# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:34:51 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 4,5-dioxo-4,5-dihydro-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]c2c(c1)C(=O)C(=O)c3nc(cc(C(O)=O)c23)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
 PQQ  PQQ  '4,5-dioxo-4,5-dihydro-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid'  ligand  27  24  .  2020-10-21  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PQQ
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
 PQQ  N1   N  NR15   0  -0.706  17.3384  51.2513  66.6750
 PQQ  C2   C  CR5    0   0.154  16.7798  50.0921  66.2116
 PQQ  C2X  C  C      0   0.354  17.1492  49.5293  64.8700
 PQQ  O2A  O  O      0  -0.598  17.9720  50.1910  64.2088
 PQQ  O2B  O  OC    -1  -0.590  16.5943  48.4604  64.5571
 PQQ  C3   C  CR15   0  -0.360  15.8990  49.6397  67.1617
 PQQ  C3A  C  CR56   0  -0.155  15.9313  50.5738  68.2253
 PQQ  C1A  C  CR56   0   0.323  16.8557  51.5676  67.8801
 PQQ  C4   C  CR6    0   0.211  15.1813  50.6238  69.4376
 PQQ  O4   O  O      0  -0.391  14.3743  49.7998  69.8200
 PQQ  C5   C  CR6    0   0.262  15.4281  51.8746  70.3010
 PQQ  O5   O  O      0  -0.343  14.7809  52.0158  71.3065
 PQQ  C6A  C  CR66   0  -0.034  16.4623  52.8768  69.8863
 PQQ  N6   N  N      0  -0.391  16.6050  53.8817  70.7310
 PQQ  C7   C  CR6    0   0.037  17.5290  54.7982  70.4878
 PQQ  C7X  C  C      0   0.387  17.6612  55.9733  71.4583
 PQQ  O7A  O  O      0  -0.586  16.8537  56.0094  72.3991
 PQQ  O7B  O  OC    -1  -0.585  18.5710  56.7843  71.2007
 PQQ  C8   C  CR16   0  -0.330  18.3736  54.6825  69.3906
 PQQ  C9   C  CR6    0   0.014  18.2369  53.6523  68.4692
 PQQ  C9X  C  C      0   0.415  19.2529  53.6511  67.3204
 PQQ  O9A  O  O      0  -0.544  20.3767  54.0732  67.6090
 PQQ  O9B  O  OC    -1  -0.597  18.8718  53.2656  66.1901
 PQQ  C9A  C  CR66   0   0.104  17.2114  52.7160  68.7023
 PQQ  HN1  H  HNR5   0   0.429  17.9982  51.8837  66.1893
 PQQ  H3   H  HCR5   0   0.253  15.2924  48.7506  67.1016
 PQQ  H8   H  HCR6   0   0.264  19.1540  55.4151  69.2524

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
 PQQ  N1   C2   aromatic  1.368  0.020  1.368
 PQQ  N1   C1A  aromatic  1.336  0.020  1.336
 PQQ  N1   HN1  single    0.860  0.020  1.020
 PQQ  C2   C2X  single    1.501  0.020  1.501
 PQQ  C2   C3   aromatic  1.372  0.020  1.372
 PQQ  C2X  O2A  deloc     1.246  0.020  1.246
 PQQ  C2X  O2B  deloc     1.244  0.020  1.244
 PQQ  C3   C3A  aromatic  1.416  0.020  1.416
 PQQ  C3   H3   single    0.930  0.020  1.080
 PQQ  C3A  C1A  aromatic  1.401  0.020  1.401
