# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:01:54 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 1-(2-carboxyphenyl)-7-chloro-6-[(2-chloro-4,6-difluorophenyl)amino]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=CN(c2ccccc2C(O)=O)c3cc(Cl)c(Nc4c(F)cc(F)cc4Cl)cc3C1=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
 AVD  AVD  '1-(2-carboxyphenyl)-7-chloro-6-[(2-chloro-4,6-difluorophenyl)amino]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid'  ligand  46  34  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AVD
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
 AVD  C5    C   CR6   0   0.536   5.6795   0.8231   1.4904
 AVD  C6    C   CR16  0  -0.562   4.4128   0.8240   2.0388
 AVD  C2    C   CR6   0   0.205   3.6258  -0.4743   0.1255
 AVD  C4    C   CR16  0  -0.395   5.9661   0.1959   0.2957
 AVD  O40   O   O     0  -0.418  -2.8794   0.5082   2.1618
 AVD  O41   O   OH1   0  -0.584  -2.4645   2.6391   2.6717
 AVD  C34   C   CR6   0  -0.027  -3.2906   2.2024   0.5324
 AVD  C33   C   CR16  0  -0.277  -3.7266   3.5189   0.4014
 AVD  C32   C   CR16  0  -0.221  -4.1744   4.0007  -0.8198
 AVD  C31   C   CR16  0  -0.252  -4.1765   3.1782  -1.9344
 AVD  C30   C   CR16  0  -0.231  -3.7274   1.8690  -1.8264
 AVD  C28   C   CR6   0   0.191  -3.3014   1.3865  -0.6029
 AVD  N21   N   NR6   0  -0.609  -2.8326   0.0375  -0.5427
 AVD  C22   C   CR16  0   0.067  -3.7183  -0.9473  -0.3909
 AVD  C23   C   CR6   0  -0.370  -3.3886  -2.2719  -0.2629
 AVD  C26   C   C     0   0.537  -4.5306  -3.1916  -0.1123
 AVD  O42   O   O     0  -0.459  -5.6869  -2.8268  -0.1475
 AVD  O27   O   OH1   0  -0.583  -4.1937  -4.4577   0.0739
 AVD  C24   C   CR6   0   0.434  -1.9954  -2.6731  -0.2679
 AVD  O25   O   O     0  -0.433  -1.5890  -3.8222  -0.1617
 AVD  C17   C   CR66  0  -0.068  -1.0416  -1.5545  -0.4180
 AVD  C18   C   CR16  0  -0.421   0.3258  -1.8193  -0.3981
 AVD  C16   C   CR66  0   0.349  -1.4716  -0.2339  -0.5591
 AVD  C15   C   CR16  0  -0.250  -0.5372   0.7856  -0.7380
 AVD  C14   C   CR6   0  -0.112   0.8058   0.4865  -0.7489
 AVD  CL29  CL  CL    0  -0.081   1.9187   1.7622  -1.0751
 AVD  C13   C   CR6   0   0.464   1.2757  -0.8231  -0.5446
 AVD  N10   N   NH1   0  -0.772   2.6222  -1.1462  -0.5657
 AVD  C3    C   CR6   0  -0.107   4.9290  -0.4319  -0.3749
 AVD  CL12  CL  CL    0  -0.085   5.2568  -1.1961  -1.8842
 AVD  F11   F   F     0  -0.305   6.6650   1.4490   2.1425
 AVD  C1    C   CR6   0   0.569   3.4224   0.1558   1.3518
 AVD  F9    F   F     0  -0.299   2.1979   0.1178   1.8844
 AVD  H6    H   HCR6  0   0.312   4.2015   1.3096   2.9824
 AVD  H4    H   HCR6  0   0.307   6.9684   0.2059  -0.1097
 AVD  HO41  H   HOH1  0   0.494  -2.2361   2.2712   3.5393
 AVD  H33   H   HCR6  0   0.284  -3.7367   4.1762   1.2593
 AVD  H32   H   HCR6  0   0.280  -4.5200   5.0225  -0.8954
 AVD  H31   H   HCR6  0   0.283  -4.5180   3.5509  -2.8901
 AVD  H30   H   HCR6  0   0.288  -3.7020   1.2206  -2.6921
 AVD  H22   H   HCR6  0   0.329  -4.7537  -0.6360  -0.3729
 AVD  HO27  H   HOH1  0   0.481  -5.0017  -4.9842   0.1718
 AVD  H18   H   HCR6  0   0.280   0.6553  -2.8402  -0.2538
 AVD  H15   H   HCR6  0   0.309  -0.8480   1.8081  -0.8998
