# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:32:40 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (5R,6R,7S,8S)-5-(hydroxymethyl)-2-[(phenylamino)methyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)c2nc(CNc3ccccc3)cn12
#
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
 IDE  IDE  (5R,6R,7S,8S)-5-(hydroxymethyl)-2-[(phenylamino)methyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol  ligand  41  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IDE
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
 IDE  O6B   O  OH1   0  -0.665   2.2273   3.4989   0.8658
 IDE  C6B   C  CH2   0  -0.149   2.8428   2.6786  -0.0984
 IDE  C5B   C  CH1   0  -0.106   2.8896   1.2440   0.4090
 IDE  C4B   C  CH1   0  -0.000   3.8962   0.4321  -0.4139
 IDE  O4B   O  OH1   0  -0.662   5.1668   0.8709  -0.0131
 IDE  C3B   C  CH1   0   0.021   3.7336  -1.0703  -0.1964
 IDE  O3B   O  OH1   0  -0.673   4.7811  -1.7018  -0.8867
 IDE  C2B   C  CH1   0  -0.057   2.3730  -1.5070  -0.7155
 IDE  O2B   O  OH1   0  -0.661   2.1756  -2.8560  -0.3846
 IDE  N1B   N  NR5   0  -0.483   1.5777   0.6077   0.3546
 IDE  C8B   C  CR15  0  -0.117   0.3881   1.1091   0.8227
 IDE  C7B   C  CR5   0   0.110  -0.5362   0.1303   0.6056
 IDE  N2B   N  N     0  -0.489   0.0578  -0.9512   0.0175
 IDE  C1B   C  CR5   0   0.439   1.3184  -0.6333  -0.1135
 IDE  C7    C  CH2   0  -0.364  -1.9917   0.1411   0.9214
 IDE  N1    N  NH1   0  -0.685  -2.7640  -0.0903  -0.2811
 IDE  C1    C  CR6   0   0.365  -4.1321  -0.2134  -0.2380
 IDE  C6    C  CR16  0  -0.349  -4.8161  -0.7533  -1.3396
 IDE  C5    C  CR16  0  -0.245  -6.1957  -0.8463  -1.3420
 IDE  C4    C  CR16  0  -0.297  -6.9438  -0.4096  -0.2523
 IDE  C3    C  CR16  0  -0.243  -6.2743   0.1179   0.8420
 IDE  C2    C  CR16  0  -0.352  -4.8888   0.2153   0.8606
 IDE  H6B   H  HOH1  0   0.462   2.0953   4.3693   0.4788
 IDE  H6B1  H  HCH2  0   0.213   2.3071   2.6918  -1.0558
 IDE  H6B2  H  HCH2  0   0.228   3.8699   3.0039  -0.2941
 IDE  H5B   H  HCH1  0   0.279   3.2270   1.2414   1.4510
 IDE  H4B   H  HCH1  0   0.230   3.7273   0.6415  -1.4829
 IDE  H3    H  HOH1  0   0.458   5.8223   0.4537  -0.5814
 IDE  H3B   H  HCH1  0   0.231   3.7857  -1.2799   0.8837
 IDE  H2    H  HOH1  0   0.461   4.8115  -2.6274  -0.6256
 IDE  H2B   H  HCH1  0   0.238   2.3635  -1.3682  -1.8080
 IDE  H1    H  HOH1  0   0.458   1.3115  -3.1259  -0.7138
 IDE  H8B   H  HCR5  0   0.294   0.3013   2.0897   1.2554
 IDE  H71   H  HCH2  0   0.229  -2.2111  -0.6131   1.6912
 IDE  H72   H  HCH2  0   0.244  -2.2532   1.1105   1.3520
 IDE  HN1   H  HNH1  0   0.378  -2.3067  -0.6901  -0.9508
 IDE  H8    H  HCR6  0   0.252  -4.2516  -1.1008  -2.1975
 IDE  H7    H  HCR6  0   0.250  -6.6925  -1.2681  -2.2068
 IDE  H6    H  HCR6  0   0.244  -8.0230  -0.4833  -0.2578
 IDE  H5    H  HCR6  0   0.249  -6.8326   0.4601   1.7046
 IDE  H4    H  HCR6  0   0.263  -4.4048   0.6299   1.7347

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
 IDE  O6B  C6B   single    1.408  0.020  1.408
 IDE  O6B  H6B   single    0.850  0.020  0.980
 IDE  C6B  C5B   single    1.522  0.020  1.522
 IDE  C6B  H6B1  single    0.970  0.020  1.090
 IDE  C6B  H6B2  single    0.970  0.020  1.090
 IDE  C5B  C4B   single    1.533  0.020  1.533
 IDE  C5B  N1B   single    1.459  0.020  1.459
