# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 19:45:22 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: N-(3,3-dimethylbutyl)-N'-{2-fluoro-5-[(5-fluoro-3-methyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]-4-methylphenyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=Nc2ccc(Nc3cc(NC(=O)NCCC(C)(C)C)c(F)cc3C)c(F)c2C1=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
 VQP  VQP  N-(3,3-dimethylbutyl)-N'-{2-fluoro-5-[(5-fluoro-3-methyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]-4-methylphenyl}urea  ligand  59  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VQP
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
 VQP  C4   C  CR6   0   0.505   8.7883  -33.2025  -33.2361
 VQP  C5   C  CR6   0   0.183   9.6514  -33.1190  -34.3213
 VQP  C6   C  CR16  0  -0.350  10.9694  -33.5101  -34.1133
 VQP  C7   C  CR6   0   0.251  11.4088  -33.9486  -32.8680
 VQP  C10  C  CR16  0  -0.287  12.2692  -36.6753  -32.3126
 VQP  C13  C  CR66  0  -0.312  14.9499  -37.0918  -31.6768
 VQP  C26  C  CH2   0  -0.289   8.8033  -33.2089  -39.1341
 VQP  C28  C  CT    0  -0.094   7.4295  -34.6851  -40.7713
 VQP  C11  C  CR16  0  -0.328  12.6947  -37.9263  -31.9306
 VQP  C12  C  CR66  0   0.246  14.0327  -38.1581  -31.6063
 VQP  C14  C  CR6   0   0.496  14.4811  -35.8337  -32.0495
 VQP  C16  C  CR6   0   0.606  16.3513  -37.3370  -31.3371
 VQP  C19  C  CR16  0   0.133  15.6487  -39.6040  -30.9443
 VQP  C2   C  CR6   0   0.087  10.5344  -33.9738  -31.7723
 VQP  C23  C  C     0   0.713   9.3940  -33.2739  -36.7505
 VQP  C27  C  CH2   0  -0.396   7.5596  -34.0614  -39.3721
 VQP  C29  C  CH3   0  -0.645   7.3788  -33.6009  -41.8495
 VQP  C3   C  CR16  0  -0.470   9.2119  -33.6028  -31.9880
 VQP  C30  C  CH3   0  -0.644   8.5962  -35.6331  -41.0553
 VQP  C31  C  CH3   0  -0.633   6.1230  -35.4801  -40.8139
 VQP  C9   C  CR6   0   0.172  13.1523  -35.5874  -32.3681
 VQP  F32  F  F     0  -0.312   7.5004  -32.8560  -33.4085
 VQP  N18  N  NR6   0  -0.513  16.6176  -38.6465  -30.9739
 VQP  N20  N  N     0  -0.456  14.4165  -39.4225  -31.2330
 VQP  N22  N  NH1   0  -0.778   9.1897  -32.6340  -35.5466
 VQP  N25  N  NH1   0  -0.671   8.8385  -32.6356  -37.8061
 VQP  N8   N  NH1   0  -0.772  12.7579  -34.3023  -32.7020
 VQP  O17  O  O     0  -0.444  17.2435  -36.5110  -31.3506
 VQP  O24  O  O     0  -0.516  10.0428  -34.3047  -36.8462
 VQP  H1   H  HCR6  0   0.274  11.6730  -33.4641  -34.9334
 VQP  H2   H  HCR6  0   0.293  11.2305  -36.5286  -32.5790
 VQP  H3   H  HCH3  0   0.261  18.0265  -40.0370  -30.3436
 VQP  H4   H  HCH3  0   0.263  18.6580  -38.8161  -31.4550
 VQP  H5   H  HCH3  0   0.263  18.3208  -38.3924  -29.7683
 VQP  H6   H  HCH2  0   0.242   9.7120  -33.7913  -39.2783
 VQP  H7   H  HCH2  0   0.243   8.8454  -32.3813  -39.8434
 VQP  H8   H  HCH3  0   0.249  11.9828  -33.9454  -30.1854
 VQP  H9   H  HCH3  0   0.256  10.3027  -33.9761  -29.6443
