# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:05:37 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2~{S},3~{S})-2-azanyl-3-[[3-[[4-(trifluoromethyl)phenyl]carbonylamino]phenyl]methoxy]butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H](OCc1cccc(NC(=O)c2ccc(cc2)C(F)(F)F)c1)C(O)=O)C(O)=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
 7O9  7O9  '(2~{S},3~{S})-2-azanyl-3-[[3-[[4-(trifluoromethyl)phenyl]carbonylamino]phenyl]methoxy]butanedioic acid'  ligand  47  30  .  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_7O9
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
 7O9  C    C  C     0   0.539  -6.6063  -0.7848   0.6381
 7O9  F2   F  F     0  -0.303   8.3716  -1.1131  -0.9232
 7O9  F    F  F     0  -0.312   8.2797  -0.5636   1.1541
 7O9  F1   F  F     0  -0.306   8.4041   0.9620  -0.3556
 7O9  C12  C  CR6   0  -0.194   6.3575  -0.1790  -0.1336
 7O9  C11  C  CR16  0  -0.260   5.6870   0.9698   0.2722
 7O9  C10  C  CR16  0  -0.251   4.3044   1.0046   0.2509
 7O9  C14  C  CR16  0  -0.260   5.6402  -1.2914  -0.5512
 7O9  C15  C  CR16  0  -0.278   4.2550  -1.2574  -0.5563
 7O9  C9   C  CR6   0  -0.037   3.5768  -0.1124  -0.1500
 7O9  C8   C  C     0   0.528   2.0844  -0.0086  -0.1728
 7O9  O5   O  O     0  -0.453   1.5351   1.0588  -0.3763
 7O9  C7   C  CR6   0   0.400   0.0514  -1.4085   0.0912
 7O9  C6   C  CR16  0  -0.373  -0.8963  -0.5598  -0.4838
 7O9  C16  C  CR16  0  -0.356  -0.3742  -2.5799   0.7158
 7O9  C17  C  CR16  0  -0.230  -1.7221  -2.8961   0.7624
 7O9  C18  C  CR16  0  -0.303  -2.6631  -2.0551   0.1902
 7O9  C5   C  CR6   0   0.091  -2.2462  -0.8857  -0.4383
 7O9  C4   C  CH2   0  -0.210  -3.2516   0.0209  -1.0886
 7O9  C2   C  CH1   0  -0.056  -5.3860   0.9548  -0.6508
 7O9  C3   C  C     0   0.536  -5.1870   2.4523  -0.8357
 7O9  O3   O  O     0  -0.426  -4.1892   3.0495  -0.5323
 7O9  O2   O  OH1   0  -0.594  -6.2502   3.0082  -1.3970
 7O9  C1   C  CH1   0  -0.243  -6.5174   0.7129   0.3575
 7O9  N1   N  NH2   0  -0.782  -6.3209   1.5244   1.5299
 7O9  O1   O  OH1   0  -0.595  -6.8032  -1.4858  -0.4708
 7O9  O    O  O     0  -0.428  -6.5292  -1.2751   1.7339
 7O9  H1   H  HCR6  0   0.282   6.2288   1.8457   0.6028
 7O9  H2   H  HCR6  0   0.275   3.7911   1.9049   0.5594
 7O9  H3   H  HCR6  0   0.282   6.1412  -2.1899  -0.8837
 7O9  H4   H  HCR6  0   0.278   3.7199  -2.1289  -0.9108
 7O9  H5   H  HNH1  0   0.422   1.9933  -1.9525   0.3676
 7O9  H6   H  HCR6  0   0.278  -0.5956   0.3537  -0.9722
 7O9  H7   H  HCR6  0   0.273   0.3517  -3.2463   1.1670
 7O9  H8   H  HCR6  0   0.263  -2.0360  -3.8098   1.2495
 7O9  H9   H  HCR6  0   0.248  -3.7130  -2.3153   0.2256
 7O9  H10  H  HCH2  0   0.236  -2.7554   0.9138  -1.4824
 7O9  H11  H  HCH2  0   0.231  -3.7174  -0.4934  -1.9397
 7O9  H12  H  HCH1  0   0.278  -5.6603   0.5235  -1.6238
