# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:10:16 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-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]c(CCc3ccccc3)c[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
 PGI  PGI  (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  43  22  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PGI
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
 PGI  O6    O  OH1   0  -0.663  -2.1293   3.5593   0.4961
 PGI  C6    C  CH2   0  -0.144  -3.0313   2.5358   0.8326
 PGI  C5    C  CH1   0  -0.121  -2.8266   1.3561  -0.1047
 PGI  C4    C  CH1   0  -0.001  -4.0123   0.3883  -0.0010
 PGI  O4    O  OH1   0  -0.657  -5.0597   1.0030  -0.6964
 PGI  C3    C  CH1   0   0.012  -3.6893  -0.9905  -0.5752
 PGI  O3    O  OH1   0  -0.665  -4.8643  -1.7482  -0.5219
 PGI  C2    C  CH1   0  -0.078  -2.5897  -1.6300   0.2693
 PGI  O2    O  OH1   0  -0.655  -2.1307  -2.8285  -0.2852
 PGI  N1    N  NR5   1  -0.478  -1.5704   0.6535   0.1872
 PGI  C8    C  CR15  0  -0.134  -0.3144   1.2185   0.2826
 PGI  C7    C  CR5   0   0.306   0.5676   0.2128   0.4998
 PGI  N2    N  NR15  0  -0.643  -0.1803  -0.9405   0.5254
 PGI  C1    C  CR5   0   0.642  -1.4589  -0.6588   0.3355
 PGI  C9    C  CH2   0  -0.521   2.0455   0.2286   0.6394
 PGI  C10   C  CH2   0  -0.517   2.7576  -0.4045  -0.5664
 PGI  C14   C  CR6   0   0.126   4.2508  -0.3451  -0.4065
 PGI  C13   C  CR16  0  -0.306   4.9412  -1.3788   0.2219
 PGI  C12   C  CR16  0  -0.240   6.3160  -1.3079   0.4044
 PGI  C15   C  CR16  0  -0.307   4.9683   0.7650  -0.8460
 PGI  C16   C  CR16  0  -0.240   6.3429   0.8402  -0.6659
 PGI  C11   C  CR16  0  -0.270   7.0217  -0.1968  -0.0387
 PGI  H6    H  HOH1  0   0.467  -2.1981   4.2539   1.1580
 PGI  H6C1  H  HCH2  0   0.223  -2.9045   2.1905   1.8661
 PGI  H6C2  H  HCH2  0   0.239  -4.0694   2.8657   0.7224
 PGI  H5    H  HCH1  0   0.308  -2.7600   1.7103  -1.1374
 PGI  H4    H  HCH1  0   0.242  -4.2662   0.2583   1.0639
 PGI  HA    H  HOH1  0   0.462  -5.8533   0.4696  -0.5806
 PGI  H3    H  HCH1  0   0.252  -3.3258  -0.8771  -1.6073
 PGI  HB    H  HOH1  0   0.467  -4.7828  -2.4962  -1.1219
 PGI  H2    H  HCH1  0   0.295  -2.9739  -1.7765   1.2873
 PGI  HC    H  HOH1  0   0.478  -2.2775  -3.5430   0.3410
 PGI  H8    H  HCR5  0   0.333  -0.1492   2.2757   0.1860
 PGI  HD    H  HNR5  0   0.448   0.1732  -1.8773   0.6688
 PGI  H9C1  H  HCH2  0   0.280   2.3622   1.2659   0.7532
 PGI  H9C2  H  HCH2  0   0.279   2.3366  -0.2904   1.5562
 PGI  H101  H  HCH2  0   0.257   2.4395  -1.4435  -0.6817
 PGI  H102  H  HCH2  0   0.263   2.4534   0.1208  -1.4742
 PGI  H13   H  HCR6  0   0.248   4.3996  -2.2516   0.5681
 PGI  H12   H  HCR6  0   0.255   6.8361  -2.1235   0.8902
 PGI  H15   H  HCR6  0   0.248   4.4467   1.5781  -1.3379
 PGI  H16   H  HCR6  0   0.255   6.8843   1.7085  -1.0193
 PGI  H11   H  HCR6  0   0.255   8.0935  -0.1409   0.1008

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
 PGI  O6   C6    single    1.405  0.020  1.405
 PGI  O6   H6    single    0.850  0.020  0.980
 PGI  C6   C5    single    1.521  0.020  1.521
 PGI  C6   H6C1  single    0.970  0.020  1.090
 PGI  C6   H6C2  single    0.970  0.020  1.090
 PGI  C5   C4    single    1.534  0.020  1.534
 PGI  C5   N1    single    1.469  0.020  1.469
 PGI  C5   H5    single    0.970  0.020  1.090
 PGI  C4   O4    single    1.399  0.020  1.399
