# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 17:19:31 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: ~{N}1-oxidanyl-~{N}3-phenyl-benzene-1,3-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1cccc(c1)C(=O)Nc2ccccc2
#
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
 GQZ  GQZ  ~{N}1-oxidanyl-~{N}3-phenyl-benzene-1,3-dicarboxamide  ligand  31  19  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GQZ
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
 GQZ  C10  C  CR6   0  -0.041  -2.8175  -0.3766  -0.1796
 GQZ  C11  C  CR16  0  -0.289  -1.5825   0.2588  -0.2041
 GQZ  C12  C  CR6   0  -0.025  -0.4311  -0.4152   0.1865
 GQZ  C13  C  CR16  0  -0.289  -0.5249  -1.7379   0.6151
 GQZ  C14  C  CR16  0  -0.226  -1.7544  -2.3774   0.6338
 GQZ  C15  C  C     0   0.503  -4.0103   0.4012  -0.6332
 GQZ  O17  O  OH1   0  -0.538  -6.2948   0.7425  -0.2966
 GQZ  C1   C  CR16  0  -0.353   4.2295  -0.9959  -0.4499
 GQZ  C2   C  CR6   0   0.381   3.3082  -0.0237  -0.0511
 GQZ  C3   C  CR16  0  -0.314   3.7716   1.2418   0.3124
 GQZ  C4   C  CR16  0  -0.245   5.1344   1.5086   0.2719
 GQZ  C5   C  CR16  0  -0.271   6.0484   0.5440  -0.1244
 GQZ  C6   C  CR16  0  -0.243   5.5839  -0.7143  -0.4855
 GQZ  N7   N  NH1   0  -0.758   1.9637  -0.4129  -0.0287
 GQZ  C8   C  C     0   0.533   0.8577   0.3443   0.1702
 GQZ  C9   C  CR16  0  -0.276  -2.8984  -1.7047   0.2340
 GQZ  N16  N  NH1   0  -0.382  -5.1712   0.0070  -0.0670
 GQZ  O18  O  O     0  -0.457   0.8727   1.5538   0.3166
 GQZ  O19  O  O     0  -0.456  -3.9292   1.2935  -1.4562
 GQZ  H1   H  HCR6  0   0.270  -1.5155   1.2887  -0.5289
 GQZ  H2   H  HCR6  0   0.273   0.3479  -2.2780   0.9602
 GQZ  H3   H  HCR6  0   0.276  -1.8218  -3.4057   0.9613
 GQZ  H4   H  HOH1  0   0.480  -6.8066   0.2484  -0.9496
 GQZ  H6   H  HCR6  0   0.280   3.0914   2.0170   0.6241
 GQZ  H7   H  HCR6  0   0.259   5.4790   2.4932   0.5605
 GQZ  H8   H  HCR6  0   0.256   7.1066   0.7673  -0.1507
 GQZ  H9   H  HCR6  0   0.261   6.2769  -1.4848  -0.7975
 GQZ  H10  H  HNH1  0   0.423   1.8106  -1.3815  -0.2648
 GQZ  H11  H  HCR6  0   0.275  -3.8432  -2.2326   0.2332
 GQZ  H12  H  HNH1  0   0.420  -5.1868  -0.5012   0.8063
 GQZ  H5   H  HCR6  0   0.271   3.8809  -1.9813  -0.7367

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
 GQZ  C14  C9   aromatic  1.386  0.020  1.386
 GQZ  C14  C13  aromatic  1.386  0.020  1.386
 GQZ  C9   C10  aromatic  1.393  0.020  1.393
 GQZ  C13  C12  aromatic  1.394  0.020  1.394
 GQZ  N16  O17  single    1.362  0.020  1.362
 GQZ  N16  C15  single    1.350  0.020  1.350
 GQZ  C10  C15  single    1.494  0.020  1.494
 GQZ  C10  C11  aromatic  1.389  0.020  1.389
 GQZ  C15  O19  double    1.217  0.020  1.217
 GQZ  C12  C11  aromatic  1.390  0.020  1.390
 GQZ  C12  C8   single    1.496  0.020  1.496
