# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 13:30:39 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: (2~{S})-2-[[(3~{S})-3-[3-[(4-iodophenyl)carbonylamino]propanoylamino]-4-oxidanyl-4-oxidanylidene-butyl]carbamoylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](NC(=O)NCC[C@H](NC(=O)CCNC(=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
 KRZ  KRZ  '(2~{S})-2-[[(3~{S})-3-[3-[(4-iodophenyl)carbonylamino]propanoylamino]-4-oxidanyl-4-oxidanylidene-butyl]carbamoylamino]pentanedioic acid'  ligand  56  34  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KRZ
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
 KRZ  O1   O  O      0  -0.488  25.9304  49.5102  44.9935
 KRZ  C1   C  C      0   0.511  24.7943  49.2938  45.3998
 KRZ  N1   N  NH1    0  -0.680  23.6864  49.6336  44.7250
 KRZ  C2   C  CH2    0  -0.321  23.7272  50.1723  43.3855
 KRZ  C3   C  CH2    0  -0.558  23.4182  49.1167  42.3132
 KRZ  C4   C  C      0   0.515  21.9946  48.6347  42.4796
 KRZ  O2   O  O      0  -0.494  21.0507  49.2249  41.9718
 KRZ  N2   N  NH1    0  -0.622  21.8369  47.5639  43.2801
 KRZ  C5   C  CH1    0  -0.180  20.5584  47.2658  43.8884
 KRZ  C6   C  CH2    0  -0.477  20.6929  45.9471  44.6643
 KRZ  C7   C  CH2    0  -0.314  19.4761  45.5591  45.5045
 KRZ  N3   N  NH1    0  -0.677  18.2200  45.6340  44.7976
 KRZ  C8   C  C      0   0.706  17.8626  44.6722  43.8972
 KRZ  O3   O  O      0  -0.549  18.3755  43.5568  43.8841
 KRZ  N4   N  NH1    0  -0.666  16.8334  45.0164  43.0721
 KRZ  C9   C  CH1    0  -0.190  16.6256  44.2686  41.8500
 KRZ  C10  C  CH2    0  -0.430  15.3193  44.7096  41.1793
 KRZ  C11  C  CH2    0  -0.594  15.2983  46.1497  40.6832
 KRZ  C12  C  C      0   0.412  13.9933  46.5978  39.9889
 KRZ  O4   O  O      0  -0.605  13.2110  45.7121  39.5899
 KRZ  O5   O  OC    -1  -0.622  13.8451  47.8309  39.8606
 KRZ  C13  C  C      0   0.404  17.8143  44.3643  40.8572
 KRZ  O6   O  O      0  -0.611  17.8050  43.5134  39.9451
 KRZ  O7   O  OC    -1  -0.602  18.6489  45.2746  41.0271
 KRZ  C14  C  C      0   0.453  20.0576  48.4323  44.7816
 KRZ  O8   O  OC    -1  -0.574  18.8260  48.5018  44.9504
 KRZ  O9   O  O      0  -0.576  20.9098  49.1998  45.2817
 KRZ  C15  C  CR6    0  -0.023  24.5898  48.6273  46.7282
 KRZ  C16  C  CR16   0  -0.262  25.6188  48.6967  47.6641
 KRZ  C17  C  CR16   0  -0.213  25.5056  48.0757  48.8979
 KRZ  C18  C  CR6    0  -0.224  24.3543  47.3570  49.1898
 KRZ  I1   I  I      0   0.061  24.1772  46.3909  51.0474
 KRZ  C19  C  CR16   0  -0.214  23.3223  47.2614  48.2691
 KRZ  C20  C  CR16   0  -0.285  23.4447  47.9027  47.0449
 KRZ  H1   H  HNH1   0   0.440  22.7507  49.4358  45.0895
 KRZ  H2   H  HCH2   0   0.263  24.7095  50.6009  43.1994
 KRZ  H3   H  HCH2   0   0.254  23.0025  50.9856  43.3154
 KRZ  H4   H  HCH2   0   0.263  23.5278  49.5726  41.3287
 KRZ  H5   H  HCH2   0   0.257  24.1391  48.3000  42.3895
 KRZ  H6   H  HNH1   0   0.391  22.6613  47.2030  43.7358
 KRZ  H7   H  HCH1   0   0.239  19.8231  47.1116  43.0952
 KRZ  H8   H  HCH2   0   0.243  20.9032  45.1537  43.9423
 KRZ  H9   H  HCH2   0   0.232  21.5585  45.9962  45.3334
 KRZ  H10  H  HCH2   0   0.245  19.6191  44.5491  45.8868
