# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 10:00:48 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 1-[2-({[(2-chloro-4,5-difluorophenyl)carbonyl]carbamoyl}amino)-4-fluorophenyl]piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1CCN(CC1)c2ccc(F)cc2NC(=O)NC(=O)c3cc(F)c(F)cc3Cl
#
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
 AVF  AVF  '1-[2-({[(2-chloro-4,5-difluorophenyl)carbonyl]carbamoyl}amino)-4-fluorophenyl]piperidine-4-carboxylic acid'  ligand  47  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AVF
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
 AVF  C1    C   CR6    0   0.412   4.5340   2.7721  -0.3340
 AVF  C2    C   CR6    0   0.426   3.6623   2.3099  -1.3048
 AVF  C3    C   CR16   0  -0.427   3.0084   1.1115  -1.1319
 AVF  C11   C   C      0   0.765   0.3433  -2.0182  -0.1319
 AVF  C13   C   C      0   0.342  -2.0940  -2.3928  -0.3055
 AVF  C14   C   C1     0  -0.494  -2.1155  -3.7760  -0.4659
 AVF  C15   C   C      0   0.550  -3.3432  -4.4009  -0.5754
 AVF  C16   C   C1     0  -0.434  -4.5457  -3.7279  -0.5342
 AVF  C24   C   CH2    0  -0.282  -3.8543   0.5103  -1.1415
 AVF  C27   C   CH2    0  -0.424  -3.5137   1.9843  -1.0035
 AVF  C28   C   CH1    0  -0.396  -3.8929   2.5187   0.3743
 AVF  C29   C   C      0   0.431  -3.5807   4.0222   0.5323
 AVF  O31   O   O      0  -0.614  -3.7308   4.7341  -0.4821
 AVF  O30   O   OC    -1  -0.607  -3.2306   4.4200   1.6616
 AVF  C26   C   CH2    0  -0.420  -3.2605   1.6449   1.4515
 AVF  C25   C   CH2    0  -0.289  -3.6036   0.1780   1.2490
 AVF  N21   N   NT     0  -0.526  -3.2103  -0.2652  -0.0867
 AVF  C18   C   C      0   0.215  -3.3020  -1.6713  -0.2582
 AVF  C17   C   C1     0  -0.260  -4.5048  -2.3495  -0.3701
 AVF  F23   F   F      0  -0.319  -3.3533  -5.7352  -0.7325
 AVF  N12   N   NH1    0  -0.784  -0.9492  -1.6151  -0.1974
 AVF  O19   O   O      0  -0.459   0.7214  -3.1673  -0.1437
 AVF  N10   N   NH1    0  -0.739   1.2134  -0.9266  -0.0541
 AVF  O20   O   O      0  -0.394   3.1980  -1.9910   0.3686
 AVF  C4    C   CR6    0   0.003   3.2317   0.3504   0.0128
 AVF  F22   F   F      0  -0.294   3.4671   3.0337  -2.4052
 AVF  F9    F   F      0  -0.292   5.1550   3.9332  -0.5171
 AVF  C6    C   CR16   0  -0.348   4.7592   2.0436   0.8141
 AVF  C5    C   CR6    0  -0.077   4.1130   0.8278   0.9779
 AVF  CL8   CL  CL     0  -0.091   4.3910  -0.0433   2.4393
 AVF  H3    H   HCR6   0   0.315   2.3384   0.7622  -1.9080
 AVF  H14   H   H      0   0.297  -1.2109  -4.3611  -0.5117
 AVF  H16   H   H      0   0.278  -5.4844  -4.2572  -0.6250
 AVF  H24   H   HCH2   0   0.199  -4.9488   0.3874  -1.1193
 AVF  H24A  H   HCH2   0   0.241  -3.5106   0.1302  -2.1055
 AVF  H27   H   HCH2   0   0.209  -2.4397   2.1184  -1.1715
 AVF  H27A  H   HCH2   0   0.228  -4.0303   2.5408  -1.7858
 AVF  H28   H   HCH1   0   0.218  -4.9859   2.4188   0.4710
 AVF  H26   H   HCH2   0   0.207  -2.1716   1.7606   1.4348
 AVF  H26A  H   HCH2   0   0.226  -3.5970   1.9514   2.4424
 AVF  H25   H   HCH2   0   0.242  -3.0791  -0.4354   1.9851
 AVF  H25A  H   HCH2   0   0.204  -4.6823   0.0224   1.4125
