# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 19:49:48 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: N-{[(1S)-1-carboxy-5-{[(4-iodophenyl)carbonyl]amino}pentyl]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](CCCCNC(=O)c1ccc(I)cc1)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
 YC2  YC2  'N-{[(1S)-1-carboxy-5-{[(4-iodophenyl)carbonyl]amino}pentyl]carbamoyl}-L-glutamic acid'  ligand  55  31  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YC2
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
 YC2  I24   I  I     0   0.069  23.9973  50.5873  50.9440
 YC2  C23   C  CR6   0  -0.223  23.6421  50.0675  48.9395
 YC2  C22   C  CR16  0  -0.213  22.9521  50.9477  48.1169
 YC2  C21   C  CR16  0  -0.260  22.7134  50.5938  46.7986
 YC2  C25   C  CR16  0  -0.209  24.0925  48.8466  48.4607
 YC2  C26   C  CR16  0  -0.285  23.8587  48.5131  47.1342
 YC2  C20   C  CR6   0  -0.022  23.1765  49.3839  46.2896
 YC2  C19   C  C     0   0.526  22.8685  49.0487  44.8631
 YC2  O27   O  O     0  -0.485  21.8646  49.4959  44.3246
 YC2  N18   N  NH1   0  -0.637  23.7580  48.2538  44.2483
 YC2  C17   C  CH2   0  -0.303  23.5985  47.7170  42.9136
 YC2  C16   C  CH2   0  -0.449  23.5544  46.1908  42.9101
 YC2  C15   C  CH2   0  -0.442  22.4780  45.5867  43.8058
 YC2  C14   C  CH2   0  -0.441  21.0623  45.9822  43.3999
 YC2  C13   C  CH1   0  -0.176  19.9534  45.2393  44.1617
 YC2  C28   C  C     0   0.542  20.0357  45.5532  45.6440
 YC2  O30   O  OH1   0  -0.583  20.7181  44.6419  46.3187
 YC2  O29   O  O     0  -0.434  19.5582  46.5408  46.1424
 YC2  N12   N  NH1   0  -0.688  18.6396  45.6128  43.6990
 YC2  C11   C  C     0   0.771  18.0259  44.9446  42.6885
 YC2  O31   O  O     0  -0.536  18.4680  43.9144  42.1925
 YC2  N10   N  NH1   0  -0.696  16.8621  45.5007  42.2521
 YC2  C6    C  CH1   0  -0.162  16.0526  44.7798  41.3078
 YC2  C7    C  C     0   0.542  16.7742  44.5400  39.9929
 YC2  O9    O  OH1   0  -0.580  17.6481  45.4832  39.6841
 YC2  O8    O  O     0  -0.447  16.5156  43.6053  39.2756
 YC2  C5    C  CH2   0  -0.493  14.7325  45.5175  41.0582
 YC2  C4    C  CH2   0  -0.589  14.8816  46.8990  40.4364
 YC2  C2    C  C     0   0.560  13.5715  47.6317  40.3390
 YC2  O1    O  O     0  -0.442  12.5116  47.2198  40.7392
 YC2  O3    O  OH1   0  -0.595  13.7157  48.8122  39.7465
 YC2  H22   H  HCR6  0   0.285  22.5950  51.8986  48.4874
 YC2  H21   H  HCR6  0   0.273  22.1659  51.2757  46.1619
 YC2  H25   H  HCR6  0   0.287  24.6156  48.1495  49.1006
 YC2  H26   H  HCR6  0   0.269  24.1992  47.5464  46.7848
 YC2  HN18  H  HNH1  0   0.403  24.6148  48.0255  44.7266
 YC2  H17   H  HCH2  0   0.253  22.6903  48.1371  42.4860
 YC2  H17A  H  HCH2  0   0.258  24.4275  48.0572  42.2891
 YC2  H16   H  HCH2  0   0.235  23.4098  45.8636  41.8765
 YC2  H16A  H  HCH2  0   0.238  24.5295  45.8035  43.2186
 YC2  H15   H  HCH2  0   0.239  22.5717  44.4976  43.7747
 YC2  H15A  H  HCH2  0   0.221  22.6765  45.8780  44.8407
 YC2  H14   H  HCH2  0   0.240  20.9077  47.0571  43.5251
 YC2  H14A  H  HCH2  0   0.248  20.9170  45.7627  42.3387
 YC2  H13   H  HCH1  0   0.284  20.0750  44.1660  44.0146
 YC2  HO30  H  HOH1  0   0.483  20.7899  44.8979  47.2515