 KRZ  H11  H  HCH2   0   0.238  19.4044  46.2076  46.3779
 KRZ  H12  H  HNH1   0   0.381  17.9420  46.5908  44.6153
 KRZ  H13  H  HNH1   0   0.372  16.6343  46.0029  43.0086
 KRZ  H14  H  HCH1   0   0.224  16.5034  43.2167  42.1204
 KRZ  H15  H  HCH2   0   0.209  14.4976  44.5520  41.8847
 KRZ  H16  H  HCH2   0   0.215  15.1343  44.0341  40.3439
 KRZ  H17  H  HCH2   0   0.225  16.1151  46.3097  39.9695
 KRZ  H18  H  HCH2   0   0.204  15.4946  46.8526  41.4995
 KRZ  H22  H  HCR6   0   0.266  26.5220  49.2454  47.4340
 KRZ  H23  H  HCR6   0   0.281  26.3141  48.1541  49.6119
 KRZ  H24  H  HCR6   0   0.282  22.4269  46.6948  48.4854
 KRZ  H25  H  HCR6   0   0.265  22.6273  47.8143  46.3430

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
 KRZ  O6   C13  deloc     1.247  0.020  1.247
 KRZ  O4   C12  deloc     1.247  0.020  1.247
 KRZ  C13  O7   deloc     1.247  0.020  1.247
 KRZ  C13  C9   single    1.552  0.020  1.552
 KRZ  C12  O5   deloc     1.249  0.020  1.249
 KRZ  C12  C11  single    1.545  0.020  1.545
 KRZ  C11  C10  single    1.523  0.020  1.523
 KRZ  C10  C9   single    1.533  0.020  1.533
 KRZ  C9   N4   single    1.448  0.020  1.448
 KRZ  C3   C2   single    1.536  0.020  1.536
 KRZ  C3   C4   single    1.512  0.020  1.512
 KRZ  O3   C8   double    1.228  0.020  1.228
 KRZ  N4   C8   single    1.363  0.020  1.363
 KRZ  C8   N3   single    1.365  0.020  1.365
 KRZ  C2   N1   single    1.444  0.020  1.444
 KRZ  N2   C4   single    1.346  0.020  1.346
 KRZ  N2   C5   single    1.447  0.020  1.447
 KRZ  C4   O2   double    1.224  0.020  1.224
 KRZ  C6   C5   single    1.536  0.020  1.536
 KRZ  C6   C7   single    1.529  0.020  1.529
 KRZ  N3   C7   single    1.443  0.020  1.443
 KRZ  C5   C14  single    1.552  0.020  1.552
 KRZ  N1   C1   single    1.341  0.020  1.341
 KRZ  O1   C1   double    1.226  0.020  1.226
 KRZ  C1   C15  single    1.500  0.020  1.500
 KRZ  C14  O9   deloc     1.251  0.020  1.251
 KRZ  C14  O8   deloc     1.245  0.020  1.245
 KRZ  C15  C20  aromatic  1.392  0.020  1.392
 KRZ  C15  C16  aromatic  1.393  0.020  1.393
 KRZ  C20  C19  aromatic  1.387  0.020  1.387
 KRZ  C16  C17  aromatic  1.386  0.020  1.386
 KRZ  C19  C18  aromatic  1.386  0.020  1.386
 KRZ  C17  C18  aromatic  1.388  0.020  1.388
 KRZ  C18  I1   single    2.101  0.020  2.101
 KRZ  N1   H1   single    0.860  0.020  1.020
 KRZ  C2   H2   single    0.970  0.020  1.090
 KRZ  C2   H3   single    0.970  0.020  1.090
 KRZ  C3   H4   single    0.970  0.020  1.090
 KRZ  C3   H5   single    0.970  0.020  1.090
 KRZ  N2   H6   single    0.890  0.020  1.040
 KRZ  C5   H7   single    0.970  0.020  1.090
 KRZ  C6   H8   single    0.970  0.020  1.090
 KRZ  C6   H9   single    0.970  0.020  1.090
 KRZ  C7   H10  single    0.970  0.020  1.090
 KRZ  C7   H11  single    0.970  0.020  1.090
 KRZ  N3   H12  single    0.890  0.020  1.040
 KRZ  N4   H13  single    0.890  0.020  1.040
 KRZ  C9   H14  single    0.970  0.020  1.090
 KRZ  C10  H15  single    0.970  0.020  1.090
 KRZ  C10  H16  single    0.970  0.020  1.090
 KRZ  C11  H17  single    0.970  0.020  1.090
 KRZ  C11  H18  single    0.970  0.020  1.090
