# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:16:22 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 1-[6,8-bis(fluoranyl)-2-methyl-quinolin-4-yl]-3-[4-(dimethylamino)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc(NC(=O)Nc2cc(C)nc3c(F)cc(F)cc23)cc1
#
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
 NVN  NVN  1-[6,8-bis(fluoranyl)-2-methyl-quinolin-4-yl]-3-[4-(dimethylamino)phenyl]urea  ligand  44  26  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NVN
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
 NVN  C1   C  CH3   0  -0.736   3.1415   4.0278   0.1490
 NVN  C10  C  CR16  0  -0.382   1.8444   1.9075  -0.1424
 NVN  C11  C  C     0   0.719  -0.6909   0.2705  -0.1768
 NVN  C12  C  CR6   0   0.287  -3.0151  -0.4413  -0.2997
 NVN  C13  C  CR16  0  -0.262  -3.7084   0.6578  -0.7931
 NVN  C14  C  CR16  0  -0.362  -5.0618   0.8132  -0.5546
 NVN  C15  C  CR6   0   0.390  -5.7910  -0.1397   0.1827
 NVN  C16  C  CR16  0  -0.360  -5.0813  -1.2612   0.6501
 NVN  C17  C  CR16  0  -0.281  -3.7218  -1.3930   0.4239
 NVN  C18  C  CH3   0  -0.537  -7.8712  -1.0533   1.0473
 NVN  C19  C  CH3   0  -0.537  -7.8554   1.0689  -0.2439
 NVN  C2   C  CR6   0   0.223   3.0971   2.5358   0.0306
 NVN  C3   C  CR66  0  -0.003   4.1764   0.5363  -0.0429
 NVN  C4   C  CR6   0   0.534   5.3927  -0.1833   0.0086
 NVN  C5   C  CR16  0  -0.583   5.4569  -1.5412  -0.0734
 NVN  C6   C  CR6   0   0.567   4.2500  -2.2360  -0.2079
 NVN  C7   C  CR16  0  -0.517   3.0373  -1.6177  -0.2693
 NVN  C8   C  CR66  0   0.059   2.9850  -0.2082  -0.1998
 NVN  C9   C  CR6   0   0.467   1.7662   0.5427  -0.2675
 NVN  F1   F  F     0  -0.308   4.3130  -3.5715  -0.2704
 NVN  F2   F  F     0  -0.293   6.5174   0.5162   0.1494
 NVN  N1   N  N     0  -0.455   4.2271   1.8794   0.0726
 NVN  N2   N  NH1   0  -0.801   0.5908  -0.1490  -0.4796
 NVN  N3   N  NH1   0  -0.783  -1.6385  -0.6240  -0.5584
 NVN  N4   N  NT    0  -0.503  -7.1283   0.0206   0.4321
 NVN  O1   O  O     0  -0.492  -0.9395   1.3279   0.3707
 NVN  H3   H  HCH3  0   0.253   2.4718   4.3776   0.9357
 NVN  H1   H  HCH3  0   0.252   4.1500   4.3694   0.3706
 NVN  H2   H  HCH3  0   0.256   2.8147   4.4986  -0.7802
 NVN  H6   H  HCR6  0   0.284   0.9618   2.5240  -0.1929
 NVN  H9   H  HCR6  0   0.257  -3.1941   1.4034  -1.3854
 NVN  H10  H  HCR6  0   0.267  -5.5506   1.6862  -0.9625
 NVN  H11  H  HCR6  0   0.266  -5.5823  -2.0418   1.2045
 NVN  H12  H  HCR6  0   0.260  -3.2070  -2.2623   0.8151
 NVN  H13  H  HCH3  0   0.238  -7.4585  -1.3164   2.0231
 NVN  H14  H  HCH3  0   0.255  -8.8968  -0.7325   1.2087
 NVN  H15  H  HCH3  0   0.226  -7.8945  -1.9632   0.4368
 NVN  H16  H  HCH3  0   0.226  -7.8285   0.9706  -1.3347
 NVN  H17  H  HCH3  0   0.255  -8.8963   1.0414   0.0666
 NVN  H18  H  HCH3  0   0.237  -7.4681   2.0578   0.0112
 NVN  H4   H  HCR6  0   0.310   6.4024  -2.0656  -0.0270
 NVN  H5   H  HCR6  0   0.277   2.1493  -2.2296  -0.3505
 NVN  H7   H  HNH1  0   0.422   0.6794  -1.0638  -0.8919
