# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 15:10:03 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-{[(1S)-1-carboxy-2-(4-hydroxy-3-iodophenyl)ethyl]carbamoyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](NC(=O)N[C@@H](Cc1ccc(O)c(I)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
 YBY  YBY  'N-{[(1S)-1-carboxy-2-(4-hydroxy-3-iodophenyl)ethyl]carbamoyl}-L-glutamic acid'  ligand  43  26  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YBY
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
 YBY  I18   I  I     0   0.040  -1.8408  -2.2419   1.0560
 YBY  C17   C  CR6   0  -0.291  -2.0498  -0.3560   0.1648
 YBY  C16   C  CR16  0  -0.272  -1.5910   0.7698   0.8275
 YBY  C19   C  CR6   0   0.424  -2.6214  -0.2600  -1.1002
 YBY  O20   O  OH1   0  -0.617  -3.0525  -1.3756  -1.7078
 YBY  C21   C  CR16  0  -0.372  -2.7356   1.0032  -1.6760
 YBY  C22   C  CR16  0  -0.280  -2.2701   2.1251  -1.0132
 YBY  C15   C  CR6   0   0.126  -1.6901   2.0292   0.2468
 YBY  C14   C  CH2   0  -0.537  -1.1208   3.2373   0.9309
 YBY  C13   C  CH1   0  -0.199   0.3165   3.5166   0.4358
 YBY  C23   C  C     0   0.549   0.9100   4.7226   1.1434
 YBY  O25   O  O     0  -0.428   1.8890   4.6953   1.8420
 YBY  O24   O  OH1   0  -0.591   0.2021   5.8175   0.9046
 YBY  N12   N  NH1   0  -0.674   1.1585   2.3725   0.6014
 YBY  C11   C  C     0   0.768   1.6558   1.6680  -0.4483
 YBY  O26   O  O     0  -0.528   1.6332   2.0684  -1.6042
 YBY  N10   N  NH1   0  -0.679   2.2413   0.4829  -0.1045
 YBY  C6    C  CH1   0  -0.176   2.7457  -0.3778  -1.1369
 YBY  C7    C  C     0   0.536   1.6262  -0.8953  -2.0291
 YBY  O9    O  OH1   0  -0.598   2.0772  -1.2075  -3.2405
 YBY  O8    O  O     0  -0.403   0.4901  -1.0491  -1.6726
 YBY  C5    C  CH2   0  -0.467   3.4837  -1.5698  -0.5194
 YBY  C4    C  CH2   0  -0.577   4.6909  -1.1237   0.2889
 YBY  C2    C  C     0   0.553   5.4716  -2.2734   0.8625
 YBY  O1    O  O     0  -0.443   5.2140  -3.4398   0.6997
 YBY  O3    O  OH1   0  -0.596   6.5033  -1.8510   1.5859
 YBY  H16   H  HCR6  0   0.263  -1.1511   0.6719   1.8120
 YBY  HO20  H  HOH1  0   0.479  -3.4168  -1.1636  -2.5749
 YBY  H21   H  HCR6  0   0.274  -3.1914   1.1061  -2.6544
 YBY  H22   H  HCR6  0   0.256  -2.3664   3.0931  -1.4908
 YBY  H14   H  HCH2  0   0.273  -1.7451   4.1104   0.7381
 YBY  H14A  H  HCH2  0   0.266  -1.1076   3.0873   2.0139
 YBY  H13   H  HCH1  0   0.305   0.2739   3.7477  -0.6309
 YBY  HO24  H  HOH1  0   0.486   0.5771   6.5713   1.3847
 YBY  HN12  H  HNH1  0   0.394   1.2723   2.0067   1.5338
 YBY  HN10  H  HNH1  0   0.392   1.9408   0.0377   0.7494
 YBY  H6    H  HCH1  0   0.281   3.4534   0.1792  -1.7562
 YBY  HO9   H  HOH1  0   0.480   1.3638  -1.5924  -3.7711
 YBY  H5    H  HCH2  0   0.254   2.7931  -2.1430   0.1051
 YBY  H5A   H  HCH2  0   0.271   3.8027  -2.2331  -1.3244
 YBY  H4    H  HCH2  0   0.287   5.3681  -0.5290  -0.3324
 YBY  H4A   H  HCH2  0   0.287   4.3979  -0.4673   1.1125
 YBY  HO3   H  HOH1  0   0.480   6.9929  -2.6089   1.9385

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
 YBY  I18  C17   single    2.096  0.020  2.096
 YBY  C16  C17   aromatic  1.385  0.020  1.385
 YBY  C17  C19   aromatic  1.392  0.020  1.392
 YBY  C16  C15   aromatic  1.390  0.020  1.390
 YBY  C16  H16   single    0.930  0.020  1.080
 YBY  C19  C21   aromatic  1.393  0.020  1.393
 YBY  C19  O20   single    1.341  0.020  1.341