 KRZ  C16  H22  single    0.930  0.020  1.080
 KRZ  C17  H23  single    0.930  0.020  1.080
 KRZ  C19  H24  single    0.930  0.020  1.080
 KRZ  C20  H25  single    0.930  0.020  1.080

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
 KRZ  C15  C1   N1   116.46  3.000
 KRZ  C15  C1   O1   119.88  3.000
 KRZ  N1   C1   O1   123.66  3.000
 KRZ  H1   N1   C2   115.35  3.000
 KRZ  H1   N1   C1   121.81  3.000
 KRZ  C2   N1   C1   122.54  3.000
 KRZ  H3   C2   H2   107.16  3.000
 KRZ  H3   C2   C3   109.48  3.000
 KRZ  H2   C2   C3   109.45  3.000
 KRZ  H3   C2   N1   108.59  3.000
 KRZ  H2   C2   N1   109.34  3.000
 KRZ  C3   C2   N1   112.67  3.000
 KRZ  H5   C3   H4   108.02  3.000
 KRZ  H5   C3   C4   112.05  3.000
 KRZ  H4   C3   C4   109.10  3.000
 KRZ  H5   C3   C2   109.41  3.000
 KRZ  H4   C3   C2   108.83  3.000
 KRZ  C4   C3   C2   109.37  3.000
 KRZ  N2   C4   O2   122.69  3.000
 KRZ  O2   C4   C3   121.79  3.000
 KRZ  N2   C4   C3   115.42  3.000
 KRZ  H6   N2   C5   117.29  3.000
 KRZ  H6   N2   C4   117.23  3.000
 KRZ  C5   N2   C4   121.16  3.000
 KRZ  H7   C5   C14  107.86  3.000
 KRZ  H7   C5   C6   107.73  3.000
 KRZ  C14  C5   C6   112.51  3.000
 KRZ  H7   C5   N2   108.58  3.000
 KRZ  C14  C5   N2   111.85  3.000
 KRZ  C6   C5   N2   108.17  3.000
 KRZ  H9   C6   H8   106.50  3.000
 KRZ  H9   C6   C7   107.74  3.000
 KRZ  H8   C6   C7   109.38  3.000
 KRZ  H9   C6   C5   109.84  3.000
 KRZ  H8   C6   C5   107.84  3.000
 KRZ  C7   C6   C5   115.21  3.000
 KRZ  H11  C7   H10  106.21  3.000
 KRZ  H11  C7   N3   107.71  3.000
 KRZ  H10  C7   N3   109.52  3.000
 KRZ  H11  C7   C6   109.98  3.000
 KRZ  H10  C7   C6   108.89  3.000
 KRZ  N3   C7   C6   114.23  3.000
 KRZ  H12  N3   C8   118.36  3.000
 KRZ  H12  N3   C7   112.09  3.000
 KRZ  C8   N3   C7   120.95  3.000
 KRZ  N4   C8   O3   122.56  3.000
 KRZ  N4   C8   N3   114.77  3.000
 KRZ  O3   C8   N3   122.53  3.000
 KRZ  H13  N4   C9   115.08  3.000
 KRZ  H13  N4   C8   115.73  3.000
 KRZ  C9   N4   C8   119.26  3.000
 KRZ  H14  C9   C13  107.66  3.000
 KRZ  H14  C9   C10  106.84  3.000
 KRZ  C13  C9   C10  110.79  3.000
 KRZ  H14  C9   N4   107.72  3.000
 KRZ  C10  C9   N4   110.06  3.000
 KRZ  C13  C9   N4   113.47  3.000
 KRZ  H16  C10  H15  106.10  3.000
 KRZ  H16  C10  C11  109.51  3.000
 KRZ  H15  C10  C11  109.62  3.000
 KRZ  H16  C10  C9   107.55  3.000
 KRZ  H15  C10  C9   108.44  3.000
 KRZ  C11  C10  C9   115.22  3.000
 KRZ  H18  C11  H17  104.95  3.000
 KRZ  H18  C11  C12  107.48  3.000
 KRZ  H17  C11  C12  107.12  3.000
 KRZ  H18  C11  C10  111.20  3.000
 KRZ  H17  C11  C10  109.86  3.000
 KRZ  C12  C11  C10  115.61  3.000
 KRZ  O5   C12  O4   126.43  3.000
 KRZ  O5   C12  C11  115.66  3.000
 KRZ  O4   C12  C11  117.89  3.000
 KRZ  O7   C13  O6   127.07  3.000
 KRZ  O7   C13  C9   118.08  3.000
 KRZ  O6   C13  C9   114.84  3.000
 KRZ  O9   C14  O8   125.82  3.000
 KRZ  O8   C14  C5   116.05  3.000
 KRZ  O9   C14  C5   118.12  3.000
 KRZ  C20  C15  C16  118.75  3.000
 KRZ  C16  C15  C1   118.18  3.000
 KRZ  C20  C15  C1   123.03  3.000
 KRZ  H22  C16  C17  119.01  3.000
 KRZ  H22  C16  C15  119.95  3.000
 KRZ  C17  C16  C15  121.04  3.000
