# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:36:25 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2S,7R,9R)-4,5-dihydroxy-2,3,6,7,8,9-hexahydro-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1C[C@@H](C(O)=O)c2c(N1)c(O)c(O)c3C[C@H](Nc23)C(O)=O
#
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
 AHQ  AHQ  '(2S,7R,9R)-4,5-dihydroxy-2,3,6,7,8,9-hexahydro-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid'  ligand  38  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AHQ
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
 AHQ  O5   O  OH1   0  -0.667   0.9682   3.4532   0.1158
 AHQ  C5   C  CR6   0   0.084   0.2590   2.2783   0.2247
 AHQ  C4   C  CR6   0   0.239  -1.1247   2.3497   0.3687
 AHQ  O4   O  OH1   0  -0.624  -1.7656   3.5272   0.4761
 AHQ  C3A  C  CR56  0  -0.097  -1.8539   1.1750   0.3946
 AHQ  C3   C  CH2   0  -0.480  -3.3262   0.9624   0.5739
 AHQ  C2   C  CR15  0  -0.246  -3.4504  -0.5480   0.2300
 AHQ  C2X  C  C     0   0.550  -3.9890  -0.7071  -1.1787
 AHQ  O2B  O  OH1   0  -0.596  -5.2913  -0.4435  -1.2199
 AHQ  O2A  O  O     0  -0.428  -3.3376  -1.0034  -2.1449
 AHQ  N1   N  NR15  0  -0.696  -2.1112  -1.1107   0.3186
 AHQ  C1A  C  CR56  0   0.308  -1.1987  -0.0448   0.3087
 AHQ  C9A  C  CR6   0  -0.007   0.1824  -0.1551   0.1815
 AHQ  C6A  C  CR6   0   0.255   0.9107   1.0433   0.1154
 AHQ  N6   N  NH1   0  -0.686   2.2813   1.0403  -0.0646
 AHQ  C7   C  CH1   0  -0.197   2.8610  -0.1185  -0.6890
 AHQ  C7X  C  C     0   0.541   4.3711   0.0049  -0.6623
 AHQ  O7B  O  OH1   0  -0.589   4.9490  -1.0285  -1.2548
 AHQ  O7A  O  O     0  -0.428   4.9738   0.9274  -0.1786
 AHQ  C8   C  CH2   0  -0.450   2.3994  -1.3629   0.0616
 AHQ  C9   C  CH1   0  -0.427   0.8653  -1.4841   0.0005
 AHQ  C9X  C  C     0   0.545   0.4872  -2.4977   1.0587
 AHQ  O9B  O  O     0  -0.436   0.0829  -2.2302   2.1633
 AHQ  O9A  O  OH1   0  -0.587   0.7094  -3.7378   0.6449
 AHQ  HO5  H  HOH1  0   0.474   1.4340   3.6313   0.9422
 AHQ  HO4  H  HOH1  0   0.469  -1.1258   4.2483   0.4121
 AHQ  H3   H  HCH2  0   0.267  -3.6446   1.1546   1.6023
 AHQ  H3A  H  HCH2  0   0.263  -3.9434   1.5918  -0.0685
 AHQ  H2   H  HCR5  0   0.302  -4.1261  -1.0573   0.9185
 AHQ  HN1  H  HNR5  0   0.383  -2.0102  -1.7346   1.1062
 AHQ  HN6  H  HNH1  0   0.378   2.6453   1.9189  -0.4031
 AHQ  H7   H  HCH1  0   0.283   2.5620  -0.2171  -1.7451
 AHQ  H8   H  HCH2  0   0.280   2.8523  -2.2563  -0.3631
 AHQ  H8A  H  HCH2  0   0.265   2.7317  -1.2781   1.0999
 AHQ  H9   H  HCH1  0   0.301   0.5919  -1.8985  -0.9762
 AHQ  HO2  H  HOH1  0   0.481  -5.6144  -0.5014  -2.1314
 AHQ  HO7  H  HOH1  0   0.489   5.9133  -0.9354  -1.2273
 AHQ  HO9  H  HOH1  0   0.484   0.5148  -4.3677   1.3556

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
 AHQ  O5   C5   single    1.377  0.020  1.377
 AHQ  C5   C4   aromatic  1.393  0.020  1.393
 AHQ  C5   C6A  aromatic  1.401  0.020  1.401
 AHQ  C4   O4   single    1.345  0.020  1.345