 YC2  HN12  H  HNH1  0   0.395  18.3162  46.5381  43.9376
 YC2  HN10  H  HNH1  0   0.401  16.4139  46.2063  42.8156
 YC2  H6    H  HCH1  0   0.291  15.7928  43.7869  41.6892
 YC2  HO9   H  HOH1  0   0.481  18.0430  45.2915  38.8202
 YC2  H5    H  HCH2  0   0.272  14.1109  44.8859  40.4223
 YC2  H5A   H  HCH2  0   0.272  14.2151  45.5887  42.0174
 YC2  H4    H  HCH2  0   0.286  15.5752  47.5262  41.0039
 YC2  H4A   H  HCH2  0   0.288  15.3014  46.8402  39.4289
 YC2  HO3   H  HOH1  0   0.480  12.8592  49.2616  39.6903

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
 YC2  C23  I24   single    2.101  0.020  2.101
 YC2  C22  C23   aromatic  1.388  0.020  1.388
 YC2  C25  C23   aromatic  1.387  0.020  1.387
 YC2  C21  C22   aromatic  1.386  0.020  1.386
 YC2  C22  H22   single    0.930  0.020  1.080
 YC2  C20  C21   aromatic  1.392  0.020  1.392
 YC2  C21  H21   single    0.930  0.020  1.080
 YC2  C26  C25   aromatic  1.388  0.020  1.388
 YC2  C25  H25   single    0.930  0.020  1.080
 YC2  C20  C26   aromatic  1.392  0.020  1.392
 YC2  C26  H26   single    0.930  0.020  1.080
 YC2  C19  C20   single    1.497  0.020  1.497
 YC2  O27  C19   double    1.224  0.020  1.224
 YC2  N18  C19   single    1.342  0.020  1.342
 YC2  C17  N18   single    1.447  0.020  1.447
 YC2  N18  HN18  single    0.860  0.020  1.020
 YC2  C16  C17   single    1.527  0.020  1.527
 YC2  C17  H17   single    0.970  0.020  1.090
 YC2  C17  H17A  single    0.970  0.020  1.090
 YC2  C16  C15   single    1.525  0.020  1.525
 YC2  C16  H16   single    0.970  0.020  1.090
 YC2  C16  H16A  single    0.970  0.020  1.090
 YC2  C14  C15   single    1.525  0.020  1.525
 YC2  C15  H15   single    0.970  0.020  1.090
 YC2  C15  H15A  single    0.970  0.020  1.090
 YC2  C14  C13   single    1.537  0.020  1.537
 YC2  C14  H14   single    0.970  0.020  1.090
 YC2  C14  H14A  single    0.970  0.020  1.090
 YC2  N12  C13   single    1.442  0.020  1.442
 YC2  C13  C28   single    1.517  0.020  1.517
 YC2  C13  H13   single    0.970  0.020  1.090
 YC2  C28  O29   double    1.205  0.020  1.205
 YC2  C28  O30   single    1.323  0.020  1.323
 YC2  O30  HO30  single    0.850  0.020  0.980
 YC2  C11  N12   single    1.358  0.020  1.358
 YC2  N12  HN12  single    0.860  0.020  1.020
 YC2  O31  C11   double    1.226  0.020  1.226
 YC2  N10  C11   single    1.362  0.020  1.362
 YC2  C6   N10   single    1.438  0.020  1.438
 YC2  N10  HN10  single    0.890  0.020  1.040
 YC2  C7   C6    single    1.519  0.020  1.519
 YC2  C5   C6    single    1.533  0.020  1.533
 YC2  C6   H6    single    0.970  0.020  1.090
 YC2  O8   C7    double    1.206  0.020  1.206
 YC2  C7   O9    single    1.322  0.020  1.322
 YC2  O9   HO9   single    0.850  0.020  0.980
 YC2  C4   C5    single    1.522  0.020  1.522
 YC2  C5   H5    single    0.970  0.020  1.090
 YC2  C5   H5A   single    0.970  0.020  1.090
 YC2  C2   C4    single    1.504  0.020  1.504
 YC2  C4   H4    single    0.970  0.020  1.090
 YC2  C4   H4A   single    0.970  0.020  1.090
 YC2  O1   C2    double    1.206  0.020  1.206
 YC2  C2   O3    single    1.329  0.020  1.329
 YC2  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
