# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 04:41:50 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: (2~{S})-3-phenyl-2-[2-[4-(trifluoromethyloxy)phenoxy]ethanoylamino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)NC(=O)COc2ccc(OC(F)(F)F)cc2
#
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
 G56  G56  "(2S)-3-phenyl-2-[2-[4-(trifluoromethyloxy)phenoxy]ethanoylamino]propanoic acid"  ligand  42  27  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G56
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
 G56  O5   O  OC    -1  -0.596  32.1906  28.6968   6.5297
 G56  C11  C  C      0   0.421  32.5013  28.8906   5.3363
 G56  O4   O  O      0  -0.585  33.5816  29.3053   4.8889
 G56  C10  C  CH1    0  -0.185  31.3873  28.6230   4.2942
 G56  C12  C  CH2    0  -0.526  30.6594  29.9376   3.9385
 G56  C13  C  CR6    0   0.160  31.4733  30.9026   3.1260
 G56  C18  C  CR16   0  -0.310  31.7817  30.6140   1.7969
 G56  C17  C  CR16   0  -0.239  32.5055  31.5082   1.0215
 G56  C16  C  CR16   0  -0.275  32.9317  32.7155   1.5629
 G56  C15  C  CR16   0  -0.240  32.6278  33.0161   2.8835
 G56  C14  C  CR16   0  -0.316  31.9062  32.1147   3.6562
 G56  N1   N  NH1    0  -0.624  30.4465  27.6772   4.8515
 G56  C9   C  C      0   0.487  29.5700  26.9744   4.1376
 G56  O3   O  O      0  -0.502  29.4883  26.9892   2.9153
 G56  C7   C  CH2    0  -0.328  28.5644  26.1527   4.9349
 G56  O1   O  O2     0  -0.483  28.9066  25.9409   6.2844
 G56  C5   C  CR6    0   0.401  29.7425  24.9309   6.6116
 G56  C6   C  CR16   0  -0.359  30.3812  24.1002   5.6960
 G56  C1   C  CR16   0  -0.287  31.1772  23.0556   6.1511
 G56  C4   C  CR16   0  -0.340  29.9473  24.7382   7.9780
 G56  C3   C  CR16   0  -0.282  30.7482  23.7066   8.4277
 G56  C2   C  CR6    0   0.288  31.3441  22.8582   7.5071
 G56  O2   O  O2     0  -0.521  32.1647  21.8254   7.9550
 G56  C8   C  CT     0   1.071  31.5726  20.6633   8.2543
 G56  F1   F  F      0  -0.278  32.5059  19.8273   8.6816
 G56  F2   F  F      0  -0.300  30.9634  20.1060   7.2054
 G56  F3   F  F      0  -0.300  30.6510  20.7835   9.2129
 G56  H2   H  HCH1   0   0.240  31.8290  28.2031   3.3877
 G56  H3   H  HCH2   0   0.242  30.3245  30.4146   4.8632
 G56  H4   H  HCH2   0   0.255  29.7593  29.6806   3.3749
 G56  H5   H  HCR6   0   0.243  31.4426  29.6804   1.3612
 G56  H6   H  HCR6   0   0.248  32.7321  31.2670  -0.0094
 G56  H7   H  HCR6   0   0.249  33.4915  33.4176   0.9585
 G56  H8   H  HCR6   0   0.248  32.9516  33.9550   3.3148
 G56  H9   H  HCR6   0   0.242  31.6725  32.3575   4.6862
 G56  H10  H  HNH1   0   0.391  30.4431  27.6439   5.8622
 G56  H11  H  HCH2   0   0.297  27.6294  26.7176   4.9503
 G56  H12  H  HCH2   0   0.261  28.3617  25.2186   4.4045
 G56  H13  H  HCR6   0   0.289  30.2747  24.2325   4.6280
 G56  H14  H  HCR6   0   0.283  31.6704  22.4097   5.4364
 G56  H15  H  HCR6   0   0.277  29.4681  25.3994   8.6882
 G56  H16  H  HCR6   0   0.281  30.9072  23.5712   9.4893

