# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 22:43:52 2022
#   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  52  31  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.061  23.3272  50.3129  50.8415
 YC2  C23   C  CR6    0  -0.222  23.2643  49.9496  48.7720
 YC2  C22   C  CR16   0  -0.214  23.5057  50.9930  47.8883
 YC2  C21   C  CR16   0  -0.260  23.4555  50.7472  46.5252
 YC2  C25   C  CR16   0  -0.216  22.9742  48.6745  48.3122
 YC2  C26   C  CR16   0  -0.287  22.9436  48.4389  46.9447
 YC2  C20   C  CR6    0  -0.037  23.1936  49.4684  46.0421
 YC2  C19   C  C      0   0.514  23.1183  49.2582  44.5619
 YC2  O27   O  O      0  -0.482  22.6814  50.1301  43.8229
 YC2  N18   N  NH1    0  -0.635  23.5488  48.0659  44.1240
 YC2  C17   C  CH2    0  -0.279  23.4346  47.6308  42.7476
 YC2  C16   C  CH2    0  -0.473  23.4223  46.1090  42.6505
 YC2  C15   C  CH2    0  -0.441  22.4185  45.4194  43.5726
 YC2  C14   C  CH2    0  -0.433  20.9786  45.8755  43.3820
 YC2  C13   C  CH1    0  -0.162  19.9858  45.2941  44.4077
 YC2  C28   C  C      0   0.423  20.1972  45.9763  45.7803
 YC2  O30   O  OC    -1  -0.600  21.0590  45.4731  46.5291
 YC2  O29   O  O      0  -0.595  19.5198  47.0005  45.9990
 YC2  N12   N  NH1    0  -0.683  18.6216  45.5067  43.9785
 YC2  C11   C  C      0   0.716  18.0426  44.7770  42.9926
 YC2  O31   O  O      0  -0.558  18.5310  43.7297  42.5730
 YC2  N10   N  NH1    0  -0.669  16.8347  45.2459  42.5529
 YC2  C6    C  CH1    0  -0.192  16.3363  44.7878  41.2722
 YC2  C7    C  C      0   0.401  17.2531  45.1612  40.0775
 YC2  O9    O  OC    -1  -0.602  18.1412  46.0147  40.2656
 YC2  O8    O  O      0  -0.615  16.9910  44.5719  39.0086
 YC2  C5    C  CH2    0  -0.427  14.9115  45.3053  41.0451
 YC2  C4    C  CH2    0  -0.593  14.7870  46.8141  40.8799
 YC2  C2    C  C      0   0.411  13.3550  47.3351  40.6318
 YC2  O1    O  O      0  -0.605  12.5033  46.5159  40.2324
 YC2  O3    O  OC    -1  -0.622  13.1772  48.5557  40.8258
 YC2  H22   H  HCR6   0   0.282  23.7272  51.9895  48.2452
 YC2  H21   H  HCR6   0   0.268  23.6335  51.5622  45.8361
 YC2  H25   H  HCR6   0   0.282  22.7632  47.8646  48.9971
 YC2  H26   H  HCR6   0   0.283  22.6871  47.4431  46.6044
 YC2  HN18  H  HNH1   0   0.405  24.0372  47.4614  44.7656
 YC2  H17   H  HCH2   0   0.240  22.5158  48.0446  42.3323
 YC2  H17A  H  HCH2   0   0.246  24.2570  48.0290  42.1456
 YC2  H16   H  HCH2   0   0.236  23.2172  45.8516  41.6081
 YC2  H16A  H  HCH2   0   0.234  24.4233  45.7239  42.8661
 YC2  H15   H  HCH2   0   0.223  22.4752  44.3412  43.3948
 YC2  H15A  H  HCH2   0   0.225  22.7194  45.5574  44.6121
 YC2  H14   H  HCH2   0   0.214  20.9053  46.9667  43.4313
 YC2  H14A  H  HCH2   0   0.221  20.6485  45.5965  42.3770
 YC2  H13   H  HCH1   0   0.215  20.1618  44.2208  44.5064
 YC2  HN12  H  HNH1   0   0.366  18.2279  46.3933  44.2563
 YC2  HN10  H  HNH1   0   0.367  16.6541  46.2185  42.7502
 YC2  H6    H  HCH1   0   0.222  16.2733  43.6972  41.3128
 YC2  H5    H  HCH2   0   0.213  14.5185  44.8124  40.1561
 YC2  H5A   H  HCH2   0   0.207  14.2847  44.9732  41.8784
