# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:45:23 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-[9-fluoranyl-5-(4-methoxyphenyl)-3-methyl-1-oxidanylidene-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2nc3ccc(F)cc3c4C(=O)N(CC(O)=O)C(=Nc24)C
#
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
 AVT  AVT  '2-[9-fluoranyl-5-(4-methoxyphenyl)-3-methyl-1-oxidanylidene-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid'  ligand  45  29  .  2022-03-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AVT
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
 AVT  F27  F  F     0  -0.313  -3.9895  -4.3632  -0.1171
 AVT  C5   C  CR6   0   0.585  -2.7910  -3.7623  -0.1186
 AVT  C3   C  CR16  0  -0.543  -2.7393  -2.4027   0.0101
 AVT  C6   C  CR16  0  -0.421  -1.6571  -4.5665  -0.2518
 AVT  C4   C  CR16  0  -0.278  -0.4323  -3.9554  -0.2575
 AVT  C2   C  CR66  0   0.146  -0.3193  -2.5570  -0.1291
 AVT  N9   N  N     0  -0.439   0.9321  -2.0351  -0.1653
 AVT  C10  C  CR6   0   0.122   1.1260  -0.7573  -0.0479
 AVT  C11  C  CR6   0   0.052   2.5244  -0.2870  -0.1016
 AVT  C13  C  CR16  0  -0.273   3.5155  -1.0440   0.5164
 AVT  C15  C  CR16  0  -0.374   4.8527  -0.6780   0.4649
 AVT  C16  C  CR6   0   0.380   5.2279   0.4639  -0.2396
 AVT  O28  O  O2    0  -0.467   6.4910   0.9056  -0.3539
 AVT  C29  C  CH3   0  -0.438   7.5244   0.1798   0.2836
 AVT  C14  C  CR16  0  -0.335   4.2452   1.2216  -0.8824
 AVT  C12  C  CR16  0  -0.255   2.9167   0.8555  -0.8062
 AVT  C8   C  CR66  0   0.169   0.0215   0.1469   0.1634
 AVT  N19  N  N     0  -0.470   0.3082   1.4590   0.3668
 AVT  C20  C  CR6   0   0.488  -0.6502   2.2918   0.5829
 AVT  C22  C  CH3   0  -0.780  -0.3107   3.7270   0.8058
 AVT  N18  N  NR6   0  -0.541  -1.9588   1.9017   0.6163
 AVT  C17  C  CR6   0   0.597  -2.3563   0.5952   0.3476
 AVT  O21  O  O     0  -0.453  -3.5448   0.3383   0.2835
 AVT  C7   C  CR66  0   0.010  -1.2690  -0.3565   0.1719
 AVT  C1   C  CR66  0   0.114  -1.4830  -1.7622   0.0122
 AVT  C23  C  CH2   0  -0.472  -3.0382   2.8443   0.8185
 AVT  C24  C  C     0   0.554  -3.6576   3.2344  -0.5061
 AVT  O25  O  OH1   0  -0.582  -4.8090   3.8545  -0.3249
 AVT  O26  O  O     0  -0.426  -3.1429   3.0299  -1.5726
 AVT  H1   H  HCR6  0   0.292  -3.6539  -1.8413   0.1111
 AVT  H2   H  HCR6  0   0.288  -1.7534  -5.6397  -0.3488
 AVT  H3   H  HCR6  0   0.278   0.4740  -4.5365  -0.3628
 AVT  H4   H  HCR6  0   0.256   3.2417  -1.9373   1.0628
 AVT  H5   H  HCR6  0   0.281   5.5808  -1.2906   0.9787
 AVT  H6   H  HCH3  0   0.230   7.3836   0.1368   1.3667
 AVT  H7   H  HCR6  0   0.264   4.5335   2.1027  -1.4420
 AVT  H8   H  HCR6  0   0.254   2.1833   1.4602  -1.3193
 AVT  H9   H  HCH3  0   0.290   0.7636   3.8445   0.7033
 AVT  H10  H  HCH3  0   0.273  -0.8005   4.3758   0.0786
 AVT  H11  H  HCH3  0   0.282  -0.6016   4.0639   1.8019
 AVT  H12  H  HCH2  0   0.331  -3.7890   2.4124   1.4779
 AVT  H13  H  HCH2  0   0.344  -2.6724   3.7403   1.3170
 AVT  H14  H  HOH1  0   0.490  -5.1832   4.1297  -1.1757