 7O9  H13  H  HOH1  0   0.486  -6.1183   3.9632  -1.4977
 7O9  H14  H  HCH1  0   0.308  -7.4595   1.0080  -0.1137
 7O9  H15  H  HNH2  0   0.366  -7.1349   1.4835   2.1281
 7O9  H16  H  HNH2  0   0.353  -5.5414   1.1840   2.0782
 7O9  H18  H  HOH1  0   0.484  -6.8626  -2.4314  -0.2666
 7O9  O4   O  O2    0  -0.487  -4.2380   0.3565  -0.1334
 7O9  N    N  NH1   0  -0.758   1.4314  -1.1730   0.0606
 7O9  C13  C  CT    0   1.055   7.8534  -0.2233  -0.0713

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
 7O9  O3   C3   double    1.202  0.020  1.202
 7O9  C4   C5   single    1.502  0.020  1.502
 7O9  C4   O4   single    1.413  0.020  1.413
 7O9  O2   C3   single    1.325  0.020  1.325
 7O9  C3   C2   single    1.522  0.020  1.522
 7O9  C18  C5   aromatic  1.391  0.020  1.391
 7O9  C18  C17  aromatic  1.386  0.020  1.386
 7O9  C5   C6   aromatic  1.389  0.020  1.389
 7O9  O4   C2   single    1.394  0.020  1.394
 7O9  C17  C16  aromatic  1.385  0.020  1.385
 7O9  C2   C1   single    1.535  0.020  1.535
 7O9  N1   C1   single    1.439  0.020  1.439
 7O9  C6   C7   aromatic  1.396  0.020  1.396
 7O9  C16  C7   aromatic  1.394  0.020  1.394
 7O9  C1   C    single    1.526  0.020  1.526
 7O9  C7   N    single    1.400  0.020  1.400
 7O9  O    C    double    1.203  0.020  1.203
 7O9  C    O1   single    1.327  0.020  1.327
 7O9  N    C8   single    1.355  0.020  1.355
 7O9  O5   C8   double    1.218  0.020  1.218
 7O9  C8   C9   single    1.496  0.020  1.496
 7O9  C9   C10  aromatic  1.392  0.020  1.392
 7O9  C9   C15  aromatic  1.391  0.020  1.391
 7O9  C10  C11  aromatic  1.383  0.020  1.383
 7O9  C15  C14  aromatic  1.386  0.020  1.386
 7O9  C11  C12  aromatic  1.391  0.020  1.391
 7O9  C14  C12  aromatic  1.388  0.020  1.388
 7O9  C12  C13  single    1.498  0.020  1.498
 7O9  C13  F    single    1.341  0.020  1.341
 7O9  C13  F1   single    1.337  0.020  1.337
 7O9  C13  F2   single    1.336  0.020  1.336
 7O9  C11  H1   single    0.930  0.020  1.080
 7O9  C10  H2   single    0.930  0.020  1.080
 7O9  C14  H3   single    0.930  0.020  1.080
 7O9  C15  H4   single    0.930  0.020  1.080
 7O9  N    H5   single    0.860  0.020  1.020
 7O9  C6   H6   single    0.930  0.020  1.080
 7O9  C16  H7   single    0.930  0.020  1.080
 7O9  C17  H8   single    0.930  0.020  1.080
 7O9  C18  H9   single    0.930  0.020  1.080
 7O9  C4   H10  single    0.970  0.020  1.090
 7O9  C4   H11  single    0.970  0.020  1.090
 7O9  C2   H12  single    0.970  0.020  1.090
 7O9  O2   H13  single    0.850  0.020  0.980
 7O9  C1   H14  single    0.970  0.020  1.090
 7O9  N1   H15  single    0.890  0.020  1.040
 7O9  N1   H16  single    0.890  0.020  1.040
 7O9  O1   H18  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
 7O9  O    C    O1   123.75  3.000
 7O9  O1   C    C1   111.93  3.000
 7O9  O    C    C1   124.31  3.000
 7O9  C14  C12  C11  120.04  3.000
