# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 00:23:48 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N-{4-[(6-oxo-5,6-dihydrobenzo[c][1,8]naphthyridin-1-yl)amino]phenyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc(Nc2ccnc3NC(=O)c4ccccc4c23)cc1)c5ccccc5
#
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
 XU2  XU2  N-{4-[(6-oxo-5,6-dihydrobenzo[c][1,8]naphthyridin-1-yl)amino]phenyl}benzamide  ligand  49  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XU2
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
 XU2  O12  O  O     0  -0.460  -4.5451   1.3579   2.9677
 XU2  C8   C  CR6   0   0.519  -4.2238   0.8152   1.9226
 XU2  C7   C  CR66  0  -0.178  -3.2896   1.3948   0.9465
 XU2  C6   C  CR16  0  -0.269  -2.8496   2.7008   1.1671
 XU2  C5   C  CR16  0  -0.261  -2.0712   3.3438   0.2291
 XU2  C1   C  CR16  0  -0.223  -1.7571   2.6847  -0.9570
 XU2  C2   C  CR16  0  -0.319  -2.1690   1.3860  -1.1751
 XU2  C3   C  CR66  0   0.224  -2.9172   0.6912  -0.2130
 XU2  C4   C  CR66  0  -0.119  -3.3808  -0.6807  -0.3880
 XU2  N1   N  NR16  0  -0.725  -4.7715  -0.3726   1.5470
 XU2  C9   C  CR66  0   0.465  -4.4073  -1.1311   0.4611
 XU2  N2   N  N     0  -0.448  -5.0822  -2.2618   0.3247
 XU2  C10  C  CR16  0  -0.059  -4.7401  -3.0470  -0.6873
 XU2  C11  C  CR16  0  -0.428  -3.6752  -2.7886  -1.5224
 XU2  C12  C  CR6   0   0.374  -2.9340  -1.6173  -1.3479
 XU2  N3   N  NH1   0  -0.779  -1.8126  -1.4414  -2.1271
 XU2  C13  C  CR6   0   0.275  -0.5433  -1.0781  -1.6542
 XU2  C14  C  CR16  0  -0.262  -0.2124  -1.0419  -0.3040
 XU2  C15  C  CR16  0  -0.294   1.0568  -0.6717   0.1124
 XU2  C18  C  CR16  0  -0.294   0.4365  -0.7436  -2.5870
 XU2  C17  C  CR16  0  -0.337   1.7090  -0.3973  -2.1766
 XU2  C16  C  CR6   0   0.362   2.0377  -0.3481  -0.8219
 XU2  N4   N  NH1   0  -0.757   3.3342   0.0646  -0.4850
 XU2  C19  C  C     0   0.524   4.0351  -0.2409   0.6346
 XU2  O38  O  O     0  -0.464   3.6056  -0.9541   1.5259
 XU2  C20  C  CR6   0  -0.044   5.4048   0.3510   0.7072
 XU2  C21  C  CR16  0  -0.265   6.3571  -0.3037   1.4866
 XU2  C22  C  CR16  0  -0.242   7.6408   0.2058   1.5994
 XU2  C23  C  CR16  0  -0.250   7.9822   1.3855   0.9499
 XU2  C24  C  CR16  0  -0.240   7.0334   2.0533   0.1880
 XU2  C25  C  CR16  0  -0.296   5.7509   1.5385   0.0642
 XU2  H1   H  HCR6  0   0.266  -3.1455   3.2102   2.0740
 XU2  H2   H  HCR6  0   0.264  -1.7313   4.3559   0.4018
 XU2  H3   H  HCR6  0   0.266  -1.1856   3.1918  -1.7233
 XU2  H4   H  HCR6  0   0.272  -1.9352   0.9267  -2.1216
 XU2  H5   H  HNR6  0   0.413  -5.4808  -0.7727   2.1481
 XU2  H6   H  HCR6  0   0.273  -5.3171  -3.9562  -0.8101
 XU2  H7   H  HCR6  0   0.279  -3.3831  -3.5120  -2.2720