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
 G56  C17  C18  aromatic  1.387  0.020  1.387
 G56  C17  C16  aromatic  1.390  0.020  1.390
 G56  C18  C13  aromatic  1.395  0.020  1.395
 G56  C16  C15  aromatic  1.388  0.020  1.388
 G56  O3   C9   double    1.225  0.020  1.225
 G56  C13  C14  aromatic  1.392  0.020  1.392
 G56  C13  C12  single    1.501  0.020  1.501
 G56  C15  C14  aromatic  1.389  0.020  1.389
 G56  O4   C11  deloc     1.241  0.020  1.241
 G56  C10  C12  single    1.544  0.020  1.544
 G56  C10  C11  single    1.549  0.020  1.549
 G56  C10  N1   single    1.446  0.020  1.446
 G56  C9   N1   single    1.331  0.020  1.331
 G56  C9   C7   single    1.524  0.020  1.524
 G56  C11  O5   deloc     1.248  0.020  1.248
 G56  C7   O1   single    1.408  0.020  1.408
 G56  C6   C1   aromatic  1.390  0.020  1.390
 G56  C6   C5   aromatic  1.392  0.020  1.392
 G56  O1   C5   single    1.351  0.020  1.351
 G56  C1   C2   aromatic  1.380  0.020  1.380
 G56  C5   C4   aromatic  1.395  0.020  1.395
 G56  F2   C8   single    1.335  0.020  1.335
 G56  C2   O2   single    1.393  0.020  1.393
 G56  C2   C3   aromatic  1.387  0.020  1.387
 G56  C4   C3   aromatic  1.381  0.020  1.381
 G56  O2   C8   single    1.338  0.020  1.338
 G56  C8   F1   single    1.324  0.020  1.324
 G56  C8   F3   single    1.335  0.020  1.335
 G56  C10  H2   single    0.970  0.020  1.090
 G56  C12  H3   single    0.970  0.020  1.090
 G56  C12  H4   single    0.970  0.020  1.090
 G56  C18  H5   single    0.930  0.020  1.080
 G56  C17  H6   single    0.930  0.020  1.080
 G56  C16  H7   single    0.930  0.020  1.080
 G56  C15  H8   single    0.930  0.020  1.080
 G56  C14  H9   single    0.930  0.020  1.080
 G56  N1   H10  single    0.860  0.020  1.020
 G56  C7   H11  single    0.970  0.020  1.090
 G56  C7   H12  single    0.970  0.020  1.090
 G56  C6   H13  single    0.930  0.020  1.080
 G56  C1   H14  single    0.930  0.020  1.080
 G56  C4   H15  single    0.930  0.020  1.080
 G56  C3   H16  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
 G56  C10  C11  O4   116.20  3.000
 G56  C10  C11  O5   115.94  3.000
 G56  O4   C11  O5   127.83  3.000
 G56  H2   C10  N1   109.37  3.000
 G56  H2   C10  C12  109.07  3.000
 G56  N1   C10  C12  109.82  3.000
 G56  H2   C10  C11  109.51  3.000
 G56  N1   C10  C11  108.77  3.000
 G56  C12  C10  C11  110.30  3.000
 G56  H4   C12  H3   106.65  3.000
 G56  H4   C12  C13  108.58  3.000
 G56  H3   C12  C13  110.08  3.000
 G56  H4   C12  C10  107.87  3.000
 G56  H3   C12  C10  108.73  3.000
 G56  C13  C12  C10  114.61  3.000
 G56  C14  C13  C18  118.32  3.000
 G56  C14  C13  C12  121.48  3.000
 G56  C18  C13  C12  120.18  3.000
 G56  H5   C18  C17  119.56  3.000
 G56  H5   C18  C13  119.46  3.000
 G56  C17  C18  C13  120.97  3.000
 G56  H6   C17  C16  120.01  3.000
 G56  H6   C17  C18  119.85  3.000
 G56  C16  C17  C18  120.14  3.000
 G56  H7   C16  C15  120.27  3.000
 G56  H7   C16  C17  120.29  3.000