 GQZ  O18  C8   double    1.219  0.020  1.219
 GQZ  C8   N7   single    1.355  0.020  1.355
 GQZ  N7   C2   single    1.400  0.020  1.400
 GQZ  C2   C1   aromatic  1.398  0.020  1.398
 GQZ  C2   C3   aromatic  1.396  0.020  1.396
 GQZ  C1   C6   aromatic  1.384  0.020  1.384
 GQZ  C3   C4   aromatic  1.389  0.020  1.389
 GQZ  C6   C5   aromatic  1.389  0.020  1.389
 GQZ  C4   C5   aromatic  1.387  0.020  1.387
 GQZ  C11  H1   single    0.930  0.020  1.080
 GQZ  C13  H2   single    0.930  0.020  1.080
 GQZ  C14  H3   single    0.930  0.020  1.080
 GQZ  O17  H4   single    0.850  0.020  0.980
 GQZ  C1   H5   single    0.930  0.020  1.080
 GQZ  C3   H6   single    0.930  0.020  1.080
 GQZ  C4   H7   single    0.930  0.020  1.080
 GQZ  C5   H8   single    0.930  0.020  1.080
 GQZ  C6   H9   single    0.930  0.020  1.080
 GQZ  N7   H10  single    0.860  0.020  1.020
 GQZ  C9   H11  single    0.930  0.020  1.080
 GQZ  N16  H12  single    0.890  0.020  1.040

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
 GQZ  C9   C10  C15  122.67  3.000
 GQZ  C15  C10  C11  117.79  3.000
 GQZ  C9   C10  C11  119.53  3.000
 GQZ  H1   C11  C12  119.64  3.000
 GQZ  H1   C11  C10  119.72  3.000
 GQZ  C12  C11  C10  120.64  3.000
 GQZ  C8   C12  C13  122.90  3.000
 GQZ  C8   C12  C11  117.67  3.000
 GQZ  C13  C12  C11  119.40  3.000
 GQZ  H2   C13  C14  118.72  3.000
 GQZ  H2   C13  C12  121.14  3.000
 GQZ  C14  C13  C12  120.12  3.000
 GQZ  H3   C14  C9   119.83  3.000
 GQZ  H3   C14  C13  119.88  3.000
 GQZ  C9   C14  C13  120.29  3.000
 GQZ  O19  C15  N16  123.71  3.000
 GQZ  O19  C15  C10  122.27  3.000
 GQZ  N16  C15  C10  114.02  3.000
 GQZ  H4   O17  N16  105.96  3.000
 GQZ  H5   C1   C6   119.54  3.000
 GQZ  H5   C1   C2   119.73  3.000
 GQZ  C6   C1   C2   120.73  3.000
 GQZ  N7   C2   C3   124.53  3.000
 GQZ  C3   C2   C1   119.09  3.000
 GQZ  N7   C2   C1   116.38  3.000
 GQZ  H6   C3   C4   119.31  3.000
 GQZ  H6   C3   C2   121.20  3.000
 GQZ  C4   C3   C2   119.48  3.000
 GQZ  H7   C4   C5   119.94  3.000
 GQZ  H7   C4   C3   118.63  3.000
 GQZ  C5   C4   C3   121.42  3.000
 GQZ  H8   C5   C6   120.51  3.000
 GQZ  H8   C5   C4   120.54  3.000
 GQZ  C6   C5   C4   118.95  3.000
 GQZ  H9   C6   C5   120.37  3.000
 GQZ  H9   C6   C1   119.29  3.000
 GQZ  C5   C6   C1   120.33  3.000
 GQZ  H10  N7   C8   116.56  3.000
 GQZ  H10  N7   C2   114.15  3.000
 GQZ  C8   N7   C2   129.11  3.000
 GQZ  O18  C8   N7   124.22  3.000
 GQZ  N7   C8   C12  114.90  3.000
 GQZ  O18  C8   C12  120.87  3.000
 GQZ  H11  C9   C14  118.95  3.000
 GQZ  H11  C9   C10  121.02  3.000
 GQZ  C14  C9   C10  120.02  3.000
 GQZ  H12  N16  O17  113.86  3.000
 GQZ  H12  N16  C15  121.49  3.000
 GQZ  O17  N16  C15  118.74  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
 GQZ  CONST_01  C13  C14  C9   C10     0.00   0.0  0