 NVN  H8   H  HNH1  0   0.408  -1.3526  -1.5296  -0.8982

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
 NVN  F1   C6   single    1.338  0.020  1.338
 NVN  C5   C6   aromatic  1.399  0.020  1.399
 NVN  C5   C4   aromatic  1.362  0.020  1.362
 NVN  C6   C7   aromatic  1.363  0.020  1.363
 NVN  F2   C4   single    1.332  0.020  1.332
 NVN  C4   C3   aromatic  1.414  0.020  1.414
 NVN  C7   C8   aromatic  1.412  0.020  1.412
 NVN  C3   C8   aromatic  1.414  0.020  1.414
 NVN  C3   N1   aromatic  1.349  0.020  1.349
 NVN  C8   C9   aromatic  1.433  0.020  1.433
 NVN  N1   C2   aromatic  1.307  0.020  1.307
 NVN  C9   N2   single    1.380  0.020  1.380
 NVN  C9   C10  aromatic  1.373  0.020  1.373
 NVN  N2   C11  single    1.382  0.020  1.382
 NVN  C2   C10  aromatic  1.412  0.020  1.412
 NVN  C2   C1   single    1.497  0.020  1.497
 NVN  N3   C11  single    1.358  0.020  1.358
 NVN  N3   C12  single    1.413  0.020  1.413
 NVN  C11  O1   double    1.216  0.020  1.216
 NVN  C13  C12  aromatic  1.390  0.020  1.390
 NVN  C13  C14  aromatic  1.383  0.020  1.383
 NVN  C12  C17  aromatic  1.389  0.020  1.389
 NVN  C14  C15  aromatic  1.408  0.020  1.408
 NVN  C17  C16  aromatic  1.385  0.020  1.385
 NVN  C15  C16  aromatic  1.407  0.020  1.407
 NVN  C15  N4   single    1.370  0.020  1.370
 NVN  C19  N4   single    1.444  0.020  1.444
 NVN  N4   C18  single    1.443  0.020  1.443
 NVN  C1   H3   single    0.970  0.020  1.090
 NVN  C1   H1   single    0.970  0.020  1.090
 NVN  C1   H2   single    0.970  0.020  1.090
 NVN  C10  H6   single    0.930  0.020  1.080
 NVN  C13  H9   single    0.930  0.020  1.080
 NVN  C14  H10  single    0.930  0.020  1.080
 NVN  C16  H11  single    0.930  0.020  1.080
 NVN  C17  H12  single    0.930  0.020  1.080
 NVN  C18  H13  single    0.970  0.020  1.090
 NVN  C18  H14  single    0.970  0.020  1.090
 NVN  C18  H15  single    0.970  0.020  1.090
 NVN  C19  H16  single    0.970  0.020  1.090
 NVN  C19  H17  single    0.970  0.020  1.090
 NVN  C19  H18  single    0.970  0.020  1.090
 NVN  C5   H4   single    0.930  0.020  1.080
 NVN  C7   H5   single    0.930  0.020  1.080
 NVN  N2   H7   single    0.860  0.020  1.020
 NVN  N3   H8   single    0.860  0.020  1.020

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
 NVN  H2   C1   H1   108.39  3.000
 NVN  H2   C1   H3   106.96  3.000
 NVN  H1   C1   H3   108.77  3.000
 NVN  H2   C1   C2   110.70  3.000
 NVN  H1   C1   C2   110.89  3.000
 NVN  H3   C1   C2   111.00  3.000
 NVN  H6   C10  C9   121.19  3.000
 NVN  H6   C10  C2   118.54  3.000
 NVN  C9   C10  C2   120.26  3.000
 NVN  O1   C11  N3   123.82  3.000
 NVN  O1   C11  N2   123.50  3.000
 NVN  N3   C11  N2   112.68  3.000
 NVN  N3   C12  C17  120.17  3.000
 NVN  C17  C12  C13  118.23  3.000
 NVN  N3   C12  C13  121.56  3.000
 NVN  H9   C13  C14  118.82  3.000
 NVN  H9   C13  C12  120.13  3.000
 NVN  C14  C13  C12  121.05  3.000
 NVN  H10  C14  C15  120.67  3.000
 NVN  H10  C14  C13  117.93  3.000