 AVF  H17   H   H      0   0.268  -5.4335  -1.7931  -0.3296
 AVF  HN12  H   HNH1   0   0.406  -1.1980  -0.6279  -0.1413
 AVF  HN10  H   HNH1   0   0.430   0.8159  -0.0010  -0.1234
 AVF  H6    H   HCR6   0   0.322   5.4314   2.4263   1.5701
 AVF  C7    C   C      0   0.534   2.5701  -0.9885   0.1367

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
 AVF  C1   C2    aromatic  1.384  0.020  1.384
 AVF  C6   C1    aromatic  1.378  0.020  1.378
 AVF  C1   F9    single    1.329  0.020  1.329
 AVF  C2   C3    aromatic  1.376  0.020  1.376
 AVF  C2   F22   single    1.332  0.020  1.332
 AVF  C3   C4    aromatic  1.393  0.020  1.393
 AVF  C3   H3    single    0.930  0.020  1.080
 AVF  O20  C7    double    1.205  0.020  1.205
 AVF  C7   N10   single    1.372  0.020  1.372
 AVF  C7   C4    single    1.499  0.020  1.499
 AVF  N12  C11   single    1.356  0.020  1.356
 AVF  C11  O19   double    1.210  0.020  1.210
 AVF  C11  N10   single    1.398  0.020  1.398
 AVF  C18  C13   aromatic  1.408  0.020  1.408
 AVF  C13  C14   aromatic  1.393  0.020  1.393
 AVF  C13  N12   single    1.388  0.020  1.388
 AVF  C15  C14   aromatic  1.382  0.020  1.382
 AVF  C14  H14   single    0.930  0.020  1.080
 AVF  C16  C15   aromatic  1.379  0.020  1.379
 AVF  C15  F23   single    1.344  0.020  1.344
 AVF  C17  C16   aromatic  1.389  0.020  1.389
 AVF  C16  H16   single    0.930  0.020  1.080
 AVF  C27  C24   single    1.519  0.020  1.519
 AVF  C24  N21   single    1.459  0.020  1.459
 AVF  C24  H24   single    0.970  0.020  1.090
 AVF  C24  H24A  single    0.970  0.020  1.090
 AVF  C27  C28   single    1.526  0.020  1.526
 AVF  C27  H27   single    0.970  0.020  1.090
 AVF  C27  H27A  single    0.970  0.020  1.090
 AVF  C29  C28   single    1.544  0.020  1.544
 AVF  C28  C26   single    1.524  0.020  1.524
 AVF  C28  H28   single    0.970  0.020  1.090
 AVF  O31  C29   deloc     1.248  0.020  1.248
 AVF  C29  O30   deloc     1.247  0.020  1.247
 AVF  C26  C25   single    1.520  0.020  1.520
 AVF  C26  H26   single    0.970  0.020  1.090
 AVF  C26  H26A  single    0.970  0.020  1.090
 AVF  N21  C25   single    1.461  0.020  1.461
 AVF  C25  H25   single    0.970  0.020  1.090
 AVF  C25  H25A  single    0.970  0.020  1.090
 AVF  N21  C18   single    1.419  0.020  1.419
 AVF  C17  C18   aromatic  1.385  0.020  1.385
 AVF  C17  H17   single    0.930  0.020  1.080
 AVF  N12  HN12  single    0.860  0.020  1.020
 AVF  N10  HN10  single    0.860  0.020  1.020
 AVF  C4   C5    aromatic  1.392  0.020  1.392
 AVF  C6   C5    aromatic  1.387  0.020  1.387
 AVF  C6   H6    single    0.930  0.020  1.080
 AVF  CL8  C5    single    1.724  0.020  1.724

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
 AVF  C6    C1   F9   120.01  3.000
 AVF  F9    C1   C2   119.29  3.000
 AVF  C6    C1   C2   120.71  3.000
 AVF  F22   C2   C3   120.51  3.000
 AVF  F22   C2   C1   119.37  3.000
 AVF  C3    C2   C1   120.13  3.000
 AVF  H3    C3   C4   120.79  3.000
 AVF  H3    C3   C2   118.99  3.000
 AVF  C4    C3   C2   120.20  3.000
 AVF  N10   C11  O19  123.21  3.000
 AVF  N10   C11  N12  111.34  3.000
 AVF  O19   C11  N12  125.45  3.000
