# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 13:58:20 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: (5R)-2-[(1S,2R)-2-amino-2-carboxy-1-hydroxyethyl]-5-{(2S)-2-carboxy-2-[(3,5-dichloro-4-hydroxybenzoyl)amino]ethyl}-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]([C@H](O)[C@]1(CC[C@H](C[C@H](NC(=O)c2cc(Cl)c(O)c(Cl)c2)C(O)=O)N1)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
 0YS  0YS  (5R)-2-[(1S,2R)-2-amino-2-carboxy-1-hydroxyethyl]-5-{(2S)-2-carboxy-2-[(3,5-dichloro-4-hydroxybenzoyl)amino]ethyl}-L-proline  ligand  50  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0YS
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
 0YS  O7   O   O      0  -0.598  -0.2983   5.0106  -0.5226
 0YS  C17  C   C      0   0.417   0.8346   4.6413  -0.1673
 0YS  O8   O   OC    -1  -0.614   1.8212   5.3609   0.0826
 0YS  C9   C   CH1    0  -0.233   1.0877   3.1209  -0.0419
 0YS  N1   N   NH1    0  -0.620  -0.1242   2.3436  -0.1811
 0YS  C10  C   C      0   0.515  -0.6586   1.5890   0.7849
 0YS  C11  C   CR6    0  -0.059  -1.7449   0.6521   0.3622
 0YS  C16  C   CR16   0  -0.252  -1.8263   0.1491  -0.9329
 0YS  C15  C   CR6    0  -0.109  -2.7610  -0.8137  -1.2484
 0YS  CL1  CL  CL     0  -0.094  -2.8178  -1.4675  -2.8436
 0YS  C14  C   CR6    0   0.490  -3.6504  -1.3092  -0.2966
 0YS  O6   O   OH1    0  -0.586  -4.5211  -2.2448  -0.6630
 0YS  C13  C   CR6    0  -0.155  -3.5620  -0.7778   0.9910
 0YS  CL   CL  CL     0  -0.102  -4.6646  -1.3662   2.1920
 0YS  C12  C   CR16   0  -0.233  -2.6183   0.1704   1.3282
 0YS  O5   O   O      0  -0.497  -0.2802   1.6029   1.9523
 0YS  C8   C   CH2    0  -0.425   2.1314   2.6663  -1.0741
 0YS  C7   C   CH1    0  -0.048   2.3532   1.1626  -1.1169
 0YS  C6   C   CH2    0  -0.425   3.4486   0.7264  -2.0804
 0YS  C5   C   CH2    0  -0.465   3.8581  -0.6557  -1.5659
 0YS  N2   N   NH1    0  -0.637   2.8506   0.6380   0.1447
 0YS  C3   C   CT     0   0.034   3.4408  -0.6782  -0.0730
 0YS  C4   C   C      0   0.404   4.7046  -0.9020   0.8038
 0YS  O4   O   OC    -1  -0.603   5.0426  -0.0216   1.6141
 0YS  O3   O   O      0  -0.635   5.3120  -1.9779   0.5975
 0YS  C2   C   CH1    0   0.066   2.4711  -1.8305   0.3051
 0YS  O2   O   OH1    0  -0.727   2.3996  -1.8078   1.7123
 0YS  C    C   CH1    0  -0.290   1.0408  -1.7575  -0.2802
 0YS  N    N   NH2    0  -0.782   1.0365  -1.8581  -1.7291
 0YS  C1   C   C      0   0.472   0.0534  -2.7677   0.3835
 0YS  O    O   OC    -1  -0.625   0.1694  -2.9626   1.6270
 0YS  O1   O   O      0  -0.566  -0.8035  -3.2912  -0.3385
 0YS  H2   H   HCH1   0   0.245   1.4797   2.9209   0.9562
 0YS  H3   H   HNH1   0   0.392  -0.5943   2.3997  -1.0696
 0YS  H4   H   HCR6   0   0.283  -1.1292   0.4598  -1.6997
 0YS  H5   H   HOH1   0   0.479  -5.0819  -2.5119   0.0776
 0YS  H6   H   HCR6   0   0.285  -2.5635   0.5319   2.3456