 IDE  C5B  H5B   single    0.970  0.020  1.090
 IDE  C4B  O4B   single    1.403  0.020  1.403
 IDE  C4B  C3B   single    1.527  0.020  1.527
 IDE  C4B  H4B   single    0.970  0.020  1.090
 IDE  O4B  H3    single    0.850  0.020  0.980
 IDE  C3B  O3B   single    1.404  0.020  1.404
 IDE  C3B  C2B   single    1.520  0.020  1.520
 IDE  C3B  H3B   single    0.970  0.020  1.090
 IDE  O3B  H2    single    0.850  0.020  0.980
 IDE  C2B  O2B   single    1.403  0.020  1.403
 IDE  C2B  C1B   single    1.496  0.020  1.496
 IDE  C2B  H2B   single    0.970  0.020  1.090
 IDE  O2B  H1    single    0.850  0.020  0.980
 IDE  N1B  C8B   aromatic  1.373  0.020  1.373
 IDE  N1B  C1B   aromatic  1.352  0.020  1.352
 IDE  C8B  C7B   aromatic  1.364  0.020  1.364
 IDE  C8B  H8B   single    0.930  0.020  1.080
 IDE  C7B  N2B   aromatic  1.367  0.020  1.367
 IDE  C7B  C7    single    1.489  0.020  1.489
 IDE  N2B  C1B   aromatic  1.307  0.020  1.307
 IDE  C7   N1    single    1.448  0.020  1.448
 IDE  C7   H71   single    0.970  0.020  1.090
 IDE  C7   H72   single    0.970  0.020  1.090
 IDE  N1   C1    single    1.374  0.020  1.374
 IDE  N1   HN1   single    0.890  0.020  1.040
 IDE  C1   C6    aromatic  1.405  0.020  1.405
 IDE  C1   C2    aromatic  1.401  0.020  1.401
 IDE  C6   C5    aromatic  1.383  0.020  1.383
 IDE  C6   H8    single    0.930  0.020  1.080
 IDE  C5   C4    aromatic  1.392  0.020  1.392
 IDE  C5   H7    single    0.930  0.020  1.080
 IDE  C4   C3    aromatic  1.387  0.020  1.387
 IDE  C4   H6    single    0.930  0.020  1.080
 IDE  C3   C2    aromatic  1.389  0.020  1.389
 IDE  C3   H5    single    0.930  0.020  1.080
 IDE  C2   H4    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
 IDE  H6B   O6B  C6B   108.17  3.000
 IDE  H6B2  C6B  H6B1  107.36  3.000
 IDE  H6B2  C6B  C5B   108.10  3.000
 IDE  H6B1  C6B  C5B   108.49  3.000
 IDE  H6B2  C6B  O6B   111.06  3.000
 IDE  H6B1  C6B  O6B   112.16  3.000
 IDE  C5B   C6B  O6B   109.53  3.000
 IDE  H5B   C5B  N1B   108.14  3.000
 IDE  H5B   C5B  C4B   107.89  3.000
 IDE  N1B   C5B  C4B   109.85  3.000
 IDE  H5B   C5B  C6B   109.19  3.000
 IDE  N1B   C5B  C6B   111.77  3.000
 IDE  C4B   C5B  C6B   109.90  3.000
 IDE  H4B   C4B  C3B   107.98  3.000
 IDE  H4B   C4B  O4B   110.88  3.000
 IDE  C3B   C4B  O4B   111.32  3.000
 IDE  H4B   C4B  C5B   108.62  3.000
 IDE  C3B   C4B  C5B   112.01  3.000
 IDE  O4B   C4B  C5B   106.01  3.000
 IDE  H3    O4B  C4B   108.21  3.000
 IDE  H3B   C3B  C2B   108.81  3.000
 IDE  H3B   C3B  O3B   111.17  3.000
 IDE  C2B   C3B  O3B   111.75  3.000
 IDE  H3B   C3B  C4B   108.78  3.000
 IDE  C2B   C3B  C4B   109.23  3.000
 IDE  O3B   C3B  C4B   107.04  3.000
 IDE  H2    O3B  C3B   108.83  3.000
 IDE  H2B   C2B  C1B   108.64  3.000
 IDE  H2B   C2B  O2B   110.73  3.000
 IDE  C1B   C2B  O2B   111.56  3.000
 IDE  H2B   C2B  C3B   108.07  3.000
 IDE  C1B   C2B  C3B   109.01  3.000
 IDE  O2B   C2B  C3B   108.75  3.000
 IDE  H1    O2B  C2B   108.36  3.000
 IDE  C1B   N1B  C8B   106.68  3.000
 IDE  C1B   N1B  C5B   125.86  3.000
 IDE  C8B   N1B  C5B   127.38  3.000
 IDE  H8B   C8B  C7B   131.60  3.000
 IDE  H8B   C8B  N1B   122.68  3.000
 IDE  C7B   C8B  N1B   105.72  3.000
 IDE  C7    C7B  N2B   121.44  3.000
 IDE  C7    C7B  C8B   128.57  3.000
 IDE  N2B   C7B  C8B   109.99  3.000
