# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 19:40:59 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  30  24  .  2020-10-21  2022-11-17
;
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  -0.715  17.5042  51.1648  66.6918
 PQQ  C2    C  CR5   0   0.231  16.9547  49.9904  66.2648
 PQQ  C2X   C  C     0   0.478  17.4322  49.3870  65.0209
 PQQ  O2A   O  O     0  -0.438  18.2945  49.8879  64.3394
 PQQ  O2B   O  OH1   0  -0.584  16.8112  48.2537  64.7508
 PQQ  C3    C  CR15  0  -0.291  15.9897  49.6081  67.1614
 PQQ  C3A   C  CR56  0  -0.166  15.9677  50.6009  68.1569
 PQQ  C1A   C  CR56  0   0.376  16.9286  51.5660  67.8341
 PQQ  C4    C  CR6   0   0.244  15.1373  50.6828  69.3272
 PQQ  O4    O  O     0  -0.351  14.2936  49.8801  69.6495
 PQQ  C5    C  CR6   0   0.279  15.3809  51.9148  70.2048
 PQQ  O5    O  O     0  -0.313  14.6969  52.0919  71.1742
 PQQ  C6A   C  CR66  0  -0.011  16.4793  52.8719  69.8383
 PQQ  N6    N  N     0  -0.376  16.6536  53.8333  70.7172
 PQQ  C7    C  CR6   0   0.108  17.6100  54.7210  70.5237
 PQQ  C7X   C  C     0   0.526  17.7402  55.7686  71.5858
 PQQ  O7A   O  O     0  -0.413  17.0177  55.8223  72.5439
 PQQ  O7B   O  OH1   0  -0.585  18.7311  56.6048  71.3359
 PQQ  C8    C  CR16  0  -0.287  18.4351  54.6751  69.4120
 PQQ  C9    C  CR6   0   0.088  18.2414  53.6912  68.4516
 PQQ  C9X   C  C     0   0.469  19.1809  53.7998  67.2895
 PQQ  O9A   O  O     0  -0.388  20.3417  54.0676  67.4279
 PQQ  O9B   O  OH1   0  -0.595  18.5800  53.6428  66.1207
 PQQ  C9A   C  CR66  0   0.179  17.2400  52.7291  68.6552
 PQQ  HN1   H  HNR5  0   0.432  18.1931  51.6746  66.1586
 PQQ  HOB2  H  HOH1  0   0.496  17.1445  47.8751  63.9230
 PQQ  H3    H  HCR5  0   0.288  15.3716  48.7265  67.1147
 PQQ  HOB7  H  HOH1  0   0.498  18.8039  57.2688  72.0385
 PQQ  H8    H  HCR6  0   0.314  19.2177  55.4064  69.2735
 PQQ  HOB9  H  HOH1  0   0.508  19.2090  53.7839  65.3932

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  1.365  0.020  1.365
 PQQ  N1   C1A   aromatic  1.341  0.020  1.341
 PQQ  N1   HN1   single    0.860  0.020  1.020
 PQQ  C2   C2X   single    1.463  0.020  1.463
 PQQ  C2   C3    aromatic  1.372  0.020  1.372
 PQQ  C2X  O2A   double    1.208  0.020  1.208
 PQQ  C2X  O2B   single    1.320  0.020  1.320
 PQQ  O2B  HOB2  single    0.850  0.020  0.980
 PQQ  C3   C3A   aromatic  1.406  0.020  1.406
 PQQ  C3   H3    single    0.930  0.020  1.080
 PQQ  C3A  C1A   aromatic  1.400  0.020  1.400
 PQQ  C3A  C4    single    1.437  0.020  1.437
 PQQ  C1A  C9A   aromatic  1.457  0.020  1.457
 PQQ  C4   O4    double    1.208  0.020  1.208
 PQQ  C4   C5    single    1.532  0.020  1.532
 PQQ  C5   O5    double    1.200  0.020  1.200
 PQQ  C5   C6A   single    1.502  0.020  1.502
 PQQ  C6A  N6    aromatic  1.314  0.020  1.314
 PQQ  C6A  C9A   aromatic  1.414  0.020  1.414
 PQQ  N6   C7    aromatic  1.319  0.020  1.319