 GQZ  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 GQZ  CONST_03  C14  C9   C10  C11     0.00   0.0  0
 GQZ  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 GQZ  CONST_05  C9   C14  C13  C12     0.00   0.0  0
 GQZ  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 GQZ  CONST_07  C4   C3   C2   C1      0.00   0.0  0
 GQZ  CONST_08  C4   C5   C6   C1      0.00   0.0  0
 GQZ  CONST_09  C5   C6   C1   C2      0.00   0.0  0
 GQZ  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 GQZ  CONST_11  C6   C1   C2   C3      0.00   0.0  0
 GQZ  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 GQZ  CONST_13  C8   C12  C11  C10   180.00   0.0  0
 GQZ  CONST_14  C15  C10  C11  C12   180.00   0.0  0
 GQZ  CONST_15  C15  C10  C9   C14   180.00   0.0  0
 GQZ  CONST_16  C8   C12  C13  C14   180.00   0.0  0
 GQZ  CONST_17  N7   C2   C3   C4    180.00   0.0  0
 GQZ  CONST_18  N7   C2   C1   C6    180.00   0.0  0
 GQZ  CONST_19  H3   C14  C9   C10   180.00   0.0  0
 GQZ  CONST_20  H11  C9   C10  C11   180.00   0.0  0
 GQZ  CONST_21  H2   C13  C12  C11   180.00   0.0  0
 GQZ  CONST_22  H1   C11  C12  C13   180.00   0.0  0
 GQZ  CONST_23  H6   C3   C2   C1    180.00   0.0  0
 GQZ  CONST_24  H8   C5   C6   C1    180.00   0.0  0
 GQZ  CONST_25  H9   C6   C1   C2    180.00   0.0  0
 GQZ  CONST_26  H7   C4   C3   C2    180.00   0.0  0
 GQZ  CONST_27  H5   C1   C2   C3    180.00   0.0  0
 GQZ  CONST_28  C2   N7   C8   C12   180.00   0.0  0
 GQZ  CONST_29  C8   N7   C2   C1    180.00   0.0  0
 GQZ  CONST_30  C8   N7   C2   C3      0.00   0.0  0
 GQZ  CONST_31  H10  N7   C2   C1      0.00   0.0  0
 GQZ  CONST_32  O17  N16  C15  C10   180.00   0.0  0
 GQZ  CONST_33  O18  C8   N7   C2      0.00   0.0  0
 GQZ  CONST_35  O19  C15  N16  O17     0.00   0.0  0
 GQZ  Var_01    N16  C15  C10  C11  -152.30  30.0  2
 GQZ  Var_02    O18  C8   C12  C11    27.27  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
 GQZ  plan-1  C10  0.020
 GQZ  plan-1  C11  0.020
 GQZ  plan-1  C12  0.020
 GQZ  plan-1  C13  0.020
 GQZ  plan-1  C14  0.020
 GQZ  plan-1  C15  0.020
 GQZ  plan-1  C8   0.020
 GQZ  plan-1  C9   0.020
 GQZ  plan-1  H1   0.020
 GQZ  plan-1  H2   0.020
 GQZ  plan-1  H3   0.020
 GQZ  plan-1  H11  0.020
 GQZ  plan-2  C1   0.020
 GQZ  plan-2  C2   0.020
 GQZ  plan-2  C3   0.020
 GQZ  plan-2  C4   0.020
 GQZ  plan-2  C5   0.020
 GQZ  plan-2  C6   0.020
 GQZ  plan-2  N7   0.020
 GQZ  plan-2  H6   0.020
 GQZ  plan-2  H7   0.020
 GQZ  plan-2  H8   0.020
 GQZ  plan-2  H9   0.020
 GQZ  plan-2  H5   0.020
 GQZ  plan-3  C10  0.020
 GQZ  plan-3  C15  0.020
 GQZ  plan-3  O17  0.020
 GQZ  plan-3  N16  0.020
 GQZ  plan-3  O19  0.020
 GQZ  plan-3  H12  0.020
 GQZ  plan-4  C12  0.020
 GQZ  plan-4  C2   0.020
 GQZ  plan-4  N7   0.020
 GQZ  plan-4  C8   0.020
 GQZ  plan-4  O18  0.020
 GQZ  plan-4  H10  0.020