 VQP  H10  H  HCH3  0   0.252  11.0578  -35.4342  -30.2688
 VQP  H11  H  HCR6  0   0.269  11.9962  -38.7511  -31.8889
 VQP  H12  H  HCR6  0   0.291  15.9854  -40.5900  -30.6458
 VQP  H13  H  HCH2  0   0.218   6.6757  -33.4429  -39.1809
 VQP  H14  H  HCH2  0   0.222   7.5411  -34.8648  -38.6278
 VQP  H15  H  HCH3  0   0.224   8.3125  -33.0399  -41.9140
 VQP  H16  H  HCH3  0   0.224   7.2006  -34.0438  -42.8318
 VQP  H17  H  HCH3  0   0.220   6.5733  -32.8882  -41.6575
 VQP  H18  H  HCR6  0   0.274   8.5043  -33.6147  -31.1678
 VQP  H19  H  HCH3  0   0.221   8.6786  -36.4038  -40.2853
 VQP  H20  H  HCH3  0   0.224   8.4571  -36.1368  -42.0142
 VQP  H21  H  HCH3  0   0.224   9.5512  -35.1069  -41.1029
 VQP  H22  H  HCH3  0   0.220   6.1148  -36.2743  -40.0637
 VQP  H23  H  HCH3  0   0.220   5.2619  -34.8350  -40.6259
 VQP  H24  H  HCH3  0   0.221   5.9816  -35.9463  -41.7914
 VQP  H25  H  HNH1  0   0.402   8.4968  -31.9024  -35.5091
 VQP  H26  H  HNH1  0   0.393   8.2495  -31.8343  -37.6441
 VQP  H27  H  HNH1  0   0.396  13.4090  -33.7827  -33.2714
 VQP  C1   C  CH3   0  -0.733  10.9936  -34.3516  -30.3974
 VQP  F15  F  F     0  -0.291  15.3192  -34.7946  -32.1211
 VQP  C21  C  CH3   0  -0.515  17.9866  -38.9864  -30.6160

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
 VQP  C29  C28  single    1.530  0.020  1.530
 VQP  C31  C28  single    1.530  0.020  1.530
 VQP  C30  C28  single    1.530  0.020  1.530
 VQP  C28  C27  single    1.537  0.020  1.537
 VQP  C27  C26  single    1.527  0.020  1.527
 VQP  C26  N25  single    1.447  0.020  1.447
 VQP  N25  C23  single    1.353  0.020  1.353
 VQP  O24  C23  double    1.222  0.020  1.222
 VQP  C23  N22  single    1.379  0.020  1.379
 VQP  N22  C5   single    1.396  0.020  1.396
 VQP  C5   C6   aromatic  1.391  0.020  1.391
 VQP  C5   C4   aromatic  1.389  0.020  1.389
 VQP  C6   C7   aromatic  1.392  0.020  1.392
 VQP  F32  C4   single    1.345  0.020  1.345
 VQP  C4   C3   aromatic  1.377  0.020  1.377
 VQP  C7   N8   single    1.405  0.020  1.405
 VQP  C7   C2   aromatic  1.402  0.020  1.402
 VQP  N8   C9   single    1.385  0.020  1.385
 VQP  C9   C10  aromatic  1.402  0.020  1.402
 VQP  C9   C14  aromatic  1.389  0.020  1.389
 VQP  C10  C11  aromatic  1.376  0.020  1.376
 VQP  F15  C14  single    1.337  0.020  1.337
 VQP  C3   C2   aromatic  1.390  0.020  1.390
 VQP  C14  C13  aromatic  1.393  0.020  1.393
 VQP  C2   C1   single    1.498  0.020  1.498
 VQP  C11  C12  aromatic  1.396  0.020  1.396
 VQP  C13  C12  aromatic  1.408  0.020  1.408
 VQP  C13  C16  single    1.463  0.020  1.463
 VQP  C12  N20  single    1.373  0.020  1.373
 VQP  O17  C16  double    1.216  0.020  1.216
 VQP  C16  N18  single    1.385  0.020  1.385
 VQP  N20  C19  double    1.278  0.020  1.278
 VQP  N18  C19  single    1.363  0.020  1.363
 VQP  N18  C21  single    1.455  0.020  1.455
 VQP  C6   H1   single    0.930  0.020  1.080