 G56  C15  C16  C17  119.44  3.000
 G56  H8   C15  C14  119.77  3.000
 G56  H8   C15  C16  120.08  3.000
 G56  C14  C15  C16  120.15  3.000
 G56  H9   C14  C15  119.68  3.000
 G56  H9   C14  C13  119.34  3.000
 G56  C15  C14  C13  120.98  3.000
 G56  H10  N1   C9   121.09  3.000
 G56  H10  N1   C10  114.14  3.000
 G56  C9   N1   C10  124.55  3.000
 G56  C7   C9   O3   118.98  3.000
 G56  C7   C9   N1   116.02  3.000
 G56  O3   C9   N1   124.94  3.000
 G56  H12  C7   H11  106.85  3.000
 G56  H12  C7   O1   112.43  3.000
 G56  H11  C7   O1   105.80  3.000
 G56  H12  C7   C9   109.23  3.000
 G56  H11  C7   C9   107.06  3.000
 G56  O1   C7   C9   114.97  3.000
 G56  C5   O1   C7   119.65  3.000
 G56  C4   C5   C6   119.65  3.000
 G56  C4   C5   O1   115.55  3.000
 G56  C6   C5   O1   124.81  3.000
 G56  H13  C6   C1   118.15  3.000
 G56  H13  C6   C5   122.11  3.000
 G56  C1   C6   C5   119.74  3.000
 G56  H14  C1   C2   120.55  3.000
 G56  H14  C1   C6   119.56  3.000
 G56  C2   C1   C6   119.89  3.000
 G56  H15  C4   C3   119.96  3.000
 G56  H15  C4   C5   119.56  3.000
 G56  C3   C4   C5   120.48  3.000
 G56  H16  C3   C2   120.78  3.000
 G56  H16  C3   C4   119.88  3.000
 G56  C2   C3   C4   119.34  3.000
 G56  O2   C2   C3   119.56  3.000
 G56  C3   C2   C1   120.85  3.000
 G56  O2   C2   C1   119.54  3.000
 G56  C8   O2   C2   117.07  3.000
 G56  F3   C8   F2   106.66  3.000
 G56  F3   C8   F1   108.16  3.000
 G56  F2   C8   F1   108.16  3.000
 G56  F3   C8   O2   112.82  3.000
 G56  F1   C8   O2   107.98  3.000
 G56  F2   C8   O2   112.88  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
 G56  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 G56  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 G56  CONST_03  C15  C16  C17  C18     0.00   0.0  0
 G56  CONST_04  C15  C14  C13  C18     0.00   0.0  0
 G56  CONST_05  C14  C13  C18  C17     0.00   0.0  0
 G56  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 G56  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 G56  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 G56  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 G56  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 G56  CONST_11  C4   C5   C6   C1      0.00   0.0  0
 G56  CONST_12  C4   C3   C2   C1      0.00   0.0  0
 G56  CONST_13  C17  C18  C13  C12   180.00   0.0  0
 G56  CONST_14  C15  C14  C13  C12   180.00   0.0  0
 G56  CONST_15  C1   C6   C5   O1    180.00   0.0  0
 G56  CONST_16  C3   C4   C5   O1    180.00   0.0  0
 G56  CONST_17  O2   C2   C1   C6    180.00   0.0  0
 G56  CONST_18  O2   C2   C3   C4    180.00   0.0  0
 G56  CONST_19  H6   C17  C18  C13   180.00   0.0  0
 G56  CONST_20  H8   C15  C14  C13   180.00   0.0  0
 G56  CONST_21  H7   C16  C17  C18   180.00   0.0  0
 G56  CONST_22  H9   C14  C13  C18   180.00   0.0  0
 G56  CONST_23  H8   C15  C16  C17   180.00   0.0  0
 G56  CONST_24  H5   C18  C17  C16   180.00   0.0  0
 G56  CONST_25  H9   C14  C15  C16   180.00   0.0  0
