# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 20:22:02 2021
#   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  53  32  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.428  -27.0522  30.1855  -12.3633
 0YS  C17  C   C     0   0.540  -26.3343  29.9279  -11.4330
 0YS  O8   O   OH1   0  -0.591  -26.6068  30.2434  -10.1745
 0YS  C9   C   CH1   0  -0.201  -24.9826  29.2385  -11.5488
 0YS  N1   N   NH1   0  -0.674  -24.8555  28.5970  -12.8286
 0YS  C10  C   C     0   0.546  -25.5967  27.5329  -13.1588
 0YS  C11  C   CR6   0  -0.065  -25.5407  27.1043  -14.5893
 0YS  C16  C   CR16  0  -0.247  -25.2749  27.9904  -15.6294
 0YS  C15  C   CR6   0  -0.147  -25.3249  27.5543  -16.9395
 0YS  CL1  CL  CL    0  -0.078  -25.0691  28.6633  -18.2364
 0YS  C14  C   CR6   0   0.489  -25.6055  26.2247  -17.2602
 0YS  O6   O   OH1   0  -0.581  -25.6261  25.8702  -18.5403
 0YS  C13  C   CR6   0  -0.155  -25.8543  25.3528  -16.1976
 0YS  CL   CL  CL    0  -0.095  -26.2021  23.6974  -16.5648
 0YS  C12  C   CR16  0  -0.230  -25.8436  25.7809  -14.8862
 0YS  O5   O   O     0  -0.492  -26.2848  26.9239  -12.3491
 0YS  C8   C   CH2   0  -0.467  -23.8417  30.2468  -11.3510
 0YS  C7   C   CH1   0  -0.076  -23.8279  31.4303  -12.3147
 0YS  C6   C   CH2   0  -0.476  -22.5850  32.3125  -12.1124
 0YS  C5   C   CH2   0  -0.458  -22.2362  32.7879  -13.5151
 0YS  N2   N   NH1   0  -0.661  -23.8021  31.0206  -13.7341
 0YS  C3   C   CT    0  -0.028  -22.6234  31.5773  -14.3781
 0YS  C4   C   C     0   0.578  -21.4602  30.5775  -14.3814
 0YS  O4   O   OH1   0  -0.566  -21.7823  29.3598  -13.9883
 0YS  O3   O   O     0  -0.450  -20.3435  30.8908  -14.7174
 0YS  C2   C   CH1   0   0.045  -22.8415  31.9287  -15.8571
 0YS  O2   O   OH1   0  -0.644  -23.0156  30.7075  -16.5371
 0YS  C    C   CH1   0  -0.290  -24.0094  32.9431  -16.1069
 0YS  N    N   NH2   0  -0.782  -23.6196  34.1797  -16.7471
 0YS  C1   C   C     0   0.576  -25.0676  32.2634  -16.9572
 0YS  O    O   OH1   0  -0.591  -25.9038  31.5359  -16.2268
 0YS  O1   O   O     0  -0.431  -25.1460  32.3692  -18.1525
 0YS  H1   H   HOH1  0   0.484  -27.4470  30.7241  -10.1234
 0YS  H2   H   HCH1  0   0.299  -24.9110  28.4946  -10.7506
 0YS  H3   H   HNH1  0   0.451  -24.3114  29.1180  -13.5130
 0YS  H4   H   HCR6  0   0.277  -25.0524  29.0322  -15.4438
 0YS  H5   H   HOH1  0   0.481  -25.8229  24.9291  -18.6450
 0YS  H6   H   HCR6  0   0.289  -26.0653  25.0800  -14.0932
 0YS  H7   H   HCH2  0   0.259  -22.9041  29.6916  -11.4282
 0YS  H8   H   HCH2  0   0.264  -23.8866  30.6309  -10.3300
 0YS  H9   H   HCH1  0   0.255  -24.7224  32.0382  -12.1472
 0YS  H10  H   HCH2  0   0.242  -21.7624  31.7264  -11.6927
 0YS  H11  H   HCH2  0   0.263  -22.7775  33.1311  -11.4204
 0YS  H12  H   HCH2  0   0.263  -21.1969  33.0908  -13.6313
 0YS  H13  H   HCH2  0   0.255  -22.8556  33.6450  -13.7908
 0YS  H14  H   HNH1  0   0.376  -24.6510  31.3210  -14.1915
 0YS  H16  H   HOH1  0   0.481  -20.9978  28.7913  -14.0240