 0YS  H7   H   HCH2   0   0.212   1.8219   2.9990  -2.0723
 0YS  H8   H   HCH2   0   0.218   3.0741   3.1693  -0.8485
 0YS  H9   H   HCH1   0   0.204   1.4209   0.6800  -1.4387
 0YS  H10  H   HCH2   0   0.215   3.1076   0.7138  -3.1165
 0YS  H11  H   HCH2   0   0.203   4.2897   1.4240  -2.0196
 0YS  H12  H   HCH2   0   0.222   3.3531  -1.4374  -2.1268
 0YS  H13  H   HCH2   0   0.219   4.9277  -0.8268  -1.6849
 0YS  H14  H   HNH1   0   0.326   2.1518   0.6127   0.8765
 0YS  H17  H   HCH1   0   0.159   2.9261  -2.7723  -0.0502
 0YS  H18  H   HOH1   0   0.435   1.5424  -2.2664   1.9254
 0YS  H19  H   HCH1   0   0.228   0.6471  -0.7676  -0.0163
 0YS  H20  H   HNH2   0   0.323   1.5185  -2.7102  -1.9966
 0YS  H21  H   HNH2   0   0.335   0.0756  -2.0216  -2.0083

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
 0YS  CL1  C15  single    1.725  0.020  1.725
 0YS  O6   C14  single    1.330  0.020  1.330
 0YS  C15  C14  aromatic  1.394  0.020  1.394
 0YS  C15  C16  aromatic  1.378  0.020  1.378
 0YS  C14  C13  aromatic  1.396  0.020  1.396
 0YS  O1   C1   deloc     1.237  0.020  1.237
 0YS  O2   C2   single    1.409  0.020  1.409
 0YS  N    C    single    1.452  0.020  1.452
 0YS  C16  C11  aromatic  1.392  0.020  1.392
 0YS  C13  CL   single    1.733  0.020  1.733
 0YS  C13  C12  aromatic  1.380  0.020  1.380
 0YS  C1   C    single    1.561  0.020  1.561
 0YS  C1   O    deloc     1.264  0.020  1.264
 0YS  C2   C    single    1.547  0.020  1.547
 0YS  C2   C3   single    1.553  0.020  1.553
 0YS  O3   C4   deloc     1.253  0.020  1.253
 0YS  C11  C12  aromatic  1.389  0.020  1.389
 0YS  C11  C10  single    1.496  0.020  1.496
 0YS  C4   O4   deloc     1.243  0.020  1.243
 0YS  C4   C3   single    1.554  0.020  1.554
 0YS  C3   N2   single    1.459  0.020  1.459
 0YS  C3   C5   single    1.550  0.020  1.550
 0YS  N2   C7   single    1.454  0.020  1.454
 0YS  C10  N1   single    1.337  0.020  1.337
 0YS  C10  O5   double    1.227  0.020  1.227
 0YS  C5   C6   single    1.531  0.020  1.531
 0YS  N1   C9   single    1.446  0.020  1.446
 0YS  C7   C6   single    1.523  0.020  1.523
 0YS  C7   C8   single    1.521  0.020  1.521
 0YS  C9   C8   single    1.537  0.020  1.537
 0YS  C9   C17  single    1.546  0.020  1.546
 0YS  O7   C17  deloc     1.243  0.020  1.243
 0YS  C17  O8   deloc     1.247  0.020  1.247
 0YS  C9   H2   single    0.970  0.020  1.090
 0YS  N1   H3   single    0.860  0.020  1.020
 0YS  C16  H4   single    0.930  0.020  1.080
 0YS  O6   H5   single    0.850  0.020  0.980
 0YS  C12  H6   single    0.930  0.020  1.080
 0YS  C8   H7   single    0.970  0.020  1.090
 0YS  C8   H8   single    0.970  0.020  1.090
 0YS  C7   H9   single    0.970  0.020  1.090
 0YS  C6   H10  single    0.970  0.020  1.090
 0YS  C6   H11  single    0.970  0.020  1.090
 0YS  C5   H12  single    0.970  0.020  1.090