 YC2  H4    H  HCH2   0   0.203  15.1909  47.3449  41.7481
 YC2  H4A   H  HCH2   0   0.224  15.4002  47.1460  40.0335

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    2.102  0.020  2.102
 YC2  C22  C23   aromatic  1.388  0.020  1.388
 YC2  C25  C23   aromatic  1.386  0.020  1.386
 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    1.341  0.020  1.341
 YC2  C17  N18   single    1.448  0.020  1.448
 YC2  N18  HN18  single    0.860  0.020  1.020
 YC2  C16  C17   single    1.525  0.020  1.525
 YC2  C17  H17   single    0.970  0.020  1.090
 YC2  C17  H17A  single    0.970  0.020  1.090
 YC2  C16  C15   single    1.528  0.020  1.528
 YC2  C16  H16   single    0.970  0.020  1.090
 YC2  C16  H16A  single    0.970  0.020  1.090
 YC2  C14  C15   single    1.522  0.020  1.522
 YC2  C15  H15   single    0.970  0.020  1.090
 YC2  C15  H15A  single    0.970  0.020  1.090
 YC2  C14  C13   single    1.541  0.020  1.541
 YC2  C14  H14   single    0.970  0.020  1.090
 YC2  C14  H14A  single    0.970  0.020  1.090
 YC2  N12  C13   single    1.446  0.020  1.446
 YC2  C13  C28   single    1.547  0.020  1.547
 YC2  C13  H13   single    0.970  0.020  1.090
 YC2  C28  O29   deloc     1.247  0.020  1.247
 YC2  C28  O30   deloc     1.248  0.020  1.248
 YC2  C11  N12   single    1.356  0.020  1.356
 YC2  N12  HN12  single    0.860  0.020  1.020
 YC2  O31  C11   double    1.229  0.020  1.229
 YC2  N10  C11   single    1.368  0.020  1.368
 YC2  C6   N10   single    1.449  0.020  1.449
 YC2  N10  HN10  single    0.890  0.020  1.040
 YC2  C7   C6    single    1.552  0.020  1.552
 YC2  C5   C6    single    1.533  0.020  1.533
 YC2  C6   H6    single    0.970  0.020  1.090
 YC2  O8   C7    deloc     1.248  0.020  1.248
 YC2  C7   O9    deloc     1.246  0.020  1.246
 YC2  C4   C5    single    1.523  0.020  1.523
 YC2  C5   H5    single    0.970  0.020  1.090
 YC2  C5   H5A   single    0.970  0.020  1.090
 YC2  C2   C4    single    1.544  0.020  1.544
 YC2  C4   H4    single    0.970  0.020  1.090
 YC2  C4   H4A   single    0.970  0.020  1.090
 YC2  O1   C2    deloc     1.247  0.020  1.247
 YC2  C2   O3    deloc     1.249  0.020  1.249

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  121.10  3.000
 YC2  C25   C23  I24  119.46  3.000
 YC2  C22   C23  I24  119.44  3.000
 YC2  H22   C22  C21  119.70  3.000
 YC2  H22   C22  C23  121.20  3.000
 YC2  C21   C22  C23  119.10  3.000
 YC2  H21   C21  C20  120.13  3.000
 YC2  H21   C21  C22  119.13  3.000
 YC2  C20   C21  C22  120.74  3.000
 YC2  H25   C25  C26  119.51  3.000
 YC2  H25   C25  C23  121.30  3.000
 YC2  C26   C25  C23  119.18  3.000
 YC2  H26   C26  C20  121.25  3.000
 YC2  H26   C26  C25  118.09  3.000
 YC2  C20   C26  C25  120.63  3.000
 YC2  C19   C20  C26  121.90  3.000
 YC2  C19   C20  C21  118.79  3.000
 YC2  C26   C20  C21  119.23  3.000
 YC2  N18   C19  O27  123.43  3.000
 YC2  N18   C19  C20  115.57  3.000
 YC2  O27   C19  C20  121.01  3.000
 YC2  HN18  N18  C17  117.59  3.000
 YC2  HN18  N18  C19  118.75  3.000
 YC2  C17   N18  C19  123.52  3.000
