O2    O  OH1    0  -0.653   3.5705  2.4435  -4.4818
 GI3  C3    C  CH1    0  -0.045   5.0699  3.4712  -2.8401
 GI3  C80   C  CR15   0  -0.106   2.6645  0.8753  -0.6659
 GI3  O3    O  OH1    0  -0.654   4.9649  4.3740  -1.7719
 GI3  C4    C  CH1    0  -0.027   5.7725  2.1650  -2.4267
 GI3  N10   N  NR5    1  -0.459   3.5938  1.5571  -1.4123
 GI3  O4    O  OH1    0  -0.665   5.9773  1.3245  -3.5341
 GI3  C5    C  CH1    0  -0.170   5.0480  1.4393  -1.2780
 GI3  C6    C  CH2    0  -0.167   5.4565  1.9097   0.1275
 GI3  O6    O  OH1    0  -0.635   6.8267  1.7062   0.3498
 GI3  N1    N  NR15   0  -0.630   1.6641  2.2235  -2.0501
 GI3  C7    C  CR5    0   0.105   1.4378  1.2968  -1.0685
 GI3  C8    C  C      0   0.385   0.0478  0.9129  -0.6234
 GI3  O8    O  OC    -1  -0.566  -0.0020  0.0575   0.2699
 GI3  O9    O  O      0  -0.583  -0.8698  1.5051  -1.2132
 GI3  H2    H  HCH1   0   0.310   3.1017  4.1512  -3.3926
 GI3  H1    H  HNR5   0   0.443   0.9274  2.7077  -2.5472
 GI3  HA    H  HOH1   0   0.483   3.7494  3.0277  -5.2287
 GI3  H3    H  HCH1   0   0.279   5.6203  3.9039  -3.6856
 GI3  HB    H  HOH1   0   0.470   5.8361  4.7347  -1.5770
 GI3  H4    H  HCH1   0   0.274   6.7678  2.4182  -2.0525
 GI3  H80   H  HCR5   0   0.354   2.9429  0.1479   0.0767
 GI3  H5    H  HCH1   0   0.341   5.2820  0.3755  -1.3613
 GI3  HC    H  HOH1   0   0.442   5.1782  1.3149  -4.0764
 GI3  H6C1  H  HCH2   0   0.235   4.8488  1.3840   0.8721
 GI3  H6C2  H  HCH2   0   0.243   5.2600  2.9739   0.2412
 GI3  H6    H  HOH1   0   0.435   6.9867  0.7614   0.4192

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
 GI3  C1   C2    single    1.488  0.020  1.488
 GI3  C1   N10   aromatic  1.329  0.020  1.329
 GI3  C1   N1    aromatic  1.322  0.020  1.322
 GI3  C2   O2    single    1.411  0.020  1.411
 GI3  C2   C3    single    1.531  0.020  1.531
 GI3  C2   H2    single    0.970  0.020  1.090
 GI3  O2   HA    single    0.850  0.020  0.980
 GI3  C3   O3    single    1.403  0.020  1.403
 GI3  C3   C4    single    1.540  0.020  1.540
 GI3  C3   H3    single    0.970  0.020  1.090
 GI3  C80  N10   aromatic  1.373  0.020  1.373
 GI3  C80  C7    aromatic  1.358  0.020  1.358
 GI3  C80  H80   single    0.930  0.020  1.080
 GI3  O3   HB    single    0.850  0.020  0.980
 GI3  C4   O4    single    1.405  0.020  1.405
 GI3  C4   C5    single    1.540  0.020  1.540
 GI3  C4   H4    single    0.970  0.020  1.090
 GI3  N10  C5    single    1.465  0.020  1.465
 GI3  O4   HC    single    0.850  0.020  0.980
 GI3  C5   C6    single    1.537  0.020  1.537
 GI3  C5   H5    single    0.970  0.020  1.090
 GI3  C6   O6    single    1.403  0.020  1.403
 GI3  C6   H6C1  single    0.970  0.020  1.090
 GI3  C6   H6C2  single    0.970  0.020  1.090
 GI3  O6   H6    single    0.850  0.020  0.980
 GI3  N1   C7    aromatic  1.369  0.020  1.369
 GI3  N1   H1    single    0.860  0.020  1.020
 GI3  C7   C8    single    1.509  0.020  1.509
 GI3  C8   O8    deloc     1.238  0.020  1.238
 GI3  C8   O9    deloc     1.241  0.020  1.241