 NVN  C15  C14  C13  121.40  3.000
 NVN  N4   C15  C16  121.68  3.000
 NVN  N4   C15  C14  121.44  3.000
 NVN  C16  C15  C14  116.88  3.000
 NVN  H11  C16  C17  118.05  3.000
 NVN  H11  C16  C15  120.82  3.000
 NVN  C17  C16  C15  121.12  3.000
 NVN  H12  C17  C16  118.95  3.000
 NVN  H12  C17  C12  119.75  3.000
 NVN  C16  C17  C12  121.30  3.000
 NVN  H15  C18  H14  107.93  3.000
 NVN  H15  C18  H13  107.81  3.000
 NVN  H14  C18  H13  107.16  3.000
 NVN  H15  C18  N4   113.03  3.000
 NVN  H14  C18  N4   109.23  3.000
 NVN  H13  C18  N4   111.45  3.000
 NVN  H18  C19  H17  107.21  3.000
 NVN  H18  C19  H16  107.76  3.000
 NVN  H17  C19  H16  107.81  3.000
 NVN  H18  C19  N4   111.68  3.000
 NVN  H17  C19  N4   109.28  3.000
 NVN  H16  C19  N4   112.87  3.000
 NVN  N1   C2   C10  123.19  3.000
 NVN  C10  C2   C1   118.64  3.000
 NVN  N1   C2   C1   118.17  3.000
 NVN  N1   C3   C8   124.44  3.000
 NVN  N1   C3   C4   118.11  3.000
 NVN  C8   C3   C4   117.44  3.000
 NVN  F2   C4   C5   119.36  3.000
 NVN  F2   C4   C3   117.57  3.000
 NVN  C5   C4   C3   123.07  3.000
 NVN  H4   C5   C6   121.14  3.000
 NVN  H4   C5   C4   121.45  3.000
 NVN  C6   C5   C4   117.41  3.000
 NVN  F1   C6   C7   119.51  3.000
 NVN  C7   C6   C5   123.14  3.000
 NVN  F1   C6   C5   117.35  3.000
 NVN  H5   C7   C8   122.55  3.000
 NVN  H5   C7   C6   118.51  3.000
 NVN  C8   C7   C6   118.93  3.000
 NVN  C9   C8   C7   123.51  3.000
 NVN  C9   C8   C3   116.49  3.000
 NVN  C7   C8   C3   120.00  3.000
 NVN  N2   C9   C8   117.97  3.000
 NVN  N2   C9   C10  124.10  3.000
 NVN  C8   C9   C10  117.92  3.000
 NVN  C3   N1   C2   117.68  3.000
 NVN  H7   N2   C9   116.30  3.000
 NVN  H7   N2   C11  116.54  3.000
 NVN  C9   N2   C11  127.15  3.000
 NVN  H8   N3   C12  117.01  3.000
 NVN  H8   N3   C11  119.23  3.000
 NVN  C12  N3   C11  122.92  3.000
 NVN  C19  N4   C18  118.72  3.000
 NVN  C18  N4   C15  119.54  3.000
 NVN  C19  N4   C15  119.43  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
 NVN  CONST_01  C7   C8   C9   C10  180.00   0.0  0
 NVN  CONST_02  C3   C8   C9   C10    0.00   0.0  0
 NVN  CONST_03  C3   N1   C2   C10    0.00   0.0  0
 NVN  CONST_04  C15  C14  C13  C12    0.00   0.0  0
 NVN  CONST_05  C15  C16  C17  C12    0.00   0.0  0
 NVN  CONST_06  C16  C17  C12  C13    0.00   0.0  0
 NVN  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 NVN  CONST_08  C17  C12  C13  C14    0.00   0.0  0
 NVN  CONST_09  C17  C16  C15  C14    0.00   0.0  0
 NVN  CONST_10  C4   C3   N1   C2   180.00   0.0  0
 NVN  CONST_11  C8   C3   N1   C2     0.00   0.0  0
 NVN  CONST_12  C8   C9   C10  C2     0.00   0.0  0
 NVN  CONST_13  C6   C5   C4   C3     0.00   0.0  0
 NVN  CONST_14  C6   C7   C8   C3     0.00   0.0  0
 NVN  CONST_15  C7   C6   C5   C4     0.00   0.0  0
 NVN  CONST_16  C7   C8   C3   C4     0.00   0.0  0
 NVN  CONST_17  C9   C8   C3   C4   180.00   0.0  0
 NVN  CONST_18  C8   C7   C6   C5     0.00   0.0  0
 NVN  CONST_19  C8   C3   C4   C5     0.00   0.0  0