 0YS  H17  H   HCH1  0   0.256  -21.9271  32.4289  -16.1960
 0YS  H18  H   HOH1  0   0.462  -22.7622  30.8125  -17.4595
 0YS  H19  H   HCH1  0   0.281  -24.4761  33.2161  -15.1560
 0YS  H20  H   HNH2  0   0.361  -23.0275  34.7133  -16.1238
 0YS  H21  H   HNH2  0   0.351  -23.0711  33.9956  -17.5783
 0YS  H23  H   HOH1  0   0.479  -26.5287  31.0649  -16.7992

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    1.726  0.020  1.726
 0YS  O6   C14  single    1.328  0.020  1.328
 0YS  C15  C14  aromatic  1.396  0.020  1.396
 0YS  C15  C16  aromatic  1.382  0.020  1.382
 0YS  C14  C13  aromatic  1.397  0.020  1.397
 0YS  O1   C1   double    1.203  0.020  1.203
 0YS  O2   C2   single    1.409  0.020  1.409
 0YS  N    C    single    1.446  0.020  1.446
 0YS  C16  C11  aromatic  1.392  0.020  1.392
 0YS  C13  CL   single    1.731  0.020  1.731
 0YS  C13  C12  aromatic  1.379  0.020  1.379
 0YS  C1   C    single    1.518  0.020  1.518
 0YS  C1   O    single    1.327  0.020  1.327
 0YS  C2   C    single    1.567  0.020  1.567
 0YS  C2   C3   single    1.536  0.020  1.536
 0YS  O3   C4   double    1.207  0.020  1.207
 0YS  C11  C12  aromatic  1.390  0.020  1.390
 0YS  C11  C10  single    1.494  0.020  1.494
 0YS  C4   O4   single    1.319  0.020  1.319
 0YS  C4   C3   single    1.534  0.020  1.534
 0YS  C3   N2   single    1.454  0.020  1.454
 0YS  C3   C5   single    1.536  0.020  1.536
 0YS  N2   C7   single    1.478  0.020  1.478
 0YS  C10  N1   single    1.338  0.020  1.338
 0YS  C10  O5   double    1.225  0.020  1.225
 0YS  C5   C6   single    1.522  0.020  1.522
 0YS  N1   C9   single    1.437  0.020  1.437
 0YS  C7   C6   single    1.538  0.020  1.538
 0YS  C7   C8   single    1.526  0.020  1.526
 0YS  C9   C8   single    1.535  0.020  1.535
 0YS  C9   C17  single    1.522  0.020  1.522
 0YS  O7   C17  double    1.203  0.020  1.203
 0YS  C17  O8   single    1.326  0.020  1.326
 0YS  O8   H1   single    0.850  0.020  0.980
 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  O4   H16  single    0.850  0.020  0.980
 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
 0YS  O    H23  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
 0YS  C9   C17  O8   111.26  3.000
 0YS  O8   C17  O7   124.09  3.000
 0YS  C9   C17  O7   124.63  3.000
 0YS  H1   O8   C17  110.25  3.000
 0YS  H2   C9   C8   107.70  3.000
 0YS  H2   C9   N1   109.91  3.000
 0YS  C8   C9   N1   110.00  3.000
 0YS  H2   C9   C17  108.11  3.000
 0YS  C8   C9   C17  110.66  3.000
 0YS  N1   C9   C17  110.40  3.000
 0YS  H3   N1   C10  122.50  3.000
 0YS  H3   N1   C9   114.68  3.000
 0YS  C10  N1   C9   121.71  3.000
 0YS  O5   C10  C11  120.75  3.000
 0YS  O5   C10  N1   122.93  3.000
 0YS  C11  C10  N1   116.33  3.000
 0YS  C12  C11  C16  119.22  3.000
 0YS  C12  C11  C10  118.00  3.000
 0YS  C16  C11  C10  122.67  3.000
 0YS  H4   C16  C15  118.31  3.000
 0YS  H4   C16  C11  121.62  3.000
 0YS  C15  C16  C11  120.05  3.000
