# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:04:04 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (3~{R})-3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CC(O)=O)c1cccc(c1)n2c(cc3ccc(OC(F)(F)F)cc23)C(N)=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
 EM8  EM8  '(3~{R})-3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]butanoic acid'  ligand  46  29  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EM8
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
 EM8  C1   C  CH3   0  -0.648   5.3825  -0.0087   0.3206
 EM8  C2   C  CH1   0  -0.345   4.0881   0.6197  -0.1988
 EM8  C3   C  CH2   0  -0.563   4.1858   2.1446  -0.2728
 EM8  C7   C  CR6   0   0.188   2.9129   0.2116   0.6589
 EM8  C8   C  CR16  0  -0.309   2.8376   0.5758   2.0035
 EM8  C9   C  CR16  0  -0.242   1.7600   0.1890   2.7845
 EM8  C10  C  CR16  0  -0.305   0.7404  -0.5819   2.2432
 EM8  C11  C  CR6   0   0.327   0.8094  -0.9427   0.9075
 EM8  C12  C  CR16  0  -0.351   1.8784  -0.5408   0.1178
 EM8  C14  C  CR56  0   0.354  -1.5232  -1.2165   0.1698
 EM8  C15  C  CR16  0  -0.355  -2.0801  -0.0076   0.5832
 EM8  C16  C  CR6   0   0.307  -3.4047   0.1909   0.2682
 EM8  C19  C  CR56  0   0.084  -2.2583  -2.1715  -0.5617
 EM8  C20  C  CR15  0  -0.411  -1.3640  -3.2388  -0.8538
 EM8  C21  C  CR5   0   0.228  -0.1565  -2.9114  -0.3041
 EM8  C22  C  C     0   0.460   1.0675  -3.7447  -0.2208
 EM8  C4   C  C     0   0.550   5.1436   2.6402  -1.3235
 EM8  O6   O  OH1   0  -0.593   5.5407   3.8852  -1.0830
 EM8  N13  N  NR5   0  -0.677  -0.2485  -1.6907   0.3319
 EM8  C17  C  CR16  0  -0.314  -4.1787  -0.7485  -0.4267
 EM8  C18  C  CR16  0  -0.336  -3.6072  -1.9302  -0.8446
 EM8  O23  O  O     0  -0.463   1.8167  -3.6846   0.7413
 EM8  N24  N  NH2   0  -0.804   1.2431  -4.5712  -1.2610
 EM8  C26  C  CT    0   1.072  -4.0288   2.4108  -0.1149
 EM8  F27  F  F     0  -0.278  -4.6272   3.4116   0.5117
 EM8  F28  F  F     0  -0.300  -2.8025   2.8066  -0.4620
 EM8  F29  F  F     0  -0.300  -4.6906   2.1732  -1.2496
 EM8  H1   H  HCH3  0   0.224   5.6203   0.3461   1.3249
 EM8  H2   H  HCH3  0   0.239   5.2949  -1.0945   0.3623
 EM8  H3   H  HCH3  0   0.238   6.2264   0.2298  -0.3269
 EM8  H4   H  HCH1  0   0.258   3.9050   0.2450  -1.2089
 EM8  H5   H  HCH2  0   0.301   3.2066   2.5686  -0.5227
 EM8  H6   H  HCH2  0   0.270   4.4561   2.5693   0.6968
 EM8  H7   H  HCR6  0   0.253   3.6266   1.1659   2.4534
 EM8  H8   H  HCR6  0   0.263   1.7165   0.4785   3.8261
 EM8  H9   H  HCR6  0   0.274  -0.0912  -0.9065   2.8555
 EM8  H10  H  HCR6  0   0.264   1.9043  -0.8182  -0.9299
 EM8  H11  H  HCR6  0   0.288  -1.5170   0.7305   1.1387
 EM8  H12  H  HCR5  0   0.274  -1.6009  -4.1565  -1.3696
 EM8  H13  H  HOH1  0   0.479   6.1194   4.1916  -1.7974
 EM8  H14  H  HCR6  0   0.276  -5.2229  -0.5464  -0.6228
 EM8  H15  H  HCR6  0   0.265  -4.1948  -2.6566  -1.3902
 EM8  H16  H  HNH2  0   0.416   0.6712  -4.5223  -2.0867
 EM8  H17  H  HNH2  0   0.409   2.0211  -5.2104  -1.2710
