# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 06:26:50 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](O)c3nccn3[C@@H]2CO)[C@H](O)[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
 IDC  IDC  '(5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucopyranoside'  D-saccharide  47  25  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IDC
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
 IDC  C1A   C  CH1   0   0.286  -0.3088   0.0705  -1.3523
 IDC  C2A   C  CH1   0  -0.033  -1.2400   0.7121  -2.3791
 IDC  C3A   C  CH1   0  -0.010  -1.1109  -0.0452  -3.6932
 IDC  C4A   C  CH1   0   0.033   0.3482  -0.1205  -4.1277
 IDC  C5A   C  CH1   0  -0.021   1.1929  -0.6945  -2.9883
 IDC  C6A   C  CH2   0  -0.151   2.6694  -0.6854  -3.3208
 IDC  O2A   O  OH1   0  -0.664  -2.5861   0.6469  -1.9788
 IDC  O3A   O  OH1   0  -0.672  -1.8306   0.5711  -4.7333
 IDC  O4A   O  OH1   0  -0.672   0.5024  -0.9492  -5.2526
 IDC  O5A   O  O2    0  -0.473   1.0062   0.0847  -1.8248
 IDC  O6A   O  OH1   0  -0.667   3.3733  -1.3484  -2.2992
 IDC  C1B   C  CR5   0   0.442   0.4321  -0.0676   3.7783
 IDC  C2B   C  CH1   0  -0.059   1.6052   0.2307   2.9025
 IDC  C3B   C  CH1   0   0.036   1.1341   0.9889   1.6681
 IDC  C4B   C  CH1   0  -0.007   0.0059   0.1920   1.0163
 IDC  C5B   C  CH1   0  -0.100  -1.2355   0.1511   1.9268
 IDC  C6B   C  CH2   0  -0.154  -2.2420  -0.8747   1.4263
 IDC  O2B   O  OH1   0  -0.663   2.5563   1.0200   3.5679
 IDC  O3B   O  OH1   0  -0.647   2.1673   1.1516   0.7423
 IDC  O4B   O  O2    0  -0.507  -0.3782   0.8159  -0.1886
 IDC  N1B   N  NR5   0  -0.481  -0.8333  -0.1201   3.3039
 IDC  O6B   O  OH1   0  -0.664  -3.4849  -0.6428   2.0456
 IDC  N2B   N  N     0  -0.474   0.4869  -0.3050   5.0621
 IDC  C7B   C  CR15  0  -0.227  -0.8071  -0.5108   5.4468
 IDC  C8B   C  CR15  0  -0.103  -1.6443  -0.3987   4.3769
 IDC  HC1A  H  HCH1  0   0.192  -0.6286  -0.9739  -1.1736
 IDC  HC2A  H  HCH1  0   0.229  -0.9148   1.7518  -2.5340
 IDC  HC3A  H  HCH1  0   0.217  -1.4659  -1.0764  -3.5310
 IDC  HC4A  H  HCH1  0   0.213   0.7017   0.9021  -4.3370
 IDC  HC5A  H  HCH1  0   0.221   0.8730  -1.7348  -2.8079
 IDC  HCA1  H  HCH2  0   0.195   2.9978   0.3572  -3.4358
 IDC  HCA2  H  HCH2  0   0.211   2.8083  -1.1752  -4.2903
 IDC  HO2A  H  HOH1  0   0.458  -2.7398   1.3099  -1.2988
 IDC  HO3A  H  HOH1  0   0.457  -2.7714   0.4775  -4.5538
 IDC  HO4A  H  HOH1  0   0.454  -0.0503  -0.5999  -5.9594
 IDC  HO6A  H  HOH1  0   0.455   4.2964  -1.3984  -2.5623
