# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 12:16:59 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: (5R,6R,7S,8S)-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]cc[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
 GIM  GIM  (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  27  14  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GIM
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
 GIM  C1    C  CR56  0   0.658   0.0291  -1.3153   0.1800
 GIM  C2    C  CR16  0  -0.071  -1.3870  -0.9577   0.4766
 GIM  N10   N  N     1  -0.481   0.9838  -0.4477  -0.1335
 GIM  C3    C  CR16  0   0.009  -1.6815   0.3580  -0.2422
 GIM  C4    C  CR16  0  -0.005  -0.6347   1.3919   0.1707
 GIM  C5    C  CR16  0  -0.118   0.7860   1.0022  -0.2576
 GIM  C6    C  CH2   0  -0.144   1.8089   1.7698   0.5666
 GIM  C7    C  CR15  0  -0.078   1.8711  -2.4521  -0.2089
 GIM  C8    C  CR15  0  -0.082   2.1494  -1.1409  -0.3853
 GIM  N1    N  NR15  0  -0.602   0.5510  -2.5289   0.1411
 GIM  O3    O  OH1   0  -0.665  -2.9340   0.8583   0.1318
 GIM  O2    O  OH1   0  -0.656  -2.2082  -2.0041   0.0480
 GIM  O4    O  OH1   0  -0.656  -0.8762   2.6339  -0.4281
 GIM  O6    O  OH1   0  -0.663   3.0732   1.6609  -0.0372
 GIM  H2    H  HCR6  0   0.294  -1.4792  -0.7914   1.5581
 GIM  H3    H  HCR6  0   0.253  -1.6175   0.1944  -1.3275
 GIM  H4    H  HCR6  0   0.243  -0.6604   1.4737   1.2696
 GIM  H5    H  HCR6  0   0.309   0.9035   1.2465  -1.3171
 GIM  H6C1  H  HCH2  0   0.227   1.8021   1.3770   1.5899
 GIM  H6C2  H  HCH2  0   0.236   1.4773   2.8126   0.6149
 GIM  H7    H  HCR5  0   0.327   2.4929  -3.3232  -0.3107
 GIM  H8    H  HCR5  0   0.334   3.0620  -0.6538  -0.6720
 GIM  H1    H  HNR5  0   0.454   0.0365  -3.3791   0.3271
 GIM  HB    H  HOH1  0   0.468  -3.6109   0.4553  -0.4199
 GIM  HA    H  HOH1  0   0.478  -2.8158  -2.2357   0.7562
 GIM  HC    H  HOH1  0   0.462  -1.6975   2.9870  -0.0699
 GIM  H6    H  HOH1  0   0.467   3.7432   1.8965   0.6111

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
 GIM  C1   C2    single    1.490  0.020  1.490
 GIM  C1   N10   aromatic  1.328  0.020  1.328
 GIM  C1   N1    aromatic  1.322  0.020  1.322
 GIM  C2   C3    single    1.528  0.020  1.528
 GIM  C2   O2    single    1.398  0.020  1.398
 GIM  C2   H2    single    0.970  0.020  1.090
 GIM  N10  C5    single    1.469  0.020  1.469
 GIM  N10  C8    aromatic  1.379  0.020  1.379
 GIM  C3   C4    single    1.528  0.020  1.528
 GIM  C3   O3    single    1.400  0.020  1.400
 GIM  C3   H3    single    0.970  0.020  1.090
 GIM  C4   C5    single    1.534  0.020  1.534
 GIM  C4   O4    single    1.400  0.020  1.400
 GIM  C4   H4    single    0.970  0.020  1.090
 GIM  C5   C6    single    1.522  0.020  1.522
 GIM  C5   H5    single    0.970  0.020  1.090
 GIM  C6   O6    single    1.405  0.020  1.405
 GIM  C6   H6C1  single    0.970  0.020  1.090
 GIM  C6   H6C2  single    0.970  0.020  1.090
 GIM  C7   C8    aromatic  1.352  0.020  1.352
 GIM  C7   N1    aromatic  1.368  0.020  1.368
 GIM  C7   H7    single    0.930  0.020  1.080
