# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:35:21 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-(4-hydroxy-3-nitrophenyl)quinazoline-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1[N+]([O-])=O)N2C(=O)NC(=O)c3ccccc23
#
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
 LM7  LM7  1-(4-hydroxy-3-nitrophenyl)quinazoline-2,4(1H,3H)-dione  ligand  31  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LM7
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
 LM7  O4   O  O      0  -0.358   3.2658   0.2418   2.3919
 LM7  N2   N  N      1   0.364   3.6799   0.2644   1.2622
 LM7  O3   O  O     -1  -0.422   4.8596   0.4419   0.9937
 LM7  C6   C  CR6    0   0.170   2.7593   0.0771   0.1736
 LM7  C5   C  CR6    0   0.384   3.2036   0.0973  -1.1630
 LM7  O2   O  OH1    0  -0.593   4.4539   0.2796  -1.5489
 LM7  C4   C  CR16   0  -0.355   2.2451  -0.0897  -2.1672
 LM7  C3   C  CR16   0  -0.209   0.9221  -0.2878  -1.8559
 LM7  C7   C  CR16   0  -0.296   1.4147  -0.1255   0.4852
 LM7  C2   C  CR6    0   0.233   0.5043  -0.3078  -0.5244
 LM7  N1   N  NR6    0  -0.706  -0.8713  -0.5020  -0.2149
 LM7  C1   C  CR6    0   0.703  -1.2866  -1.8011  -0.0450
 LM7  O1   O  O      0  -0.464  -0.5321  -2.7439  -0.1364
 LM7  N    N  NR16   0  -0.731  -2.6206  -1.9617   0.2376
 LM7  C8   C  CR66   0   0.426  -1.7337   0.5874  -0.1267
 LM7  C13  C  CR66   0  -0.134  -3.0852   0.3750   0.1583
 LM7  C    C  CR6    0   0.571  -3.5810  -0.9858   0.3596
 LM7  O    O  O      0  -0.433  -4.7329  -1.2715   0.6133
 LM7  C12  C  CR16   0  -0.274  -3.9601   1.4568   0.2502
 LM7  C11  C  CR16   0  -0.259  -3.5027   2.7440   0.0622
 LM7  C10  C  CR16   0  -0.234  -2.1550   2.9502  -0.2225
 LM7  C9   C  CR16   0  -0.316  -1.2722   1.8908  -0.3178
 LM7  H1   H  HOH1   0   0.486   5.0186   0.3966  -0.7624
 LM7  H2   H  HCR6   0   0.298   2.5696  -0.0739  -3.1991
 LM7  H3   H  HCR6   0   0.294   0.1990  -0.4257  -2.6492
 LM7  H4   H  HCR6   0   0.314   1.0879  -0.1393   1.5157
 LM7  H5   H  HNR6   0   0.431  -2.9220  -2.9201   0.3668
 LM7  H6   H  HCR6   0   0.274  -5.0031   1.2722   0.4695
 LM7  H7   H  HCR6   0   0.270  -4.1816   3.5818   0.1345
 LM7  H8   H  HCR6   0   0.277  -1.7830   3.9547  -0.3740
 LM7  H9   H  HCR6   0   0.288  -0.2328   2.0853  -0.5392

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
 LM7  O2   C5   single    1.321  0.020  1.321
 LM7  C5   C4   aromatic  1.401  0.020  1.401
 LM7  C5   C6   aromatic  1.409  0.020  1.409
 LM7  C4   C3   aromatic  1.374  0.020  1.374
 LM7  O3   N2   single    1.223  0.020  1.223
 LM7  C3   C2   aromatic  1.396  0.020  1.396
 LM7  C6   N2   single    1.438  0.020  1.438
 LM7  C6   C7   aromatic  1.395  0.020  1.395
 LM7  N2   O4   double    1.203  0.020  1.203
 LM7  O1   C1   double    1.211  0.020  1.211
 LM7  C7   C2   aromatic  1.372  0.020  1.372
 LM7  C2   N1   single    1.423  0.020  1.423