 XU2  H8   H  HNH1  0   0.404  -1.7839  -2.0397  -2.9402
 XU2  H9   H  HCR6  0   0.273  -0.9435  -1.3019   0.4497
 XU2  H10  H  HCR6  0   0.274   1.2617  -0.6388   1.1704
 XU2  H11  H  HCR6  0   0.271   0.2031  -0.7589  -3.6447
 XU2  H12  H  HCR6  0   0.272   2.4562  -0.1527  -2.9224
 XU2  H13  H  HNH1  0   0.419   3.8386   0.5216  -1.2289
 XU2  H14  H  HCR6  0   0.262   6.0955  -1.2206   1.9975
 XU2  H15  H  HCR6  0   0.265   8.3748  -0.3163   2.1986
 XU2  H16  H  HCR6  0   0.266   8.9835   1.7852   1.0415
 XU2  H17  H  HCR6  0   0.266   7.2879   2.9812  -0.3064
 XU2  H18  H  HCR6  0   0.263   5.0251   2.0924  -0.5182

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
 XU2  C5   C6   aromatic  1.378  0.020  1.378
 XU2  C5   C1   aromatic  1.393  0.020  1.393
 XU2  C6   C7   aromatic  1.396  0.020  1.396
 XU2  C1   C2   aromatic  1.380  0.020  1.380
 XU2  C7   C8   single    1.470  0.020  1.470
 XU2  C7   C3   aromatic  1.407  0.020  1.407
 XU2  C2   C3   aromatic  1.403  0.020  1.403
 XU2  O12  C8   double    1.221  0.020  1.221
 XU2  C8   N1   single    1.361  0.020  1.361
 XU2  C3   C4   aromatic  1.459  0.020  1.459
 XU2  N1   C9   single    1.374  0.020  1.374
 XU2  C4   C9   aromatic  1.406  0.020  1.406
 XU2  C4   C12  aromatic  1.414  0.020  1.414
 XU2  N3   C12  single    1.377  0.020  1.377
 XU2  N3   C13  single    1.402  0.020  1.402
 XU2  C9   N2   aromatic  1.324  0.020  1.324
 XU2  C12  C11  aromatic  1.397  0.020  1.397
 XU2  C13  C18  aromatic  1.394  0.020  1.394
 XU2  C13  C14  aromatic  1.391  0.020  1.391
 XU2  C18  C17  aromatic  1.381  0.020  1.381
 XU2  C14  C15  aromatic  1.386  0.020  1.386
 XU2  N2   C10  aromatic  1.326  0.020  1.326
 XU2  C17  C16  aromatic  1.395  0.020  1.395
 XU2  C11  C10  aromatic  1.378  0.020  1.378
 XU2  C15  C16  aromatic  1.393  0.020  1.393
 XU2  C16  N4   single    1.402  0.020  1.402
 XU2  O38  C19  double    1.220  0.020  1.220
 XU2  N4   C19  single    1.356  0.020  1.356
 XU2  C19  C20  single    1.494  0.020  1.494
 XU2  C20  C21  aromatic  1.394  0.020  1.394
 XU2  C20  C25  aromatic  1.394  0.020  1.394
 XU2  C21  C22  aromatic  1.386  0.020  1.386
 XU2  C25  C24  aromatic  1.388  0.020  1.388
 XU2  C22  C23  aromatic  1.389  0.020  1.389
 XU2  C24  C23  aromatic  1.388  0.020  1.388
 XU2  C6   H1   single    0.930  0.020  1.080
 XU2  C5   H2   single    0.930  0.020  1.080
 XU2  C1   H3   single    0.930  0.020  1.080
 XU2  C2   H4   single    0.930  0.020  1.080
 XU2  N1   H5   single    0.860  0.020  1.020
 XU2  C10  H6   single    0.930  0.020  1.080
 XU2  C11  H7   single    0.930  0.020  1.080
 XU2  N3   H8   single    0.890  0.020  1.040
 XU2  C14  H9   single    0.930  0.020  1.080
