# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:16:30 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: [2-(benzylcarbamoyl)-5-fluorophenoxy]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1cc(F)ccc1C(=O)NCc2ccccc2
#
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
 2YZ  2YZ  '[2-(benzylcarbamoyl)-5-fluorophenoxy]acetic acid'  ligand  36  22  .  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_2YZ
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
 2YZ  O1   O  O2    0  -0.439  -2.3449  -0.5762  -0.1474
 2YZ  C2   C  CH2   0  -0.280  -3.7165  -0.7873   0.0319
 2YZ  C3   C  C     0   0.519  -3.9368  -2.2775   0.1344
 2YZ  O4   O  O     0  -0.406  -3.0716  -3.1061   0.1375
 2YZ  O6   O  OH1   0  -0.578  -5.2339  -2.5391   0.2283
 2YZ  C9   C  CR6   0   0.425  -1.8856   0.6819  -0.2074
 2YZ  C10  C  CR6   0  -0.189  -0.4987   0.8234  -0.3405
 2YZ  C11  C  C     0   0.524   0.3760  -0.3803  -0.5080
 2YZ  N12  N  NH1   0  -0.601   1.2819  -0.5313   0.4757
 2YZ  C14  C  CH2   0  -0.363   2.3105  -1.5464   0.4892
 2YZ  C15  C  CR6   0   0.127   3.6873  -0.9682   0.2812
 2YZ  C16  C  CR16  0  -0.281   3.9857  -0.2688  -0.8869
 2YZ  C17  C  CR16  0  -0.218   5.2481   0.2673  -1.0846
 2YZ  C19  C  CR16  0  -0.248   6.2326   0.1111  -0.1156
 2YZ  C20  C  CR16  0  -0.220   5.9452  -0.5849   1.0484
 2YZ  C21  C  CR16  0  -0.289   4.6770  -1.1190   1.2445
 2YZ  O28  O  O     0  -0.466   0.2819  -1.1197  -1.4712
 2YZ  C29  C  CR16  0  -0.211   0.0542   2.0933  -0.3738
 2YZ  C31  C  CR16  0  -0.415  -0.7347   3.2332  -0.2958
 2YZ  C33  C  CR6   0   0.570  -2.0943   3.0574  -0.1666
 2YZ  F34  F  F     0  -0.307  -2.8853   4.1322  -0.0775
 2YZ  C35  C  CR16  0  -0.528  -2.6926   1.8100  -0.1167
 2YZ  H1   H  HCH2  0   0.267  -4.0897  -0.3147   0.9490
 2YZ  H2   H  HCH2  0   0.265  -4.3068  -0.3937  -0.8040
 2YZ  H3   H  HOH1  0   0.465  -5.3684  -3.4936   0.2978
 2YZ  H4   H  HNH1  0   0.385   1.2616   0.1147   1.2471
 2YZ  H5   H  HCH2  0   0.252   2.2677  -2.0833   1.4383
 2YZ  H6   H  HCH2  0   0.267   2.0778  -2.2685  -0.2924
 2YZ  H7   H  HCR6  0   0.238   3.2289  -0.1504  -1.6534
 2YZ  H8   H  HCR6  0   0.236   5.4678   0.8064  -1.9966
 2YZ  H9   H  HCR6  0   0.237   7.2178   0.5305  -0.2703
 2YZ  H10  H  HCR6  0   0.237   6.7058  -0.7122   1.8071
 2YZ  H11  H  HCR6  0   0.227   4.4596  -1.6596   2.1581
 2YZ  H12  H  HCR6  0   0.254   1.1257   2.2060  -0.4794
 2YZ  H13  H  HCR6  0   0.262  -0.3008   4.2220  -0.3357
 2YZ  H14  H  HCR6  0   0.280  -3.7648   1.7505   0.0082

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
 2YZ  C17  C19  aromatic  1.390  0.020  1.390
 2YZ  C17  C16  aromatic  1.386  0.020  1.386
 2YZ  C19  C20  aromatic  1.386  0.020  1.386
 2YZ  C16  C15  aromatic  1.394  0.020  1.394
 2YZ  C20  C21  aromatic  1.390  0.020  1.390
 2YZ  C15  C21  aromatic  1.389  0.020  1.389
 2YZ  C15  C14  single    1.508  0.020  1.508
 2YZ  C14  N12  single    1.445  0.020  1.445
 2YZ  O28  C11  double    1.218  0.020  1.218
 2YZ  N12  C11  single    1.346  0.020  1.346
 2YZ  C11  C10  single    1.497  0.020  1.497
 2YZ  C29  C10  aromatic  1.386  0.020  1.386