 PQQ  C3A  C4   single    1.426  0.020  1.426
 PQQ  C1A  C9A  aromatic  1.456  0.020  1.456
 PQQ  C4   O4   double    1.215  0.020  1.215
 PQQ  C4   C5   single    1.540  0.020  1.540
 PQQ  C5   O5   double    1.204  0.020  1.204
 PQQ  C5   C6A  single    1.499  0.020  1.499
 PQQ  C6A  N6   aromatic  1.321  0.020  1.321
 PQQ  C6A  C9A  aromatic  1.410  0.020  1.410
 PQQ  N6   C7   aromatic  1.324  0.020  1.324
 PQQ  C7   C7X  single    1.530  0.020  1.530
 PQQ  C7   C8   aromatic  1.389  0.020  1.389
 PQQ  C7X  O7A  deloc     1.240  0.020  1.240
 PQQ  C7X  O7B  deloc     1.246  0.020  1.246
 PQQ  C8   C9   aromatic  1.389  0.020  1.389
 PQQ  C8   H8   single    0.930  0.020  1.080
 PQQ  C9   C9X  single    1.534  0.020  1.534
 PQQ  C9   C9A  aromatic  1.408  0.020  1.408
 PQQ  C9X  O9A  deloc     1.235  0.020  1.235
 PQQ  C9X  O9B  deloc     1.254  0.020  1.254

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
 PQQ  HN1  N1   C1A  120.59  3.000
 PQQ  HN1  N1   C2   128.27  3.000
 PQQ  C1A  N1   C2   111.02  3.000
 PQQ  C3   C2   C2X  130.78  3.000
 PQQ  C3   C2   N1   107.88  3.000
 PQQ  C2X  C2   N1   121.34  3.000
 PQQ  O2B  C2X  O2A  128.12  3.000
 PQQ  O2B  C2X  C2   115.92  3.000
 PQQ  O2A  C2X  C2   115.96  3.000
 PQQ  H3   C3   C3A  126.79  3.000
 PQQ  H3   C3   C2   126.47  3.000
 PQQ  C3A  C3   C2   106.74  3.000
 PQQ  C4   C3A  C1A  122.12  3.000
 PQQ  C4   C3A  C3   130.51  3.000
 PQQ  C1A  C3A  C3   107.34  3.000
 PQQ  C9A  C1A  C3A  125.56  3.000
 PQQ  C9A  C1A  N1   127.42  3.000
 PQQ  C3A  C1A  N1   107.02  3.000
 PQQ  C5   C4   O4   118.74  3.000
 PQQ  C5   C4   C3A  114.88  3.000
 PQQ  O4   C4   C3A  126.36  3.000
 PQQ  C6A  C5   O5   121.57  3.000
 PQQ  C6A  C5   C4   119.91  3.000
 PQQ  O5   C5   C4   118.51  3.000
 PQQ  C9A  C6A  N6   124.50  3.000
 PQQ  C9A  C6A  C5   121.51  3.000
 PQQ  N6   C6A  C5   113.98  3.000
 PQQ  C7   N6   C6A  118.99  3.000
 PQQ  C8   C7   C7X  120.82  3.000
 PQQ  C8   C7   N6   120.78  3.000
 PQQ  C7X  C7   N6   118.39  3.000
 PQQ  O7B  C7X  O7A  127.84  3.000
 PQQ  O7B  C7X  C7   115.59  3.000
 PQQ  O7A  C7X  C7   116.57  3.000
 PQQ  H8   C8   C9   119.33  3.000
 PQQ  H8   C8   C7   118.96  3.000
 PQQ  C9   C8   C7   121.72  3.000
 PQQ  C9A  C9   C9X  127.30  3.000
 PQQ  C9A  C9   C8   117.08  3.000
 PQQ  C9X  C9   C8   115.61  3.000
 PQQ  O9B  C9X  O9A  126.34  3.000
 PQQ  O9B  C9X  C9   118.31  3.000
 PQQ  O9A  C9X  C9   115.32  3.000
 PQQ  C9   C9A  C6A  116.75  3.000
 PQQ  C9   C9A  C1A  127.50  3.000
 PQQ  C6A  C9A  C1A  115.73  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