 VQP  C10  H2   single    0.930  0.020  1.080
 VQP  C21  H3   single    0.970  0.020  1.090
 VQP  C21  H4   single    0.970  0.020  1.090
 VQP  C21  H5   single    0.970  0.020  1.090
 VQP  C26  H6   single    0.970  0.020  1.090
 VQP  C26  H7   single    0.970  0.020  1.090
 VQP  C1   H8   single    0.970  0.020  1.090
 VQP  C1   H9   single    0.970  0.020  1.090
 VQP  C1   H10  single    0.970  0.020  1.090
 VQP  C11  H11  single    0.930  0.020  1.080
 VQP  C19  H12  single    0.930  0.020  1.080
 VQP  C27  H13  single    0.970  0.020  1.090
 VQP  C27  H14  single    0.970  0.020  1.090
 VQP  C29  H15  single    0.970  0.020  1.090
 VQP  C29  H16  single    0.970  0.020  1.090
 VQP  C29  H17  single    0.970  0.020  1.090
 VQP  C3   H18  single    0.930  0.020  1.080
 VQP  C30  H19  single    0.970  0.020  1.090
 VQP  C30  H20  single    0.970  0.020  1.090
 VQP  C30  H21  single    0.970  0.020  1.090
 VQP  C31  H22  single    0.970  0.020  1.090
 VQP  C31  H23  single    0.970  0.020  1.090
 VQP  C31  H24  single    0.970  0.020  1.090
 VQP  N22  H25  single    0.860  0.020  1.020
 VQP  N25  H26  single    0.860  0.020  1.020
 VQP  N8   H27  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
 VQP  F32  C4   C3   119.05  3.000
 VQP  C3   C4   C5   122.30  3.000
 VQP  F32  C4   C5   118.64  3.000
 VQP  N22  C5   C6   122.84  3.000
 VQP  C6   C5   C4   117.08  3.000
 VQP  N22  C5   C4   120.07  3.000
 VQP  H1   C6   C7   119.12  3.000
 VQP  H1   C6   C5   119.43  3.000
 VQP  C7   C6   C5   121.45  3.000
 VQP  N8   C7   C2   120.15  3.000
 VQP  C2   C7   C6   120.54  3.000
 VQP  N8   C7   C6   119.23  3.000
 VQP  H2   C10  C9   119.31  3.000
 VQP  H2   C10  C11  119.24  3.000
 VQP  C9   C10  C11  121.45  3.000
 VQP  C16  C13  C14  122.40  3.000
 VQP  C16  C13  C12  119.04  3.000
 VQP  C14  C13  C12  118.55  3.000
 VQP  H7   C26  H6   106.71  3.000
 VQP  H7   C26  N25  107.18  3.000
 VQP  H6   C26  N25  108.25  3.000
 VQP  H7   C26  C27  110.72  3.000
 VQP  H6   C26  C27  111.13  3.000
 VQP  N25  C26  C27  112.59  3.000
 VQP  C31  C28  C30  108.91  3.000
 VQP  C30  C28  C29  109.48  3.000
 VQP  C31  C28  C29  108.68  3.000
 VQP  C30  C28  C27  110.84  3.000
 VQP  C31  C28  C27  107.96  3.000
 VQP  C29  C28  C27  110.90  3.000
 VQP  H11  C11  C12  118.90  3.000
 VQP  H11  C11  C10  120.30  3.000
 VQP  C12  C11  C10  120.80  3.000
 VQP  N20  C12  C11  118.95  3.000
 VQP  N20  C12  C13  121.92  3.000
 VQP  C11  C12  C13  119.13  3.000
 VQP  F15  C14  C9   116.73  3.000
 VQP  F15  C14  C13  120.35  3.000
 VQP  C9   C14  C13  122.92  3.000
 VQP  O17  C16  N18  120.27  3.000
 VQP  N18  C16  C13  113.81  3.000
 VQP  O17  C16  C13  125.91  3.000
 VQP  H12  C19  N20  119.39  3.000
 VQP  H12  C19  N18  115.11  3.000
 VQP  N20  C19  N18  125.50  3.000
 VQP  C3   C2   C1   120.09  3.000
 VQP  C1   C2   C7   122.05  3.000
 VQP  C3   C2   C7   117.85  3.000
 VQP  O24  C23  N25  123.71  3.000