 2YZ  C29  C31  aromatic  1.388  0.020  1.388
 2YZ  C10  C9   aromatic  1.400  0.020  1.400
 2YZ  C31  C33  aromatic  1.377  0.020  1.377
 2YZ  O4   C3   double    1.198  0.020  1.198
 2YZ  C9   O1   single    1.341  0.020  1.341
 2YZ  C9   C35  aromatic  1.390  0.020  1.390
 2YZ  O1   C2   single    1.399  0.020  1.399
 2YZ  C33  C35  aromatic  1.384  0.020  1.384
 2YZ  C33  F34  single    1.337  0.020  1.337
 2YZ  C3   C2   single    1.510  0.020  1.510
 2YZ  C3   O6   single    1.327  0.020  1.327
 2YZ  C2   H1   single    0.970  0.020  1.090
 2YZ  C2   H2   single    0.970  0.020  1.090
 2YZ  O6   H3   single    0.850  0.020  0.980
 2YZ  N12  H4   single    0.860  0.020  1.020
 2YZ  C14  H5   single    0.970  0.020  1.090
 2YZ  C14  H6   single    0.970  0.020  1.090
 2YZ  C16  H7   single    0.930  0.020  1.080
 2YZ  C17  H8   single    0.930  0.020  1.080
 2YZ  C19  H9   single    0.930  0.020  1.080
 2YZ  C20  H10  single    0.930  0.020  1.080
 2YZ  C21  H11  single    0.930  0.020  1.080
 2YZ  C29  H12  single    0.930  0.020  1.080
 2YZ  C31  H13  single    0.930  0.020  1.080
 2YZ  C35  H14  single    0.930  0.020  1.080

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
 2YZ  C9   O1   C2   118.89  3.000
 2YZ  H2   C2   H1   107.43  3.000
 2YZ  H2   C2   C3   109.12  3.000
 2YZ  H1   C2   C3   108.59  3.000
 2YZ  H2   C2   O1   112.07  3.000
 2YZ  H1   C2   O1   112.06  3.000
 2YZ  C3   C2   O1   107.49  3.000
 2YZ  O6   C3   O4   124.73  3.000
 2YZ  O6   C3   C2   110.00  3.000
 2YZ  O4   C3   C2   125.27  3.000
 2YZ  H3   O6   C3   109.63  3.000
 2YZ  C35  C9   C10  119.95  3.000
 2YZ  C35  C9   O1   124.04  3.000
 2YZ  C10  C9   O1   116.00  3.000
 2YZ  C29  C10  C11  120.07  3.000
 2YZ  C29  C10  C9   119.35  3.000
 2YZ  C11  C10  C9   120.53  3.000
 2YZ  O28  C11  N12  124.20  3.000
 2YZ  N12  C11  C10  113.68  3.000
 2YZ  O28  C11  C10  122.10  3.000
 2YZ  H4   N12  C14  117.26  3.000
 2YZ  H4   N12  C11  118.34  3.000
 2YZ  C14  N12  C11  124.38  3.000
 2YZ  H6   C14  H5   106.83  3.000
 2YZ  H6   C14  C15  110.51  3.000
 2YZ  H5   C14  C15  110.15  3.000
 2YZ  H6   C14  N12  107.87  3.000
 2YZ  H5   C14  N12  109.01  3.000
 2YZ  C15  C14  N12  112.29  3.000
 2YZ  C21  C15  C16  118.89  3.000
 2YZ  C21  C15  C14  120.88  3.000
 2YZ  C16  C15  C14  120.23  3.000
 2YZ  H7   C16  C17  119.54  3.000
 2YZ  H7   C16  C15  119.87  3.000
 2YZ  C17  C16  C15  120.58  3.000
 2YZ  H8   C17  C19  119.98  3.000
 2YZ  H8   C17  C16  119.87  3.000
 2YZ  C19  C17  C16  120.15  3.000
 2YZ  H9   C19  C20  120.23  3.000
 2YZ  H9   C19  C17  120.11  3.000
 2YZ  C20  C19  C17  119.66  3.000
 2YZ  H10  C20  C21  119.83  3.000
 2YZ  H10  C20  C19  120.14  3.000
 2YZ  C21  C20  C19  120.03  3.000
 2YZ  H11  C21  C20  119.58  3.000
 2YZ  H11  C21  C15  119.72  3.000
 2YZ  C20  C21  C15  120.69  3.000
 2YZ  H12  C29  C31  118.84  3.000
 2YZ  H12  C29  C10  119.52  3.000
 2YZ  C31  C29  C10  121.63  3.000
 2YZ  H13  C31  C33  121.11  3.000
 2YZ  H13  C31  C29  121.40  3.000
 2YZ  C33  C31  C29  117.48  3.000
 2YZ  C35  C33  F34  117.78  3.000
