# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:40:11 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc2ccc(OC(F)(F)F)cc2n1c3cccc(CCC(O)=O)c3
#
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
 AYZ  AYZ  '3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]propanoic acid'  ligand  42  28  .  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_AYZ
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
 AYZ  C1   C  CR16   0  -0.336   3.1678   2.1600  -1.1120
 AYZ  C2   C  CR16   0  -0.314   3.9443   1.0244  -1.0398
 AYZ  C3   C  CR6    0   0.309   3.4026  -0.1564  -0.5141
 AYZ  C8   C  CR5    0   0.226  -0.2882   2.4228  -0.0416
 AYZ  C9   C  CR15   0  -0.411   0.7862   3.0583  -0.5973
 AYZ  C10  C  C      0   0.461  -1.5933   3.0075   0.3540
 AYZ  C13  C  CR6    0   0.324  -0.8282   0.1001   0.7180
 AYZ  C15  C  CT     0   1.071   4.9376  -1.5556   0.5609
 AYZ  C19  C  CR16   0  -0.312  -0.5474  -0.5714   1.8982
 AYZ  C20  C  CR16   0  -0.243  -1.3886  -1.5990   2.3019
 AYZ  C21  C  CR16   0  -0.307  -2.5010  -1.9332   1.5445
 AYZ  C22  C  CR6    0   0.142  -2.7918  -1.2566   0.3603
 AYZ  C24  C  CH2    0  -0.502  -4.0280  -1.5830  -0.4282
 AYZ  O28  O  O      0  -0.607  -6.5803  -2.0314  -1.4702
 AYZ  C4   C  CR16   0  -0.358   2.1114  -0.2528  -0.0486
 AYZ  C5   C  CR56   0   0.083   1.8488   2.1131  -0.6478
 AYZ  C6   C  CR56   0   0.355   1.3467   0.9108  -0.1090
 AYZ  N7   N  NR5    0  -0.674   0.0474   1.1217   0.2698
 AYZ  N11  N  NH2    0  -0.803  -2.0261   3.9866  -0.4518
 AYZ  O12  O  O      0  -0.463  -2.1838   2.6306   1.3536
 AYZ  O14  O  O2     0  -0.526   4.1939  -1.3032  -0.5217
 AYZ  F16  F  F      0  -0.299   4.2068  -1.7230   1.6651
 AYZ  F17  F  F      0  -0.278   5.6103  -2.6733   0.3352
 AYZ  F18  F  F      0  -0.300   5.8152  -0.5850   0.8255
 AYZ  C23  C  CR16   0  -0.332  -1.9315  -0.2446  -0.0501
 AYZ  C25  C  CH2    0  -0.575  -5.2500  -0.8595   0.1329
 AYZ  C26  C  C      0   0.414  -6.5760  -1.1439  -0.5951
 AYZ  O27  O  OC    -1  -0.629  -7.5531  -0.4558  -0.2325
 AYZ  H1   H  HCR6   0   0.265   3.5737   3.0724  -1.5286
 AYZ  H2   H  HCR6   0   0.274   4.9622   1.0324  -1.4059
 AYZ  H3   H  HCR5   0   0.274   0.8302   4.0949  -0.8927
 AYZ  H4   H  HCR6   0   0.271   0.3092  -0.2908   2.4975
 AYZ  H5   H  HCR6   0   0.259  -1.1767  -2.1336   3.2187
 AYZ  H6   H  HCR6   0   0.248  -3.1526  -2.7330   1.8767
 AYZ  H7   H  HCH2   0   0.232  -3.8822  -1.3042  -1.4741
 AYZ  H8   H  HCH2   0   0.233  -4.2017  -2.6605  -0.4129
 AYZ  H9   H  HCR6   0   0.289   1.7159  -1.1859   0.3296
 AYZ  H10  H  HNH2   0   0.416  -1.5643   4.2148  -1.3155
 AYZ  H11  H  HNH2   0   0.409  -2.8733   4.4844  -0.2304
 AYZ  H12  H  HCR6   0   0.258  -2.1232   0.2777  -0.9809
 AYZ  H13  H  HCH2   0   0.232  -5.3775  -1.1257   1.1888