 IDC  HC2B  H  HCH1  0   0.239   2.0540  -0.7178   2.5676
 IDC  HC3B  H  HCH1  0   0.225   0.7301   1.9624   1.9931
 IDC  HC4B  H  HCH1  0   0.254   0.3577  -0.8328   0.8294
 IDC  HC5B  H  HCH1  0   0.279  -1.6980   1.1438   1.8968
 IDC  HCB1  H  HCH2  0   0.220  -2.3336  -0.7763   0.3403
 IDC  HCB2  H  HCH2  0   0.218  -1.8556  -1.8802   1.6343
 IDC  HO2B  H  HOH1  0   0.459   2.8545   0.5406   4.3483
 IDC  HO3B  H  HOH1  0   0.452   2.8642   1.6636   1.1660
 IDC  HO6B  H  HOH1  0   0.463  -4.0821  -1.3547   1.7980
 IDC  HC7B  H  HCR5  0   0.250  -1.0723  -0.7264   6.4704
 IDC  HC8B  H  HCR5  0   0.292  -2.7113  -0.4888   4.2894

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
 IDC  C1A  C2A   single    1.527  0.020  1.527
 IDC  C1A  O5A   single    1.397  0.020  1.397
 IDC  C1A  O4B   single    1.384  0.020  1.384
 IDC  C1A  HC1A  single    0.970  0.020  1.090
 IDC  C2A  C3A   single    1.522  0.020  1.522
 IDC  C2A  O2A   single    1.406  0.020  1.406
 IDC  C2A  HC2A  single    0.970  0.020  1.090
 IDC  C3A  C4A   single    1.524  0.020  1.524
 IDC  C3A  O3A   single    1.407  0.020  1.407
 IDC  C3A  HC3A  single    0.970  0.020  1.090
 IDC  C4A  C5A   single    1.530  0.020  1.530
 IDC  C4A  O4A   single    1.406  0.020  1.406
 IDC  C4A  HC4A  single    0.970  0.020  1.090
 IDC  C5A  C6A   single    1.514  0.020  1.514
 IDC  C5A  O5A   single    1.413  0.020  1.413
 IDC  C5A  HC5A  single    0.970  0.020  1.090
 IDC  C6A  O6A   single    1.407  0.020  1.407
 IDC  C6A  HCA1  single    0.970  0.020  1.090
 IDC  C6A  HCA2  single    0.970  0.020  1.090
 IDC  O2A  HO2A  single    0.850  0.020  0.980
 IDC  O3A  HO3A  single    0.850  0.020  0.980
 IDC  O4A  HO4A  single    0.850  0.020  0.980
 IDC  O6A  HO6A  single    0.850  0.020  0.980
 IDC  C1B  C2B   single    1.494  0.020  1.494
 IDC  C1B  N1B   aromatic  1.352  0.020  1.352
 IDC  C1B  N2B   aromatic  1.307  0.020  1.307
 IDC  C2B  C3B   single    1.523  0.020  1.523
 IDC  C2B  O2B   single    1.404  0.020  1.404
 IDC  C2B  HC2B  single    0.970  0.020  1.090
 IDC  C3B  C4B   single    1.527  0.020  1.527
 IDC  C3B  O3B   single    1.397  0.020  1.397
 IDC  C3B  HC3B  single    0.970  0.020  1.090
 IDC  C4B  C5B   single    1.540  0.020  1.540
 IDC  C4B  O4B   single    1.410  0.020  1.410
 IDC  C4B  HC4B  single    0.970  0.020  1.090
 IDC  C5B  C6B   single    1.522  0.020  1.522
 IDC  C5B  N1B   single    1.460  0.020  1.460