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
 GI3  N1    C1   N10   107.58  3.000
 GI3  N1    C1   C2    127.68  3.000
 GI3  N10   C1   C2    124.54  3.000
 GI3  H2    C2   C3    109.13  3.000
 GI3  H2    C2   O2    111.45  3.000
 GI3  C3    C2   O2    112.67  3.000
 GI3  H2    C2   C1    109.21  3.000
 GI3  C3    C2   C1    108.43  3.000
 GI3  O2    C2   C1    105.83  3.000
 GI3  HA    O2   C2    108.71  3.000
 GI3  H3    C3   C4    108.20  3.000
 GI3  H3    C3   O3    111.74  3.000
 GI3  C4    C3   O3    112.07  3.000
 GI3  H3    C3   C2    108.30  3.000
 GI3  C4    C3   C2    110.88  3.000
 GI3  O3    C3   C2    105.59  3.000
 GI3  H80   C80  C7    130.39  3.000
 GI3  H80   C80  N10   122.39  3.000
 GI3  C7    C80  N10   107.22  3.000
 GI3  HB    O3   C3    109.12  3.000
 GI3  H4    C4   C5    106.39  3.000
 GI3  H4    C4   O4    106.00  3.000
 GI3  C5    C4   O4    112.00  3.000
 GI3  H4    C4   C3    108.11  3.000
 GI3  C5    C4   C3    112.67  3.000
 GI3  O4    C4   C3    111.25  3.000
 GI3  C5    N10  C80   125.59  3.000
 GI3  C5    N10  C1    125.38  3.000
 GI3  C80   N10  C1    109.00  3.000
 GI3  HC    O4   C4    109.13  3.000
 GI3  H5    C5   C6    108.11  3.000
 GI3  H5    C5   N10   106.49  3.000
 GI3  C6    C5   N10   108.84  3.000
 GI3  H5    C5   C4    107.53  3.000
 GI3  C6    C5   C4    114.38  3.000
 GI3  N10   C5   C4    111.14  3.000
 GI3  H6C2  C6   H6C1  107.34  3.000
 GI3  H6C2  C6   O6    107.56  3.000
 GI3  H6C1  C6   O6    111.38  3.000
 GI3  H6C2  C6   C5    110.29  3.000
 GI3  H6C1  C6   C5    109.09  3.000
 GI3  O6    C6   C5    111.10  3.000
 GI3  H6    O6   C6    108.46  3.000
 GI3  H1    N1   C7    123.76  3.000
 GI3  H1    N1   C1    125.90  3.000
 GI3  C7    N1   C1    110.33  3.000
 GI3  C8    C7   N1    122.41  3.000
 GI3  C8    C7   C80   131.73  3.000
 GI3  N1    C7   C80   105.86  3.000
 GI3  O9    C8   O8    130.01  3.000
 GI3  O9    C8   C7    114.80  3.000
 GI3  O8    C8   C7    115.19  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
 GI3  CONST_01  C7   C80  N10  C1     0.00   0.0  0
 GI3  CONST_02  C80  C7   N1   C1     0.00   0.0  0
 GI3  CONST_03  N1   C1   N10  C80    0.00   0.0  0
 GI3  CONST_04  C7   N1   C1   N10    0.00   0.0  0
 GI3  CONST_05  N1   C7   C80  N10    0.00   0.0  0
 GI3  CONST_06  C8   C7   N1   C1   180.00   0.0  0
 GI3  CONST_07  C8   C7   C80  N10  180.00   0.0  0
 GI3  CONST_08  H80  C80  N10  C1   180.00   0.0  0
 GI3  CONST_09  H1   N1   C1   C2     0.00   0.0  0
 GI3  Var_01    O8   C8   C7   C80   -0.11  30.0  2

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
 GI3  chir_01  C2  C1   O2  C3  positiv
 GI3  chir_02  C3  O3   C2  C4  positiv
 GI3  chir_03  C4  O4   C5  C3  positiv
 GI3  chir_04  C5  N10  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
 GI3  plan-1  C7   0.020
 GI3  plan-1  C8   0.020
 GI3  plan-1  O8   0.020
 GI3  plan-1  O9   0.020
 GI3  plan-2  C1   0.020
 GI3  plan-2  C2   0.020
 GI3  plan-2  C80  0.020
 GI3  plan-2  N10  0.020
 GI3  plan-2  C5   0.020
 GI3  plan-2  N1   0.020
 GI3  plan-2  C7   0.020
 GI3  plan-2  C8   0.020
 GI3  plan-2  H1   0.020
 GI3  plan-2  H80  0.020