 0YS  C14  C15  CL1  117.98  3.000
 0YS  C14  C15  C16  121.71  3.000
 0YS  CL1  C15  C16  120.29  3.000
 0YS  C13  C14  O6   124.31  3.000
 0YS  C13  C14  C15  117.09  3.000
 0YS  O6   C14  C15  118.60  3.000
 0YS  H5   O6   C14  111.54  3.000
 0YS  C12  C13  CL   120.00  3.000
 0YS  C12  C13  C14  121.87  3.000
 0YS  CL   C13  C14  118.12  3.000
 0YS  H6   C12  C13  119.63  3.000
 0YS  H6   C12  C11  120.34  3.000
 0YS  C13  C12  C11  120.02  3.000
 0YS  H8   C8   H7   106.27  3.000
 0YS  H8   C8   C7   108.55  3.000
 0YS  H7   C8   C7   109.98  3.000
 0YS  H8   C8   C9   108.72  3.000
 0YS  H7   C8   C9   107.15  3.000
 0YS  C7   C8   C9   115.76  3.000
 0YS  H9   C7   N2   108.38  3.000
 0YS  H9   C7   C6   108.78  3.000
 0YS  N2   C7   C6   105.74  3.000
 0YS  H9   C7   C8   109.07  3.000
 0YS  C6   C7   C8   111.66  3.000
 0YS  N2   C7   C8   113.05  3.000
 0YS  H11  C6   H10  106.97  3.000
 0YS  H11  C6   C5   113.04  3.000
 0YS  H10  C6   C5   110.41  3.000
 0YS  H11  C6   C7   111.83  3.000
 0YS  H10  C6   C7   110.55  3.000
 0YS  C5   C6   C7   104.08  3.000
 0YS  H13  C5   H12  107.22  3.000
 0YS  H13  C5   C3   109.48  3.000
 0YS  H12  C5   C3   113.56  3.000
 0YS  H13  C5   C6   110.35  3.000
 0YS  H12  C5   C6   113.84  3.000
 0YS  C3   C5   C6   102.35  3.000
 0YS  H14  N2   C3   111.52  3.000
 0YS  H14  N2   C7   109.74  3.000
 0YS  C3   N2   C7   109.48  3.000
 0YS  C2   C3   C4   104.76  3.000
 0YS  C4   C3   N2   111.48  3.000
 0YS  C2   C3   N2   113.52  3.000
 0YS  N2   C3   C5   104.90  3.000
 0YS  C4   C3   C5   108.89  3.000
 0YS  C2   C3   C5   113.36  3.000
 0YS  O3   C4   O4   123.24  3.000
 0YS  O4   C4   C3   114.56  3.000
 0YS  O3   C4   C3   122.19  3.000
 0YS  H16  O4   C4   109.42  3.000
 0YS  H17  C2   C    106.09  3.000
 0YS  H17  C2   O2   110.46  3.000
 0YS  C    C2   O2   113.09  3.000
 0YS  H17  C2   C3   106.49  3.000
 0YS  C    C2   C3   114.05  3.000
 0YS  O2   C2   C3   106.50  3.000
 0YS  H18  O2   C2   109.61  3.000
 0YS  H19  C    C1   107.53  3.000
 0YS  H19  C    N    106.65  3.000
 0YS  C1   C    N    108.84  3.000
 0YS  H19  C    C2   109.94  3.000
 0YS  C1   C    C2   108.60  3.000
 0YS  N    C    C2   115.04  3.000
 0YS  H21  N    H20  106.53  3.000
 0YS  H21  N    C    110.72  3.000
 0YS  H20  N    C    109.63  3.000
 0YS  O1   C1   O    123.65  3.000
 0YS  O    C1   C    112.11  3.000
 0YS  O1   C1   C    124.25  3.000
 0YS  H23  O    C1   110.33  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  H16  O4   C4   C3   180.00   0.0  0
 0YS  CONST_20  O5   C10  N1   C9     0.00   0.0  0
 0YS  CONST_21  H1   O8   C17  O7     0.00   0.0  0
 0YS  CONST_22  H23  O    C1   C    180.00   0.0  0
 0YS  Var_01    C3   C5   C6   C7   -34.40  30.0  1
 0YS  Var_02    C16  C11  C10  N1   -27.86  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-3  H1   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-4  H16  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
 0YS  plan-5  H23  0.020