 PGI  C4   C3    single    1.528  0.020  1.528
 PGI  C4   H4    single    0.970  0.020  1.090
 PGI  O4   HA    single    0.850  0.020  0.980
 PGI  C3   O3    single    1.399  0.020  1.399
 PGI  C3   C2    single    1.527  0.020  1.527
 PGI  C3   H3    single    0.970  0.020  1.090
 PGI  O3   HB    single    0.850  0.020  0.980
 PGI  C2   O2    single    1.398  0.020  1.398
 PGI  C2   C1    single    1.492  0.020  1.492
 PGI  C2   H2    single    0.970  0.020  1.090
 PGI  O2   HC    single    0.850  0.020  0.980
 PGI  N1   C8    aromatic  1.381  0.020  1.381
 PGI  N1   C1    aromatic  1.325  0.020  1.325
 PGI  C8   C7    aromatic  1.355  0.020  1.355
 PGI  C8   H8    single    0.930  0.020  1.080
 PGI  C7   N2    aromatic  1.375  0.020  1.375
 PGI  C7   C9    single    1.485  0.020  1.485
 PGI  N2   C1    aromatic  1.323  0.020  1.323
 PGI  N2   HD    single    0.860  0.020  1.020
 PGI  C9   C10   single    1.537  0.020  1.537
 PGI  C9   H9C1  single    0.970  0.020  1.090
 PGI  C9   H9C2  single    0.970  0.020  1.090
 PGI  C10  C14   single    1.503  0.020  1.503
 PGI  C10  H101  single    0.970  0.020  1.090
 PGI  C10  H102  single    0.970  0.020  1.090
 PGI  C14  C13   aromatic  1.393  0.020  1.393
 PGI  C14  C15   aromatic  1.393  0.020  1.393
 PGI  C13  C12   aromatic  1.389  0.020  1.389
 PGI  C13  H13   single    0.930  0.020  1.080
 PGI  C12  C11   aromatic  1.389  0.020  1.389
 PGI  C12  H12   single    0.930  0.020  1.080
 PGI  C15  C16   aromatic  1.388  0.020  1.388
 PGI  C15  H15   single    0.930  0.020  1.080
 PGI  C16  C11   aromatic  1.389  0.020  1.389
 PGI  C16  H16   single    0.930  0.020  1.080
 PGI  C11  H11   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
 PGI  H6    O6   C6    108.37  3.000
 PGI  H6C2  C6   H6C1  107.42  3.000
 PGI  H6C2  C6   C5    107.42  3.000
 PGI  H6C1  C6   C5    108.72  3.000
 PGI  H6C2  C6   O6    111.41  3.000
 PGI  H6C1  C6   O6    112.37  3.000
 PGI  C5    C6   O6    109.33  3.000
 PGI  H5    C5   N1    106.89  3.000
 PGI  H5    C5   C4    108.37  3.000
 PGI  N1    C5   C4    110.24  3.000
 PGI  H5    C5   C6    109.82  3.000
 PGI  N1    C5   C6    111.33  3.000
 PGI  C4    C5   C6    110.10  3.000
 PGI  H4    C4   C3    107.78  3.000
 PGI  H4    C4   O4    111.06  3.000
 PGI  C3    C4   O4    111.58  3.000
 PGI  H4    C4   C5    108.52  3.000
 PGI  C3    C4   C5    112.36  3.000
 PGI  O4    C4   C5    105.53  3.000
 PGI  HA    O4   C4    108.28  3.000
 PGI  H3    C3   C2    108.92  3.000
 PGI  H3    C3   O3    111.66  3.000
 PGI  C2    C3   O3    110.91  3.000
 PGI  H3    C3   C4    109.23  3.000
 PGI  C2    C3   C4    108.80  3.000
 PGI  O3    C3   C4    107.26  3.000
 PGI  HB    O3   C3    109.03  3.000
 PGI  H2    C2   C1    108.12  3.000
 PGI  H2    C2   O2    111.61  3.000
 PGI  C1    C2   O2    109.07  3.000
 PGI  H2    C2   C3    108.47  3.000
 PGI  C1    C2   C3    107.32  3.000
 PGI  O2    C2   C3    112.09  3.000
 PGI  HC    O2   C2    109.19  3.000
 PGI  C1    N1   C8    108.72  3.000
 PGI  C1    N1   C5    124.60  3.000
 PGI  C8    N1   C5    126.60  3.000
 PGI  H8    C8   C7    130.14  3.000
 PGI  H8    C8   N1    122.44  3.000
 PGI  C7    C8   N1    107.43  3.000
 PGI  C9    C7   N2    123.28  3.000
 PGI  C9    C7   C8    130.92  3.000
 PGI  N2    C7   C8    105.75  3.000
 PGI  HD    N2   C1    123.73  3.000
 PGI  HD    N2   C7    126.12  3.000
 PGI  C1    N2   C7    110.15  3.000
