# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 15:52:32 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-{[(2S)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)CONC(=O)c1ccc(F)c(F)c1Nc2ccc(I)cc2F
#
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
 5Y0  5Y0  N-{[(2S)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]benzamide  ligand  40  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5Y0
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
 5Y0  C13   C  CR6   0   0.150  -0.1152  -0.6644   0.2814
 5Y0  C14   C  CR16  0  -0.274   0.2549  -0.3479  -1.0237
 5Y0  C15   C  CR16  0  -0.231   0.2157   0.9576  -1.4897
 5Y0  C16   C  CR6   0  -0.234  -0.2126   1.9707  -0.6472
 5Y0  C17   C  CR16  0  -0.378  -0.5916   1.6925   0.6598
 5Y0  C18   C  CR6   0   0.507  -0.5262   0.3875   1.0970
 5Y0  N9    N  NH1   0  -0.770  -0.1052  -1.9599   0.7781
 5Y0  C5    C  CR6   0   0.177   0.7486  -2.9445   0.3210
 5Y0  C6    C  CR6   0  -0.109   2.1228  -2.7278   0.1315
 5Y0  C1    C  CR16  0  -0.260   2.9276  -3.7477  -0.3610
 5Y0  C2    C  CR16  0  -0.418   2.4135  -5.0049  -0.6397
 5Y0  C3    C  CR6   0   0.409   1.0690  -5.2215  -0.4279
 5Y0  C4    C  CR6   0   0.349   0.2473  -4.2077   0.0268
 5Y0  C10   C  C     0   0.488   2.7516  -1.4536   0.5982
 5Y0  N12   N  NH1   0  -0.344   3.4971  -0.8523  -0.3432
 5Y0  O11   O  O     0  -0.447   2.6096  -1.0249   1.7276
 5Y0  O21   O  O2    0  -0.382   4.2307   0.2439  -0.0297
 5Y0  C22   C  CH2   0  -0.154   3.4828   1.4464  -0.2132
 5Y0  C24   C  CH2   0  -0.164   3.5634   3.8905   0.1891
 5Y0  O26   O  OH1   0  -0.656   5.5379   2.6884  -0.5860
 5Y0  O23   O  OH1   0  -0.666   4.3676   4.9353   0.6759
 5Y0  C25   C  CH1   0  -0.050   4.3746   2.6038   0.2002
 5Y0  I20   I  I     0   0.068  -0.3070   3.9471  -1.3477
 5Y0  F19   F  F     0  -0.303  -0.8887   0.1064   2.3555
 5Y0  F7    F  F     0  -0.298  -1.0591  -4.4444   0.1829
 5Y0  F8    F  F     0  -0.299   0.5252  -6.4116  -0.6842
 5Y0  H17   H  HCR6  0   0.302  -0.9238   2.4644   1.3415
 5Y0  H14   H  HCR6  0   0.293   0.5655  -1.1351  -1.6988
 5Y0  H9    H  HNH1  0   0.409  -0.9023  -2.2503   1.3223
 5Y0  H15   H  HCR6  0   0.287   0.5079   1.1610  -2.5104
 5Y0  H242  H  HCH2  0   0.197   3.2139   4.0914  -0.8345
 5Y0  H25   H  HCH1  0   0.243   4.7172   2.4240   1.2249
 5Y0  H23   H  HOH1  0   0.457   3.8645   5.7518   0.6112
 5Y0  H1    H  HCR6  0   0.287   3.9882  -3.5793  -0.4922
 5Y0  H2    H  HCR6  0   0.297   3.0461  -5.8051  -0.9980
 5Y0  H12   H  HNH1  0   0.423   3.5802  -1.1856  -1.2944
 5Y0  H221  H  HCH2  0   0.223   3.1790   1.5468  -1.2622
 5Y0  H222  H  HCH2  0   0.226   2.5803   1.4294   0.4050
 5Y0  H26   H  HOH1  0   0.445   5.2849   2.9176  -1.4873
 5Y0  H241  H  HCH2  0   0.199   2.6652   3.7462   0.8048

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
 5Y0  I20  C16   single    2.099  0.020  2.099
 5Y0  C17  C18   aromatic  1.378  0.020  1.378
 5Y0  C17  C16   aromatic  1.389  0.020  1.389
 5Y0  C18  C13   aromatic  1.393  0.020  1.393
 5Y0  C18  F19   single    1.339  0.020  1.339
 5Y0  C13  C14   aromatic  1.393  0.020  1.393
 5Y0  C13  N9    single    1.387  0.020  1.387
 5Y0  C14  C15   aromatic  1.387  0.020  1.387
 5Y0  C15  C16   aromatic  1.385  0.020  1.385
 5Y0  C24  C25   single    1.521  0.020  1.521
 5Y0  C24  O23   single    1.406  0.020  1.406
 5Y0  N9   C5    single    1.381  0.020  1.381