 NVN  CONST_20  N1   C3   C4   C5   180.00   0.0  0
 NVN  CONST_21  C9   C8   C7   C6   180.00   0.0  0
 NVN  CONST_22  N1   C3   C8   C7   180.00   0.0  0
 NVN  CONST_23  N1   C3   C8   C9     0.00   0.0  0
 NVN  CONST_24  N1   C2   C10  C9     0.00   0.0  0
 NVN  CONST_25  C3   N1   C2   C1   180.00   0.0  0
 NVN  CONST_26  C9   C10  C2   C1   180.00   0.0  0
 NVN  CONST_27  N4   C15  C14  C13  180.00   0.0  0
 NVN  CONST_28  N3   C12  C13  C14  180.00   0.0  0
 NVN  CONST_29  N3   C12  C17  C16  180.00   0.0  0
 NVN  CONST_30  N4   C15  C16  C17  180.00   0.0  0
 NVN  CONST_31  N2   C9   C10  C2   180.00   0.0  0
 NVN  CONST_32  N2   C9   C8   C3   180.00   0.0  0
 NVN  CONST_33  F1   C6   C5   C4   180.00   0.0  0
 NVN  CONST_34  F2   C4   C5   C6   180.00   0.0  0
 NVN  CONST_35  N2   C9   C8   C7     0.00   0.0  0
 NVN  CONST_36  F1   C6   C7   C8   180.00   0.0  0
 NVN  CONST_37  F2   C4   C3   C8   180.00   0.0  0
 NVN  CONST_38  N1   C3   C4   F2     0.00   0.0  0
 NVN  CONST_39  H10  C14  C13  C12  180.00   0.0  0
 NVN  CONST_40  H11  C16  C17  C12  180.00   0.0  0
 NVN  CONST_41  H12  C17  C12  C13  180.00   0.0  0
 NVN  CONST_42  H9   C13  C14  C15  180.00   0.0  0
 NVN  CONST_43  H4   C5   C4   C3   180.00   0.0  0
 NVN  CONST_44  H5   C7   C8   C3   180.00   0.0  0
 NVN  CONST_45  H6   C10  C9   C8   180.00   0.0  0
 NVN  CONST_50  C19  N4   C15  C14    0.00   0.0  0
 NVN  CONST_51  C18  N4   C15  C14  180.00   0.0  0
 NVN  CONST_52  C19  N4   C15  C16  180.00   0.0  0
 NVN  CONST_53  C18  N4   C15  C16    0.00   0.0  0
 NVN  CONST_56  O1   C11  N3   C12    0.00   0.0  0
 NVN  CONST_57  O1   C11  N2   C9     0.00   0.0  0
 NVN  CONST_58  N2   C11  N3   C12  180.00   0.0  0
 NVN  CONST_59  N3   C11  N2   C9   180.00   0.0  0
 NVN  Var_01    H3   C1   C2   C10   53.67  30.0  2
 NVN  Var_02    H16  C19  N4   C15   59.55  30.0  3
 NVN  Var_03    H13  C18  N4   C15   59.18  30.0  3

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
 NVN  plan-1  C12  0.020
 NVN  plan-1  C13  0.020
 NVN  plan-1  C14  0.020
 NVN  plan-1  C15  0.020
 NVN  plan-1  C16  0.020
 NVN  plan-1  C17  0.020
 NVN  plan-1  N3   0.020
 NVN  plan-1  N4   0.020
 NVN  plan-1  H9   0.020
 NVN  plan-1  H10  0.020
 NVN  plan-1  H11  0.020
 NVN  plan-1  H12  0.020
 NVN  plan-2  C1   0.020
 NVN  plan-2  C10  0.020
 NVN  plan-2  C2   0.020
 NVN  plan-2  C3   0.020
 NVN  plan-2  C4   0.020
 NVN  plan-2  C5   0.020
 NVN  plan-2  C6   0.020
 NVN  plan-2  C7   0.020
 NVN  plan-2  C8   0.020
 NVN  plan-2  C9   0.020
 NVN  plan-2  F1   0.020
 NVN  plan-2  F2   0.020
 NVN  plan-2  N1   0.020
 NVN  plan-2  N2   0.020
 NVN  plan-2  H6   0.020
 NVN  plan-2  H4   0.020
 NVN  plan-2  H5   0.020
 NVN  plan-3  C11  0.020
 NVN  plan-3  C12  0.020
 NVN  plan-3  C9   0.020
 NVN  plan-3  N2   0.020
 NVN  plan-3  N3   0.020
 NVN  plan-3  O1   0.020
 NVN  plan-3  H7   0.020
 NVN  plan-3  H8   0.020
 NVN  plan-4  C15  0.020
 NVN  plan-4  C18  0.020
 NVN  plan-4  C19  0.020
 NVN  plan-4  N4   0.020