 AHQ  C4   C3A  aromatic  1.383  0.020  1.383
 AHQ  C3A  C3   single    1.498  0.020  1.498
 AHQ  C3A  C1A  aromatic  1.387  0.020  1.387
 AHQ  C3   C2   single    1.554  0.020  1.554
 AHQ  C2   C2X  single    1.516  0.020  1.516
 AHQ  C2   N1   single    1.455  0.020  1.455
 AHQ  C2X  O2B  single    1.329  0.020  1.329
 AHQ  C2X  O2A  double    1.202  0.020  1.202
 AHQ  N1   C1A  single    1.403  0.020  1.403
 AHQ  C1A  C9A  aromatic  1.391  0.020  1.391
 AHQ  C9A  C6A  aromatic  1.404  0.020  1.404
 AHQ  C9A  C9   single    1.505  0.020  1.505
 AHQ  C6A  N6   single    1.382  0.020  1.382
 AHQ  N6   C7   single    1.438  0.020  1.438
 AHQ  C7   C7X  single    1.515  0.020  1.515
 AHQ  C7   C8   single    1.525  0.020  1.525
 AHQ  C7X  O7B  single    1.324  0.020  1.324
 AHQ  C7X  O7A  double    1.203  0.020  1.203
 AHQ  C8   C9   single    1.540  0.020  1.540
 AHQ  C9   C9X  single    1.513  0.020  1.513
 AHQ  C9X  O9B  double    1.206  0.020  1.206
 AHQ  C9X  O9A  single    1.326  0.020  1.326
 AHQ  O5   HO5  single    0.850  0.020  0.980
 AHQ  O4   HO4  single    0.850  0.020  0.980
 AHQ  C3   H3   single    0.970  0.020  1.090
 AHQ  C3   H3A  single    0.970  0.020  1.090
 AHQ  C2   H2   single    0.970  0.020  1.090
 AHQ  N1   HN1  single    0.890  0.020  1.040
 AHQ  N6   HN6  single    0.890  0.020  1.040
 AHQ  C7   H7   single    0.970  0.020  1.090
 AHQ  C8   H8   single    0.970  0.020  1.090
 AHQ  C8   H8A  single    0.970  0.020  1.090
 AHQ  C9   H9   single    0.970  0.020  1.090
 AHQ  O2B  HO2  single    0.850  0.020  0.980
 AHQ  O7B  HO7  single    0.850  0.020  0.980
 AHQ  O9A  HO9  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
 AHQ  HO5  O5   C5   109.78  3.000
 AHQ  C6A  C5   C4   121.03  3.000
 AHQ  C6A  C5   O5   120.44  3.000
 AHQ  C4   C5   O5   118.43  3.000
 AHQ  C3A  C4   O4   119.40  3.000
 AHQ  C3A  C4   C5   118.83  3.000
 AHQ  O4   C4   C5   121.77  3.000
 AHQ  HO4  O4   C4   109.42  3.000
 AHQ  C1A  C3A  C3   110.29  3.000
 AHQ  C1A  C3A  C4   119.79  3.000
 AHQ  C3   C3A  C4   129.86  3.000
 AHQ  H3A  C3   H3   106.72  3.000
 AHQ  H3A  C3   C2   112.66  3.000
 AHQ  H3   C3   C2   110.83  3.000
 AHQ  H3A  C3   C3A  113.81  3.000
 AHQ  H3   C3   C3A  111.94  3.000
 AHQ  C2   C3   C3A  100.95  3.000
 AHQ  H2   C2   N1   110.55  3.000
 AHQ  H2   C2   C2X  108.50  3.000
 AHQ  N1   C2   C2X  110.05  3.000
 AHQ  H2   C2   C3   111.32  3.000
 AHQ  N1   C2   C3   106.79  3.000
 AHQ  C2X  C2   C3   109.63  3.000
 AHQ  O2A  C2X  O2B  123.69  3.000
 AHQ  O2A  C2X  C2   125.45  3.000
 AHQ  O2B  C2X  C2   110.85  3.000
 AHQ  HO2  O2B  C2X  110.12  3.000
 AHQ  HN1  N1   C1A  114.19  3.000
 AHQ  HN1  N1   C2   112.23  3.000
 AHQ  C1A  N1   C2   107.72  3.000
 AHQ  C9A  C1A  N1   125.87  3.000
 AHQ  C9A  C1A  C3A  122.96  3.000
 AHQ  N1   C1A  C3A  111.12  3.000
 AHQ  C9   C9A  C6A  120.85  3.000
 AHQ  C9   C9A  C1A  122.09  3.000
 AHQ  C6A  C9A  C1A  116.85  3.000
 AHQ  N6   C6A  C9A  121.24  3.000