 0YS  C5   H13  single    0.970  0.020  1.090
 0YS  N2   H14  single    0.890  0.020  1.040
 0YS  C2   H17  single    0.970  0.020  1.090
 0YS  O2   H18  single    0.850  0.020  0.980
 0YS  C    H19  single    0.970  0.020  1.090
 0YS  N    H20  single    0.890  0.020  1.040
 0YS  N    H21  single    0.890  0.020  1.040

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
 0YS  C9   C17  O8   114.94  3.000
 0YS  O8   C17  O7   127.37  3.000
 0YS  C9   C17  O7   117.67  3.000
 0YS  H2   C9   C8   108.44  3.000
 0YS  H2   C9   N1   106.89  3.000
 0YS  C8   C9   N1   110.21  3.000
 0YS  H2   C9   C17  108.25  3.000
 0YS  C8   C9   C17  110.34  3.000
 0YS  N1   C9   C17  112.54  3.000
 0YS  H3   N1   C10  118.84  3.000
 0YS  H3   N1   C9   116.50  3.000
 0YS  C10  N1   C9   124.65  3.000
 0YS  O5   C10  C11  119.99  3.000
 0YS  O5   C10  N1   123.89  3.000
 0YS  C11  C10  N1   116.08  3.000
 0YS  C12  C11  C16  119.02  3.000
 0YS  C12  C11  C10  118.53  3.000
 0YS  C16  C11  C10  122.14  3.000
 0YS  H4   C16  C15  118.38  3.000
 0YS  H4   C16  C11  121.20  3.000
 0YS  C15  C16  C11  120.34  3.000
 0YS  C14  C15  CL1  118.41  3.000
 0YS  C14  C15  C16  121.65  3.000
 0YS  CL1  C15  C16  119.91  3.000
 0YS  C13  C14  O6   124.31  3.000
 0YS  C13  C14  C15  117.01  3.000
 0YS  O6   C14  C15  118.68  3.000
 0YS  H5   O6   C14  111.30  3.000
 0YS  C12  C13  CL   119.94  3.000
 0YS  C12  C13  C14  122.04  3.000
 0YS  CL   C13  C14  118.01  3.000
 0YS  H6   C12  C13  119.64  3.000
 0YS  H6   C12  C11  120.45  3.000
 0YS  C13  C12  C11  119.91  3.000
 0YS  H8   C8   H7   106.97  3.000
 0YS  H8   C8   C7   109.60  3.000
 0YS  H7   C8   C7   108.40  3.000
 0YS  H8   C8   C9   108.13  3.000
 0YS  H7   C8   C9   109.26  3.000
 0YS  C7   C8   C9   114.23  3.000
 0YS  H9   C7   N2   112.71  3.000
 0YS  H9   C7   C6   107.43  3.000
 0YS  N2   C7   C6   101.51  3.000
 0YS  H9   C7   C8   108.61  3.000
 0YS  C6   C7   C8   113.95  3.000
 0YS  N2   C7   C8   112.47  3.000
 0YS  H11  C6   H10  107.48  3.000
 0YS  H11  C6   C5   110.56  3.000
 0YS  H10  C6   C5   113.11  3.000
 0YS  H11  C6   C7   109.58  3.000
 0YS  H10  C6   C7   112.30  3.000
 0YS  C5   C6   C7   103.80  3.000
 0YS  H13  C5   H12  106.66  3.000
 0YS  H13  C5   C3   111.53  3.000
 0YS  H12  C5   C3   111.19  3.000
 0YS  H13  C5   C6   111.58  3.000
 0YS  H12  C5   C6   110.60  3.000
 0YS  C3   C5   C6   105.36  3.000
 0YS  H14  N2   C3   111.38  3.000
 0YS  H14  N2   C7   113.59  3.000
 0YS  C3   N2   C7   109.54  3.000
 0YS  C2   C3   C4   105.28  3.000
 0YS  C4   C3   N2   112.01  3.000
 0YS  C2   C3   N2   112.37  3.000
 0YS  N2   C3   C5   103.85  3.000
 0YS  C4   C3   C5   109.05  3.000
 0YS  C2   C3   C5   114.42  3.000
 0YS  O3   C4   O4   125.71  3.000
 0YS  O4   C4   C3   119.12  3.000
 0YS  O3   C4   C3   115.15  3.000
 0YS  H17  C2   C    107.42  3.000