 7O9  C14  C12  C13  120.33  3.000
 7O9  C11  C12  C13  119.59  3.000
 7O9  H1   C11  C10  119.02  3.000
 7O9  H1   C11  C12  121.10  3.000
 7O9  C10  C11  C12  119.88  3.000
 7O9  H2   C10  C9   120.14  3.000
 7O9  H2   C10  C11  119.41  3.000
 7O9  C9   C10  C11  120.45  3.000
 7O9  H3   C14  C15  118.85  3.000
 7O9  H3   C14  C12  121.27  3.000
 7O9  C15  C14  C12  119.87  3.000
 7O9  H4   C15  C9   121.14  3.000
 7O9  H4   C15  C14  118.40  3.000
 7O9  C9   C15  C14  120.43  3.000
 7O9  C8   C9   C15  122.61  3.000
 7O9  C15  C9   C10  119.31  3.000
 7O9  C8   C9   C10  118.04  3.000
 7O9  N    C8   O5   124.37  3.000
 7O9  O5   C8   C9   120.89  3.000
 7O9  N    C8   C9   114.73  3.000
 7O9  C16  C7   C6   119.22  3.000
 7O9  C16  C7   N    116.87  3.000
 7O9  C6   C7   N    123.90  3.000
 7O9  H6   C6   C5   118.97  3.000
 7O9  H6   C6   C7   120.80  3.000
 7O9  C5   C6   C7   120.23  3.000
 7O9  H7   C16  C17  119.83  3.000
 7O9  H7   C16  C7   119.91  3.000
 7O9  C17  C16  C7   120.26  3.000
 7O9  H8   C17  C18  120.09  3.000
 7O9  H8   C17  C16  119.35  3.000
 7O9  C18  C17  C16  120.55  3.000
 7O9  H9   C18  C5   120.50  3.000
 7O9  H9   C18  C17  119.96  3.000
 7O9  C5   C18  C17  119.54  3.000
 7O9  C4   C5   C18  120.15  3.000
 7O9  C18  C5   C6   120.20  3.000
 7O9  C4   C5   C6   119.64  3.000
 7O9  H11  C4   H10  107.18  3.000
 7O9  H11  C4   O4   109.81  3.000
 7O9  H10  C4   O4   111.45  3.000
 7O9  H11  C4   C5   109.68  3.000
 7O9  H10  C4   C5   110.16  3.000
 7O9  O4   C4   C5   108.53  3.000
 7O9  H12  C2   C1   109.62  3.000
 7O9  H12  C2   C3   108.13  3.000
 7O9  C1   C2   C3   109.35  3.000
 7O9  H12  C2   O4   111.45  3.000
 7O9  C1   C2   O4   107.19  3.000
 7O9  C3   C2   O4   111.08  3.000
 7O9  O2   C3   O3   124.40  3.000
 7O9  O2   C3   C2   111.07  3.000
 7O9  O3   C3   C2   124.53  3.000
 7O9  H13  O2   C3   110.39  3.000
 7O9  H14  C1   N1   108.44  3.000
 7O9  H14  C1   C2   108.03  3.000
 7O9  N1   C1   C2   110.22  3.000
 7O9  H14  C1   C    107.08  3.000
 7O9  N1   C1   C    114.29  3.000
 7O9  C2   C1   C    108.57  3.000
 7O9  H16  N1   H15  106.62  3.000
 7O9  H16  N1   C1   110.91  3.000
 7O9  H15  N1   C1   110.45  3.000
 7O9  H18  O1   C    110.40  3.000
 7O9  C2   O4   C4   115.19  3.000
 7O9  H5   N    C7   114.35  3.000
 7O9  H5   N    C8   116.61  3.000
 7O9  C7   N    C8   128.55  3.000
 7O9  C12  C13  F1   112.10  3.000
 7O9  F1   C13  F    106.75  3.000
 7O9  C12  C13  F    111.27  3.000
 7O9  F1   C13  F2   107.16  3.000
 7O9  F    C13  F2   106.87  3.000
 7O9  C12  C13  F2   112.36  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
 7O9  CONST_01  C9   C10  C11  C12     0.00   0.0  0
 7O9  CONST_02  C9   C15  C14  C12     0.00   0.0  0
 7O9  CONST_03  C15  C9   C10  C11     0.00   0.0  0
 7O9  CONST_04  C15  C14  C12  C11     0.00   0.0  0