 VQP  O24  C23  N22  122.60  3.000
 VQP  N25  C23  N22  113.67  3.000
 VQP  H14  C27  H13  106.37  3.000
 VQP  H14  C27  C28  108.63  3.000
 VQP  H13  C27  C28  108.64  3.000
 VQP  H14  C27  C26  108.51  3.000
 VQP  H13  C27  C26  108.35  3.000
 VQP  C28  C27  C26  115.94  3.000
 VQP  H17  C29  H16  107.60  3.000
 VQP  H17  C29  H15  107.81  3.000
 VQP  H16  C29  H15  107.16  3.000
 VQP  H17  C29  C28  111.28  3.000
 VQP  H16  C29  C28  110.60  3.000
 VQP  H15  C29  C28  112.19  3.000
 VQP  H18  C3   C2   120.06  3.000
 VQP  H18  C3   C4   119.23  3.000
 VQP  C2   C3   C4   120.70  3.000
 VQP  H21  C30  H20  107.19  3.000
 VQP  H21  C30  H19  107.75  3.000
 VQP  H20  C30  H19  107.64  3.000
 VQP  H21  C30  C28  112.12  3.000
 VQP  H20  C30  C28  110.59  3.000
 VQP  H19  C30  C28  111.33  3.000
 VQP  H24  C31  H23  107.70  3.000
 VQP  H24  C31  H22  107.66  3.000
 VQP  H23  C31  H22  107.77  3.000
 VQP  H24  C31  C28  110.93  3.000
 VQP  H23  C31  C28  111.20  3.000
 VQP  H22  C31  C28  111.41  3.000
 VQP  N8   C9   C14  119.50  3.000
 VQP  C14  C9   C10  117.13  3.000
 VQP  N8   C9   C10  123.37  3.000
 VQP  C19  N18  C16  122.24  3.000
 VQP  C19  N18  C21  119.97  3.000
 VQP  C16  N18  C21  117.79  3.000
 VQP  C19  N20  C12  117.48  3.000
 VQP  H25  N22  C23  118.11  3.000
 VQP  H25  N22  C5   116.52  3.000
 VQP  C23  N22  C5   123.79  3.000
 VQP  H26  N25  C23  119.33  3.000
 VQP  H26  N25  C26  116.64  3.000
 VQP  C23  N25  C26  122.63  3.000
 VQP  H27  N8   C9   115.47  3.000
 VQP  H27  N8   C7   115.06  3.000
 VQP  C9   N8   C7   122.39  3.000
 VQP  H10  C1   H9   107.32  3.000
 VQP  H10  C1   H8   107.04  3.000
 VQP  H9   C1   H8   108.23  3.000
 VQP  H10  C1   C2   112.10  3.000
 VQP  H9   C1   C2   110.69  3.000
 VQP  H8   C1   C2   111.27  3.000
 VQP  H5   C21  H4   109.02  3.000
 VQP  H5   C21  H3   108.75  3.000
 VQP  H4   C21  H3   108.80  3.000
 VQP  H5   C21  N18  110.68  3.000
 VQP  H4   C21  N18  110.76  3.000
 VQP  H3   C21  N18  108.79  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
 VQP  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 VQP  CONST_02  C7   C2   C3   C4      0.00   0.0  0
 VQP  CONST_03  C2   C7   C6   C5      0.00   0.0  0
 VQP  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 VQP  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 VQP  CONST_06  C3   C2   C7   C6      0.00   0.0  0
 VQP  CONST_07  C13  C14  C9   C10     0.00   0.0  0
 VQP  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 VQP  CONST_09  C14  C9   C10  C11     0.00   0.0  0
 VQP  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 VQP  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 VQP  CONST_12  C9   C14  C13  C12     0.00   0.0  0
 VQP  CONST_13  C19  N18  C16  C13     0.00   0.0  0
 VQP  CONST_14  N18  C19  N20  C12     0.00   0.0  0
 VQP  CONST_15  N20  C19  N18  C16     0.00   0.0  0
