# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:42:17 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: (5~{R},6~{R},7~{S},8~{S})-5-(hydroxymethyl)-2-(3-phenylpropyl)-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(CCCc3ccccc3)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
 KG8  KG8  (5~{R},6~{R},7~{S},8~{S})-5-(hydroxymethyl)-2-(3-phenylpropyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol  ligand  45  23  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KG8
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
 KG8  N1   N  NR5   0  -0.489  48.9319  -14.8031   -7.4289
 KG8  C4   C  CH1   0  -0.108  47.9941  -15.2787   -8.4386
 KG8  C5   C  CH2   0  -0.150  48.6570  -15.4379   -9.7997
 KG8  C6   C  CR5   0   0.424  48.6772  -13.8629   -6.4952
 KG8  C7   C  CR5   0   0.126  50.6428  -14.5892   -6.0788
 KG8  C8   C  CH2   0  -0.516  51.9693  -14.6788   -5.3962
 KG8  C10  C  CH2   0  -0.512  52.1929  -17.2196   -5.1913
 KG8  C13  C  CR16  0  -0.240  54.6708  -20.0960   -5.4142
 KG8  C15  C  CR16  0  -0.240  53.3611  -20.0584   -7.4243
 KG8  C17  C  CR15  0  -0.119  50.1935  -15.2829   -7.1669
 KG8  O1   O  OH1   0  -0.674  45.1555  -13.1085   -7.3666
 KG8  C1   C  CH1   0   0.016  46.3115  -13.8810   -7.1599
 KG8  C2   C  CH1   0  -0.046  47.3979  -13.0908   -6.4491
 KG8  O2   O  OH1   0  -0.663  46.9933  -12.8428   -5.1280
 KG8  C3   C  CH1   0   0.006  46.8132  -14.3071   -8.5382
 KG8  O3   O  OH1   0  -0.664  45.8126  -14.9776   -9.2564
 KG8  O4   O  OH1   0  -0.664  49.4917  -16.5722   -9.7867
 KG8  N2   N  N     0  -0.496  49.6810  -13.7040   -5.6730
 KG8  C9   C  CH2   0  -0.448  52.7735  -15.9222   -5.7603
 KG8  C11  C  CR6   0   0.141  52.9373  -18.4277   -5.6852
 KG8  C12  C  CR16  0  -0.317  53.9567  -19.0057   -4.9325
 KG8  C14  C  CR16  0  -0.275  54.3760  -20.6259   -6.6631
 KG8  C16  C  CR16  0  -0.307  52.6505  -18.9706   -6.9373
 KG8  H1   H  HCH1  0   0.275  47.6039  -16.2509   -8.1164
 KG8  H2   H  HCH2  0   0.213  49.2103  -14.5190  -10.0299
 KG8  H3   H  HCH2  0   0.228  47.8678  -15.5402  -10.5517
 KG8  H4   H  HCH2  0   0.234  51.8189  -14.6353   -4.3132
 KG8  H5   H  HCH2  0   0.249  52.5601  -13.7918   -5.6463
 KG8  H6   H  HCH2  0   0.241  52.2309  -17.1781   -4.0997
 KG8  H7   H  HCH2  0   0.245  51.1378  -17.3039   -5.4627
 KG8  H9   H  HCR6  0   0.252  53.1208  -20.4657   -8.3983
 KG8  H10  H  HCR5  0   0.288  50.6452  -16.0527   -7.7659
 KG8  H11  H  HOH1  0   0.462  44.6866  -13.0176   -6.5314
 KG8  H12  H  HCH1  0   0.232  46.0841  -14.7840   -6.5722
 KG8  H13  H  HCH1  0   0.234  47.5414  -12.1444   -6.9950
 KG8  H14  H  HOH1  0   0.456  47.7364  -12.4496   -4.6567
 KG8  H15  H  HCH1  0   0.227  47.1466  -13.4030   -9.0747
 KG8  H16  H  HOH1  0   0.457  45.0605  -14.3831   -9.3466
 KG8  H17  H  HOH1  0   0.462  50.0071  -16.5753  -10.5985
 KG8  H18  H  HCH2  0   0.242  53.7958  -15.8032   -5.3932
 KG8  H19  H  HCH2  0   0.228  52.8576  -16.0009   -6.8487
 KG8  H20  H  HCR6  0   0.245  54.1924  -18.5999   -3.9552
 KG8  H21  H  HCR6  0   0.252  54.9298  -21.4762   -7.0401
 KG8  H22  H  HCR6  0   0.240  51.8575  -18.5388   -7.5387
 KG8  H8   H  HCR6  0   0.252  55.4564  -20.5333   -4.8111

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
 KG8  O4   C5   single    1.408  0.020  1.408
 KG8  C5   C4   single    1.522  0.020  1.522
 KG8  O3   C3   single    1.402  0.020  1.402
 KG8  C4   C3   single    1.532  0.020  1.532
 KG8  C4   N1   single    1.458  0.020  1.458