 7O9  CONST_05  C14  C15  C9   C10     0.00   0.0  0
 7O9  CONST_06  C14  C12  C11  C10     0.00   0.0  0
 7O9  CONST_07  C18  C5   C6   C7      0.00   0.0  0
 7O9  CONST_08  C18  C17  C16  C7      0.00   0.0  0
 7O9  CONST_09  C17  C18  C5   C6      0.00   0.0  0
 7O9  CONST_10  C17  C16  C7   C6      0.00   0.0  0
 7O9  CONST_11  C5   C18  C17  C16     0.00   0.0  0
 7O9  CONST_12  C5   C6   C7   C16     0.00   0.0  0
 7O9  CONST_13  C10  C11  C12  C13   180.00   0.0  0
 7O9  CONST_14  C15  C14  C12  C13   180.00   0.0  0
 7O9  CONST_15  C8   C9   C10  C11   180.00   0.0  0
 7O9  CONST_16  C8   C9   C15  C14   180.00   0.0  0
 7O9  CONST_17  C5   C6   C7   N     180.00   0.0  0
 7O9  CONST_18  C17  C16  C7   N     180.00   0.0  0
 7O9  CONST_19  C4   C5   C6   C7    180.00   0.0  0
 7O9  CONST_20  C4   C5   C18  C17   180.00   0.0  0
 7O9  CONST_21  H2   C10  C11  C12   180.00   0.0  0
 7O9  CONST_22  H4   C15  C14  C12   180.00   0.0  0
 7O9  CONST_23  H3   C14  C12  C11   180.00   0.0  0
 7O9  CONST_24  H1   C11  C12  C14   180.00   0.0  0
 7O9  CONST_25  H8   C17  C16  C7    180.00   0.0  0
 7O9  CONST_26  H9   C18  C5   C6    180.00   0.0  0
 7O9  CONST_27  H7   C16  C7   C6    180.00   0.0  0
 7O9  CONST_28  H6   C6   C7   C16   180.00   0.0  0
 7O9  CONST_29  C7   N    C8   C9    180.00   0.0  0
 7O9  CONST_32  H5   N    C7   C6    180.00   0.0  0
 7O9  CONST_33  C7   N    C8   O5      0.00   0.0  0
 7O9  CONST_34  H13  O2   C3   C2    180.00   0.0  0
 7O9  CONST_35  H18  O1   C    C1    180.00   0.0  0
 7O9  Var_01    C11  C12  C13  F2   -156.08  30.0  3
 7O9  Var_02    N    C8   C9   C10  -150.10  30.0  2
 7O9  Var_03    O4   C4   C5   C6   -126.25  30.0  1

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
 7O9  chir_01  C2  C3  O4  C1  negativ
 7O9  chir_02  C1  N1  C2  C   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
 7O9  plan-1  C12  0.020
 7O9  plan-1  C11  0.020
 7O9  plan-1  C10  0.020
 7O9  plan-1  C14  0.020
 7O9  plan-1  C15  0.020
 7O9  plan-1  C9   0.020
 7O9  plan-1  C8   0.020
 7O9  plan-1  H1   0.020
 7O9  plan-1  H2   0.020
 7O9  plan-1  H3   0.020
 7O9  plan-1  H4   0.020
 7O9  plan-1  C13  0.020
 7O9  plan-2  C7   0.020
 7O9  plan-2  C6   0.020
 7O9  plan-2  C16  0.020
 7O9  plan-2  C17  0.020
 7O9  plan-2  C18  0.020
 7O9  plan-2  C5   0.020
 7O9  plan-2  C4   0.020
 7O9  plan-2  H6   0.020
 7O9  plan-2  H7   0.020
 7O9  plan-2  H8   0.020
 7O9  plan-2  H9   0.020
 7O9  plan-2  N    0.020
 7O9  plan-3  C9   0.020
 7O9  plan-3  C8   0.020
 7O9  plan-3  O5   0.020
 7O9  plan-3  C7   0.020
 7O9  plan-3  H5   0.020
 7O9  plan-3  N    0.020
 7O9  plan-4  C    0.020
 7O9  plan-4  C1   0.020
 7O9  plan-4  O1   0.020
 7O9  plan-4  O    0.020
 7O9  plan-4  H18  0.020
 7O9  plan-5  C2   0.020
 7O9  plan-5  C3   0.020
 7O9  plan-5  O3   0.020
 7O9  plan-5  O2   0.020
 7O9  plan-5  H13  0.020