 AVT  H15  H  HCH3  0   0.231   7.6054  -0.8395  -0.1025
 AVT  H16  H  HCH3  0   0.261   8.4496   0.7095   0.0711

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
 AVT  C29  O28  single    1.415  0.020  1.415
 AVT  O28  C16  single    1.343  0.020  1.343
 AVT  C16  C14  aromatic  1.398  0.020  1.398
 AVT  C16  C15  aromatic  1.393  0.020  1.393
 AVT  C22  C20  single    1.492  0.020  1.492
 AVT  C14  C12  aromatic  1.380  0.020  1.380
 AVT  C15  C13  aromatic  1.387  0.020  1.387
 AVT  C12  C11  aromatic  1.398  0.020  1.398
 AVT  C13  C11  aromatic  1.392  0.020  1.392
 AVT  C20  N19  double    1.288  0.020  1.288
 AVT  C20  N18  single    1.366  0.020  1.366
 AVT  N19  C8   single    1.358  0.020  1.358
 AVT  C11  C10  single    1.476  0.020  1.476
 AVT  C23  N18  single    1.447  0.020  1.447
 AVT  C23  C24  single    1.513  0.020  1.513
 AVT  N18  C17  single    1.392  0.020  1.392
 AVT  C8   C10  aromatic  1.443  0.020  1.443
 AVT  C8   C7   aromatic  1.385  0.020  1.385
 AVT  C10  N9   aromatic  1.298  0.020  1.298
 AVT  C24  O26  double    1.202  0.020  1.202
 AVT  C24  O25  single    1.320  0.020  1.320
 AVT  C17  C7   single    1.456  0.020  1.456
 AVT  C17  O21  double    1.218  0.020  1.218
 AVT  N9   C2   aromatic  1.356  0.020  1.356
 AVT  C7   C1   aromatic  1.431  0.020  1.431
 AVT  C2   C1   aromatic  1.416  0.020  1.416
 AVT  C2   C4   aromatic  1.409  0.020  1.409
 AVT  C1   C3   aromatic  1.410  0.020  1.410
 AVT  C4   C6   aromatic  1.369  0.020  1.369
 AVT  C3   C5   aromatic  1.367  0.020  1.367
 AVT  C6   C5   aromatic  1.397  0.020  1.397
 AVT  C5   F27  single    1.341  0.020  1.341
 AVT  C3   H1   single    0.930  0.020  1.080
 AVT  C6   H2   single    0.930  0.020  1.080
 AVT  C4   H3   single    0.930  0.020  1.080
 AVT  C13  H4   single    0.930  0.020  1.080
 AVT  C15  H5   single    0.930  0.020  1.080
 AVT  C29  H6   single    0.970  0.020  1.090
 AVT  C14  H7   single    0.930  0.020  1.080
 AVT  C12  H8   single    0.930  0.020  1.080
 AVT  C22  H9   single    0.970  0.020  1.090
 AVT  C22  H10  single    0.970  0.020  1.090
 AVT  C22  H11  single    0.970  0.020  1.090
 AVT  C23  H12  single    0.970  0.020  1.090
 AVT  C23  H13  single    0.970  0.020  1.090
 AVT  O25  H14  single    0.850  0.020  0.980
 AVT  C29  H15  single    0.970  0.020  1.090
 AVT  C29  H16  single    0.970  0.020  1.090

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
 AVT  C6   C5   C3   123.45  3.000
 AVT  C6   C5   F27  117.89  3.000
 AVT  C3   C5   F27  118.66  3.000
 AVT  H1   C3   C1   121.28  3.000
 AVT  H1   C3   C5   119.66  3.000
 AVT  C1   C3   C5   119.06  3.000
 AVT  H2   C6   C4   121.48  3.000
 AVT  H2   C6   C5   120.50  3.000
 AVT  C4   C6   C5   118.02  3.000
 AVT  H3   C4   C2   118.35  3.000
 AVT  H3   C4   C6   120.68  3.000
 AVT  C2   C4   C6   120.97  3.000
 AVT  C1   C2   N9   123.01  3.000
 AVT  C1   C2   C4   120.01  3.000
 AVT  N9   C2   C4   116.97  3.000
 AVT  C10  N9   C2   120.95  3.000
 AVT  C8   C10  C11  122.06  3.000
 AVT  C8   C10  N9   121.06  3.000