 G56  CONST_26  H6   C17  C16  C15   180.00   0.0  0
 G56  CONST_27  H5   C18  C13  C14   180.00   0.0  0
 G56  CONST_28  H7   C16  C15  C14   180.00   0.0  0
 G56  CONST_29  H14  C1   C6   C5    180.00   0.0  0
 G56  CONST_30  H16  C3   C4   C5    180.00   0.0  0
 G56  CONST_31  H15  C4   C5   C6    180.00   0.0  0
 G56  CONST_32  H16  C3   C2   C1    180.00   0.0  0
 G56  CONST_33  H13  C6   C5   C4    180.00   0.0  0
 G56  CONST_34  H14  C1   C2   C3    180.00   0.0  0
 G56  CONST_35  H13  C6   C1   C2    180.00   0.0  0
 G56  CONST_36  H15  C4   C3   C2    180.00   0.0  0
 G56  CONST_37  O3   C9   N1   C10     0.00   0.0  0
 G56  CONST_38  C7   C9   N1   C10   180.00   0.0  0
 G56  CONST_39  H10  N1   C9   O3    180.00   0.0  0
 G56  CONST_40  H10  N1   C9   C7      0.00   0.0  0
 G56  Var_01    C18  C13  C12  C10    69.89  30.0  2
 G56  Var_02    C14  C13  C12  C10  -111.93  30.0  2
 G56  Var_03    C6   C5   O1   C7      4.15  30.0  2
 G56  Var_04    C4   C5   O1   C7   -175.56  30.0  2
 G56  Var_05    C8   O2   C2   C1    -94.88  30.0  2
 G56  Var_06    C8   O2   C2   C3     87.65  30.0  2
 G56  Var_07    H3   C12  C13  C18  -167.18  30.0  2
 G56  Var_08    H4   C12  C13  C18   -50.77  30.0  2
 G56  Var_09    H3   C12  C13  C14    11.00  30.0  2
 G56  Var_10    H4   C12  C13  C14   127.41  30.0  2
 G56  Var_11    C5   O1   C7   C9    -83.63  30.0  3
 G56  Var_12    F2   C8   O2   C2     61.71  30.0  3
 G56  Var_13    F1   C8   O2   C2   -178.78  30.0  3
 G56  Var_14    F3   C8   O2   C2    -59.31  30.0  3
 G56  Var_15    H11  C7   O1   C5    158.46  30.0  2
 G56  Var_16    H12  C7   O1   C5     42.18  30.0  2
 G56  Var_17    O1   C7   C9   N1    -16.85  30.0  3
 G56  Var_18    O1   C7   C9   O3    166.04  30.0  3
 G56  Var_19    H11  C7   C9   N1    100.35  30.0  3
 G56  Var_20    H12  C7   C9   N1   -144.30  30.0  3
 G56  Var_21    H11  C7   C9   O3    -76.76  30.0  3
 G56  Var_22    H12  C7   C9   O3     38.59  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
 G56  chir_01  C10  C12  C11  N1  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
 G56  plan-1  C12  0.020
 G56  plan-1  C13  0.020
 G56  plan-1  C18  0.020
 G56  plan-1  C17  0.020
 G56  plan-1  C16  0.020
 G56  plan-1  C15  0.020
 G56  plan-1  C14  0.020
 G56  plan-1  H5   0.020
 G56  plan-1  H6   0.020
 G56  plan-1  H7   0.020
 G56  plan-1  H8   0.020
 G56  plan-1  H9   0.020
 G56  plan-2  O1   0.020
 G56  plan-2  C5   0.020
 G56  plan-2  C6   0.020
 G56  plan-2  C1   0.020
 G56  plan-2  C4   0.020
 G56  plan-2  C3   0.020
 G56  plan-2  C2   0.020
 G56  plan-2  O2   0.020
 G56  plan-2  H13  0.020
 G56  plan-2  H14  0.020
 G56  plan-2  H15  0.020
 G56  plan-2  H16  0.020
 G56  plan-3  C10  0.020
 G56  plan-3  N1   0.020
 G56  plan-3  C9   0.020
 G56  plan-3  O3   0.020
 G56  plan-3  C7   0.020
 G56  plan-3  H10  0.020
 G56  plan-4  O5   0.020
 G56  plan-4  C11  0.020
 G56  plan-4  O4   0.020
 G56  plan-4  C10  0.020