 KG8  C3   C1   single    1.527  0.020  1.527
 KG8  N1   C17  aromatic  1.375  0.020  1.375
 KG8  N1   C6   aromatic  1.349  0.020  1.349
 KG8  C17  C7   aromatic  1.366  0.020  1.366
 KG8  C1   O1   single    1.406  0.020  1.406
 KG8  C1   C2   single    1.520  0.020  1.520
 KG8  C16  C15  aromatic  1.388  0.020  1.388
 KG8  C16  C11  aromatic  1.394  0.020  1.394
 KG8  C9   C10  single    1.531  0.020  1.531
 KG8  C9   C8   single    1.525  0.020  1.525
 KG8  C6   C2   single    1.495  0.020  1.495
 KG8  C6   N2   aromatic  1.307  0.020  1.307
 KG8  C10  C11  single    1.502  0.020  1.502
 KG8  C7   C8   single    1.495  0.020  1.495
 KG8  C7   N2   aromatic  1.369  0.020  1.369
 KG8  C15  C14  aromatic  1.390  0.020  1.390
 KG8  C2   O2   single    1.404  0.020  1.404
 KG8  C11  C12  aromatic  1.393  0.020  1.393
 KG8  C14  C13  aromatic  1.388  0.020  1.388
 KG8  C12  C13  aromatic  1.390  0.020  1.390
 KG8  C4   H1   single    0.970  0.020  1.090
 KG8  C5   H2   single    0.970  0.020  1.090
 KG8  C5   H3   single    0.970  0.020  1.090
 KG8  C8   H4   single    0.970  0.020  1.090
 KG8  C8   H5   single    0.970  0.020  1.090
 KG8  C10  H6   single    0.970  0.020  1.090
 KG8  C10  H7   single    0.970  0.020  1.090
 KG8  C13  H8   single    0.930  0.020  1.080
 KG8  C15  H9   single    0.930  0.020  1.080
 KG8  C17  H10  single    0.930  0.020  1.080
 KG8  O1   H11  single    0.850  0.020  0.980
 KG8  C1   H12  single    0.970  0.020  1.090
 KG8  C2   H13  single    0.970  0.020  1.090
 KG8  O2   H14  single    0.850  0.020  0.980
 KG8  C3   H15  single    0.970  0.020  1.090
 KG8  O3   H16  single    0.850  0.020  0.980
 KG8  O4   H17  single    0.850  0.020  0.980
 KG8  C9   H18  single    0.970  0.020  1.090
 KG8  C9   H19  single    0.970  0.020  1.090
 KG8  C12  H20  single    0.930  0.020  1.080
 KG8  C14  H21  single    0.930  0.020  1.080
 KG8  C16  H22  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
 KG8  C17  N1   C6   106.53  3.000
 KG8  C6   N1   C4   125.81  3.000
 KG8  C17  N1   C4   127.48  3.000
 KG8  H1   C4   C3   107.89  3.000
 KG8  H1   C4   C5   108.97  3.000
 KG8  C3   C4   C5   110.11  3.000
 KG8  H1   C4   N1   108.35  3.000
 KG8  C3   C4   N1   109.51  3.000
 KG8  C5   C4   N1   111.92  3.000
 KG8  H3   C5   H2   107.32  3.000
 KG8  H3   C5   O4   111.00  3.000
 KG8  H2   C5   O4   112.18  3.000
 KG8  H3   C5   C4   108.06  3.000
 KG8  H2   C5   C4   108.64  3.000
 KG8  O4   C5   C4   109.52  3.000
 KG8  N2   C6   C2   125.10  3.000
 KG8  N2   C6   N1   112.02  3.000
 KG8  C2   C6   N1   122.87  3.000
 KG8  N2   C7   C17  109.47  3.000
 KG8  N2   C7   C8   121.81  3.000
 KG8  C17  C7   C8   128.70  3.000
 KG8  H5   C8   H4   105.55  3.000
 KG8  H5   C8   C9   108.75  3.000
 KG8  H4   C8   C9   109.96  3.000
 KG8  H5   C8   C7   109.03  3.000
 KG8  H4   C8   C7   109.13  3.000
 KG8  C9   C8   C7   114.07  3.000
 KG8  H7   C10  H6   106.53  3.000
 KG8  H7   C10  C11  109.55  3.000
 KG8  H6   C10  C11  109.98  3.000
 KG8  H7   C10  C9   109.83  3.000
 KG8  H6   C10  C9   109.01  3.000
 KG8  C11  C10  C9   111.79  3.000
 KG8  H8   C13  C14  120.07  3.000
 KG8  H8   C13  C12  119.79  3.000
 KG8  C14  C13  C12  120.15  3.000
 KG8  H9   C15  C16  119.80  3.000
 KG8  H9   C15  C14  120.08  3.000
 KG8  C16  C15  C14  120.12  3.000
 KG8  H10  C17  C7   132.00  3.000
 KG8  H10  C17  N1   121.96  3.000
 KG8  C7   C17  N1   106.04  3.000
 KG8  H11  O1   C1   108.97  3.000
 KG8  H12  C1   C3   108.71  3.000