 5Y0  C5   C6    aromatic  1.404  0.020  1.404
 5Y0  C5   C4    aromatic  1.391  0.020  1.391
 5Y0  C6   C1    aromatic  1.389  0.020  1.389
 5Y0  C6   C10   single    1.496  0.020  1.496
 5Y0  C1   C2    aromatic  1.387  0.020  1.387
 5Y0  C2   C3    aromatic  1.378  0.020  1.378
 5Y0  C3   C4    aromatic  1.382  0.020  1.382
 5Y0  C3   F8    single    1.333  0.020  1.333
 5Y0  C4   F7    single    1.337  0.020  1.337
 5Y0  C10  O11   double    1.216  0.020  1.216
 5Y0  C10  N12   single    1.343  0.020  1.343
 5Y0  N12  O21   single    1.356  0.020  1.356
 5Y0  O21  C22   single    1.428  0.020  1.428
 5Y0  C22  C25   single    1.518  0.020  1.518
 5Y0  C25  O26   single    1.407  0.020  1.407
 5Y0  C17  H17   single    0.930  0.020  1.080
 5Y0  C14  H14   single    0.930  0.020  1.080
 5Y0  N9   H9    single    0.860  0.020  1.020
 5Y0  C15  H15   single    0.930  0.020  1.080
 5Y0  C24  H241  single    0.970  0.020  1.090
 5Y0  C24  H242  single    0.970  0.020  1.090
 5Y0  C25  H25   single    0.970  0.020  1.090
 5Y0  O23  H23   single    0.850  0.020  0.980
 5Y0  C1   H1    single    0.930  0.020  1.080
 5Y0  C2   H2    single    0.930  0.020  1.080
 5Y0  N12  H12   single    0.860  0.020  1.020
 5Y0  C22  H221  single    0.970  0.020  1.090
 5Y0  C22  H222  single    0.970  0.020  1.090
 5Y0  O26  H26   single    0.850  0.020  0.980

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
 5Y0  N9    C13  C18   119.84  3.000
 5Y0  N9    C13  C14   123.07  3.000
 5Y0  C18   C13  C14   117.08  3.000
 5Y0  H14   C14  C15   118.89  3.000
 5Y0  H14   C14  C13   119.69  3.000
 5Y0  C15   C14  C13   121.42  3.000
 5Y0  H15   C15  C16   121.34  3.000
 5Y0  H15   C15  C14   119.13  3.000
 5Y0  C16   C15  C14   119.52  3.000
 5Y0  I20   C16  C17   119.36  3.000
 5Y0  C17   C16  C15   120.67  3.000
 5Y0  I20   C16  C15   119.96  3.000
 5Y0  H17   C17  C18   119.36  3.000
 5Y0  H17   C17  C16   122.25  3.000
 5Y0  C18   C17  C16   118.38  3.000
 5Y0  F19   C18  C17   118.95  3.000
 5Y0  F19   C18  C13   118.13  3.000
 5Y0  C17   C18  C13   122.92  3.000
 5Y0  H9    N9   C5    117.53  3.000
 5Y0  H9    N9   C13   117.16  3.000
 5Y0  C5    N9   C13   123.48  3.000
 5Y0  C4    C5   C6    117.68  3.000
 5Y0  C4    C5   N9    119.66  3.000
 5Y0  C6    C5   N9    122.66  3.000
 5Y0  C10   C6   C1    119.50  3.000
 5Y0  C10   C6   C5    120.06  3.000
 5Y0  C1    C6   C5    120.10  3.000
 5Y0  H1    C1   C2    118.70  3.000
 5Y0  H1    C1   C6    119.77  3.000
 5Y0  C2    C1   C6    121.47  3.000
 5Y0  H2    C2   C3    120.36  3.000
 5Y0  H2    C2   C1    121.38  3.000
 5Y0  C3    C2   C1    118.25  3.000
 5Y0  F8    C3   C4    118.39  3.000
 5Y0  F8    C3   C2    120.58  3.000
 5Y0  C4    C3   C2    121.02  3.000
 5Y0  F7    C4   C3    119.31  3.000
 5Y0  F7    C4   C5    119.24  3.000
 5Y0  C3    C4   C5    121.45  3.000
 5Y0  O11   C10  N12   123.91  3.000
 5Y0  N12   C10  C6    113.33  3.000
 5Y0  O11   C10  C6    122.75  3.000
 5Y0  H12   N12  O21   116.07  3.000
 5Y0  H12   N12  C10   123.87  3.000
 5Y0  O21   N12  C10   120.02  3.000
 5Y0  C22   O21  N12   111.58  3.000
 5Y0  H222  C22  H221  108.26  3.000
 5Y0  H222  C22  C25   110.03  3.000
 5Y0  H221  C22  C25   110.69  3.000
 5Y0  H222  C22  O21   110.27  3.000
 5Y0  H221  C22  O21   110.19  3.000
 5Y0  C25   C22  O21   107.41  3.000
 5Y0  H242  C24  H241  106.61  3.000
 5Y0  H242  C24  C25   109.31  3.000
