# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:14:06 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (6R,7S,8S)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1Cn2ccnc2[C@H](O)[C@H]1O
#
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
 XIM  XIM  (6R,7S,8S)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol  ligand  22  12  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XIM
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
 XIM  C1   C  CR5   0   0.441   1.0671  -0.4137   0.1093
 XIM  C2   C  CH1   0  -0.066  -0.1847  -1.2186   0.2819
 XIM  C3   C  CH1   0   0.034  -1.3980  -0.4557  -0.2476
 XIM  C4   C  CH1   0   0.006  -1.3732   0.9624   0.3106
 XIM  C5   C  CH2   0  -0.317  -0.1624   1.7081  -0.2529
 XIM  N1   N  NR5   0  -0.456   1.0404   0.9229  -0.0718
 XIM  C17  C  CR15  0  -0.106   2.3376   1.3479  -0.1452
 XIM  C18  C  CR15  0  -0.224   3.0950   0.2216   0.0037
 XIM  N21  N  N     0  -0.471   2.2918  -0.8714   0.1671
 XIM  O2   O  OH1   0  -0.661  -0.1143  -2.4470  -0.3962
 XIM  O3   O  OH1   0  -0.665  -2.5931  -1.0750   0.1416
 XIM  O4   O  OH1   0  -0.659  -2.5540   1.6175  -0.0640
 XIM  H2   H  HCH1  0   0.239  -0.3430  -1.3798   1.3594
 XIM  H3   H  HCH1  0   0.222  -1.3179  -0.3985  -1.3461
 XIM  H4   H  HCH1  0   0.231  -1.2795   0.9075   1.4053
 XIM  H51  H  HCH2  0   0.264  -0.3193   1.8980  -1.3175
 XIM  H52  H  HCH2  0   0.277  -0.0387   2.6687   0.2483
 XIM  H17  H  HCR5  0   0.287   2.5959   2.3833  -0.2922
 XIM  H18  H  HCR5  0   0.250   4.1714   0.1446   0.0049
 XIM  HO2  H  HOH1  0   0.460   0.5657  -2.9855   0.0212
 XIM  HO3  H  HOH1  0   0.453  -2.5878  -1.9753  -0.2001
 XIM  HO4  H  HOH1  0   0.460  -2.6319   2.4232   0.4562

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
 XIM  C1   C2   single    1.498  0.020  1.498
 XIM  C1   N1   aromatic  1.349  0.020  1.349
 XIM  C1   N21  aromatic  1.309  0.020  1.309
 XIM  C2   C3   single    1.528  0.020  1.528
 XIM  C2   O2   single    1.405  0.020  1.405
 XIM  C2   H2   single    0.970  0.020  1.090
 XIM  C3   C4   single    1.524  0.020  1.524
 XIM  C3   O3   single    1.401  0.020  1.401
 XIM  C3   H3   single    0.970  0.020  1.090
 XIM  C4   C5   single    1.530  0.020  1.530
 XIM  C4   O4   single    1.401  0.020  1.401
 XIM  C4   H4   single    0.970  0.020  1.090
 XIM  C5   N1   single    1.448  0.020  1.448
 XIM  C5   H51  single    0.970  0.020  1.090
 XIM  C5   H52  single    0.970  0.020  1.090
 XIM  N1   C17  aromatic  1.367  0.020  1.367
 XIM  C17  C18  aromatic  1.365  0.020  1.365
 XIM  C17  H17  single    0.930  0.020  1.080
 XIM  C18  N21  aromatic  1.366  0.020  1.366
 XIM  C18  H18  single    0.930  0.020  1.080
 XIM  O2   HO2  single    0.850  0.020  0.980
 XIM  O3   HO3  single    0.850  0.020  0.980
 XIM  O4   HO4  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
 XIM  N21  C1   N1   111.77  3.000
 XIM  N21  C1   C2   126.08  3.000
 XIM  N1   C1   C2   122.09  3.000
 XIM  H2   C2   O2   110.58  3.000
 XIM  H2   C2   C3   107.35  3.000
 XIM  O2   C2   C3   108.01  3.000
 XIM  H2   C2   C1   108.15  3.000
 XIM  O2   C2   C1   111.85  3.000
 XIM  C3   C2   C1   110.81  3.000
 XIM  H3   C3   O3   111.19  3.000
 XIM  H3   C3   C4   108.39  3.000
 XIM  O3   C3   C4   108.87  3.000
 XIM  H3   C3   C2   108.26  3.000
 XIM  O3   C3   C2   111.12  3.000
 XIM  C4   C3   C2   108.95  3.000
 XIM  H4   C4   O4   111.17  3.000
 XIM  H4   C4   C5   108.88  3.000
 XIM  O4   C4   C5   109.91  3.000
 XIM  H4   C4   C3   108.63  3.000
 XIM  O4   C4   C3   108.86  3.000
 XIM  C5   C4   C3   109.36  3.000
 XIM  H52  C5   H51  108.12  3.000
 XIM  H52  C5   N1   109.03  3.000
 XIM  H51  C5   N1   109.60  3.000
 XIM  H52  C5   C4   110.48  3.000
 XIM  H51  C5   C4   109.27  3.000
 XIM  N1   C5   C4   110.31  3.000
 XIM  C17  N1   C5   127.81  3.000
 XIM  C17  N1   C1   107.25  3.000
 XIM  C5   N1   C1   124.79  3.000
 XIM  H17  C17  C18  132.44  3.000
 XIM  H17  C17  N1   122.25  3.000
 XIM  C18  C17  N1   105.31  3.000
 XIM  H18  C18  N21  121.95  3.000
 XIM  H18  C18  C17  127.75  3.000
 XIM  N21  C18  C17  110.30  3.000
 XIM  C18  N21  C1   105.37  3.000
 XIM  HO2  O2   C2   108.38  3.000
 XIM  HO3  O3   C3   108.06  3.000
 XIM  HO4  O4   C4   108.37  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
 XIM  CONST_01  C18  C17  N1   C1     0.00   0.0  0
 XIM  CONST_02  C17  C18  N21  C1     0.00   0.0  0
 XIM  CONST_03  C18  N21  C1   N1     0.00   0.0  0
 XIM  CONST_04  N21  C18  C17  N1     0.00   0.0  0
 XIM  CONST_05  N21  C1   N1   C17    0.00   0.0  0
 XIM  CONST_06  H17  C17  N1   C1   180.00   0.0  0
 XIM  CONST_07  H18  C18  N21  C1   180.00   0.0  0
 XIM  Var_01    C4   C5   N1   C1    21.84  30.0  1

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
 XIM  chir_01  C2  C1  C3  O2  negativ
 XIM  chir_02  C3  O3  C4  C2  negativ
 XIM  chir_03  C4  O4  C3  C5  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
 XIM  plan-1  C1   0.020
 XIM  plan-1  C2   0.020
 XIM  plan-1  C5   0.020
 XIM  plan-1  N1   0.020
 XIM  plan-1  C17  0.020
 XIM  plan-1  C18  0.020
 XIM  plan-1  N21  0.020
 XIM  plan-1  H17  0.020
 XIM  plan-1  H18  0.020