 EM8  O25  O  O2    0  -0.526  -4.0203   1.3593   0.7122
 EM8  O5   O  O     0  -0.443   5.4922   2.0152  -2.2943

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
 EM8  F27  C26  single    1.324  0.020  1.324
 EM8  F28  C26  single    1.335  0.020  1.335
 EM8  C26  O25  single    1.338  0.020  1.338
 EM8  C26  F29  single    1.335  0.020  1.335
 EM8  O25  C16  single    1.393  0.020  1.393
 EM8  C16  C17  aromatic  1.402  0.020  1.402
 EM8  C16  C15  aromatic  1.376  0.020  1.376
 EM8  C1   C2   single    1.530  0.020  1.530
 EM8  C17  C18  aromatic  1.378  0.020  1.378
 EM8  C15  C14  aromatic  1.394  0.020  1.394
 EM8  C2   C7   single    1.511  0.020  1.511
 EM8  C2   C3   single    1.530  0.020  1.530
 EM8  C18  C19  aromatic  1.399  0.020  1.399
 EM8  C14  C19  aromatic  1.410  0.020  1.410
 EM8  C14  N13  aromatic  1.370  0.020  1.370
 EM8  C8   C7   aromatic  1.395  0.020  1.395
 EM8  C8   C9   aromatic  1.386  0.020  1.386
 EM8  C7   C12  aromatic  1.389  0.020  1.389
 EM8  C9   C10  aromatic  1.388  0.020  1.388
 EM8  C12  C11  aromatic  1.389  0.020  1.389
 EM8  C10  C11  aromatic  1.385  0.020  1.385
 EM8  C19  C20  aromatic  1.423  0.020  1.423
 EM8  C11  N13  single    1.418  0.020  1.418
 EM8  N13  C21  aromatic  1.380  0.020  1.380
 EM8  C3   C4   single    1.506  0.020  1.506
 EM8  C20  C21  aromatic  1.366  0.020  1.366
 EM8  C21  C22  single    1.483  0.020  1.483
 EM8  C4   O5   double    1.206  0.020  1.206
 EM8  C4   O6   single    1.329  0.020  1.329
 EM8  C22  N24  single    1.340  0.020  1.340
 EM8  C22  O23  double    1.221  0.020  1.221
 EM8  C1   H1   single    0.970  0.020  1.090
 EM8  C1   H2   single    0.970  0.020  1.090
 EM8  C1   H3   single    0.970  0.020  1.090
 EM8  C2   H4   single    0.970  0.020  1.090
 EM8  C3   H5   single    0.970  0.020  1.090
 EM8  C3   H6   single    0.970  0.020  1.090
 EM8  C8   H7   single    0.930  0.020  1.080
 EM8  C9   H8   single    0.930  0.020  1.080
 EM8  C10  H9   single    0.930  0.020  1.080
 EM8  C12  H10  single    0.930  0.020  1.080
 EM8  C15  H11  single    0.930  0.020  1.080
 EM8  C20  H12  single    0.930  0.020  1.080
 EM8  O6   H13  single    0.850  0.020  0.980
 EM8  C17  H14  single    0.930  0.020  1.080
 EM8  C18  H15  single    0.930  0.020  1.080
 EM8  N24  H16  single    0.860  0.020  1.020
 EM8  N24  H17  single    0.860  0.020  1.020

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
 EM8  H3   C1   H2   107.63  3.000
 EM8  H3   C1   H1   107.87  3.000
 EM8  H2   C1   H1   107.82  3.000
 EM8  H3   C1   C2   111.31  3.000
 EM8  H2   C1   C2   110.74  3.000
 EM8  H1   C1   C2   111.30  3.000
 EM8  H4   C2   C7   107.56  3.000
 EM8  H4   C2   C3   107.92  3.000
 EM8  C7   C2   C3   110.27  3.000
 EM8  H4   C2   C1   108.34  3.000
 EM8  C3   C2   C1   111.83  3.000
 EM8  C7   C2   C1   110.76  3.000
 EM8  H6   C3   H5   105.84  3.000
 EM8  H6   C3   C4   109.51  3.000
 EM8  H5   C3   C4   106.38  3.000
 EM8  H6   C3   C2   111.12  3.000