 PQQ  C7   C7X   single    1.498  0.020  1.498
 PQQ  C7   C8    aromatic  1.385  0.020  1.385
 PQQ  C7X  O7A   double    1.201  0.020  1.201
 PQQ  C7X  O7B   single    1.321  0.020  1.321
 PQQ  O7B  HOB7  single    0.850  0.020  0.980
 PQQ  C8   C9    aromatic  1.388  0.020  1.388
 PQQ  C8   H8    single    0.930  0.020  1.080
 PQQ  C9   C9X   single    1.498  0.020  1.498
 PQQ  C9   C9A   aromatic  1.403  0.020  1.403
 PQQ  C9X  O9A   double    1.199  0.020  1.199
 PQQ  C9X  O9B   single    1.324  0.020  1.324
 PQQ  O9B  HOB9  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
 PQQ  HN1   N1   C1A  126.30  3.000
 PQQ  HN1   N1   C2   122.96  3.000
 PQQ  C1A   N1   C2   110.56  3.000
 PQQ  C3    C2   C2X  132.11  3.000
 PQQ  C3    C2   N1   108.58  3.000
 PQQ  C2X   C2   N1   119.31  3.000
 PQQ  O2B   C2X  O2A  125.19  3.000
 PQQ  O2B   C2X  C2   112.00  3.000
 PQQ  O2A   C2X  C2   122.81  3.000
 PQQ  HOB2  O2B  C2X  110.38  3.000
 PQQ  H3    C3   C3A  126.82  3.000
 PQQ  H3    C3   C2   127.10  3.000
 PQQ  C3A   C3   C2   106.08  3.000
 PQQ  C4    C3A  C1A  123.03  3.000
 PQQ  C4    C3A  C3   128.74  3.000
 PQQ  C1A   C3A  C3   108.23  3.000
 PQQ  C9A   C1A  C3A  124.55  3.000
 PQQ  C9A   C1A  N1   128.84  3.000
 PQQ  C3A   C1A  N1   106.55  3.000
 PQQ  C5    C4   O4   119.50  3.000
 PQQ  C5    C4   C3A  114.86  3.000
 PQQ  O4    C4   C3A  125.64  3.000
 PQQ  C6A   C5   O5   121.33  3.000
 PQQ  C6A   C5   C4   119.27  3.000
 PQQ  O5    C5   C4   119.40  3.000
 PQQ  C9A   C6A  N6   124.20  3.000
 PQQ  C9A   C6A  C5   122.22  3.000
 PQQ  N6    C6A  C5   113.58  3.000
 PQQ  C7    N6   C6A  119.36  3.000
 PQQ  C8    C7   C7X  122.73  3.000
 PQQ  C8    C7   N6   121.82  3.000
 PQQ  C7X   C7   N6   115.45  3.000
 PQQ  O7B   C7X  O7A  125.03  3.000
 PQQ  O7B   C7X  C7   111.96  3.000
 PQQ  O7A   C7X  C7   123.01  3.000
 PQQ  HOB7  O7B  C7X  110.67  3.000
 PQQ  H8    C8   C9   119.49  3.000
 PQQ  H8    C8   C7   120.80  3.000
 PQQ  C9    C8   C7   119.70  3.000
 PQQ  C9A   C9   C9X  127.56  3.000
 PQQ  C9A   C9   C8   119.01  3.000
 PQQ  C9X   C9   C8   113.43  3.000
 PQQ  O9B   C9X  O9A  124.59  3.000
 PQQ  O9B   C9X  C9   113.06  3.000
 PQQ  O9A   C9X  C9   122.25  3.000
 PQQ  HOB9  O9B  C9X  110.49  3.000
 PQQ  C9    C9A  C6A  115.85  3.000
 PQQ  C9    C9A  C1A  128.16  3.000
 PQQ  C6A   C9A  C1A  115.92  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  CONST_30  HOB2  O2B  C2X  C2   180.00   0.0  0
 PQQ  CONST_31  HOB7  O7B  C7X  C7   180.00   0.0  0
 PQQ  CONST_32  HOB9  O9B  C9X  C9   180.00   0.0  0
 PQQ  Var_01    O2A   C2X  C2   N1    -0.49  30.0  2
 PQQ  Var_02    O7A   C7X  C7   N6    -1.09  30.0  2
 PQQ  Var_03    O9A   C9X  C9   C8    41.05  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-2  HOB2  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-3  HOB7  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
 PQQ  plan-4  HOB9  0.020