 YBY  O20  HO20  single    0.850  0.020  0.980
 YBY  C22  C21   aromatic  1.384  0.020  1.384
 YBY  C21  H21   single    0.930  0.020  1.080
 YBY  C15  C22   aromatic  1.390  0.020  1.390
 YBY  C22  H22   single    0.930  0.020  1.080
 YBY  C14  C15   single    1.501  0.020  1.501
 YBY  C14  C13   single    1.546  0.020  1.546
 YBY  C14  H14   single    0.970  0.020  1.090
 YBY  C14  H14A  single    0.970  0.020  1.090
 YBY  N12  C13   single    1.430  0.020  1.430
 YBY  C13  C23   single    1.519  0.020  1.519
 YBY  C13  H13   single    0.970  0.020  1.090
 YBY  C23  O25   double    1.203  0.020  1.203
 YBY  C23  O24   single    1.325  0.020  1.325
 YBY  O24  HO24  single    0.850  0.020  0.980
 YBY  C11  N12   single    1.358  0.020  1.358
 YBY  N12  HN12  single    0.860  0.020  1.020
 YBY  O26  C11   double    1.223  0.020  1.223
 YBY  N10  C11   single    1.366  0.020  1.366
 YBY  C6   N10   single    1.436  0.020  1.436
 YBY  N10  HN10  single    0.890  0.020  1.040
 YBY  C7   C6    single    1.522  0.020  1.522
 YBY  C5   C6    single    1.532  0.020  1.532
 YBY  C6   H6    single    0.970  0.020  1.090
 YBY  O8   C7    double    1.201  0.020  1.201
 YBY  O9   C7    single    1.330  0.020  1.330
 YBY  O9   HO9   single    0.850  0.020  0.980
 YBY  C4   C5    single    1.520  0.020  1.520
 YBY  C5   H5    single    0.970  0.020  1.090
 YBY  C5   H5A   single    0.970  0.020  1.090
 YBY  C2   C4    single    1.503  0.020  1.503
 YBY  C4   H4    single    0.970  0.020  1.090
 YBY  C4   H4A   single    0.970  0.020  1.090
 YBY  O1   C2    double    1.206  0.020  1.206
 YBY  C2   O3    single    1.329  0.020  1.329
 YBY  O3   HO3   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
 YBY  C19   C17  C16  121.01  3.000
 YBY  C19   C17  I18  119.31  3.000
 YBY  C16   C17  I18  119.67  3.000
 YBY  H16   C16  C15  119.38  3.000
 YBY  H16   C16  C17  119.76  3.000
 YBY  C15   C16  C17  120.86  3.000
 YBY  C21   C19  O20  122.73  3.000
 YBY  O20   C19  C17  119.10  3.000
 YBY  C21   C19  C17  118.16  3.000
 YBY  HO20  O20  C19  110.23  3.000
 YBY  H21   C21  C22  119.79  3.000
 YBY  H21   C21  C19  119.57  3.000
 YBY  C22   C21  C19  120.64  3.000
 YBY  H22   C22  C15  119.88  3.000
 YBY  H22   C22  C21  118.89  3.000
 YBY  C15   C22  C21  121.23  3.000
 YBY  C14   C15  C22  121.05  3.000
 YBY  C14   C15  C16  120.79  3.000
 YBY  C22   C15  C16  118.08  3.000
 YBY  H14A  C14  H14  106.97  3.000
 YBY  H14A  C14  C13  109.31  3.000
 YBY  H14   C14  C13  109.34  3.000
 YBY  H14A  C14  C15  110.22  3.000
 YBY  H14   C14  C15  110.29  3.000
 YBY  C13   C14  C15  110.62  3.000
 YBY  H13   C13  N12  107.78  3.000
 YBY  H13   C13  C23  107.59  3.000
 YBY  N12   C13  C23  110.56  3.000
 YBY  H13   C13  C14  108.34  3.000
 YBY  C23   C13  C14  110.95  3.000
 YBY  N12   C13  C14  111.46  3.000
 YBY  O24   C23  O25  123.91  3.000
 YBY  O24   C23  C13  111.30  3.000
 YBY  O25   C23  C13  124.79  3.000
 YBY  HO24  O24  C23  110.28  3.000
 YBY  HN12  N12  C11  119.03  3.000
 YBY  HN12  N12  C13  117.64  3.000
 YBY  C11   N12  C13  122.74  3.000
 YBY  N10   C11  O26  121.98  3.000
 YBY  N10   C11  N12  114.35  3.000
 YBY  O26   C11  N12  123.61  3.000
 YBY  HN10  N10  C6   116.67  3.000
 YBY  HN10  N10  C11  117.92  3.000
 YBY  C6    N10  C11  119.33  3.000
 YBY  H6    C6   C5   108.24  3.000
 YBY  H6    C6   C7   108.50  3.000