 AVT  C11  C10  N9   116.86  3.000
 AVT  C12  C11  C13  117.93  3.000
 AVT  C13  C11  C10  119.02  3.000
 AVT  C12  C11  C10  122.97  3.000
 AVT  H4   C13  C15  118.71  3.000
 AVT  H4   C13  C11  119.53  3.000
 AVT  C15  C13  C11  121.76  3.000
 AVT  H5   C15  C16  121.55  3.000
 AVT  H5   C15  C13  118.80  3.000
 AVT  C16  C15  C13  119.65  3.000
 AVT  C14  C16  O28  116.35  3.000
 AVT  C14  C16  C15  119.18  3.000
 AVT  O28  C16  C15  124.47  3.000
 AVT  C29  O28  C16  118.68  3.000
 AVT  H16  C29  H15  108.80  3.000
 AVT  H16  C29  H6   108.81  3.000
 AVT  H15  C29  H6   108.84  3.000
 AVT  H16  C29  O28  106.48  3.000
 AVT  H15  C29  O28  111.93  3.000
 AVT  H6   C29  O28  111.88  3.000
 AVT  H7   C14  C12  120.05  3.000
 AVT  H7   C14  C16  119.44  3.000
 AVT  C12  C14  C16  120.51  3.000
 AVT  H8   C12  C14  118.61  3.000
 AVT  H8   C12  C11  120.42  3.000
 AVT  C14  C12  C11  120.97  3.000
 AVT  C7   C8   N19  123.15  3.000
 AVT  C7   C8   C10  119.09  3.000
 AVT  N19  C8   C10  117.76  3.000
 AVT  C20  N19  C8   119.51  3.000
 AVT  N18  C20  C22  119.29  3.000
 AVT  N18  C20  N19  122.16  3.000
 AVT  C22  C20  N19  118.55  3.000
 AVT  H11  C22  H10  107.78  3.000
 AVT  H11  C22  H9   108.45  3.000
 AVT  H10  C22  H9   108.49  3.000
 AVT  H11  C22  C20  111.89  3.000
 AVT  H10  C22  C20  111.75  3.000
 AVT  H9   C22  C20  108.38  3.000
 AVT  C23  N18  C17  115.17  3.000
 AVT  C17  N18  C20  122.48  3.000
 AVT  C23  N18  C20  122.14  3.000
 AVT  C7   C17  O21  125.78  3.000
 AVT  O21  C17  N18  119.15  3.000
 AVT  C7   C17  N18  115.07  3.000
 AVT  C1   C7   C17  122.97  3.000
 AVT  C1   C7   C8   119.72  3.000
 AVT  C17  C7   C8   117.32  3.000
 AVT  C7   C1   C2   116.08  3.000
 AVT  C2   C1   C3   118.49  3.000
 AVT  C7   C1   C3   125.42  3.000
 AVT  H13  C23  H12  106.32  3.000
 AVT  H13  C23  C24  109.03  3.000
 AVT  H12  C23  C24  110.49  3.000
 AVT  H13  C23  N18  110.46  3.000
 AVT  H12  C23  N18  109.92  3.000
 AVT  C24  C23  N18  110.54  3.000
 AVT  O26  C24  O25  125.12  3.000
 AVT  O25  C24  C23  110.97  3.000
 AVT  O26  C24  C23  123.89  3.000
 AVT  H14  O25  C24  110.46  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
 AVT  CONST_01  C7   C1   C3   C5   180.00   0.0  0
 AVT  CONST_02  C2   C1   C3   C5     0.00   0.0  0
 AVT  CONST_03  C2   C4   C6   C5     0.00   0.0  0
 AVT  CONST_04  C8   C7   C1   C3   180.00   0.0  0
 AVT  CONST_05  N9   C2   C1   C3   180.00   0.0  0
 AVT  CONST_06  C4   C2   C1   C3     0.00   0.0  0
 AVT  CONST_07  C4   C6   C5   C3     0.00   0.0  0
 AVT  CONST_08  N9   C2   C4   C6   180.00   0.0  0
 AVT  CONST_09  C1   C2   C4   C6     0.00   0.0  0
 AVT  CONST_10  C1   C3   C5   C6     0.00   0.0  0
 AVT  CONST_11  C10  N9   C2   C4   180.00   0.0  0
 AVT  CONST_12  C7   C1   C2   C4   180.00   0.0  0
 AVT  CONST_13  C11  C10  N9   C2   180.00   0.0  0
 AVT  CONST_14  C8   C10  N9   C2     0.00   0.0  0
 AVT  CONST_15  C8   C7   C1   C2     0.00   0.0  0
 AVT  CONST_18  C7   C8   C10  N9     0.00   0.0  0
 AVT  CONST_19  C7   C1   C2   N9     0.00   0.0  0