 LM7  C1   N1   single    1.374  0.020  1.374
 LM7  C1   N    single    1.373  0.020  1.373
 LM7  N1   C8   single    1.392  0.020  1.392
 LM7  N    C    single    1.375  0.020  1.375
 LM7  C8   C9   aromatic  1.396  0.020  1.396
 LM7  C8   C13  aromatic  1.398  0.020  1.398
 LM7  C9   C10  aromatic  1.382  0.020  1.382
 LM7  C    C13  single    1.462  0.020  1.462
 LM7  C    O    double    1.214  0.020  1.214
 LM7  C13  C12  aromatic  1.394  0.020  1.394
 LM7  C10  C11  aromatic  1.393  0.020  1.393
 LM7  C12  C11  aromatic  1.379  0.020  1.379
 LM7  O2   H1   single    0.850  0.020  0.980
 LM7  C4   H2   single    0.930  0.020  1.080
 LM7  C3   H3   single    0.930  0.020  1.080
 LM7  C7   H4   single    0.930  0.020  1.080
 LM7  N    H5   single    0.860  0.020  1.020
 LM7  C12  H6   single    0.930  0.020  1.080
 LM7  C11  H7   single    0.930  0.020  1.080
 LM7  C10  H8   single    0.930  0.020  1.080
 LM7  C9   H9   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
 LM7  C6   N2   O3   118.06  3.000
 LM7  C6   N2   O4   119.20  3.000
 LM7  O3   N2   O4   122.74  3.000
 LM7  C7   C6   C5   121.20  3.000
 LM7  C7   C6   N2   117.84  3.000
 LM7  C5   C6   N2   120.96  3.000
 LM7  C4   C5   O2   117.17  3.000
 LM7  C4   C5   C6   117.55  3.000
 LM7  O2   C5   C6   125.29  3.000
 LM7  H1   O2   C5   109.20  3.000
 LM7  H2   C4   C3   120.48  3.000
 LM7  H2   C4   C5   118.47  3.000
 LM7  C3   C4   C5   121.06  3.000
 LM7  H3   C3   C2   119.84  3.000
 LM7  H3   C3   C4   119.72  3.000
 LM7  C2   C3   C4   120.44  3.000
 LM7  H4   C7   C2   119.95  3.000
 LM7  H4   C7   C6   120.40  3.000
 LM7  C2   C7   C6   119.65  3.000
 LM7  N1   C2   C7   119.97  3.000
 LM7  N1   C2   C3   119.92  3.000
 LM7  C7   C2   C3   120.11  3.000
 LM7  C8   N1   C1   123.00  3.000
 LM7  C8   N1   C2   120.38  3.000
 LM7  C1   N1   C2   116.61  3.000
 LM7  N    C1   O1   121.99  3.000
 LM7  N    C1   N1   115.44  3.000
 LM7  O1   C1   N1   122.57  3.000
 LM7  H5   N    C    116.90  3.000
 LM7  H5   N    C1   115.22  3.000
 LM7  C    N    C1   127.88  3.000
 LM7  C9   C8   C13  119.32  3.000
 LM7  C13  C8   N1   119.54  3.000
 LM7  C9   C8   N1   121.15  3.000
 LM7  C12  C13  C    120.01  3.000
 LM7  C12  C13  C8   120.15  3.000
 LM7  C    C13  C8   119.84  3.000
 LM7  O    C    C13  124.74  3.000
 LM7  O    C    N    120.96  3.000
 LM7  C13  C    N    114.30  3.000
 LM7  H6   C12  C11  120.45  3.000
 LM7  H6   C12  C13  119.08  3.000
 LM7  C11  C12  C13  120.47  3.000
 LM7  H7   C11  C10  120.45  3.000
 LM7  H7   C11  C12  120.41  3.000
 LM7  C10  C11  C12  119.15  3.000
 LM7  H8   C10  C9   118.84  3.000
 LM7  H8   C10  C11  119.93  3.000
 LM7  C9   C10  C11  121.24  3.000
 LM7  H9   C9   C10  119.38  3.000
 LM7  H9   C9   C8   120.95  3.000
 LM7  C10  C9   C8   119.67  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
 LM7  CONST_01  C3   C4   C5   C6     0.00   0.0  0