 AVD  HN10  H   HNH1  0   0.409   2.8210  -2.1138  -0.7745
 AVD  C39   C   C     0   0.512  -2.8614   1.6742   1.8577

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
 AVD  C4    C5    aromatic  1.379  0.020  1.379
 AVD  C5    F11   single    1.337  0.020  1.337
 AVD  C5    C6    aromatic  1.380  0.020  1.380
 AVD  C1    C6    aromatic  1.378  0.020  1.378
 AVD  C6    H6    single    0.930  0.020  1.080
 AVD  C3    C2    aromatic  1.397  0.020  1.397
 AVD  N10   C2    single    1.392  0.020  1.392
 AVD  C2    C1    aromatic  1.394  0.020  1.394
 AVD  C3    C4    aromatic  1.385  0.020  1.385
 AVD  C4    H4    single    0.930  0.020  1.080
 AVD  O40   C39   double    1.205  0.020  1.205
 AVD  C34   C39   single    1.490  0.020  1.490
 AVD  C39   O41   single    1.323  0.020  1.323
 AVD  O41   HO41  single    0.850  0.020  0.980
 AVD  C33   C34   aromatic  1.393  0.020  1.393
 AVD  C28   C34   aromatic  1.398  0.020  1.398
 AVD  C32   C33   aromatic  1.387  0.020  1.387
 AVD  C33   H33   single    0.930  0.020  1.080
 AVD  C31   C32   aromatic  1.385  0.020  1.385
 AVD  C32   H32   single    0.930  0.020  1.080
 AVD  C31   C30   aromatic  1.388  0.020  1.388
 AVD  C31   H31   single    0.930  0.020  1.080
 AVD  C30   C28   aromatic  1.383  0.020  1.383
 AVD  C30   H30   single    0.930  0.020  1.080
 AVD  C28   N21   single    1.429  0.020  1.429
 AVD  C22   N21   single    1.333  0.020  1.333
 AVD  N21   C16   single    1.388  0.020  1.388
 AVD  C22   C23   double    1.371  0.020  1.371
 AVD  C22   H22   single    0.930  0.020  1.080
 AVD  C26   C23   single    1.474  0.020  1.474
 AVD  C23   C24   single    1.450  0.020  1.450
 AVD  O42   C26   double    1.213  0.020  1.213
 AVD  C26   O27   single    1.323  0.020  1.323
 AVD  O27   HO27  single    0.850  0.020  0.980
 AVD  C24   C17   single    1.478  0.020  1.478
 AVD  C24   O25   double    1.224  0.020  1.224
 AVD  C16   C17   aromatic  1.396  0.020  1.396
 AVD  C17   C18   aromatic  1.393  0.020  1.393
 AVD  C18   C13   aromatic  1.384  0.020  1.384
 AVD  C18   H18   single    0.930  0.020  1.080
 AVD  C16   C15   aromatic  1.394  0.020  1.394
 AVD  C15   C14   aromatic  1.376  0.020  1.376
 AVD  C15   H15   single    0.930  0.020  1.080
 AVD  C14   CL29  single    1.724  0.020  1.724
 AVD  C14   C13   aromatic  1.406  0.020  1.406
 AVD  C13   N10   single    1.385  0.020  1.385
 AVD  N10   HN10  single    0.890  0.020  1.040
 AVD  CL12  C3    single    1.723  0.020  1.723
 AVD  C1    F9    single    1.336  0.020  1.336

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
 AVD  F11   C5   C4    118.82  3.000
 AVD  F11   C5   C6    118.84  3.000
 AVD  C4    C5   C6    122.34  3.000
 AVD  H6    C6   C1    120.79  3.000
 AVD  H6    C6   C5    121.73  3.000
 AVD  C1    C6   C5    117.46  3.000
 AVD  C1    C2   C3    115.96  3.000
 AVD  C1    C2   N10   123.38  3.000
 AVD  C3    C2   N10   120.64  3.000
 AVD  H4    C4   C3    121.11  3.000
 AVD  H4    C4   C5    120.87  3.000
 AVD  C3    C4   C5    118.02  3.000
 AVD  HO41  O41  C39   110.14  3.000
 AVD  C28   C34  C33   118.21  3.000
 AVD  C28   C34  C39   121.18  3.000
 AVD  C33   C34  C39   120.59  3.000
 AVD  H33   C33  C32   118.99  3.000