 EM8  H5   C3   C2   109.85  3.000
 EM8  C4   C3   C2   113.73  3.000
 EM8  C12  C7   C8   118.47  3.000
 EM8  C12  C7   C2   120.30  3.000
 EM8  C8   C7   C2   121.23  3.000
 EM8  H7   C8   C9   118.97  3.000
 EM8  H7   C8   C7   120.21  3.000
 EM8  C9   C8   C7   120.81  3.000
 EM8  H8   C9   C10  119.63  3.000
 EM8  H8   C9   C8   119.94  3.000
 EM8  C10  C9   C8   120.42  3.000
 EM8  H9   C10  C11  120.36  3.000
 EM8  H9   C10  C9   120.68  3.000
 EM8  C11  C10  C9   118.95  3.000
 EM8  N13  C11  C12  119.76  3.000
 EM8  N13  C11  C10  119.45  3.000
 EM8  C12  C11  C10  120.75  3.000
 EM8  H10  C12  C11  119.60  3.000
 EM8  H10  C12  C7   119.82  3.000
 EM8  C11  C12  C7   120.58  3.000
 EM8  N13  C14  C19  108.19  3.000
 EM8  N13  C14  C15  129.57  3.000
 EM8  C19  C14  C15  122.22  3.000
 EM8  H11  C15  C16  121.35  3.000
 EM8  H11  C15  C14  122.42  3.000
 EM8  C16  C15  C14  116.23  3.000
 EM8  O25  C16  C17  118.43  3.000
 EM8  C17  C16  C15  123.26  3.000
 EM8  O25  C16  C15  118.25  3.000
 EM8  C18  C19  C20  133.94  3.000
 EM8  C20  C19  C14  106.67  3.000
 EM8  C18  C19  C14  119.39  3.000
 EM8  H12  C20  C21  126.17  3.000
 EM8  H12  C20  C19  126.73  3.000
 EM8  C21  C20  C19  107.04  3.000
 EM8  N13  C21  C22  121.76  3.000
 EM8  C22  C21  C20  128.11  3.000
 EM8  N13  C21  C20  109.79  3.000
 EM8  N24  C22  O23  124.17  3.000
 EM8  O23  C22  C21  121.54  3.000
 EM8  N24  C22  C21  114.27  3.000
 EM8  O6   C4   O5   123.02  3.000
 EM8  O6   C4   C3   111.85  3.000
 EM8  O5   C4   C3   125.10  3.000
 EM8  H13  O6   C4   109.95  3.000
 EM8  C21  N13  C14  108.29  3.000
 EM8  C21  N13  C11  127.18  3.000
 EM8  C14  N13  C11  124.05  3.000
 EM8  H14  C17  C18  120.39  3.000
 EM8  H14  C17  C16  119.86  3.000
 EM8  C18  C17  C16  119.75  3.000
 EM8  H15  C18  C17  120.23  3.000
 EM8  H15  C18  C19  120.65  3.000
 EM8  C17  C18  C19  119.12  3.000
 EM8  H17  N24  H16  117.53  3.000
 EM8  H17  N24  C22  120.03  3.000
 EM8  H16  N24  C22  122.20  3.000
 EM8  F29  C26  F28  106.70  3.000
 EM8  F29  C26  F27  108.23  3.000
 EM8  F28  C26  F27  108.32  3.000
 EM8  F29  C26  O25  112.88  3.000
 EM8  F28  C26  O25  112.83  3.000
 EM8  F27  C26  O25  107.72  3.000
 EM8  C26  O25  C16  117.70  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
 EM8  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 EM8  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 EM8  CONST_03  N13  C11  C12  C7    180.00   0.0  0
 EM8  CONST_04  C11  C12  C7   C8      0.00   0.0  0
 EM8  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 EM8  CONST_06  C12  C7   C8   C9      0.00   0.0  0
 EM8  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 EM8  CONST_08  N13  C11  C10  C9    180.00   0.0  0
 EM8  CONST_11  C15  C14  N13  C11     0.00   0.0  0
 EM8  CONST_12  C19  C14  N13  C11   180.00   0.0  0
 EM8  CONST_13  C20  C21  N13  C11   180.00   0.0  0
 EM8  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 EM8  CONST_17  C17  C18  C19  C14     0.00   0.0  0