 GIM  C8   H8    single    0.930  0.020  1.080
 GIM  N1   H1    single    0.860  0.020  1.020
 GIM  O3   HB    single    0.850  0.020  0.980
 GIM  O2   HA    single    0.850  0.020  0.980
 GIM  O4   HC    single    0.850  0.020  0.980
 GIM  O6   H6    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
 GIM  N1    C1   N10   108.01  3.000
 GIM  N1    C1   C2    126.97  3.000
 GIM  N10   C1   C2    124.99  3.000
 GIM  H2    C2   O2    111.47  3.000
 GIM  H2    C2   C3    108.47  3.000
 GIM  O2    C2   C3    112.78  3.000
 GIM  H2    C2   C1    108.19  3.000
 GIM  O2    C2   C1    108.52  3.000
 GIM  C3    C2   C1    107.23  3.000
 GIM  C8    N10  C5    126.48  3.000
 GIM  C8    N10  C1    108.80  3.000
 GIM  C5    N10  C1    124.63  3.000
 GIM  H3    C3   O3    111.66  3.000
 GIM  H3    C3   C4    109.12  3.000
 GIM  O3    C3   C4    107.40  3.000
 GIM  H3    C3   C2    108.96  3.000
 GIM  O3    C3   C2    110.77  3.000
 GIM  C4    C3   C2    108.87  3.000
 GIM  H4    C4   O4    110.89  3.000
 GIM  H4    C4   C5    108.59  3.000
 GIM  O4    C4   C5    105.41  3.000
 GIM  H4    C4   C3    107.67  3.000
 GIM  O4    C4   C3    111.50  3.000
 GIM  C5    C4   C3    112.77  3.000
 GIM  H5    C5   C6    109.87  3.000
 GIM  H5    C5   C4    108.25  3.000
 GIM  C6    C5   C4    110.07  3.000
 GIM  H5    C5   N10   106.73  3.000
 GIM  C6    C5   N10   111.21  3.000
 GIM  C4    C5   N10   110.61  3.000
 GIM  H6C2  C6   H6C1  107.35  3.000
 GIM  H6C2  C6   O6    111.41  3.000
 GIM  H6C1  C6   O6    112.27  3.000
 GIM  H6C2  C6   C5    107.49  3.000
 GIM  H6C1  C6   C5    108.71  3.000
 GIM  O6    C6   C5    109.45  3.000
 GIM  H7    C7   N1    122.47  3.000
 GIM  H7    C7   C8    130.88  3.000
 GIM  N1    C7   C8    106.65  3.000
 GIM  H8    C8   C7    130.53  3.000
 GIM  H8    C8   N10   122.63  3.000
 GIM  C7    C8   N10   106.84  3.000
 GIM  H1    N1   C7    125.84  3.000
 GIM  H1    N1   C1    124.46  3.000
 GIM  C7    N1   C1    109.70  3.000
 GIM  HB    O3   C3    109.07  3.000
 GIM  HA    O2   C2    109.02  3.000
 GIM  HC    O4   C4    108.26  3.000
 GIM  H6    O6   C6    108.55  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
 GIM  CONST_01  C7  C8  N10  C1     0.00  0.0  0
 GIM  CONST_02  C8  C7  N1   C1     0.00  0.0  0
 GIM  CONST_03  C7  N1  C1   N10    0.00  0.0  0
 GIM  CONST_04  N1  C7  C8   N10    0.00  0.0  0
 GIM  CONST_05  N1  C1  N10  C8     0.00  0.0  0
 GIM  CONST_06  H8  C8  N10  C1   180.00  0.0  0
 GIM  CONST_07  H7  C7  N1   C1   180.00  0.0  0
 GIM  CONST_08  H1  N1  C1   C2     0.00  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
 GIM  chir_01  C2  C1   C3  O2  negativ
 GIM  chir_02  C3  O3   C2  C4  positiv
 GIM  chir_03  C4  O4   C5  C3  positiv
 GIM  chir_04  C5  N10  C4  C6  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
 GIM  plan-1  C1   0.020
 GIM  plan-1  C2   0.020
 GIM  plan-1  N10  0.020
 GIM  plan-1  C5   0.020
 GIM  plan-1  C7   0.020
 GIM  plan-1  C8   0.020
 GIM  plan-1  N1   0.020
 GIM  plan-1  H7   0.020
 GIM  plan-1  H8   0.020
 GIM  plan-1  H1   0.020