 AYZ  H14  H  HCH2   0   0.227  -5.0713   0.2206   0.1306

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
 AYZ  F18  C15  single    1.335  0.020  1.335
 AYZ  F17  C15  single    1.324  0.020  1.324
 AYZ  C15  O14  single    1.337  0.020  1.337
 AYZ  C15  F16  single    1.335  0.020  1.335
 AYZ  O14  C3   single    1.393  0.020  1.393
 AYZ  C3   C4   aromatic  1.376  0.020  1.376
 AYZ  C3   C2   aromatic  1.401  0.020  1.401
 AYZ  C4   C6   aromatic  1.394  0.020  1.394
 AYZ  C2   C1   aromatic  1.378  0.020  1.378
 AYZ  C21  C20  aromatic  1.387  0.020  1.387
 AYZ  C21  C22  aromatic  1.395  0.020  1.395
 AYZ  C24  C22  single    1.502  0.020  1.502
 AYZ  C24  C25  single    1.527  0.020  1.527
 AYZ  C20  C19  aromatic  1.388  0.020  1.388
 AYZ  C6   C5   aromatic  1.410  0.020  1.410
 AYZ  C6   N7   aromatic  1.370  0.020  1.370
 AYZ  C1   C5   aromatic  1.399  0.020  1.399
 AYZ  C22  C23  aromatic  1.390  0.020  1.390
 AYZ  C19  C13  aromatic  1.387  0.020  1.387
 AYZ  C23  C13  aromatic  1.388  0.020  1.388
 AYZ  C13  N7   single    1.418  0.020  1.418
 AYZ  C5   C9   aromatic  1.423  0.020  1.423
 AYZ  N7   C8   aromatic  1.379  0.020  1.379
 AYZ  C25  C26  single    1.539  0.020  1.539
 AYZ  C9   C8   aromatic  1.366  0.020  1.366
 AYZ  C8   C10  single    1.484  0.020  1.484
 AYZ  O28  C26  deloc     1.246  0.020  1.246
 AYZ  C26  O27  deloc     1.249  0.020  1.249
 AYZ  C10  N11  single    1.340  0.020  1.340
 AYZ  C10  O12  double    1.221  0.020  1.221
 AYZ  C1   H1   single    0.930  0.020  1.080
 AYZ  C2   H2   single    0.930  0.020  1.080
 AYZ  C9   H3   single    0.930  0.020  1.080
 AYZ  C19  H4   single    0.930  0.020  1.080
 AYZ  C20  H5   single    0.930  0.020  1.080
 AYZ  C21  H6   single    0.930  0.020  1.080
 AYZ  C24  H7   single    0.970  0.020  1.090
 AYZ  C24  H8   single    0.970  0.020  1.090
 AYZ  C4   H9   single    0.930  0.020  1.080
 AYZ  N11  H10  single    0.860  0.020  1.020
 AYZ  N11  H11  single    0.860  0.020  1.020
 AYZ  C23  H12  single    0.930  0.020  1.080
 AYZ  C25  H13  single    0.970  0.020  1.090
 AYZ  C25  H14  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
 AYZ  H1   C1   C5   120.64  3.000
 AYZ  H1   C1   C2   120.25  3.000
 AYZ  C5   C1   C2   119.10  3.000
 AYZ  H2   C2   C3   119.79  3.000
 AYZ  H2   C2   C1   120.44  3.000
 AYZ  C3   C2   C1   119.76  3.000
 AYZ  O14  C3   C4   118.50  3.000
 AYZ  C4   C3   C2   123.28  3.000
 AYZ  O14  C3   C2   118.16  3.000
 AYZ  N7   C8   C10  121.70  3.000
 AYZ  C10  C8   C9   128.08  3.000
 AYZ  N7   C8   C9   109.84  3.000
 AYZ  H3   C9   C5   126.73  3.000
 AYZ  H3   C9   C8   126.19  3.000
 AYZ  C5   C9   C8   107.02  3.000
 AYZ  O12  C10  N11  124.18  3.000
 AYZ  O12  C10  C8   121.48  3.000
 AYZ  N11  C10  C8   114.31  3.000
 AYZ  C23  C13  N7   119.66  3.000