 AHQ  N6   C6A  C5   118.25  3.000
 AHQ  C9A  C6A  C5   120.51  3.000
 AHQ  HN6  N6   C7   114.22  3.000
 AHQ  HN6  N6   C6A  113.54  3.000
 AHQ  C7   N6   C6A  117.25  3.000
 AHQ  H7   C7   C8   108.46  3.000
 AHQ  H7   C7   C7X  107.13  3.000
 AHQ  C8   C7   C7X  111.07  3.000
 AHQ  H7   C7   N6   112.25  3.000
 AHQ  C8   C7   N6   108.77  3.000
 AHQ  C7X  C7   N6   109.17  3.000
 AHQ  O7A  C7X  O7B  124.03  3.000
 AHQ  O7A  C7X  C7   124.65  3.000
 AHQ  O7B  C7X  C7   111.32  3.000
 AHQ  HO7  O7B  C7X  110.28  3.000
 AHQ  H8A  C8   H8   107.93  3.000
 AHQ  H8A  C8   C9   110.27  3.000
 AHQ  H8   C8   C9   109.54  3.000
 AHQ  H8A  C8   C7   108.19  3.000
 AHQ  H8   C8   C7   110.61  3.000
 AHQ  C9   C8   C7   110.26  3.000
 AHQ  H9   C9   C9X  107.92  3.000
 AHQ  H9   C9   C8   108.28  3.000
 AHQ  C9X  C9   C8   105.90  3.000
 AHQ  H9   C9   C9A  109.15  3.000
 AHQ  C9X  C9   C9A  113.20  3.000
 AHQ  C8   C9   C9A  112.19  3.000
 AHQ  O9A  C9X  O9B  123.32  3.000
 AHQ  O9A  C9X  C9   111.49  3.000
 AHQ  O9B  C9X  C9   125.14  3.000
 AHQ  HO9  O9A  C9X  110.20  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
 AHQ  CONST_01  C1A  C3A  C4   C5      0.00   0.0  0
 AHQ  CONST_02  C1A  C9A  C6A  C5      0.00   0.0  0
 AHQ  CONST_03  C9A  C6A  C5   C4      0.00   0.0  0
 AHQ  CONST_04  C9A  C1A  C3A  C4      0.00   0.0  0
 AHQ  CONST_05  C6A  C5   C4   C3A     0.00   0.0  0
 AHQ  CONST_06  C6A  C9A  C1A  C3A     0.00   0.0  0
 AHQ  CONST_07  C3A  C4   C5   O5    180.00   0.0  0
 AHQ  CONST_08  C9A  C6A  C5   O5    180.00   0.0  0
 AHQ  CONST_09  N6   C6A  C5   O5      0.00   0.0  0
 AHQ  CONST_10  C6A  C5   C4   O4    180.00   0.0  0
 AHQ  CONST_11  C3   C3A  C4   O4      0.00   0.0  0
 AHQ  CONST_12  C1A  C3A  C4   O4    180.00   0.0  0
 AHQ  CONST_13  HO2  O2B  C2X  C2    180.00   0.0  0
 AHQ  CONST_14  HO7  O7B  C7X  C7    180.00   0.0  0
 AHQ  CONST_15  HO9  O9A  C9X  C9    180.00   0.0  0
 AHQ  Var_01    C7   N6   C6A  C5   -155.93  30.0  1
 AHQ  Var_02    C2   C3   C3A  C4    169.86  30.0  1
 AHQ  Var_03    C2   N1   C1A  C3A     7.76  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
 AHQ  chir_01  C2  C3   C2X  N1   negativ
 AHQ  chir_02  C7  N6   C8   C7X  positiv
 AHQ  chir_03  C9  C9X  C8   C9A  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
 AHQ  plan-1  C2   0.020
 AHQ  plan-1  C2X  0.020
 AHQ  plan-1  O2B  0.020
 AHQ  plan-1  O2A  0.020
 AHQ  plan-1  HO2  0.020
 AHQ  plan-2  O5   0.020
 AHQ  plan-2  C5   0.020
 AHQ  plan-2  C4   0.020
 AHQ  plan-2  O4   0.020
 AHQ  plan-2  C3A  0.020
 AHQ  plan-2  C3   0.020
 AHQ  plan-2  N1   0.020
 AHQ  plan-2  C1A  0.020
 AHQ  plan-2  C9A  0.020
 AHQ  plan-2  C6A  0.020
 AHQ  plan-2  N6   0.020
 AHQ  plan-2  C9   0.020
 AHQ  plan-3  C7   0.020
 AHQ  plan-3  C7X  0.020
 AHQ  plan-3  O7B  0.020
 AHQ  plan-3  O7A  0.020
 AHQ  plan-3  HO7  0.020
 AHQ  plan-4  C9   0.020
 AHQ  plan-4  C9X  0.020
 AHQ  plan-4  O9B  0.020
 AHQ  plan-4  O9A  0.020
 AHQ  plan-4  HO9  0.020