 AVD  H33   C33  C34   120.20  3.000
 AVD  C32   C33  C34   120.80  3.000
 AVD  H32   C32  C31   120.29  3.000
 AVD  H32   C32  C33   119.53  3.000
 AVD  C31   C32  C33   120.18  3.000
 AVD  H31   C31  C30   119.74  3.000
 AVD  H31   C31  C32   120.47  3.000
 AVD  C30   C31  C32   119.79  3.000
 AVD  H30   C30  C28   119.45  3.000
 AVD  H30   C30  C31   120.70  3.000
 AVD  C28   C30  C31   119.85  3.000
 AVD  N21   C28  C30   117.89  3.000
 AVD  N21   C28  C34   120.93  3.000
 AVD  C30   C28  C34   121.15  3.000
 AVD  C16   N21  C22   120.56  3.000
 AVD  C16   N21  C28   120.37  3.000
 AVD  C22   N21  C28   118.95  3.000
 AVD  H22   C22  C23   120.45  3.000
 AVD  H22   C22  N21   115.18  3.000
 AVD  C23   C22  N21   124.37  3.000
 AVD  C24   C23  C26   124.90  3.000
 AVD  C24   C23  C22   119.88  3.000
 AVD  C26   C23  C22   115.22  3.000
 AVD  O27   C26  O42   122.31  3.000
 AVD  O27   C26  C23   114.46  3.000
 AVD  O42   C26  C23   123.23  3.000
 AVD  HO27  O27  C26   108.76  3.000
 AVD  C17   C24  O25   120.36  3.000
 AVD  O25   C24  C23   125.37  3.000
 AVD  C17   C24  C23   114.28  3.000
 AVD  C16   C17  C18   118.92  3.000
 AVD  C18   C17  C24   119.23  3.000
 AVD  C16   C17  C24   121.84  3.000
 AVD  H18   C18  C13   118.94  3.000
 AVD  H18   C18  C17   118.68  3.000
 AVD  C13   C18  C17   122.37  3.000
 AVD  C15   C16  C17   119.88  3.000
 AVD  C15   C16  N21   121.05  3.000
 AVD  C17   C16  N21   119.07  3.000
 AVD  H15   C15  C14   119.02  3.000
 AVD  H15   C15  C16   121.21  3.000
 AVD  C14   C15  C16   119.74  3.000
 AVD  C13   C14  CL29  120.06  3.000
 AVD  C13   C14  C15   121.83  3.000
 AVD  CL29  C14  C15   118.08  3.000
 AVD  N10   C13  C14   122.68  3.000
 AVD  N10   C13  C18   120.07  3.000
 AVD  C14   C13  C18   117.14  3.000
 AVD  HN10  N10  C13   114.72  3.000
 AVD  HN10  N10  C2    115.05  3.000
 AVD  C13   N10  C2    125.52  3.000
 AVD  CL12  C3   C4    118.85  3.000
 AVD  CL12  C3   C2    118.54  3.000
 AVD  C4    C3   C2    122.61  3.000
 AVD  F9    C1   C2    118.15  3.000
 AVD  F9    C1   C6    118.28  3.000
 AVD  C2    C1   C6    123.57  3.000
 AVD  C34   C39  O41   112.03  3.000
 AVD  O41   C39  O40   123.69  3.000
 AVD  C34   C39  O40   124.27  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
 AVD  CONST_01  C2    C3   C4   C5       0.00   0.0  0
 AVD  CONST_02  C2    C1   C6   C5       0.00   0.0  0
 AVD  CONST_03  C3    C4   C5   C6       0.00   0.0  0
 AVD  CONST_04  C3    C2   C1   C6       0.00   0.0  0
 AVD  CONST_05  C1    C6   C5   C4       0.00   0.0  0
 AVD  CONST_06  C1    C2   C3   C4       0.00   0.0  0
 AVD  CONST_07  C31   C32  C33  C34      0.00   0.0  0
 AVD  CONST_08  C31   C30  C28  C34      0.00   0.0  0
 AVD  CONST_09  C30   C28  C34  C33      0.00   0.0  0
 AVD  CONST_10  C30   C31  C32  C33      0.00   0.0  0
 AVD  CONST_11  C28   C34  C33  C32      0.00   0.0  0
 AVD  CONST_12  C28   C30  C31  C32      0.00   0.0  0
 AVD  CONST_13  C14   C15  C16  C17      0.00   0.0  0
 AVD  CONST_14  C14   C13  C18  C17      0.00   0.0  0
 AVD  CONST_15  C15   C16  C17  C18      0.00   0.0  0
 AVD  CONST_16  C15   C14  C13  C18      0.00   0.0  0
 AVD  CONST_17  C13   C18  C17  C16      0.00   0.0  0