 KRZ  H23  C17  C18  121.24  3.000
 KRZ  H23  C17  C16  119.62  3.000
 KRZ  C18  C17  C16  119.14  3.000
 KRZ  C19  C18  I1   119.51  3.000
 KRZ  I1   C18  C17  119.59  3.000
 KRZ  C19  C18  C17  120.89  3.000
 KRZ  H24  C19  C20  119.45  3.000
 KRZ  H24  C19  C18  121.31  3.000
 KRZ  C20  C19  C18  119.24  3.000
 KRZ  H25  C20  C19  117.94  3.000
 KRZ  H25  C20  C15  121.12  3.000
 KRZ  C19  C20  C15  120.94  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
 KRZ  CONST_01  C18  C19  C20  C15     0.00   0.0  0
 KRZ  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 KRZ  CONST_03  C19  C20  C15  C16     0.00   0.0  0
 KRZ  CONST_04  C19  C18  C17  C16     0.00   0.0  0
 KRZ  CONST_05  C20  C15  C16  C17     0.00   0.0  0
 KRZ  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 KRZ  CONST_07  C19  C20  C15  C1    180.00   0.0  0
 KRZ  CONST_08  C17  C16  C15  C1    180.00   0.0  0
 KRZ  CONST_09  I1   C18  C17  C16   180.00   0.0  0
 KRZ  CONST_10  C20  C19  C18  I1    180.00   0.0  0
 KRZ  CONST_11  H24  C19  C20  C15   180.00   0.0  0
 KRZ  CONST_12  H23  C17  C16  C15   180.00   0.0  0
 KRZ  CONST_13  H25  C20  C15  C16   180.00   0.0  0
 KRZ  CONST_14  H22  C16  C17  C18   180.00   0.0  0
 KRZ  CONST_15  C15  C1   N1   C2    180.00   0.0  0
 KRZ  CONST_16  H1   N1   C1   C15     0.00   0.0  0
 KRZ  CONST_17  C2   N1   C1   O1      0.00   0.0  0
 KRZ  CONST_24  H6   N2   C4   C3      0.00   0.0  0
 KRZ  CONST_25  H13  N4   C8   O3    180.00   0.0  0
 KRZ  Var_01    C20  C15  C1   O1   -154.92  30.0  2
 KRZ  Var_02    C3   C2   N1   C1    100.07  30.0  1
 KRZ  Var_03    C4   C3   C2   N1     64.46  30.0  2
 KRZ  Var_04    N2   C4   C3   C2    -90.85  30.0  3
 KRZ  Var_05    N3   C7   C6   C5     48.85  30.0  3
 KRZ  Var_06    C8   N3   C7   C6     76.21  30.0  2
 KRZ  Var_07    C12  C11  C10  C9    179.21  30.0  2
 KRZ  Var_08    O4   C12  C11  C10   -17.37  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
 KRZ  chir_01  C5  N2   C6   C14  negativ
 KRZ  chir_02  C9  C13  C10  N4   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
 KRZ  plan-1  C1   0.020
 KRZ  plan-1  C15  0.020
 KRZ  plan-1  C16  0.020
 KRZ  plan-1  C17  0.020
 KRZ  plan-1  C18  0.020
 KRZ  plan-1  I1   0.020
 KRZ  plan-1  C19  0.020
 KRZ  plan-1  C20  0.020
 KRZ  plan-1  H22  0.020
 KRZ  plan-1  H23  0.020
 KRZ  plan-1  H24  0.020
 KRZ  plan-1  H25  0.020
 KRZ  plan-2  C11  0.020
 KRZ  plan-2  C12  0.020
 KRZ  plan-2  O4   0.020
 KRZ  plan-2  O5   0.020
 KRZ  plan-3  C9   0.020
 KRZ  plan-3  C13  0.020
 KRZ  plan-3  O6   0.020
 KRZ  plan-3  O7   0.020
 KRZ  plan-4  C5   0.020
 KRZ  plan-4  C14  0.020
 KRZ  plan-4  O8   0.020
 KRZ  plan-4  O9   0.020
 KRZ  plan-5  O1   0.020
 KRZ  plan-5  C1   0.020
 KRZ  plan-5  N1   0.020
 KRZ  plan-5  C2   0.020
 KRZ  plan-5  C15  0.020
 KRZ  plan-5  H1   0.020
 KRZ  plan-6  C3   0.020
 KRZ  plan-6  C4   0.020
 KRZ  plan-6  O2   0.020
 KRZ  plan-6  N2   0.020
 KRZ  plan-6  C5   0.020
 KRZ  plan-6  H6   0.020
 KRZ  plan-7  C7   0.020
 KRZ  plan-7  N3   0.020
 KRZ  plan-7  C8   0.020
 KRZ  plan-7  O3   0.020
 KRZ  plan-7  N4   0.020
 KRZ  plan-7  C9   0.020
 KRZ  plan-7  H12  0.020
 KRZ  plan-7  H13  0.020