 IDE  C1B   N2B  C7B   105.66  3.000
 IDE  N2B   C1B  N1B   111.95  3.000
 IDE  N2B   C1B  C2B   125.34  3.000
 IDE  N1B   C1B  C2B   122.71  3.000
 IDE  H72   C7   H71   106.55  3.000
 IDE  H72   C7   N1    109.97  3.000
 IDE  H71   C7   N1    111.43  3.000
 IDE  H72   C7   C7B   108.89  3.000
 IDE  H71   C7   C7B   109.78  3.000
 IDE  N1    C7   C7B   110.13  3.000
 IDE  HN1   N1   C1    114.76  3.000
 IDE  HN1   N1   C7    113.87  3.000
 IDE  C1    N1   C7    121.29  3.000
 IDE  C2    C1   C6    118.00  3.000
 IDE  C2    C1   N1    122.33  3.000
 IDE  C6    C1   N1    119.65  3.000
 IDE  H8    C6   C5    119.77  3.000
 IDE  H8    C6   C1    119.35  3.000
 IDE  C5    C6   C1    120.87  3.000
 IDE  H7    C5   C4    120.05  3.000
 IDE  H7    C5   C6    119.03  3.000
 IDE  C4    C5   C6    120.91  3.000
 IDE  H6    C4   C3    120.76  3.000
 IDE  H6    C4   C5    120.71  3.000
 IDE  C3    C4   C5    118.52  3.000
 IDE  H5    C3   C2    118.77  3.000
 IDE  H5    C3   C4    119.98  3.000
 IDE  C2    C3   C4    121.25  3.000
 IDE  H4    C2   C3    118.95  3.000
 IDE  H4    C2   C1    120.61  3.000
 IDE  C3    C2   C1    120.44  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
 IDE  CONST_01  N2B  C7B  C8B  N1B    0.00   0.0  0
 IDE  CONST_02  C7B  N2B  C1B  N1B    0.00   0.0  0
 IDE  CONST_03  N2B  C1B  N1B  C8B    0.00   0.0  0
 IDE  CONST_04  C1B  N2B  C7B  C8B    0.00   0.0  0
 IDE  CONST_05  C1B  N1B  C8B  C7B    0.00   0.0  0
 IDE  CONST_06  C4   C5   C6   C1     0.00   0.0  0
 IDE  CONST_07  C4   C3   C2   C1     0.00   0.0  0
 IDE  CONST_08  C3   C2   C1   C6     0.00   0.0  0
 IDE  CONST_09  C3   C4   C5   C6     0.00   0.0  0
 IDE  CONST_10  C2   C1   C6   C5     0.00   0.0  0
 IDE  CONST_11  C2   C3   C4   C5     0.00   0.0  0
 IDE  CONST_12  C7   C7B  C8B  N1B  180.00   0.0  0
 IDE  CONST_13  C7   C7B  N2B  C1B  180.00   0.0  0
 IDE  CONST_14  C5   C6   C1   N1   180.00   0.0  0
 IDE  CONST_15  C3   C2   C1   N1   180.00   0.0  0
 IDE  CONST_16  H8B  C8B  N1B  C5B    0.00   0.0  0
 IDE  CONST_17  H7   C5   C6   C1   180.00   0.0  0
 IDE  CONST_18  H5   C3   C2   C1   180.00   0.0  0
 IDE  CONST_19  H4   C2   C1   C6   180.00   0.0  0
 IDE  CONST_20  H6   C4   C5   C6   180.00   0.0  0
 IDE  CONST_21  H8   C6   C5   C4   180.00   0.0  0
 IDE  Var_01    N1   C7   C7B  C8B  122.46  30.0  2
 IDE  Var_02    C1   N1   C7   C7B  175.70  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
 IDE  chir_01  C5B  C6B  C4B  N1B  positiv
 IDE  chir_02  C4B  O4B  C5B  C3B  positiv
 IDE  chir_03  C3B  O3B  C2B  C4B  positiv
 IDE  chir_04  C2B  O2B  C3B  C1B  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
 IDE  plan-1  N1   0.020
 IDE  plan-1  C1   0.020
 IDE  plan-1  C6   0.020
 IDE  plan-1  C5   0.020
 IDE  plan-1  C4   0.020
 IDE  plan-1  C3   0.020
 IDE  plan-1  C2   0.020
 IDE  plan-1  H8   0.020
 IDE  plan-1  H7   0.020
 IDE  plan-1  H6   0.020
 IDE  plan-1  H5   0.020
 IDE  plan-1  H4   0.020
 IDE  plan-2  C5B  0.020
 IDE  plan-2  C2B  0.020
 IDE  plan-2  N1B  0.020
 IDE  plan-2  C8B  0.020
 IDE  plan-2  C7B  0.020
 IDE  plan-2  N2B  0.020
 IDE  plan-2  C1B  0.020
 IDE  plan-2  C7   0.020
 IDE  plan-2  H8B  0.020
 IDE  plan-3  C7   0.020
 IDE  plan-3  N1   0.020
 IDE  plan-3  C1   0.020
 IDE  plan-3  HN1  0.020