 AVD  CONST_18  C13   C14  C15  C16      0.00   0.0  0
 AVD  CONST_19  N21   C28  C34  C33    180.00   0.0  0
 AVD  CONST_20  N21   C28  C30  C31    180.00   0.0  0
 AVD  CONST_21  CL12  C3   C4   C5     180.00   0.0  0
 AVD  CONST_22  F9    C1   C6   C5     180.00   0.0  0
 AVD  CONST_23  N10   C2   C1   C6     180.00   0.0  0
 AVD  CONST_24  N10   C2   C3   C4     180.00   0.0  0
 AVD  CONST_25  C32   C33  C34  C39    180.00   0.0  0
 AVD  CONST_26  C30   C28  C34  C39    180.00   0.0  0
 AVD  CONST_27  N21   C28  C34  C39      0.00   0.0  0
 AVD  CONST_28  N10   C13  C18  C17    180.00   0.0  0
 AVD  CONST_29  CL29  C14  C13  C18    180.00   0.0  0
 AVD  CONST_30  CL29  C14  C15  C16    180.00   0.0  0
 AVD  CONST_31  N10   C13  C14  C15    180.00   0.0  0
 AVD  CONST_32  F9    C1   C2   C3     180.00   0.0  0
 AVD  CONST_33  F11   C5   C4   C3     180.00   0.0  0
 AVD  CONST_34  C1    C2   C3   CL12   180.00   0.0  0
 AVD  CONST_35  C1    C6   C5   F11    180.00   0.0  0
 AVD  CONST_36  H4    C4   C5   C6     180.00   0.0  0
 AVD  CONST_37  H6    C6   C1   C2     180.00   0.0  0
 AVD  CONST_38  H32   C32  C33  C34    180.00   0.0  0
 AVD  CONST_39  H30   C30  C28  C34    180.00   0.0  0
 AVD  CONST_40  H31   C31  C32  C33    180.00   0.0  0
 AVD  CONST_41  H33   C33  C32  C31    180.00   0.0  0
 AVD  CONST_42  H15   C15  C16  N21      0.00   0.0  0
 AVD  CONST_43  H18   C18  C17  C24      0.00   0.0  0
 AVD  CONST_44  HO41  O41  C39  C34    180.00   0.0  0
 AVD  CONST_45  HO27  O27  C26  C23    180.00   0.0  0
 AVD  Var_01    C22   N21  C28  C34     97.27  30.0  2
 AVD  Var_02    C18   C13  N10  C2    -135.08  30.0  3
 AVD  Var_03    C3    C2   N10  C13   -150.51  30.0  2
 AVD  Var_04    C33   C34  C39  O40    155.42  30.0  1
 AVD  Var_05    O42   C26  C23  C22      2.69  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
 AVD  plan-1  C5    0.020
 AVD  plan-1  C6    0.020
 AVD  plan-1  C2    0.020
 AVD  plan-1  C4    0.020
 AVD  plan-1  N10   0.020
 AVD  plan-1  C3    0.020
 AVD  plan-1  CL12  0.020
 AVD  plan-1  F11   0.020
 AVD  plan-1  C1    0.020
 AVD  plan-1  F9    0.020
 AVD  plan-1  H6    0.020
 AVD  plan-1  H4    0.020
 AVD  plan-2  C34   0.020
 AVD  plan-2  C33   0.020
 AVD  plan-2  C32   0.020
 AVD  plan-2  C31   0.020
 AVD  plan-2  C30   0.020
 AVD  plan-2  C28   0.020
 AVD  plan-2  N21   0.020
 AVD  plan-2  H33   0.020
 AVD  plan-2  H32   0.020
 AVD  plan-2  H31   0.020
 AVD  plan-2  H30   0.020
 AVD  plan-2  C39   0.020
 AVD  plan-3  C28   0.020
 AVD  plan-3  N21   0.020
 AVD  plan-3  C22   0.020
 AVD  plan-3  C23   0.020
 AVD  plan-3  C26   0.020
 AVD  plan-3  C24   0.020
 AVD  plan-3  O25   0.020
 AVD  plan-3  C17   0.020
 AVD  plan-3  C18   0.020
 AVD  plan-3  C16   0.020
 AVD  plan-3  C15   0.020
 AVD  plan-3  C14   0.020
 AVD  plan-3  CL29  0.020
 AVD  plan-3  C13   0.020
 AVD  plan-3  N10   0.020
 AVD  plan-3  H22   0.020
 AVD  plan-3  H18   0.020
 AVD  plan-3  H15   0.020
 AVD  plan-4  C23   0.020
 AVD  plan-4  C26   0.020
 AVD  plan-4  O42   0.020
 AVD  plan-4  O27   0.020
 AVD  plan-4  HO27  0.020
 AVD  plan-5  O40   0.020
 AVD  plan-5  O41   0.020
 AVD  plan-5  C34   0.020
 AVD  plan-5  HO41  0.020
 AVD  plan-5  C39   0.020