 YBY  C5    C6   C7   109.03  3.000
 YBY  H6    C6   N10  109.24  3.000
 YBY  C5    C6   N10  110.24  3.000
 YBY  C7    C6   N10  111.53  3.000
 YBY  O8    C7   O9   124.15  3.000
 YBY  O9    C7   C6   111.37  3.000
 YBY  O8    C7   C6   124.43  3.000
 YBY  HO9   O9   C7   110.02  3.000
 YBY  H5A   C5   H5   106.71  3.000
 YBY  H5A   C5   C4   109.80  3.000
 YBY  H5    C5   C4   110.60  3.000
 YBY  H5A   C5   C6   108.46  3.000
 YBY  H5    C5   C6   109.50  3.000
 YBY  C4    C5   C6   111.63  3.000
 YBY  H4A   C4   H4   105.50  3.000
 YBY  H4A   C4   C2   108.11  3.000
 YBY  H4    C4   C2   108.10  3.000
 YBY  H4A   C4   C5   111.35  3.000
 YBY  H4    C4   C5   110.43  3.000
 YBY  C2    C4   C5   113.01  3.000
 YBY  O3    C2   O1   123.15  3.000
 YBY  O3    C2   C4   111.58  3.000
 YBY  O1    C2   C4   125.27  3.000
 YBY  HO3   O3   C2   109.99  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
 YBY  CONST_01  C22   C15  C16  C17     0.00   0.0  0
 YBY  CONST_02  C22   C21  C19  C17     0.00   0.0  0
 YBY  CONST_03  C21   C19  C17  C16     0.00   0.0  0
 YBY  CONST_04  C21   C22  C15  C16     0.00   0.0  0
 YBY  CONST_05  C15   C16  C17  C19     0.00   0.0  0
 YBY  CONST_06  C15   C22  C21  C19     0.00   0.0  0
 YBY  CONST_07  C15   C16  C17  I18   180.00   0.0  0
 YBY  CONST_08  C21   C19  C17  I18   180.00   0.0  0
 YBY  CONST_09  C14   C15  C16  C17   180.00   0.0  0
 YBY  CONST_10  O20   C19  C17  C16   180.00   0.0  0
 YBY  CONST_11  C22   C21  C19  O20   180.00   0.0  0
 YBY  CONST_12  C14   C15  C22  C21   180.00   0.0  0
 YBY  CONST_13  H21   C21  C19  C17   180.00   0.0  0
 YBY  CONST_14  H22   C22  C15  C16   180.00   0.0  0
 YBY  CONST_15  H16   C16  C17  C19   180.00   0.0  0
 YBY  CONST_16  O26   C11  N12  C13     0.00   0.0  0
 YBY  CONST_17  C6    N10  C11  O26     0.00   0.0  0
 YBY  CONST_18  N10   C11  N12  C13   180.00   0.0  0
 YBY  CONST_19  C6    N10  C11  N12   180.00   0.0  0
 YBY  CONST_20  HN12  N12  C11  O26   180.00   0.0  0
 YBY  CONST_22  HO24  O24  C23  C13   180.00   0.0  0
 YBY  CONST_23  HO9   O9   C7   C6    180.00   0.0  0
 YBY  CONST_24  HO3   O3   C2   C4    180.00   0.0  0
 YBY  Var_01    C13   C14  C15  C16    93.62  30.0  2
 YBY  Var_02    C2    C4   C5   C6   -177.63  30.0  1
 YBY  Var_03    O1    C2   C4   C5      1.36  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
 YBY  chir_01  C13  C14  N12  C23  positiv
 YBY  chir_02  C6   N10  C7   C5   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
 YBY  plan-1  I18   0.020
 YBY  plan-1  C17   0.020
 YBY  plan-1  C16   0.020
 YBY  plan-1  C19   0.020
 YBY  plan-1  O20   0.020
 YBY  plan-1  C21   0.020
 YBY  plan-1  C22   0.020
 YBY  plan-1  C15   0.020
 YBY  plan-1  C14   0.020
 YBY  plan-1  H16   0.020
 YBY  plan-1  H21   0.020
 YBY  plan-1  H22   0.020
 YBY  plan-2  C13   0.020
 YBY  plan-2  N12   0.020
 YBY  plan-2  C11   0.020
 YBY  plan-2  O26   0.020
 YBY  plan-2  N10   0.020
 YBY  plan-2  C6    0.020
 YBY  plan-2  HN12  0.020
 YBY  plan-2  HN10  0.020
 YBY  plan-3  C13   0.020
 YBY  plan-3  C23   0.020
 YBY  plan-3  O25   0.020
 YBY  plan-3  O24   0.020
 YBY  plan-3  HO24  0.020
 YBY  plan-4  C6    0.020
 YBY  plan-4  C7    0.020
 YBY  plan-4  O9    0.020
 YBY  plan-4  O8    0.020
 YBY  plan-4  HO9   0.020
 YBY  plan-5  C4    0.020
 YBY  plan-5  C2    0.020
 YBY  plan-5  O1    0.020
 YBY  plan-5  O3    0.020
 YBY  plan-5  HO3   0.020