 KG8  H12  C1   C2   108.93  3.000
 KG8  C3   C1   C2   109.41  3.000
 KG8  H12  C1   O1   111.06  3.000
 KG8  C2   C1   O1   111.77  3.000
 KG8  C3   C1   O1   106.90  3.000
 KG8  H13  C2   O2   110.61  3.000
 KG8  H13  C2   C1   107.94  3.000
 KG8  O2   C2   C1   109.03  3.000
 KG8  H13  C2   C6   108.47  3.000
 KG8  O2   C2   C6   111.52  3.000
 KG8  C1   C2   C6   109.19  3.000
 KG8  H14  O2   C2   108.07  3.000
 KG8  H15  C3   O3   111.01  3.000
 KG8  H15  C3   C1   108.03  3.000
 KG8  O3   C3   C1   111.17  3.000
 KG8  H15  C3   C4   108.57  3.000
 KG8  C1   C3   C4   111.79  3.000
 KG8  O3   C3   C4   106.26  3.000
 KG8  H16  O3   C3   108.06  3.000
 KG8  H17  O4   C5   108.21  3.000
 KG8  C7   N2   C6   105.93  3.000
 KG8  H19  C9   H18  105.67  3.000
 KG8  H19  C9   C10  109.74  3.000
 KG8  H18  C9   C10  108.80  3.000
 KG8  H19  C9   C8   109.67  3.000
 KG8  H18  C9   C8   108.93  3.000
 KG8  C10  C9   C8   113.72  3.000
 KG8  C16  C11  C12  118.31  3.000
 KG8  C12  C11  C10  121.24  3.000
 KG8  C16  C11  C10  120.42  3.000
 KG8  H20  C12  C11  119.41  3.000
 KG8  H20  C12  C13  119.63  3.000
 KG8  C11  C12  C13  120.96  3.000
 KG8  H21  C14  C15  120.24  3.000
 KG8  H21  C14  C13  120.30  3.000
 KG8  C15  C14  C13  119.47  3.000
 KG8  H22  C16  C11  119.55  3.000
 KG8  H22  C16  C15  119.45  3.000
 KG8  C11  C16  C15  121.00  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
 KG8  CONST_01  N2   C7   C17  N1     0.00   0.0  0
 KG8  CONST_02  C7   N2   C6   N1     0.00   0.0  0
 KG8  CONST_03  C7   C17  N1   C6     0.00   0.0  0
 KG8  CONST_04  C17  C7   N2   C6     0.00   0.0  0
 KG8  CONST_05  C16  C15  C14  C13    0.00   0.0  0
 KG8  CONST_06  C16  C11  C12  C13    0.00   0.0  0
 KG8  CONST_07  C12  C11  C16  C15    0.00   0.0  0
 KG8  CONST_08  C12  C13  C14  C15    0.00   0.0  0
 KG8  CONST_09  N2   C6   N1   C17    0.00   0.0  0
 KG8  CONST_10  C14  C15  C16  C11    0.00   0.0  0
 KG8  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 KG8  CONST_12  C8   C7   C17  N1   180.00   0.0  0
 KG8  CONST_13  C8   C7   N2   C6   180.00   0.0  0
 KG8  CONST_14  C15  C16  C11  C10  180.00   0.0  0
 KG8  CONST_15  C13  C12  C11  C10  180.00   0.0  0
 KG8  CONST_16  H10  C17  N1   C4     0.00   0.0  0
 KG8  CONST_17  H9   C15  C14  C13  180.00   0.0  0
 KG8  CONST_18  H8   C13  C14  C15  180.00   0.0  0
 KG8  CONST_19  H22  C16  C11  C12  180.00   0.0  0
 KG8  CONST_20  H21  C14  C13  C12  180.00   0.0  0
 KG8  CONST_21  H20  C12  C13  C14  180.00   0.0  0
 KG8  Var_01    C9   C8   C7   C17  -15.80  30.0  2
 KG8  Var_02    C16  C11  C10  C9   -81.83  30.0  2
 KG8  Var_03    C10  C9   C8   C7   -70.43  30.0  1
 KG8  Var_04    C11  C10  C9   C8   174.40  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
 KG8  chir_01  C4  C5  C3  N1  positiv
 KG8  chir_02  C1  O1  C3  C2  negativ
 KG8  chir_03  C2  O2  C1  C6  positiv
 KG8  chir_04  C3  O3  C1  C4  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
 KG8  plan-1  C10  0.020
 KG8  plan-1  C13  0.020
 KG8  plan-1  C15  0.020
 KG8  plan-1  C11  0.020
 KG8  plan-1  C12  0.020
 KG8  plan-1  C14  0.020
 KG8  plan-1  C16  0.020
 KG8  plan-1  H9   0.020
 KG8  plan-1  H20  0.020
 KG8  plan-1  H21  0.020
 KG8  plan-1  H22  0.020
 KG8  plan-1  H8   0.020
 KG8  plan-2  N1   0.020
 KG8  plan-2  C4   0.020
 KG8  plan-2  C6   0.020
 KG8  plan-2  C7   0.020
 KG8  plan-2  C8   0.020
 KG8  plan-2  C17  0.020
 KG8  plan-2  C2   0.020
 KG8  plan-2  N2   0.020
 KG8  plan-2  H10  0.020