 AYZ  N7   C13  C19  119.53  3.000
 AYZ  C23  C13  C19  120.78  3.000
 AYZ  F18  C15  F17  108.27  3.000
 AYZ  F17  C15  F16  108.26  3.000
 AYZ  F18  C15  F16  106.69  3.000
 AYZ  F16  C15  O14  112.88  3.000
 AYZ  F17  C15  O14  107.69  3.000
 AYZ  F18  C15  O14  112.88  3.000
 AYZ  H4   C19  C20  120.70  3.000
 AYZ  H4   C19  C13  120.39  3.000
 AYZ  C20  C19  C13  118.91  3.000
 AYZ  H5   C20  C21  120.05  3.000
 AYZ  H5   C20  C19  119.56  3.000
 AYZ  C21  C20  C19  120.38  3.000
 AYZ  H6   C21  C22  119.53  3.000
 AYZ  H6   C21  C20  119.52  3.000
 AYZ  C22  C21  C20  120.95  3.000
 AYZ  C23  C22  C24  120.83  3.000
 AYZ  C23  C22  C21  118.35  3.000
 AYZ  C24  C22  C21  120.80  3.000
 AYZ  H8   C24  H7   106.66  3.000
 AYZ  H8   C24  C25  109.58  3.000
 AYZ  H7   C24  C25  109.74  3.000
 AYZ  H8   C24  C22  109.76  3.000
 AYZ  H7   C24  C22  109.72  3.000
 AYZ  C25  C24  C22  111.27  3.000
 AYZ  H9   C4   C6   122.33  3.000
 AYZ  H9   C4   C3   121.45  3.000
 AYZ  C6   C4   C3   116.22  3.000
 AYZ  C6   C5   C9   106.67  3.000
 AYZ  C9   C5   C1   133.91  3.000
 AYZ  C6   C5   C1   119.41  3.000
 AYZ  N7   C6   C5   108.19  3.000
 AYZ  N7   C6   C4   129.57  3.000
 AYZ  C5   C6   C4   122.21  3.000
 AYZ  C6   N7   C13  124.20  3.000
 AYZ  C13  N7   C8   126.92  3.000
 AYZ  C6   N7   C8   108.27  3.000
 AYZ  H11  N11  H10  117.57  3.000
 AYZ  H11  N11  C10  120.05  3.000
 AYZ  H10  N11  C10  122.27  3.000
 AYZ  C15  O14  C3   117.82  3.000
 AYZ  H12  C23  C22  119.64  3.000
 AYZ  H12  C23  C13  119.73  3.000
 AYZ  C22  C23  C13  120.62  3.000
 AYZ  H14  C25  H13  105.10  3.000
 AYZ  H14  C25  C26  108.78  3.000
 AYZ  H13  C25  C26  108.09  3.000
 AYZ  H14  C25  C24  109.63  3.000
 AYZ  H13  C25  C24  109.38  3.000
 AYZ  C26  C25  C24  115.35  3.000
 AYZ  O27  C26  C25  115.78  3.000
 AYZ  O27  C26  O28  126.40  3.000
 AYZ  C25  C26  O28  117.82  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
 AYZ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 AYZ  CONST_02  C4   C6   C5   C1      0.00   0.0  0
 AYZ  CONST_03  N7   C6   C5   C1    180.00   0.0  0
 AYZ  CONST_04  C8   C9   C5   C1    180.00   0.0  0
 AYZ  CONST_05  C6   C4   C3   C2      0.00   0.0  0
 AYZ  CONST_06  C6   C5   C1   C2      0.00   0.0  0
 AYZ  CONST_07  C9   C5   C1   C2    180.00   0.0  0
 AYZ  CONST_08  C5   C6   C4   C3      0.00   0.0  0
 AYZ  CONST_09  N7   C6   C4   C3    180.00   0.0  0
 AYZ  CONST_10  C5   C1   C2   C3      0.00   0.0  0
 AYZ  CONST_11  C4   C6   N7   C8    180.00   0.0  0
 AYZ  CONST_12  C5   C6   N7   C8      0.00   0.0  0
 AYZ  CONST_15  C6   C5   C9   C8      0.00   0.0  0
 AYZ  CONST_16  C4   C6   C5   C9    180.00   0.0  0
 AYZ  CONST_17  N7   C6   C5   C9      0.00   0.0  0
 AYZ  CONST_18  C6   N7   C8   C9      0.00   0.0  0
 AYZ  CONST_19  C13  N7   C8   C9    180.00   0.0  0