 IDC  C5B  HC5B  single    0.970  0.020  1.090
 IDC  C6B  O6B   single    1.408  0.020  1.408
 IDC  C6B  HCB1  single    0.970  0.020  1.090
 IDC  C6B  HCB2  single    0.970  0.020  1.090
 IDC  O2B  HO2B  single    0.850  0.020  0.980
 IDC  O3B  HO3B  single    0.850  0.020  0.980
 IDC  N1B  C8B   aromatic  1.374  0.020  1.374
 IDC  O6B  HO6B  single    0.850  0.020  0.980
 IDC  N2B  C7B   aromatic  1.366  0.020  1.366
 IDC  C7B  C8B   aromatic  1.363  0.020  1.363
 IDC  C7B  HC7B  single    0.930  0.020  1.080
 IDC  C8B  HC8B  single    0.930  0.020  1.080

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
 IDC  HC1A  C1A  O4B   110.98  3.000
 IDC  HC1A  C1A  O5A   109.64  3.000
 IDC  O4B   C1A  O5A   109.03  3.000
 IDC  HC1A  C1A  C2A   109.20  3.000
 IDC  O4B   C1A  C2A   107.97  3.000
 IDC  O5A   C1A  C2A   110.01  3.000
 IDC  HC2A  C2A  O2A   111.53  3.000
 IDC  HC2A  C2A  C3A   108.88  3.000
 IDC  O2A   C2A  C3A   107.69  3.000
 IDC  HC2A  C2A  C1A   108.14  3.000
 IDC  O2A   C2A  C1A   111.89  3.000
 IDC  C3A   C2A  C1A   108.64  3.000
 IDC  HC3A  C3A  O3A   110.72  3.000
 IDC  HC3A  C3A  C4A   107.69  3.000
 IDC  O3A   C3A  C4A   107.49  3.000
 IDC  HC3A  C3A  C2A   108.12  3.000
 IDC  O3A   C3A  C2A   112.14  3.000
 IDC  C4A   C3A  C2A   110.60  3.000
 IDC  HC4A  C4A  O4A   111.09  3.000
 IDC  HC4A  C4A  C5A   108.21  3.000
 IDC  O4A   C4A  C5A   108.31  3.000
 IDC  HC4A  C4A  C3A   108.39  3.000
 IDC  O4A   C4A  C3A   111.24  3.000
 IDC  C5A   C4A  C3A   109.55  3.000
 IDC  HC5A  C5A  O5A   110.31  3.000
 IDC  HC5A  C5A  C6A   108.93  3.000
 IDC  O5A   C5A  C6A   107.85  3.000
 IDC  HC5A  C5A  C4A   108.39  3.000
 IDC  O5A   C5A  C4A   109.48  3.000
 IDC  C6A   C5A  C4A   111.88  3.000
 IDC  HCA2  C6A  HCA1  107.08  3.000
 IDC  HCA2  C6A  O6A   111.64  3.000
 IDC  HCA1  C6A  O6A   111.93  3.000
 IDC  HCA2  C6A  C5A   108.40  3.000
 IDC  HCA1  C6A  C5A   108.67  3.000
 IDC  O6A   C6A  C5A   109.01  3.000
 IDC  HO2A  O2A  C2A   108.80  3.000
 IDC  HO3A  O3A  C3A   108.63  3.000
 IDC  HO4A  O4A  C4A   108.09  3.000
 IDC  C5A   O5A  C1A   113.40  3.000
 IDC  HO6A  O6A  C6A   107.84  3.000
 IDC  N2B   C1B  N1B   112.14  3.000
 IDC  N2B   C1B  C2B   125.40  3.000
 IDC  N1B   C1B  C2B   122.46  3.000
 IDC  HC2B  C2B  O2B   110.62  3.000
 IDC  HC2B  C2B  C3B   107.95  3.000
 IDC  O2B   C2B  C3B   108.29  3.000
 IDC  HC2B  C2B  C1B   109.04  3.000
 IDC  O2B   C2B  C1B   111.49  3.000
 IDC  C3B   C2B  C1B   109.37  3.000
 IDC  HC3B  C3B  O3B   111.31  3.000