 AVF  N12   C13  C18  114.70  3.000
 AVF  N12   C13  C14  125.32  3.000
 AVF  C18   C13  C14  119.97  3.000
 AVF  H14   C14  C15  119.77  3.000
 AVF  H14   C14  C13  122.07  3.000
 AVF  C15   C14  C13  118.16  3.000
 AVF  F23   C15  C16  118.80  3.000
 AVF  F23   C15  C14  117.71  3.000
 AVF  C16   C15  C14  123.49  3.000
 AVF  H16   C16  C17  121.42  3.000
 AVF  H16   C16  C15  121.04  3.000
 AVF  C17   C16  C15  117.54  3.000
 AVF  H24A  C24  H24  106.96  3.000
 AVF  H24A  C24  N21  108.32  3.000
 AVF  H24   C24  N21  111.40  3.000
 AVF  H24A  C24  C27  110.33  3.000
 AVF  H24   C24  C27  109.21  3.000
 AVF  N21   C24  C27  110.56  3.000
 AVF  H27A  C27  H27  106.99  3.000
 AVF  H27A  C27  C28  110.57  3.000
 AVF  H27   C27  C28  109.83  3.000
 AVF  H27A  C27  C24  108.90  3.000
 AVF  H27   C27  C24  108.95  3.000
 AVF  C28   C27  C24  111.48  3.000
 AVF  H28   C28  C26  107.31  3.000
 AVF  H28   C28  C29  106.26  3.000
 AVF  C26   C28  C29  113.71  3.000
 AVF  H28   C28  C27  107.10  3.000
 AVF  C26   C28  C27  109.53  3.000
 AVF  C29   C28  C27  112.54  3.000
 AVF  O30   C29  O31  125.98  3.000
 AVF  O30   C29  C28  117.39  3.000
 AVF  O31   C29  C28  116.61  3.000
 AVF  H26A  C26  H26  106.92  3.000
 AVF  H26A  C26  C25  108.82  3.000
 AVF  H26   C26  C25  108.93  3.000
 AVF  H26A  C26  C28  110.67  3.000
 AVF  H26   C26  C28  109.95  3.000
 AVF  C25   C26  C28  111.43  3.000
 AVF  H25A  C25  H25  106.90  3.000
 AVF  H25A  C25  N21  110.87  3.000
 AVF  H25   C25  N21  108.44  3.000
 AVF  H25A  C25  C26  109.72  3.000
 AVF  H25   C25  C26  110.11  3.000
 AVF  N21   C25  C26  110.71  3.000
 AVF  C18   N21  C25  113.17  3.000
 AVF  C18   N21  C24  114.25  3.000
 AVF  C25   N21  C24  112.38  3.000
 AVF  C17   C18  N21  123.42  3.000
 AVF  C17   C18  C13  119.43  3.000
 AVF  N21   C18  C13  117.14  3.000
 AVF  H17   C17  C18  119.33  3.000
 AVF  H17   C17  C16  119.27  3.000
 AVF  C18   C17  C16  121.40  3.000
 AVF  HN12  N12  C13  110.21  3.000
 AVF  HN12  N12  C11  121.19  3.000
 AVF  C13   N12  C11  128.57  3.000
 AVF  HN10  N10  C11  117.84  3.000
 AVF  HN10  N10  C7   116.13  3.000
 AVF  C11   N10  C7   126.02  3.000
 AVF  C5    C4   C7   121.93  3.000
 AVF  C5    C4   C3   118.95  3.000
 AVF  C7    C4   C3   119.05  3.000
 AVF  H6    C6   C5   121.15  3.000
 AVF  H6    C6   C1   119.79  3.000
 AVF  C5    C6   C1   119.06  3.000
 AVF  CL8   C5   C6   117.92  3.000
 AVF  CL8   C5   C4   121.11  3.000
 AVF  C6    C5   C4   120.94  3.000
 AVF  C4    C7   O20  121.94  3.000
 AVF  C4    C7   N10  112.63  3.000
 AVF  O20   C7   N10  125.42  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
 AVF  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 AVF  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 AVF  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 AVF  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 AVF  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 AVF  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 AVF  CONST_07  C16   C17  C18  C13    0.00   0.0  0
 AVF  CONST_08  C16   C15  C14  C13    0.00   0.0  0
 AVF  CONST_09  C17   C18  C13  C14    0.00   0.0  0