 AYZ  CONST_20  C21  C20  C19  C13     0.00   0.0  0
 AYZ  CONST_21  C21  C22  C23  C13     0.00   0.0  0
 AYZ  CONST_22  C4   C6   N7   C13     0.00   0.0  0
 AYZ  CONST_23  C5   C6   N7   C13   180.00   0.0  0
 AYZ  CONST_24  C22  C21  C20  C19     0.00   0.0  0
 AYZ  CONST_25  C22  C23  C13  C19     0.00   0.0  0
 AYZ  CONST_27  C23  C22  C21  C20     0.00   0.0  0
 AYZ  CONST_28  C23  C13  C19  C20     0.00   0.0  0
 AYZ  CONST_29  N7   C13  C19  C20   180.00   0.0  0
 AYZ  CONST_30  N7   C13  C23  C22   180.00   0.0  0
 AYZ  CONST_31  N7   C8   C9   C5      0.00   0.0  0
 AYZ  CONST_33  O14  C3   C2   C1    180.00   0.0  0
 AYZ  CONST_34  C6   N7   C8   C10   180.00   0.0  0
 AYZ  CONST_35  C13  N7   C8   C10     0.00   0.0  0
 AYZ  CONST_36  C5   C9   C8   C10   180.00   0.0  0
 AYZ  CONST_37  C24  C22  C23  C13   180.00   0.0  0
 AYZ  CONST_38  C24  C22  C21  C20   180.00   0.0  0
 AYZ  CONST_39  O14  C3   C4   C6    180.00   0.0  0
 AYZ  CONST_40  H3   C9   C5   C1      0.00   0.0  0
 AYZ  CONST_41  H9   C4   C3   C2    180.00   0.0  0
 AYZ  CONST_42  H1   C1   C2   C3    180.00   0.0  0
 AYZ  CONST_43  H5   C20  C19  C13   180.00   0.0  0
 AYZ  CONST_44  H6   C21  C20  C19   180.00   0.0  0
 AYZ  CONST_45  H12  C23  C13  C19   180.00   0.0  0
 AYZ  CONST_46  H4   C19  C20  C21   180.00   0.0  0
 AYZ  CONST_47  H2   C2   C3   C4    180.00   0.0  0
 AYZ  CONST_48  H10  N11  C10  C8      0.00   0.0  0
 AYZ  CONST_49  H11  N11  C10  C8    180.00   0.0  0
 AYZ  Var_01    N11  C10  C8   C9     35.45  30.0  2
 AYZ  Var_02    C4   C3   O14  C15   -90.89  30.0  2
 AYZ  Var_03    C25  C24  C22  C21    82.75  30.0  3
 AYZ  Var_04    F18  C15  O14  C3    -59.99  30.0  3
 AYZ  Var_05    C26  C25  C24  C22  -179.16  30.0  3
 AYZ  Var_06    O28  C26  C25  C24     7.56  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
 AYZ  plan-1  C13  0.020
 AYZ  plan-1  C19  0.020
 AYZ  plan-1  C20  0.020
 AYZ  plan-1  C21  0.020
 AYZ  plan-1  C22  0.020
 AYZ  plan-1  C24  0.020
 AYZ  plan-1  N7   0.020
 AYZ  plan-1  C23  0.020
 AYZ  plan-1  H4   0.020
 AYZ  plan-1  H5   0.020
 AYZ  plan-1  H6   0.020
 AYZ  plan-1  H12  0.020
 AYZ  plan-2  C1   0.020
 AYZ  plan-2  C2   0.020
 AYZ  plan-2  C3   0.020
 AYZ  plan-2  C8   0.020
 AYZ  plan-2  C9   0.020
 AYZ  plan-2  C10  0.020
 AYZ  plan-2  C13  0.020
 AYZ  plan-2  C4   0.020
 AYZ  plan-2  C5   0.020
 AYZ  plan-2  C6   0.020
 AYZ  plan-2  N7   0.020
 AYZ  plan-2  O14  0.020
 AYZ  plan-2  H1   0.020
 AYZ  plan-2  H2   0.020
 AYZ  plan-2  H3   0.020
 AYZ  plan-2  H9   0.020
 AYZ  plan-3  C8   0.020
 AYZ  plan-3  C10  0.020
 AYZ  plan-3  N11  0.020
 AYZ  plan-3  O12  0.020
 AYZ  plan-3  H10  0.020
 AYZ  plan-3  H11  0.020
 AYZ  plan-4  O28  0.020
 AYZ  plan-4  C25  0.020
 AYZ  plan-4  C26  0.020
 AYZ  plan-4  O27  0.020