 PQQ  CONST_01  C3A  C3   C2   N1     0.00   0.0  0
 PQQ  CONST_02  C3   C3A  C1A  N1     0.00   0.0  0
 PQQ  CONST_03  C6A  C9A  C1A  N1   180.00   0.0  0
 PQQ  CONST_04  C9   C9A  C1A  N1     0.00   0.0  0
 PQQ  CONST_05  C3A  C1A  N1   C2     0.00   0.0  0
 PQQ  CONST_06  C9A  C1A  N1   C2   180.00   0.0  0
 PQQ  CONST_07  C1A  C3A  C3   C2     0.00   0.0  0
 PQQ  CONST_08  C1A  N1   C2   C3     0.00   0.0  0
 PQQ  CONST_09  C9A  C1A  C3A  C3   180.00   0.0  0
 PQQ  CONST_10  C6A  C9A  C1A  C3A    0.00   0.0  0
 PQQ  CONST_11  C9   C9A  C1A  C3A  180.00   0.0  0
 PQQ  CONST_12  N6   C6A  C9A  C1A  180.00   0.0  0
 PQQ  CONST_13  C8   C9   C9A  C1A  180.00   0.0  0
 PQQ  CONST_14  C8   C7   N6   C6A    0.00   0.0  0
 PQQ  CONST_15  C8   C9   C9A  C6A    0.00   0.0  0
 PQQ  CONST_16  C9   C9A  C6A  N6     0.00   0.0  0
 PQQ  CONST_17  C9   C8   C7   N6     0.00   0.0  0
 PQQ  CONST_18  C9A  C6A  N6   C7     0.00   0.0  0
 PQQ  CONST_19  C9A  C9   C8   C7     0.00   0.0  0
 PQQ  CONST_20  C1A  N1   C2   C2X  180.00   0.0  0
 PQQ  CONST_21  C3A  C3   C2   C2X  180.00   0.0  0
 PQQ  CONST_22  C9X  C9   C9A  C1A    0.00   0.0  0
 PQQ  CONST_23  C7X  C7   N6   C6A  180.00   0.0  0
 PQQ  CONST_24  C9X  C9   C9A  C6A  180.00   0.0  0
 PQQ  CONST_25  C9X  C9   C8   C7   180.00   0.0  0
 PQQ  CONST_26  C9   C8   C7   C7X  180.00   0.0  0
 PQQ  CONST_27  H3   C3   C2   N1   180.00   0.0  0
 PQQ  CONST_28  HN1  N1   C2   C3   180.00   0.0  0
 PQQ  CONST_29  H8   C8   C7   N6   180.00   0.0  0
 PQQ  Var_01    O2A  C2X  C2   N1    -1.02  30.0  2
 PQQ  Var_02    O7A  C7X  C7   N6    -2.17  30.0  2
 PQQ  Var_03    O9A  C9X  C9   C8    33.07  30.0  2

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
 PQQ  plan-1  N1   0.020
 PQQ  plan-1  C2   0.020
 PQQ  plan-1  C2X  0.020
 PQQ  plan-1  C3   0.020
 PQQ  plan-1  C3A  0.020
 PQQ  plan-1  C1A  0.020
 PQQ  plan-1  C4   0.020
 PQQ  plan-1  O4   0.020
 PQQ  plan-1  C5   0.020
 PQQ  plan-1  O5   0.020
 PQQ  plan-1  C6A  0.020
 PQQ  plan-1  N6   0.020
 PQQ  plan-1  C7   0.020
 PQQ  plan-1  C7X  0.020
 PQQ  plan-1  C8   0.020
 PQQ  plan-1  C9   0.020
 PQQ  plan-1  C9X  0.020
 PQQ  plan-1  C9A  0.020
 PQQ  plan-1  HN1  0.020
 PQQ  plan-1  H3   0.020
 PQQ  plan-1  H8   0.020
 PQQ  plan-2  C2   0.020
 PQQ  plan-2  C2X  0.020
 PQQ  plan-2  O2A  0.020
 PQQ  plan-2  O2B  0.020
 PQQ  plan-3  C7   0.020
 PQQ  plan-3  C7X  0.020
 PQQ  plan-3  O7A  0.020
 PQQ  plan-3  O7B  0.020
 PQQ  plan-4  C9   0.020
 PQQ  plan-4  C9X  0.020
 PQQ  plan-4  O9A  0.020
 PQQ  plan-4  O9B  0.020