 XU2  C15  H10  single    0.930  0.020  1.080
 XU2  C18  H11  single    0.930  0.020  1.080
 XU2  C17  H12  single    0.930  0.020  1.080
 XU2  N4   H13  single    0.860  0.020  1.020
 XU2  C21  H14  single    0.930  0.020  1.080
 XU2  C22  H15  single    0.930  0.020  1.080
 XU2  C23  H16  single    0.930  0.020  1.080
 XU2  C24  H17  single    0.930  0.020  1.080
 XU2  C25  H18  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
 XU2  N1   C8   C7   114.62  3.000
 XU2  N1   C8   O12  121.23  3.000
 XU2  C7   C8   O12  124.08  3.000
 XU2  C3   C7   C6   120.99  3.000
 XU2  C3   C7   C8   121.22  3.000
 XU2  C6   C7   C8   117.67  3.000
 XU2  H1   C6   C5   120.37  3.000
 XU2  H1   C6   C7   119.15  3.000
 XU2  C5   C6   C7   120.47  3.000
 XU2  H2   C5   C1   120.54  3.000
 XU2  H2   C5   C6   120.36  3.000
 XU2  C1   C5   C6   119.09  3.000
 XU2  H3   C1   C2   119.13  3.000
 XU2  H3   C1   C5   120.02  3.000
 XU2  C2   C1   C5   120.85  3.000
 XU2  H4   C2   C3   120.46  3.000
 XU2  H4   C2   C1   118.37  3.000
 XU2  C3   C2   C1   121.13  3.000
 XU2  C4   C3   C2   123.58  3.000
 XU2  C4   C3   C7   119.03  3.000
 XU2  C2   C3   C7   117.31  3.000
 XU2  C12  C4   C9   115.37  3.000
 XU2  C12  C4   C3   127.17  3.000
 XU2  C9   C4   C3   117.44  3.000
 XU2  H5   N1   C9   115.91  3.000
 XU2  H5   N1   C8   117.59  3.000
 XU2  C9   N1   C8   126.40  3.000
 XU2  N2   C9   N1   114.70  3.000
 XU2  N2   C9   C4   125.69  3.000
 XU2  N1   C9   C4   119.60  3.000
 XU2  C10  N2   C9   116.93  3.000
 XU2  H6   C10  C11  120.01  3.000
 XU2  H6   C10  N2   116.48  3.000
 XU2  C11  C10  N2   123.44  3.000
 XU2  H7   C11  C12  120.26  3.000
 XU2  H7   C11  C10  120.21  3.000
 XU2  C12  C11  C10  119.45  3.000
 XU2  N3   C12  C11  117.94  3.000
 XU2  C11  C12  C4   118.21  3.000
 XU2  N3   C12  C4   123.85  3.000
 XU2  H8   N3   C13  113.54  3.000
 XU2  H8   N3   C12  113.77  3.000
 XU2  C13  N3   C12  125.41  3.000
 XU2  C18  C13  C14  118.45  3.000
 XU2  C14  C13  N3   123.33  3.000
 XU2  C18  C13  N3   118.22  3.000
 XU2  H9   C14  C15  118.28  3.000
 XU2  H9   C14  C13  120.63  3.000
 XU2  C15  C14  C13  121.10  3.000
 XU2  H10  C15  C16  121.16  3.000
 XU2  H10  C15  C14  118.49  3.000
 XU2  C16  C15  C14  120.36  3.000
 XU2  H11  C18  C17  119.49  3.000
 XU2  H11  C18  C13  119.91  3.000
 XU2  C17  C18  C13  120.60  3.000
 XU2  H12  C17  C16  119.87  3.000
 XU2  H12  C17  C18  119.17  3.000
 XU2  C16  C17  C18  120.97  3.000
 XU2  N4   C16  C17  117.50  3.000
 XU2  N4   C16  C15  123.96  3.000
 XU2  C17  C16  C15  118.52  3.000
 XU2  H13  N4   C19  116.92  3.000
 XU2  H13  N4   C16  114.77  3.000
 XU2  C19  N4   C16  127.61  3.000
 XU2  C20  C19  O38  121.27  3.000