 0YS  H17  C2   O2   110.84  3.000
 0YS  C    C2   O2   109.28  3.000
 0YS  H17  C2   C3   107.29  3.000
 0YS  C    C2   C3   116.76  3.000
 0YS  O2   C2   C3   105.24  3.000
 0YS  H18  O2   C2   104.48  3.000
 0YS  H19  C    C1   104.75  3.000
 0YS  H19  C    N    107.54  3.000
 0YS  C1   C    N    112.17  3.000
 0YS  H19  C    C2   106.46  3.000
 0YS  C1   C    C2   113.17  3.000
 0YS  N    C    C2   112.14  3.000
 0YS  H21  N    H20  104.01  3.000
 0YS  H21  N    C    106.78  3.000
 0YS  H20  N    C    108.65  3.000
 0YS  O1   C1   O    124.94  3.000
 0YS  O    C1   C    117.39  3.000
 0YS  O1   C1   C    117.65  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
 0YS  CONST_01  C14  C15  C16  C11    0.00   0.0  0
 0YS  CONST_02  C14  C13  C12  C11    0.00   0.0  0
 0YS  CONST_03  C13  C14  C15  C16    0.00   0.0  0
 0YS  CONST_04  C13  C12  C11  C16    0.00   0.0  0
 0YS  CONST_05  C12  C13  C14  C15    0.00   0.0  0
 0YS  CONST_06  C12  C11  C16  C15    0.00   0.0  0
 0YS  CONST_07  C15  C16  C11  C10  180.00   0.0  0
 0YS  CONST_08  C13  C12  C11  C10  180.00   0.0  0
 0YS  CONST_09  CL1  C15  C16  C11  180.00   0.0  0
 0YS  CONST_10  CL   C13  C12  C11  180.00   0.0  0
 0YS  CONST_11  O6   C14  C15  C16  180.00   0.0  0
 0YS  CONST_12  CL   C13  C14  C15  180.00   0.0  0
 0YS  CONST_13  C13  C14  C15  CL1  180.00   0.0  0
 0YS  CONST_14  C12  C13  C14  O6   180.00   0.0  0
 0YS  CONST_15  H6   C12  C11  C16  180.00   0.0  0
 0YS  CONST_16  H4   C16  C15  C14  180.00   0.0  0
 0YS  CONST_17  C11  C10  N1   C9   180.00   0.0  0
 0YS  CONST_18  H3   N1   C10  C11    0.00   0.0  0
 0YS  CONST_19  O5   C10  N1   C9     0.00   0.0  0
 0YS  Var_01    C3   C5   C6   C7   -23.01  30.0  1
 0YS  Var_02    C16  C11  C10  N1    26.82  30.0  2

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
 0YS  chir_01  C9  N1  C8  C17  negativ
 0YS  chir_02  C7  N2  C6  C8   positiv
 0YS  chir_03  C3  N2  C4  C5   positiv
 0YS  chir_04  C2  O2  C3  C    positiv
 0YS  chir_05  C   N   C2  C1   positiv

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
 0YS  plan-1  C10  0.020
 0YS  plan-1  C11  0.020
 0YS  plan-1  C16  0.020
 0YS  plan-1  C15  0.020
 0YS  plan-1  CL1  0.020
 0YS  plan-1  C14  0.020
 0YS  plan-1  O6   0.020
 0YS  plan-1  C13  0.020
 0YS  plan-1  CL   0.020
 0YS  plan-1  C12  0.020
 0YS  plan-1  H4   0.020
 0YS  plan-1  H6   0.020
 0YS  plan-2  C9   0.020
 0YS  plan-2  N1   0.020
 0YS  plan-2  C10  0.020
 0YS  plan-2  C11  0.020
 0YS  plan-2  O5   0.020
 0YS  plan-2  H3   0.020
 0YS  plan-3  O7   0.020
 0YS  plan-3  C17  0.020
 0YS  plan-3  O8   0.020
 0YS  plan-3  C9   0.020
 0YS  plan-4  C3   0.020
 0YS  plan-4  C4   0.020
 0YS  plan-4  O4   0.020
 0YS  plan-4  O3   0.020
 0YS  plan-5  C    0.020
 0YS  plan-5  C1   0.020
 0YS  plan-5  O    0.020
 0YS  plan-5  O1   0.020