 LM7  CONST_02  C3   C2   C7   C6     0.00   0.0  0
 LM7  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 LM7  CONST_04  C2   C7   C6   C5     0.00   0.0  0
 LM7  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 LM7  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 LM7  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 LM7  CONST_08  C11  C12  C13  C8     0.00   0.0  0
 LM7  CONST_09  C10  C9   C8   C13    0.00   0.0  0
 LM7  CONST_10  C10  C11  C12  C13    0.00   0.0  0
 LM7  CONST_11  C9   C8   C13  C12    0.00   0.0  0
 LM7  CONST_12  C9   C10  C11  C12    0.00   0.0  0
 LM7  CONST_13  N1   C2   C7   C6   180.00   0.0  0
 LM7  CONST_14  N1   C2   C3   C4   180.00   0.0  0
 LM7  CONST_15  N    C1   N1   C2   180.00   0.0  0
 LM7  CONST_16  C    N    C1   N1     0.00   0.0  0
 LM7  CONST_17  C13  C    N    C1     0.00   0.0  0
 LM7  CONST_18  C8   N1   C1   N      0.00   0.0  0
 LM7  CONST_19  C4   C5   C6   N2   180.00   0.0  0
 LM7  CONST_20  C2   C7   C6   N2   180.00   0.0  0
 LM7  CONST_21  C3   C4   C5   O2   180.00   0.0  0
 LM7  CONST_22  C7   C6   C5   O2   180.00   0.0  0
 LM7  CONST_23  O1   C1   N1   C2     0.00   0.0  0
 LM7  CONST_24  O    C    N    C1   180.00   0.0  0
 LM7  CONST_25  C8   N1   C1   O1   180.00   0.0  0
 LM7  CONST_26  C    N    C1   O1   180.00   0.0  0
 LM7  CONST_27  H2   C4   C5   C6   180.00   0.0  0
 LM7  CONST_28  H3   C3   C4   C5   180.00   0.0  0
 LM7  CONST_29  H4   C7   C6   C5   180.00   0.0  0
 LM7  CONST_30  H9   C9   C8   N1     0.00   0.0  0
 LM7  CONST_31  H8   C10  C9   C8   180.00   0.0  0
 LM7  CONST_32  H6   C12  C13  C8   180.00   0.0  0
 LM7  CONST_33  H7   C11  C12  C13  180.00   0.0  0
 LM7  CONST_34  H5   N    C1   N1   180.00   0.0  0
 LM7  CONST_35  C5   C6   N2   O4   180.00   0.0  0
 LM7  CONST_36  C7   C6   N2   O4     0.00   0.0  0
 LM7  CONST_37  C5   C6   N2   O3     0.00   0.0  0
 LM7  CONST_38  C7   C6   N2   O3   180.00   0.0  0
 LM7  Var_01    C1   N1   C2   C3    89.90  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
 LM7  plan-1  N2   0.020
 LM7  plan-1  C6   0.020
 LM7  plan-1  C5   0.020
 LM7  plan-1  O2   0.020
 LM7  plan-1  C4   0.020
 LM7  plan-1  C3   0.020
 LM7  plan-1  C7   0.020
 LM7  plan-1  C2   0.020
 LM7  plan-1  N1   0.020
 LM7  plan-1  H2   0.020
 LM7  plan-1  H3   0.020
 LM7  plan-1  H4   0.020
 LM7  plan-2  C2   0.020
 LM7  plan-2  N1   0.020
 LM7  plan-2  C1   0.020
 LM7  plan-2  O1   0.020
 LM7  plan-2  N    0.020
 LM7  plan-2  C8   0.020
 LM7  plan-2  C13  0.020
 LM7  plan-2  C    0.020
 LM7  plan-2  O    0.020
 LM7  plan-2  C12  0.020
 LM7  plan-2  C11  0.020
 LM7  plan-2  C10  0.020
 LM7  plan-2  C9   0.020
 LM7  plan-2  H5   0.020
 LM7  plan-2  H6   0.020
 LM7  plan-2  H7   0.020
 LM7  plan-2  H8   0.020
 LM7  plan-2  H9   0.020
 LM7  plan-3  O4   0.020
 LM7  plan-3  N2   0.020
 LM7  plan-3  O3   0.020
 LM7  plan-3  C6   0.020