 VQP  CONST_16  C1   C2   C3   C4    180.00   0.0  0
 VQP  CONST_17  N8   C7   C6   C5    180.00   0.0  0
 VQP  CONST_18  F32  C4   C5   C6    180.00   0.0  0
 VQP  CONST_19  C1   C2   C7   C6    180.00   0.0  0
 VQP  CONST_20  N22  C5   C6   C7    180.00   0.0  0
 VQP  CONST_21  F15  C14  C9   C10   180.00   0.0  0
 VQP  CONST_22  N8   C9   C14  C13   180.00   0.0  0
 VQP  CONST_23  N8   C9   C10  C11   180.00   0.0  0
 VQP  CONST_24  F15  C14  C13  C12   180.00   0.0  0
 VQP  CONST_25  F15  C14  C13  C16     0.00   0.0  0
 VQP  CONST_26  F32  C4   C3   C2    180.00   0.0  0
 VQP  CONST_27  N22  C5   C4   C3    180.00   0.0  0
 VQP  CONST_28  N8   C7   C2   C3    180.00   0.0  0
 VQP  CONST_29  C21  N18  C16  C13   180.00   0.0  0
 VQP  CONST_30  N20  C19  N18  C21   180.00   0.0  0
 VQP  CONST_31  O17  C16  N18  C19   180.00   0.0  0
 VQP  CONST_32  H1   C6   C5   C4    180.00   0.0  0
 VQP  CONST_33  H18  C3   C4   C5    180.00   0.0  0
 VQP  CONST_34  H11  C11  C12  C13   180.00   0.0  0
 VQP  CONST_35  H2   C10  C11  C12   180.00   0.0  0
 VQP  CONST_36  H12  C19  N20  C12   180.00   0.0  0
 VQP  CONST_39  O17  C16  N18  C21     0.00   0.0  0
 VQP  CONST_41  O24  C23  N22  C5      0.00   0.0  0
 VQP  CONST_42  N25  C23  N22  C5    180.00   0.0  0
 VQP  CONST_43  O24  C23  N25  C26     0.00   0.0  0
 VQP  CONST_44  N22  C23  N25  C26   180.00   0.0  0
 VQP  CONST_45  H26  N25  C23  O24   180.00   0.0  0
 VQP  Var_01    C9   N8   C7   C6   -117.17  30.0  2
 VQP  Var_02    C10  C9   N8   C7      7.36  30.0  2
 VQP  Var_03    H8   C1   C2   C7     39.10  30.0  2
 VQP  Var_04    H3   C21  N18  C16   179.14  30.0  3
 VQP  Var_05    C29  C28  C27  C26   -60.40  30.0  3
 VQP  Var_06    N25  C26  C27  C28   178.77  30.0  3
 VQP  Var_07    C27  C26  N25  C23    88.93  30.0  2
 VQP  Var_08    H15  C29  C28  C27    65.27  30.0  3
 VQP  Var_09    H22  C31  C28  C27   -60.06  30.0  3
 VQP  Var_10    H19  C30  C28  C27    55.66  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
 VQP  plan-1  C4   0.020
 VQP  plan-1  C5   0.020
 VQP  plan-1  C6   0.020
 VQP  plan-1  C7   0.020
 VQP  plan-1  C2   0.020
 VQP  plan-1  C3   0.020
 VQP  plan-1  F32  0.020
 VQP  plan-1  N22  0.020
 VQP  plan-1  N8   0.020
 VQP  plan-1  H1   0.020
 VQP  plan-1  H18  0.020
 VQP  plan-1  C1   0.020
 VQP  plan-2  C10  0.020
 VQP  plan-2  C13  0.020
 VQP  plan-2  C11  0.020
 VQP  plan-2  C12  0.020
 VQP  plan-2  C14  0.020
 VQP  plan-2  C16  0.020
 VQP  plan-2  C19  0.020
 VQP  plan-2  C9   0.020
 VQP  plan-2  N18  0.020
 VQP  plan-2  N20  0.020
 VQP  plan-2  N8   0.020
 VQP  plan-2  O17  0.020
 VQP  plan-2  H2   0.020
 VQP  plan-2  H11  0.020
 VQP  plan-2  H12  0.020
 VQP  plan-2  F15  0.020
 VQP  plan-2  C21  0.020
 VQP  plan-3  C5   0.020
 VQP  plan-3  C26  0.020
 VQP  plan-3  C23  0.020
 VQP  plan-3  N22  0.020
 VQP  plan-3  N25  0.020
 VQP  plan-3  O24  0.020
 VQP  plan-3  H25  0.020
 VQP  plan-3  H26  0.020