 5Y0  H241  C24  C25   108.72  3.000
 5Y0  H242  C24  O23   111.61  3.000
 5Y0  H241  C24  O23   111.80  3.000
 5Y0  C25   C24  O23   108.73  3.000
 5Y0  H26   O26  C25   108.66  3.000
 5Y0  H23   O23  C24   107.98  3.000
 5Y0  H25   C25  O26   105.91  3.000
 5Y0  H25   C25  C24   108.21  3.000
 5Y0  O26   C25  C24   112.71  3.000
 5Y0  H25   C25  C22   108.26  3.000
 5Y0  O26   C25  C22   112.29  3.000
 5Y0  C24   C25  C22   109.24  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
 5Y0  CONST_01  C16  C17  C18  C13    0.00   0.0  0
 5Y0  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 5Y0  CONST_03  C17  C18  C13  C14    0.00   0.0  0
 5Y0  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 5Y0  CONST_05  C18  C13  C14  C15    0.00   0.0  0
 5Y0  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 5Y0  CONST_07  C2   C1   C6   C5     0.00   0.0  0
 5Y0  CONST_08  C2   C3   C4   C5     0.00   0.0  0
 5Y0  CONST_09  C3   C4   C5   C6     0.00   0.0  0
 5Y0  CONST_10  C3   C2   C1   C6     0.00   0.0  0
 5Y0  CONST_11  C4   C5   C6   C1     0.00   0.0  0
 5Y0  CONST_12  C4   C3   C2   C1     0.00   0.0  0
 5Y0  CONST_13  F19  C18  C13  C14  180.00   0.0  0
 5Y0  CONST_14  I20  C16  C15  C14  180.00   0.0  0
 5Y0  CONST_15  N9   C13  C14  C15  180.00   0.0  0
 5Y0  CONST_16  F19  C18  C17  C16  180.00   0.0  0
 5Y0  CONST_17  N9   C13  C18  C17  180.00   0.0  0
 5Y0  CONST_18  I20  C16  C17  C18  180.00   0.0  0
 5Y0  CONST_19  C1   C6   C5   N9   180.00   0.0  0
 5Y0  CONST_20  C3   C4   C5   N9   180.00   0.0  0
 5Y0  CONST_21  F8   C3   C4   C5   180.00   0.0  0
 5Y0  CONST_22  F7   C4   C5   C6   180.00   0.0  0
 5Y0  CONST_23  F8   C3   C2   C1   180.00   0.0  0
 5Y0  CONST_24  C10  C6   C1   C2   180.00   0.0  0
 5Y0  CONST_25  F7   C4   C3   C2   180.00   0.0  0
 5Y0  CONST_26  C10  C6   C5   C4   180.00   0.0  0
 5Y0  CONST_27  H17  C17  C18  C13  180.00   0.0  0
 5Y0  CONST_28  H15  C15  C14  C13  180.00   0.0  0
 5Y0  CONST_29  H14  C14  C15  C16  180.00   0.0  0
 5Y0  CONST_30  H1   C1   C6   C5   180.00   0.0  0
 5Y0  CONST_31  H2   C2   C1   C6   180.00   0.0  0
 5Y0  CONST_32  O21  N12  C10  C6   180.00   0.0  0
 5Y0  CONST_33  H12  N12  C10  C6     0.00   0.0  0
 5Y0  CONST_34  O21  N12  C10  O11    0.00   0.0  0
 5Y0  Var_01    C6   C5   N9   C13   46.52  30.0  2
 5Y0  Var_02    C5   N9   C13  C14   28.66  30.0  2
 5Y0  Var_03    O11  C10  C6   C5    51.19  30.0  2
 5Y0  Var_04    C25  C22  O21  N12  178.41  30.0  3

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
 5Y0  chir_01  C25  C24  C22  O26  negativ

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
 5Y0  plan-1  C13  0.020
 5Y0  plan-1  C14  0.020
 5Y0  plan-1  C15  0.020
 5Y0  plan-1  C16  0.020
 5Y0  plan-1  C17  0.020
 5Y0  plan-1  C18  0.020
 5Y0  plan-1  N9   0.020
 5Y0  plan-1  I20  0.020
 5Y0  plan-1  F19  0.020
 5Y0  plan-1  H17  0.020
 5Y0  plan-1  H14  0.020
 5Y0  plan-1  H15  0.020
 5Y0  plan-2  N9   0.020
 5Y0  plan-2  C5   0.020
 5Y0  plan-2  C6   0.020
 5Y0  plan-2  C1   0.020
 5Y0  plan-2  C2   0.020
 5Y0  plan-2  C3   0.020
 5Y0  plan-2  C4   0.020
 5Y0  plan-2  C10  0.020
 5Y0  plan-2  F7   0.020
 5Y0  plan-2  F8   0.020
 5Y0  plan-2  H1   0.020
 5Y0  plan-2  H2   0.020
 5Y0  plan-3  C6   0.020
 5Y0  plan-3  C10  0.020
 5Y0  plan-3  N12  0.020
 5Y0  plan-3  O11  0.020
 5Y0  plan-3  O21  0.020
 5Y0  plan-3  H12  0.020