 2YZ  F34  C33  C31  119.18  3.000
 2YZ  C35  C33  C31  123.04  3.000
 2YZ  H14  C35  C33  118.85  3.000
 2YZ  H14  C35  C9   122.59  3.000
 2YZ  C33  C35  C9   118.55  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
 2YZ  CONST_01  C31  C29  C10  C9     0.00   0.0  0
 2YZ  CONST_02  C31  C33  C35  C9     0.00   0.0  0
 2YZ  CONST_03  C33  C31  C29  C10    0.00   0.0  0
 2YZ  CONST_04  C33  C35  C9   C10    0.00   0.0  0
 2YZ  CONST_05  C19  C17  C16  C15    0.00   0.0  0
 2YZ  CONST_06  C19  C20  C21  C15    0.00   0.0  0
 2YZ  CONST_07  C20  C19  C17  C16    0.00   0.0  0
 2YZ  CONST_08  C20  C21  C15  C16    0.00   0.0  0
 2YZ  CONST_09  C21  C20  C19  C17    0.00   0.0  0
 2YZ  CONST_10  C21  C15  C16  C17    0.00   0.0  0
 2YZ  CONST_11  C35  C9   C10  C29    0.00   0.0  0
 2YZ  CONST_12  C35  C33  C31  C29    0.00   0.0  0
 2YZ  CONST_13  C29  C10  C9   O1   180.00   0.0  0
 2YZ  CONST_14  C33  C35  C9   O1   180.00   0.0  0
 2YZ  CONST_15  F34  C33  C35  C9   180.00   0.0  0
 2YZ  CONST_16  C31  C29  C10  C11  180.00   0.0  0
 2YZ  CONST_17  C35  C9   C10  C11  180.00   0.0  0
 2YZ  CONST_18  C17  C16  C15  C14  180.00   0.0  0
 2YZ  CONST_19  C20  C21  C15  C14  180.00   0.0  0
 2YZ  CONST_20  F34  C33  C31  C29  180.00   0.0  0
 2YZ  CONST_21  H12  C29  C10  C9   180.00   0.0  0
 2YZ  CONST_22  H13  C31  C29  C10  180.00   0.0  0
 2YZ  CONST_23  H14  C35  C9   C10  180.00   0.0  0
 2YZ  CONST_24  H8   C17  C16  C15  180.00   0.0  0
 2YZ  CONST_25  H10  C20  C21  C15  180.00   0.0  0
 2YZ  CONST_26  H9   C19  C17  C16  180.00   0.0  0
 2YZ  CONST_27  H11  C21  C15  C16  180.00   0.0  0
 2YZ  CONST_28  H7   C16  C17  C19  180.00   0.0  0
 2YZ  CONST_29  C14  N12  C11  C10  180.00   0.0  0
 2YZ  CONST_30  H4   N12  C11  C10    0.00   0.0  0
 2YZ  CONST_31  O28  C11  N12  C14    0.00   0.0  0
 2YZ  CONST_32  H3   O6   C3   C2   180.00   0.0  0
 2YZ  Var_01    C10  C9   O1   C2   177.82  30.0  1
 2YZ  Var_02    O28  C11  C10  C9    62.88  30.0  2
 2YZ  Var_03    C16  C15  C14  N12  -60.06  30.0  2
 2YZ  Var_04    C15  C14  N12  C11  109.63  30.0  2
 2YZ  Var_05    H1   C2   O1   C9   -57.85  30.0  3
 2YZ  Var_06    O4   C3   C2   O1     3.92  30.0  1

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
 2YZ  plan-1  C14  0.020
 2YZ  plan-1  C15  0.020
 2YZ  plan-1  C16  0.020
 2YZ  plan-1  C17  0.020
 2YZ  plan-1  C19  0.020
 2YZ  plan-1  C20  0.020
 2YZ  plan-1  C21  0.020
 2YZ  plan-1  H7   0.020
 2YZ  plan-1  H8   0.020
 2YZ  plan-1  H9   0.020
 2YZ  plan-1  H10  0.020
 2YZ  plan-1  H11  0.020
 2YZ  plan-2  O1   0.020
 2YZ  plan-2  C9   0.020
 2YZ  plan-2  C10  0.020
 2YZ  plan-2  C11  0.020
 2YZ  plan-2  C29  0.020
 2YZ  plan-2  C31  0.020
 2YZ  plan-2  C33  0.020
 2YZ  plan-2  F34  0.020
 2YZ  plan-2  C35  0.020
 2YZ  plan-2  H12  0.020
 2YZ  plan-2  H13  0.020
 2YZ  plan-2  H14  0.020
 2YZ  plan-3  C10  0.020
 2YZ  plan-3  C11  0.020
 2YZ  plan-3  N12  0.020
 2YZ  plan-3  C14  0.020
 2YZ  plan-3  O28  0.020
 2YZ  plan-3  H4   0.020
 2YZ  plan-4  C2   0.020
 2YZ  plan-4  C3   0.020
 2YZ  plan-4  O4   0.020
 2YZ  plan-4  O6   0.020
 2YZ  plan-4  H3   0.020