 IDC  HC3B  C3B  C4B   108.40  3.000
 IDC  O3B   C3B  C4B   108.92  3.000
 IDC  HC3B  C3B  C2B   108.29  3.000
 IDC  O3B   C3B  C2B   111.49  3.000
 IDC  C4B   C3B  C2B   108.33  3.000
 IDC  HC4B  C4B  O4B   110.75  3.000
 IDC  HC4B  C4B  C5B   109.49  3.000
 IDC  O4B   C4B  C5B   107.30  3.000
 IDC  HC4B  C4B  C3B   108.82  3.000
 IDC  O4B   C4B  C3B   109.57  3.000
 IDC  C5B   C4B  C3B   110.92  3.000
 IDC  HC5B  C5B  N1B   108.08  3.000
 IDC  HC5B  C5B  C6B   108.82  3.000
 IDC  N1B   C5B  C6B   111.55  3.000
 IDC  HC5B  C5B  C4B   107.46  3.000
 IDC  N1B   C5B  C4B   109.91  3.000
 IDC  C6B   C5B  C4B   110.89  3.000
 IDC  HCB2  C6B  HCB1  107.46  3.000
 IDC  HCB2  C6B  O6B   112.24  3.000
 IDC  HCB1  C6B  O6B   110.35  3.000
 IDC  HCB2  C6B  C5B   108.82  3.000
 IDC  HCB1  C6B  C5B   108.74  3.000
 IDC  O6B   C6B  C5B   109.16  3.000
 IDC  HO2B  O2B  C2B   108.30  3.000
 IDC  HO3B  O3B  C3B   107.79  3.000
 IDC  C4B   O4B  C1A   117.81  3.000
 IDC  C8B   N1B  C5B   127.72  3.000
 IDC  C8B   N1B  C1B   106.64  3.000
 IDC  C5B   N1B  C1B   125.55  3.000
 IDC  HO6B  O6B  C6B   108.24  3.000
 IDC  C7B   N2B  C1B   105.33  3.000
 IDC  HC7B  C7B  C8B   127.59  3.000
 IDC  HC7B  C7B  N2B   122.01  3.000
 IDC  C8B   C7B  N2B   110.40  3.000
 IDC  HC8B  C8B  C7B   131.84  3.000
 IDC  HC8B  C8B  N1B   122.67  3.000
 IDC  C7B   C8B  N1B   105.49  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
 IDC  CONST_01  C7B   C8B  N1B  C1B    0.00  0.0  0
 IDC  CONST_02  C8B   C7B  N2B  C1B    0.00  0.0  0
 IDC  CONST_03  C7B   N2B  C1B  N1B    0.00  0.0  0
 IDC  CONST_04  N2B   C7B  C8B  N1B    0.00  0.0  0
 IDC  CONST_05  C8B   N1B  C1B  N2B    0.00  0.0  0
 IDC  CONST_06  HC8B  C8B  N1B  C1B  180.00  0.0  0
 IDC  CONST_07  HC7B  C7B  N2B  C1B  180.00  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
 IDC  chir_01  C1A  C2A  O5A  O4B  negativ
 IDC  chir_02  C2A  O2A  C1A  C3A  negativ
 IDC  chir_03  C3A  O3A  C2A  C4A  positiv
 IDC  chir_04  C4A  O4A  C5A  C3A  positiv
 IDC  chir_05  C5A  O5A  C4A  C6A  negativ
 IDC  chir_06  C2B  O2B  C1B  C3B  negativ
 IDC  chir_07  C3B  O3B  C2B  C4B  positiv
 IDC  chir_08  C4B  O4B  C5B  C3B  positiv
 IDC  chir_09  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
 IDC  plan-1  C1B   0.020
 IDC  plan-1  C2B   0.020
 IDC  plan-1  C5B   0.020
 IDC  plan-1  N1B   0.020
 IDC  plan-1  N2B   0.020
 IDC  plan-1  C7B   0.020
 IDC  plan-1  C8B   0.020
 IDC  plan-1  HC7B  0.020
 IDC  plan-1  HC8B  0.020