 PGI  N2    C1   N1    107.95  3.000
 PGI  N2    C1   C2    126.88  3.000
 PGI  N1    C1   C2    125.16  3.000
 PGI  H9C2  C9   H9C1  106.67  3.000
 PGI  H9C2  C9   C10   109.83  3.000
 PGI  H9C1  C9   C10   109.82  3.000
 PGI  H9C2  C9   C7    109.81  3.000
 PGI  H9C1  C9   C7    108.00  3.000
 PGI  C10   C9   C7    112.53  3.000
 PGI  H102  C10  H101  106.77  3.000
 PGI  H102  C10  C14   110.26  3.000
 PGI  H101  C10  C14   109.75  3.000
 PGI  H102  C10  C9    108.97  3.000
 PGI  H101  C10  C9    109.85  3.000
 PGI  C14   C10  C9    111.14  3.000
 PGI  C15   C14  C13   118.59  3.000
 PGI  C15   C14  C10   120.64  3.000
 PGI  C13   C14  C10   120.74  3.000
 PGI  H13   C13  C12   119.59  3.000
 PGI  H13   C13  C14   119.60  3.000
 PGI  C12   C13  C14   120.80  3.000
 PGI  H12   C12  C11   120.13  3.000
 PGI  H12   C12  C13   119.74  3.000
 PGI  C11   C12  C13   120.13  3.000
 PGI  H15   C15  C16   119.65  3.000
 PGI  H15   C15  C14   119.54  3.000
 PGI  C16   C15  C14   120.81  3.000
 PGI  H16   C16  C11   120.12  3.000
 PGI  H16   C16  C15   119.75  3.000
 PGI  C11   C16  C15   120.13  3.000
 PGI  H11   C11  C16   120.24  3.000
 PGI  H11   C11  C12   120.22  3.000
 PGI  C16   C11  C12   119.54  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
 PGI  CONST_01  N2   C7   C8   N1      0.00   0.0  0
 PGI  CONST_02  C7   N2   C1   N1      0.00   0.0  0
 PGI  CONST_03  N2   C1   N1   C8      0.00   0.0  0
 PGI  CONST_04  C1   N2   C7   C8      0.00   0.0  0
 PGI  CONST_05  C1   N1   C8   C7      0.00   0.0  0
 PGI  CONST_06  C11  C12  C13  C14     0.00   0.0  0
 PGI  CONST_07  C11  C16  C15  C14     0.00   0.0  0
 PGI  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 PGI  CONST_09  C16  C11  C12  C13     0.00   0.0  0
 PGI  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 PGI  CONST_11  C15  C16  C11  C12     0.00   0.0  0
 PGI  CONST_12  C9   C7   C8   N1    180.00   0.0  0
 PGI  CONST_13  C9   C7   N2   C1    180.00   0.0  0
 PGI  CONST_14  C12  C13  C14  C10   180.00   0.0  0
 PGI  CONST_15  C16  C15  C14  C10   180.00   0.0  0
 PGI  CONST_16  H8   C8   N1   C5      0.00   0.0  0
 PGI  CONST_17  HD   N2   C1   C2      0.00   0.0  0
 PGI  CONST_18  H12  C12  C13  C14   180.00   0.0  0
 PGI  CONST_19  H16  C16  C15  C14   180.00   0.0  0
 PGI  CONST_20  H15  C15  C14  C13   180.00   0.0  0
 PGI  CONST_21  H11  C11  C12  C13   180.00   0.0  0
 PGI  CONST_22  H13  C13  C14  C15   180.00   0.0  0
 PGI  Var_01    C10  C9   C7   C8   -109.29  30.0  2
 PGI  Var_02    C14  C10  C9   C7    178.76  30.0  3
 PGI  Var_03    C13  C14  C10  C9     89.79  30.0  2

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
 PGI  chir_01  C5  C6  C4  N1  positiv
 PGI  chir_02  C4  O4  C5  C3  positiv
 PGI  chir_03  C3  O3  C2  C4  positiv
 PGI  chir_04  C2  O2  C1  C3  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
 PGI  plan-1  C10  0.020
 PGI  plan-1  C14  0.020
 PGI  plan-1  C13  0.020
 PGI  plan-1  C12  0.020
 PGI  plan-1  C15  0.020
 PGI  plan-1  C16  0.020
 PGI  plan-1  C11  0.020
 PGI  plan-1  H13  0.020
 PGI  plan-1  H12  0.020
 PGI  plan-1  H15  0.020
 PGI  plan-1  H16  0.020
 PGI  plan-1  H11  0.020
 PGI  plan-2  C5   0.020
 PGI  plan-2  C2   0.020
 PGI  plan-2  N1   0.020
 PGI  plan-2  C8   0.020
 PGI  plan-2  C7   0.020
 PGI  plan-2  N2   0.020
 PGI  plan-2  C1   0.020
 PGI  plan-2  C9   0.020
 PGI  plan-2  H8   0.020
 PGI  plan-2  HD   0.020