 YC2  C25   C23  C22  121.00  3.000
 YC2  C25   C23  I24  119.49  3.000
 YC2  C22   C23  I24  119.50  3.000
 YC2  H22   C22  C21  119.59  3.000
 YC2  H22   C22  C23  121.24  3.000
 YC2  C21   C22  C23  119.17  3.000
 YC2  H21   C21  C20  120.07  3.000
 YC2  H21   C21  C22  119.09  3.000
 YC2  C20   C21  C22  120.84  3.000
 YC2  H25   C25  C26  119.49  3.000
 YC2  H25   C25  C23  121.36  3.000
 YC2  C26   C25  C23  119.14  3.000
 YC2  H26   C26  C20  121.12  3.000
 YC2  H26   C26  C25  118.04  3.000
 YC2  C20   C26  C25  120.82  3.000
 YC2  C19   C20  C26  122.61  3.000
 YC2  C19   C20  C21  118.33  3.000
 YC2  C26   C20  C21  119.01  3.000
 YC2  N18   C19  O27  123.95  3.000
 YC2  N18   C19  C20  115.64  3.000
 YC2  O27   C19  C20  120.40  3.000
 YC2  HN18  N18  C17  116.58  3.000
 YC2  HN18  N18  C19  118.71  3.000
 YC2  C17   N18  C19  124.69  3.000
 YC2  H17A  C17  H17  106.77  3.000
 YC2  H17A  C17  C16  109.39  3.000
 YC2  H17   C17  C16  111.15  3.000
 YC2  H17A  C17  N18  109.15  3.000
 YC2  H17   C17  N18  108.12  3.000
 YC2  C16   C17  N18  112.09  3.000
 YC2  H16A  C16  H16  106.17  3.000
 YC2  H16A  C16  C15  108.86  3.000
 YC2  H16   C16  C15  110.07  3.000
 YC2  H16A  C16  C17  109.12  3.000
 YC2  H16   C16  C17  107.76  3.000
 YC2  C15   C16  C17  114.52  3.000
 YC2  H15A  C15  H15  106.07  3.000
 YC2  H15A  C15  C14  110.57  3.000
 YC2  H15   C15  C14  109.29  3.000
 YC2  H15A  C15  C16  108.80  3.000
 YC2  H15   C15  C16  108.50  3.000
 YC2  C14   C15  C16  113.33  3.000
 YC2  H14A  C14  H14  106.84  3.000
 YC2  H14A  C14  C13  106.74  3.000
 YC2  H14   C14  C13  108.45  3.000
 YC2  H14A  C14  C15  109.25  3.000
 YC2  H14   C14  C15  110.85  3.000
 YC2  C13   C14  C15  114.36  3.000
 YC2  H13   C13  N12  108.26  3.000
 YC2  H13   C13  C28  109.23  3.000
 YC2  N12   C13  C28  108.02  3.000
 YC2  H13   C13  C14  109.18  3.000
 YC2  C28   C13  C14  110.19  3.000
 YC2  N12   C13  C14  111.91  3.000
 YC2  O29   C28  O30  123.91  3.000
 YC2  O30   C28  C13  112.56  3.000
 YC2  O29   C28  C13  123.51  3.000
 YC2  HO30  O30  C28  110.29  3.000
 YC2  HN12  N12  C11  118.84  3.000
 YC2  HN12  N12  C13  116.98  3.000
 YC2  C11   N12  C13  121.54  3.000
 YC2  N10   C11  O31  121.45  3.000
 YC2  N10   C11  N12  115.08  3.000
 YC2  O31   C11  N12  123.47  3.000
 YC2  HN10  N10  C6   117.89  3.000
 YC2  HN10  N10  C11  119.12  3.000
 YC2  C6    N10  C11  119.14  3.000
 YC2  H6    C6   C5   106.79  3.000
 YC2  H6    C6   C7   105.73  3.000
 YC2  C5    C6   C7   110.13  3.000
 YC2  H6    C6   N10  111.08  3.000
 YC2  C5    C6   N10  110.52  3.000
 YC2  C7    C6   N10  112.35  3.000
 YC2  O8    C7   O9   123.74  3.000
 YC2  O9    C7   C6   113.80  3.000
 YC2  O8    C7   C6   122.36  3.000
 YC2  HO9   O9   C7   109.66  3.000
 YC2  H5A   C5   H5   106.25  3.000
 YC2  H5A   C5   C4   110.24  3.000
 YC2  H5    C5   C4   110.07  3.000
 YC2  H5A   C5   C6   107.24  3.000
 YC2  H5    C5   C6   107.88  3.000
 YC2  C4    C5   C6   114.77  3.000
 YC2  H4A   C4   H4   105.40  3.000
 YC2  H4A   C4   C2   107.51  3.000
 YC2  H4    C4   C2   107.85  3.000
 YC2  H4A   C4   C5   111.43  3.000
 YC2  H4    C4   C5   111.75  3.000
 YC2  C2    C4   C5   112.53  3.000