 AVT  CONST_20  C14  C12  C11  C10  180.00   0.0  0
 AVT  CONST_21  C15  C13  C11  C10  180.00   0.0  0
 AVT  CONST_22  C1   C7   C8   C10    0.00   0.0  0
 AVT  CONST_23  C1   C2   N9   C10    0.00   0.0  0
 AVT  CONST_24  C16  C14  C12  C11    0.00   0.0  0
 AVT  CONST_25  C16  C15  C13  C11    0.00   0.0  0
 AVT  CONST_26  C7   C8   C10  C11  180.00   0.0  0
 AVT  CONST_27  C14  C16  C15  C13    0.00   0.0  0
 AVT  CONST_28  C14  C12  C11  C13    0.00   0.0  0
 AVT  CONST_30  C12  C14  C16  C15    0.00   0.0  0
 AVT  CONST_31  C12  C11  C13  C15    0.00   0.0  0
 AVT  CONST_33  N19  C8   C10  C11    0.00   0.0  0
 AVT  CONST_34  N18  C20  N19  C8     0.00   0.0  0
 AVT  CONST_35  C17  N18  C20  N19    0.00   0.0  0
 AVT  CONST_36  C7   C17  N18  C20    0.00   0.0  0
 AVT  CONST_37  C1   C3   C5   F27  180.00   0.0  0
 AVT  CONST_38  C4   C6   C5   F27  180.00   0.0  0
 AVT  CONST_39  O28  C16  C15  C13  180.00   0.0  0
 AVT  CONST_40  C12  C14  C16  O28  180.00   0.0  0
 AVT  CONST_41  C22  C20  N19  C8   180.00   0.0  0
 AVT  CONST_42  C23  N18  C20  N19  180.00   0.0  0
 AVT  CONST_43  O21  C17  N18  C20  180.00   0.0  0
 AVT  CONST_44  C17  N18  C20  C22  180.00   0.0  0
 AVT  CONST_45  C23  N18  C17  C7   180.00   0.0  0
 AVT  CONST_46  H3   C4   C6   C5   180.00   0.0  0
 AVT  CONST_47  H2   C6   C5   C3   180.00   0.0  0
 AVT  CONST_48  H1   C3   C5   C6   180.00   0.0  0
 AVT  CONST_49  H8   C12  C11  C10    0.00   0.0  0
 AVT  CONST_50  H4   C13  C11  C10    0.00   0.0  0
 AVT  CONST_51  H7   C14  C12  C11  180.00   0.0  0
 AVT  CONST_52  H5   C15  C13  C11  180.00   0.0  0
 AVT  CONST_53  C23  N18  C20  C22    0.00   0.0  0
 AVT  CONST_54  C23  N18  C17  O21    0.00   0.0  0
 AVT  CONST_55  H14  O25  C24  C23  180.00   0.0  0
 AVT  Var_01    C14  C16  O28  C29  179.67  30.0  2
 AVT  Var_02    C24  C23  N18  C20   98.01  30.0  2
 AVT  Var_03    H9   C22  C20  N19    2.30  30.0  3
 AVT  Var_04    O26  C24  C23  N18  -15.27  30.0  3
 AVT  Var_05    H6   C29  O28  C16  -60.79  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
 AVT  plan-1  C10  0.020
 AVT  plan-1  C11  0.020
 AVT  plan-1  C13  0.020
 AVT  plan-1  C15  0.020
 AVT  plan-1  C16  0.020
 AVT  plan-1  O28  0.020
 AVT  plan-1  C14  0.020
 AVT  plan-1  C12  0.020
 AVT  plan-1  H4   0.020
 AVT  plan-1  H5   0.020
 AVT  plan-1  H7   0.020
 AVT  plan-1  H8   0.020
 AVT  plan-2  F27  0.020
 AVT  plan-2  C5   0.020
 AVT  plan-2  C3   0.020
 AVT  plan-2  C6   0.020
 AVT  plan-2  C4   0.020
 AVT  plan-2  C2   0.020
 AVT  plan-2  N9   0.020
 AVT  plan-2  C10  0.020
 AVT  plan-2  C11  0.020
 AVT  plan-2  C8   0.020
 AVT  plan-2  N19  0.020
 AVT  plan-2  C20  0.020
 AVT  plan-2  C22  0.020
 AVT  plan-2  N18  0.020
 AVT  plan-2  C17  0.020
 AVT  plan-2  O21  0.020
 AVT  plan-2  C7   0.020
 AVT  plan-2  C1   0.020
 AVT  plan-2  C23  0.020
 AVT  plan-2  H1   0.020
 AVT  plan-2  H2   0.020
 AVT  plan-2  H3   0.020
 AVT  plan-3  C23  0.020
 AVT  plan-3  C24  0.020
 AVT  plan-3  O25  0.020
 AVT  plan-3  O26  0.020
 AVT  plan-3  H14  0.020