 YC2  H17A  C17  H17  106.61  3.000
 YC2  H17A  C17  C16  109.52  3.000
 YC2  H17   C17  C16  110.36  3.000
 YC2  H17A  C17  N18  110.75  3.000
 YC2  H17   C17  N18  108.34  3.000
 YC2  C16   C17  N18  111.16  3.000
 YC2  H16A  C16  H16  106.06  3.000
 YC2  H16A  C16  C15  108.87  3.000
 YC2  H16   C16  C15  110.24  3.000
 YC2  H16A  C16  C17  109.35  3.000
 YC2  H16   C16  C17  107.29  3.000
 YC2  C15   C16  C17  114.67  3.000
 YC2  H15A  C15  H15  105.37  3.000
 YC2  H15A  C15  C14  110.01  3.000
 YC2  H15   C15  C14  108.90  3.000
 YC2  H15A  C15  C16  109.69  3.000
 YC2  H15   C15  C16  108.23  3.000
 YC2  C14   C15  C16  114.25  3.000
 YC2  H14A  C14  H14  105.98  3.000
 YC2  H14A  C14  C13  108.70  3.000
 YC2  H14   C14  C13  107.63  3.000
 YC2  H14A  C14  C15  108.90  3.000
 YC2  H14   C14  C15  110.88  3.000
 YC2  C13   C14  C15  114.39  3.000
 YC2  H13   C13  N12  108.87  3.000
 YC2  H13   C13  C28  109.33  3.000
 YC2  N12   C13  C28  109.11  3.000
 YC2  H13   C13  C14  109.09  3.000
 YC2  C28   C13  C14  109.63  3.000
 YC2  N12   C13  C14  110.78  3.000
 YC2  O29   C28  O30  126.95  3.000
 YC2  O30   C28  C13  116.67  3.000
 YC2  O29   C28  C13  116.32  3.000
 YC2  HN12  N12  C11  120.41  3.000
 YC2  HN12  N12  C13  114.56  3.000
 YC2  C11   N12  C13  122.64  3.000
 YC2  N10   C11  O31  122.20  3.000
 YC2  N10   C11  N12  115.22  3.000
 YC2  O31   C11  N12  122.47  3.000
 YC2  HN10  N10  C6   114.60  3.000
 YC2  HN10  N10  C11  115.19  3.000
 YC2  C6    N10  C11  118.65  3.000
 YC2  H6    C6   C5   106.78  3.000
 YC2  H6    C6   C7   107.62  3.000
 YC2  C5    C6   C7   110.73  3.000
 YC2  H6    C6   N10  107.61  3.000
 YC2  C5    C6   N10  110.13  3.000
 YC2  C7    C6   N10  113.66  3.000
 YC2  O8    C7   O9   127.03  3.000
 YC2  O9    C7   C6   118.02  3.000
 YC2  O8    C7   C6   114.94  3.000
 YC2  H5A   C5   H5   106.10  3.000
 YC2  H5A   C5   C4   109.66  3.000
 YC2  H5    C5   C4   109.27  3.000
 YC2  H5A   C5   C6   108.49  3.000
 YC2  H5    C5   C6   107.66  3.000
 YC2  C4    C5   C6   115.25  3.000
 YC2  H4A   C4   H4   105.01  3.000
 YC2  H4A   C4   C2   107.01  3.000
 YC2  H4    C4   C2   107.82  3.000
 YC2  H4A   C4   C5   109.74  3.000
 YC2  H4    C4   C5   111.35  3.000
 YC2  C2    C4   C5   115.32  3.000
 YC2  O3    C2   O1   126.48  3.000
 YC2  O3    C2   C4   115.91  3.000
 YC2  O1    C2   C4   117.58  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_20  N10   C11  N12  C13   180.00   0.0  0
 YC2  CONST_22  HN12  N12  C11  O31   180.00   0.0  0
 YC2  Var_01    O27   C19  C20  C21   -33.56  30.0  2
 YC2  Var_02    C16   C17  N18  C19  -155.25  30.0  2
 YC2  Var_03    C15   C16  C17  N18    50.68  30.0  1
 YC2  Var_04    C14   C15  C16  C17    56.70  30.0  3
 YC2  Var_05    C13   C14  C15  C16  -173.87  30.0  2
 YC2  Var_06    C2    C4   C5   C6    179.20  30.0  1
 YC2  Var_07    O1    C2   C4   C5    -18.87  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-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-6  C6    0.020
 YC2  plan-6  C7    0.020
 YC2  plan-6  O9    0.020
 YC2  plan-6  O8    0.020