 AVF  CONST_10  C17   C16  C15  C14    0.00   0.0  0
 AVF  CONST_11  C18   C13  C14  C15    0.00   0.0  0
 AVF  CONST_12  C18   C17  C16  C15    0.00   0.0  0
 AVF  CONST_13  N21   C18  C13  C14  180.00   0.0  0
 AVF  CONST_14  N21   C18  C17  C16  180.00   0.0  0
 AVF  CONST_15  CL8   C5   C6   C1   180.00   0.0  0
 AVF  CONST_16  C7    C4   C3   C2   180.00   0.0  0
 AVF  CONST_17  F9    C1   C2   C3   180.00   0.0  0
 AVF  CONST_18  CL8   C5   C4   C3   180.00   0.0  0
 AVF  CONST_19  C6    C5   C4   C7   180.00   0.0  0
 AVF  CONST_20  F23   C15  C14  C13  180.00   0.0  0
 AVF  CONST_21  N12   C13  C14  C15  180.00   0.0  0
 AVF  CONST_22  N12   C13  C18  N21    0.00   0.0  0
 AVF  CONST_23  F23   C15  C16  C17  180.00   0.0  0
 AVF  CONST_24  N12   C13  C18  C17  180.00   0.0  0
 AVF  CONST_25  F22   C2   C3   C4   180.00   0.0  0
 AVF  CONST_26  C6    C1   C2   F22  180.00   0.0  0
 AVF  CONST_27  C5    C6   C1   F9   180.00   0.0  0
 AVF  CONST_28  H3    C3   C2   C1   180.00   0.0  0
 AVF  CONST_29  H6    C6   C1   C2   180.00   0.0  0
 AVF  CONST_30  H17   C17  C18  C13  180.00   0.0  0
 AVF  CONST_31  H16   C16  C15  C14  180.00   0.0  0
 AVF  CONST_32  H14   C14  C15  C16  180.00   0.0  0
 AVF  CONST_33  C18   C13  N12  C11  180.00   0.0  0
 AVF  CONST_34  C14   C13  N12  C11    0.00   0.0  0
 AVF  CONST_35  HN12  N12  C13  C14  180.00   0.0  0
 AVF  CONST_36  C4    C7   N10  C11  180.00   0.0  0
 AVF  CONST_37  O19   C11  N12  C13    0.00   0.0  0
 AVF  CONST_38  N10   C11  N12  C13  180.00   0.0  0
 AVF  CONST_39  HN10  N10  C7   C4     0.00   0.0  0
 AVF  CONST_40  O19   C11  N10  C7     0.00   0.0  0
 AVF  CONST_41  O20   C7   N10  C11    0.00   0.0  0
 AVF  CONST_42  N12   C11  N10  C7   180.00   0.0  0
 AVF  Var_01    C24   N21  C18  C13  122.80  30.0  2
 AVF  Var_02    C26   C25  N21  C24  -58.52  30.0  1
 AVF  Var_03    N21   C24  C27  C28  -56.13  30.0  1
 AVF  Var_04    N21   C25  C26  C28   55.78  30.0  1
 AVF  Var_05    O20   C7   C4   C3   126.31  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 AVF  chir_01  C28  C27  C29  C26  positiv

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
 AVF  plan-1  C1    0.020
 AVF  plan-1  C2    0.020
 AVF  plan-1  C3    0.020
 AVF  plan-1  C4    0.020
 AVF  plan-1  F22   0.020
 AVF  plan-1  F9    0.020
 AVF  plan-1  C6    0.020
 AVF  plan-1  C5    0.020
 AVF  plan-1  CL8   0.020
 AVF  plan-1  H3    0.020
 AVF  plan-1  H6    0.020
 AVF  plan-1  C7    0.020
 AVF  plan-2  C13   0.020
 AVF  plan-2  C14   0.020
 AVF  plan-2  C15   0.020
 AVF  plan-2  C16   0.020
 AVF  plan-2  N21   0.020
 AVF  plan-2  C18   0.020
 AVF  plan-2  C17   0.020
 AVF  plan-2  F23   0.020
 AVF  plan-2  N12   0.020
 AVF  plan-2  H14   0.020
 AVF  plan-2  H16   0.020
 AVF  plan-2  H17   0.020
 AVF  plan-3  C11   0.020
 AVF  plan-3  C13   0.020
 AVF  plan-3  N12   0.020
 AVF  plan-3  O19   0.020
 AVF  plan-3  N10   0.020
 AVF  plan-3  O20   0.020
 AVF  plan-3  C4    0.020
 AVF  plan-3  HN12  0.020
 AVF  plan-3  HN10  0.020
 AVF  plan-3  C7    0.020
 AVF  plan-4  C28   0.020
 AVF  plan-4  C29   0.020
 AVF  plan-4  O31   0.020
 AVF  plan-4  O30   0.020