 XU2  C20  C19  N4   115.14  3.000
 XU2  O38  C19  N4   123.59  3.000
 XU2  C25  C20  C21  119.23  3.000
 XU2  C25  C20  C19  122.87  3.000
 XU2  C21  C20  C19  117.87  3.000
 XU2  H14  C21  C22  119.82  3.000
 XU2  H14  C21  C20  119.80  3.000
 XU2  C22  C21  C20  120.38  3.000
 XU2  H15  C22  C23  120.13  3.000
 XU2  H15  C22  C21  119.75  3.000
 XU2  C23  C22  C21  120.12  3.000
 XU2  H16  C23  C24  120.08  3.000
 XU2  H16  C23  C22  120.10  3.000
 XU2  C24  C23  C22  119.81  3.000
 XU2  H17  C24  C25  119.66  3.000
 XU2  H17  C24  C23  120.19  3.000
 XU2  C25  C24  C23  120.16  3.000
 XU2  H18  C25  C24  118.54  3.000
 XU2  H18  C25  C20  121.15  3.000
 XU2  C24  C25  C20  120.29  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
 XU2  CONST_01  C1   C5   C6   C7      0.00   0.0  0
 XU2  CONST_02  C1   C2   C3   C7      0.00   0.0  0
 XU2  CONST_03  C9   C4   C3   C7      0.00   0.0  0
 XU2  CONST_04  C12  C4   C3   C7    180.00   0.0  0
 XU2  CONST_05  C2   C1   C5   C6      0.00   0.0  0
 XU2  CONST_06  C2   C3   C7   C6      0.00   0.0  0
 XU2  CONST_07  C4   C3   C7   C6    180.00   0.0  0
 XU2  CONST_08  C3   C7   C6   C5      0.00   0.0  0
 XU2  CONST_09  C3   C2   C1   C5      0.00   0.0  0
 XU2  CONST_10  C4   C3   C2   C1    180.00   0.0  0
 XU2  CONST_13  N2   C9   C4   C3    180.00   0.0  0
 XU2  CONST_14  C11  C12  C4   C3    180.00   0.0  0
 XU2  CONST_15  C10  N2   C9   C4      0.00   0.0  0
 XU2  CONST_16  C10  C11  C12  C4      0.00   0.0  0
 XU2  CONST_17  C11  C12  C4   C9      0.00   0.0  0
 XU2  CONST_18  C11  C10  N2   C9      0.00   0.0  0
 XU2  CONST_19  C12  C4   C9   N2      0.00   0.0  0
 XU2  CONST_20  C12  C11  C10  N2      0.00   0.0  0
 XU2  CONST_21  C16  C17  C18  C13     0.00   0.0  0
 XU2  CONST_22  C16  C15  C14  C13     0.00   0.0  0
 XU2  CONST_23  C17  C18  C13  C14     0.00   0.0  0
 XU2  CONST_24  C17  C16  C15  C14     0.00   0.0  0
 XU2  CONST_25  C18  C13  C14  C15     0.00   0.0  0
 XU2  CONST_26  C18  C17  C16  C15     0.00   0.0  0
 XU2  CONST_27  C23  C22  C21  C20     0.00   0.0  0
 XU2  CONST_28  C23  C24  C25  C20     0.00   0.0  0
 XU2  CONST_29  C24  C25  C20  C21     0.00   0.0  0
 XU2  CONST_30  C24  C23  C22  C21     0.00   0.0  0
 XU2  CONST_31  C25  C20  C21  C22     0.00   0.0  0
 XU2  CONST_32  C25  C24  C23  C22     0.00   0.0  0
 XU2  CONST_33  C9   N1   C8   C7      0.00   0.0  0
 XU2  CONST_34  N3   C12  C4   C3      0.00   0.0  0
 XU2  CONST_35  N3   C12  C4   C9    180.00   0.0  0
 XU2  CONST_36  N3   C12  C11  C10   180.00   0.0  0
 XU2  CONST_37  C17  C18  C13  N3    180.00   0.0  0
 XU2  CONST_38  C15  C14  C13  N3    180.00   0.0  0
 XU2  CONST_39  N4   C16  C15  C14   180.00   0.0  0