 YC2  O3    C2   O1   123.16  3.000
 YC2  O3    C2   C4   111.55  3.000
 YC2  O1    C2   C4   125.30  3.000
 YC2  HO3   O3   C2   110.00  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
 YC2  CONST_01  C20   C21  C22  C23     0.00   0.0  0
 YC2  CONST_02  C20   C26  C25  C23     0.00   0.0  0
 YC2  CONST_03  C26   C25  C23  C22     0.00   0.0  0
 YC2  CONST_04  C26   C20  C21  C22     0.00   0.0  0
 YC2  CONST_05  C25   C23  C22  C21     0.00   0.0  0
 YC2  CONST_06  C25   C26  C20  C21     0.00   0.0  0
 YC2  CONST_07  C21   C22  C23  I24   180.00   0.0  0
 YC2  CONST_08  C26   C25  C23  I24   180.00   0.0  0
 YC2  CONST_09  C19   C20  C21  C22   180.00   0.0  0
 YC2  CONST_10  C19   C20  C26  C25   180.00   0.0  0
 YC2  CONST_11  H21   C21  C22  C23   180.00   0.0  0
 YC2  CONST_12  H26   C26  C25  C23   180.00   0.0  0
 YC2  CONST_13  H25   C25  C23  C22   180.00   0.0  0
 YC2  CONST_14  H22   C22  C23  C25   180.00   0.0  0
 YC2  CONST_15  C17   N18  C19  C20   180.00   0.0  0
 YC2  CONST_16  HN18  N18  C19  C20     0.00   0.0  0
 YC2  CONST_17  C17   N18  C19  O27     0.00   0.0  0
 YC2  CONST_18  O31   C11  N12  C13     0.00   0.0  0
 YC2  CONST_19  C6    N10  C11  O31     0.00   0.0  0
 YC2  CONST_20  N10   C11  N12  C13   180.00   0.0  0
 YC2  CONST_21  C6    N10  C11  N12   180.00   0.0  0
 YC2  CONST_22  HN12  N12  C11  O31   180.00   0.0  0
 YC2  CONST_23  HN10  N10  C11  O31   180.00   0.0  0
 YC2  CONST_24  HO30  O30  C28  C13   180.00   0.0  0
 YC2  CONST_25  HO9   O9   C7   C6    180.00   0.0  0
 YC2  CONST_26  HO3   O3   C2   C4    180.00   0.0  0
 YC2  Var_01    O27   C19  C20  C21   -28.08  30.0  2
 YC2  Var_02    C16   C17  N18  C19  -118.19  30.0  2
 YC2  Var_03    C15   C16  C17  N18    55.87  30.0  1
 YC2  Var_04    C14   C15  C16  C17    61.69  30.0  3
 YC2  Var_05    C13   C14  C15  C16   172.09  30.0  2
 YC2  Var_06    C2    C4   C5   C6   -174.32  30.0  1
 YC2  Var_07    O1    C2   C4   C5      2.38  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
 YC2  chir_01  C13  C14  N12  C28  positiv
 YC2  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
 YC2  plan-1  I24   0.020
 YC2  plan-1  C23   0.020
 YC2  plan-1  C22   0.020
 YC2  plan-1  C21   0.020
 YC2  plan-1  C25   0.020
 YC2  plan-1  C26   0.020
 YC2  plan-1  C20   0.020
 YC2  plan-1  C19   0.020
 YC2  plan-1  H22   0.020
 YC2  plan-1  H21   0.020
 YC2  plan-1  H25   0.020
 YC2  plan-1  H26   0.020
 YC2  plan-2  C4    0.020
 YC2  plan-2  C2    0.020
 YC2  plan-2  O1    0.020
 YC2  plan-2  O3    0.020
 YC2  plan-2  HO3   0.020
 YC2  plan-3  C20   0.020
 YC2  plan-3  C19   0.020
 YC2  plan-3  O27   0.020
 YC2  plan-3  N18   0.020
 YC2  plan-3  C17   0.020
 YC2  plan-3  HN18  0.020
 YC2  plan-4  C13   0.020
 YC2  plan-4  N12   0.020
 YC2  plan-4  C11   0.020
 YC2  plan-4  O31   0.020
 YC2  plan-4  N10   0.020
 YC2  plan-4  C6    0.020
 YC2  plan-4  HN12  0.020
 YC2  plan-4  HN10  0.020
 YC2  plan-5  C13   0.020
 YC2  plan-5  C28   0.020
 YC2  plan-5  O30   0.020
 YC2  plan-5  O29   0.020
 YC2  plan-5  HO30  0.020
 YC2  plan-6  C6    0.020
 YC2  plan-6  C7    0.020
 YC2  plan-6  O9    0.020
 YC2  plan-6  O8    0.020
 YC2  plan-6  HO9   0.020