 EM8  CONST_18  C21  C20  C19  C14     0.00   0.0  0
 EM8  CONST_19  C20  C21  N13  C14     0.00   0.0  0
 EM8  CONST_20  C18  C17  C16  C15     0.00   0.0  0
 EM8  CONST_21  C18  C19  C14  C15     0.00   0.0  0
 EM8  CONST_22  C20  C19  C14  C15   180.00   0.0  0
 EM8  CONST_23  C21  N13  C14  C15   180.00   0.0  0
 EM8  CONST_24  C19  C18  C17  C16     0.00   0.0  0
 EM8  CONST_25  C19  C14  C15  C16     0.00   0.0  0
 EM8  CONST_26  N13  C14  C15  C16   180.00   0.0  0
 EM8  CONST_27  C21  N13  C14  C19     0.00   0.0  0
 EM8  CONST_28  N13  C21  C20  C19     0.00   0.0  0
 EM8  CONST_29  C17  C18  C19  C20   180.00   0.0  0
 EM8  CONST_30  N13  C14  C19  C20     0.00   0.0  0
 EM8  CONST_31  C18  C19  C20  C21   180.00   0.0  0
 EM8  CONST_32  C18  C19  C14  N13   180.00   0.0  0
 EM8  CONST_33  C9   C8   C7   C2    180.00   0.0  0
 EM8  CONST_34  C11  C12  C7   C2    180.00   0.0  0
 EM8  CONST_35  C22  C21  N13  C11     0.00   0.0  0
 EM8  CONST_36  O25  C16  C15  C14   180.00   0.0  0
 EM8  CONST_37  C22  C21  N13  C14   180.00   0.0  0
 EM8  CONST_38  C22  C21  C20  C19   180.00   0.0  0
 EM8  CONST_39  O25  C16  C17  C18   180.00   0.0  0
 EM8  CONST_40  H8   C9   C8   C7    180.00   0.0  0
 EM8  CONST_41  H10  C12  C7   C8    180.00   0.0  0
 EM8  CONST_42  H9   C10  C9   C8    180.00   0.0  0
 EM8  CONST_43  H7   C8   C9   C10   180.00   0.0  0
 EM8  CONST_44  H15  C18  C19  C14   180.00   0.0  0
 EM8  CONST_45  H12  C20  C19  C14   180.00   0.0  0
 EM8  CONST_46  H14  C17  C16  C15   180.00   0.0  0
 EM8  CONST_47  H11  C15  C14  C19   180.00   0.0  0
 EM8  CONST_48  H16  N24  C22  C21     0.00   0.0  0
 EM8  CONST_49  H17  N24  C22  C21   180.00   0.0  0
 EM8  CONST_50  H13  O6   C4   C3    180.00   0.0  0
 EM8  Var_01    N24  C22  C21  C20    33.52  30.0  2
 EM8  Var_02    F27  C26  O25  C16  -178.48  30.0  3
 EM8  Var_03    O5   C4   C3   C2     22.77  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
 EM8  chir_01  C2  C1  C7  C3  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
 EM8  plan-1  C2   0.020
 EM8  plan-1  C7   0.020
 EM8  plan-1  C8   0.020
 EM8  plan-1  C9   0.020
 EM8  plan-1  C10  0.020
 EM8  plan-1  C11  0.020
 EM8  plan-1  C12  0.020
 EM8  plan-1  N13  0.020
 EM8  plan-1  H7   0.020
 EM8  plan-1  H8   0.020
 EM8  plan-1  H9   0.020
 EM8  plan-1  H10  0.020
 EM8  plan-2  C11  0.020
 EM8  plan-2  C14  0.020
 EM8  plan-2  C15  0.020
 EM8  plan-2  C16  0.020
 EM8  plan-2  C19  0.020
 EM8  plan-2  C20  0.020
 EM8  plan-2  C21  0.020
 EM8  plan-2  C22  0.020
 EM8  plan-2  N13  0.020
 EM8  plan-2  C17  0.020
 EM8  plan-2  C18  0.020
 EM8  plan-2  H11  0.020
 EM8  plan-2  H12  0.020
 EM8  plan-2  H14  0.020
 EM8  plan-2  H15  0.020
 EM8  plan-2  O25  0.020
 EM8  plan-3  C21  0.020
 EM8  plan-3  C22  0.020
 EM8  plan-3  O23  0.020
 EM8  plan-3  N24  0.020
 EM8  plan-3  H16  0.020
 EM8  plan-3  H17  0.020
 EM8  plan-4  C3   0.020
 EM8  plan-4  C4   0.020
 EM8  plan-4  O6   0.020
 EM8  plan-4  H13  0.020
 EM8  plan-4  O5   0.020