 XU2  CONST_40  N4   C16  C17  C18   180.00   0.0  0
 XU2  CONST_41  C22  C21  C20  C19   180.00   0.0  0
 XU2  CONST_42  C24  C25  C20  C19   180.00   0.0  0
 XU2  CONST_43  C9   N1   C8   O12   180.00   0.0  0
 XU2  CONST_44  H1   C6   C7   C8      0.00   0.0  0
 XU2  CONST_45  H2   C5   C6   C7    180.00   0.0  0
 XU2  CONST_46  H4   C2   C3   C7    180.00   0.0  0
 XU2  CONST_47  H3   C1   C5   C6    180.00   0.0  0
 XU2  CONST_48  H7   C11  C12  C4    180.00   0.0  0
 XU2  CONST_49  H6   C10  N2   C9    180.00   0.0  0
 XU2  CONST_50  H12  C17  C18  C13   180.00   0.0  0
 XU2  CONST_51  H10  C15  C14  C13   180.00   0.0  0
 XU2  CONST_52  H11  C18  C13  C14   180.00   0.0  0
 XU2  CONST_53  H9   C14  C13  C18   180.00   0.0  0
 XU2  CONST_54  H15  C22  C21  C20   180.00   0.0  0
 XU2  CONST_55  H17  C24  C25  C20   180.00   0.0  0
 XU2  CONST_56  H18  C25  C20  C21   180.00   0.0  0
 XU2  CONST_57  H16  C23  C22  C21   180.00   0.0  0
 XU2  CONST_58  H14  C21  C22  C23   180.00   0.0  0
 XU2  CONST_59  H5   N1   C8   C7    180.00   0.0  0
 XU2  CONST_60  C20  C19  N4   C16   180.00   0.0  0
 XU2  CONST_64  O38  C19  N4   C16     0.00   0.0  0
 XU2  Var_01    C13  N3   C12  C4     49.74  30.0  2
 XU2  Var_02    C18  C13  N3   C12  -170.43  30.0  2
 XU2  Var_03    C21  C20  C19  N4   -154.48  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
 XU2  plan-1  N3   0.020
 XU2  plan-1  C13  0.020
 XU2  plan-1  C14  0.020
 XU2  plan-1  C15  0.020
 XU2  plan-1  C18  0.020
 XU2  plan-1  C17  0.020
 XU2  plan-1  C16  0.020
 XU2  plan-1  N4   0.020
 XU2  plan-1  H9   0.020
 XU2  plan-1  H10  0.020
 XU2  plan-1  H11  0.020
 XU2  plan-1  H12  0.020
 XU2  plan-2  C19  0.020
 XU2  plan-2  C20  0.020
 XU2  plan-2  C21  0.020
 XU2  plan-2  C22  0.020
 XU2  plan-2  C23  0.020
 XU2  plan-2  C24  0.020
 XU2  plan-2  C25  0.020
 XU2  plan-2  H14  0.020
 XU2  plan-2  H15  0.020
 XU2  plan-2  H16  0.020
 XU2  plan-2  H17  0.020
 XU2  plan-2  H18  0.020
 XU2  plan-3  O12  0.020
 XU2  plan-3  C8   0.020
 XU2  plan-3  C7   0.020
 XU2  plan-3  C6   0.020
 XU2  plan-3  C5   0.020
 XU2  plan-3  C1   0.020
 XU2  plan-3  C2   0.020
 XU2  plan-3  C3   0.020
 XU2  plan-3  C4   0.020
 XU2  plan-3  N1   0.020
 XU2  plan-3  C9   0.020
 XU2  plan-3  N2   0.020
 XU2  plan-3  C10  0.020
 XU2  plan-3  C11  0.020
 XU2  plan-3  C12  0.020
 XU2  plan-3  N3   0.020
 XU2  plan-3  H1   0.020
 XU2  plan-3  H2   0.020
 XU2  plan-3  H3   0.020
 XU2  plan-3  H4   0.020
 XU2  plan-3  H5   0.020
 XU2  plan-3  H6   0.020
 XU2  plan-3  H7   0.020
 XU2  plan-4  C16  0.020
 XU2  plan-4  N4   0.020
 XU2  plan-4  C19  0.020
 XU2  plan-4  O38  0.020
 XU2  plan-4  C20  0.020
 XU2  plan-4  H13  0.020

