# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 17:13:07 2021
#   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  59  34  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.477  26.2636  48.5143  44.9065
 KRZ  C1   C  C     0   0.533  25.3311  49.0708  45.4706
 KRZ  N1   N  NH1   0  -0.631  24.3235  49.6624  44.8113
 KRZ  C2   C  CH2   0  -0.289  24.1899  49.6158  43.3719
 KRZ  C3   C  CH2   0  -0.562  23.5596  48.3183  42.8857
 KRZ  C4   C  C     0   0.588  22.1776  48.1236  43.4648
 KRZ  O2   O  O     0  -0.487  21.4044  49.0552  43.6432
 KRZ  N2   N  NH1   0  -0.637  21.8334  46.8594  43.7566
 KRZ  C5   C  CH1   0  -0.128  20.5330  46.5491  44.2911
 KRZ  C6   C  CH2   0  -0.484  20.4215  45.0350  44.4882
 KRZ  C7   C  CH2   0  -0.298  19.0713  44.5529  45.0108
 KRZ  N3   N  NH1   0  -0.672  17.9354  44.9985  44.2416
 KRZ  C8   C  C     0   0.789  17.5960  44.4348  43.0593
 KRZ  O3   O  O     0  -0.522  18.1958  43.4819  42.5721
 KRZ  N4   N  NH1   0  -0.685  16.5300  45.0020  42.4242
 KRZ  C9   C  CH1   0  -0.152  15.9987  44.3636  41.2515
 KRZ  C10  C  CH2   0  -0.481  14.7263  45.0749  40.7759
 KRZ  C11  C  CH2   0  -0.555  14.9248  46.5218  40.3479
 KRZ  C12  C  C     0   0.579  13.6300  47.1971  39.9872
 KRZ  O4   O  O     0  -0.451  12.5440  46.6738  40.0021
 KRZ  O5   O  OH1   0  -0.587  13.8206  48.4648  39.6370
 KRZ  C13  C  C     0   0.547  17.0112  44.2989  40.1213
 KRZ  O6   O  O     0  -0.469  16.9761  43.4443  39.2702
 KRZ  O7   O  OH1   0  -0.559  17.8770  45.2984  40.1224
 KRZ  C14  C  C     0   0.535  20.3312  47.2721  45.6149
 KRZ  O8   O  OH1   0  -0.583  19.0786  47.6798  45.7680
 KRZ  O9   O  O     0  -0.401  21.1893  47.4086  46.4470
 KRZ  C15  C  CR6   0  -0.022  25.2687  49.1435  46.9632
 KRZ  C16  C  CR16  0  -0.239  26.4649  49.1666  47.6742
 KRZ  C17  C  CR16  0  -0.194  26.4654  49.2237  49.0587
 KRZ  C18  C  CR6   0  -0.211  25.2529  49.2324  49.7352
 KRZ  I1   I  I     0   0.076  25.2417  49.3072  51.8351
 KRZ  C19  C  CR16  0  -0.187  24.0496  49.1851  49.0475
 KRZ  C20  C  CR16  0  -0.273  24.0645  49.1440  47.6604
 KRZ  H1   H  HNH1  0   0.386  23.6166  50.1582  45.3278
 KRZ  H2   H  HCH2  0   0.261  25.1678  49.7426  42.9086
 KRZ  H3   H  HCH2  0   0.255  23.5807  50.4655  43.0710
 KRZ  H4   H  HCH2  0   0.277  23.4664  48.3564  41.7962
 KRZ  H5   H  HCH2  0   0.244  24.2079  47.4700  43.1116
 KRZ  H6   H  HNH1  0   0.382  22.5152  46.1227  43.6712
 KRZ  H7   H  HCH1  0   0.267  19.7595  46.8739  43.5899
 KRZ  H8   H  HCH2  0   0.266  20.6254  44.5620  43.5257
 KRZ  H9   H  HCH2  0   0.252  21.1982  44.6981  45.1801
 KRZ  H10  H  HCH2  0   0.268  19.0890  43.4633  45.0392
 KRZ  H11  H  HCH2  0   0.247  18.9139  44.8769  46.0393
 KRZ  H12  H  HNH1  0   0.367  17.4504  45.8237  44.5534
 KRZ  H13  H  HNH1  0   0.369  15.9189  45.6146  42.9413
 KRZ  H14  H  HCH1  0   0.297  15.7178  43.3256  41.4586
 KRZ  H15  H  HCH2  0   0.269  14.0016  45.0195  41.5911
 KRZ  H16  H  HCH2  0   0.265  14.3072  44.4925  39.9546
 KRZ  H17  H  HCH2  0   0.276  15.5864  46.5970  39.4808
 KRZ  H18  H  HCH2  0   0.272  15.4066  47.1133  41.1315
 KRZ  H19  H  HOH1  0   0.453  12.9744  48.8742  39.4028
 KRZ  H20  H  HOH1  0   0.449  18.4658  45.2208  39.3566
 KRZ  H21  H  HOH1  0   0.453  18.9604  48.0784  46.6439
 KRZ  H22  H  HCR6  0   0.247  27.4092  49.1502  47.1464
 KRZ  H23  H  HCR6  0   0.254  27.4053  49.2575  49.5921
 KRZ  H24  H  HCR6  0   0.252  23.1036  49.1733  49.5710
 KRZ  H25  H  HCR6  0   0.260  23.1181  49.0765  47.1395

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  double    1.207  0.020  1.207
 KRZ  O4   C12  double    1.206  0.020  1.206
 KRZ  C13  O7   single    1.322  0.020  1.322
 KRZ  C13  C9   single    1.519  0.020  1.519
 KRZ  C12  O5   single    1.329  0.020  1.329
 KRZ  C12  C11  single    1.504  0.020  1.504
 KRZ  C11  C10  single    1.522  0.020  1.522
 KRZ  C10  C9   single    1.533  0.020  1.533
 KRZ  C9   N4   single    1.437  0.020  1.437
 KRZ  C3   C2   single    1.522  0.020  1.522
 KRZ  C3   C4   single    1.511  0.020  1.511
 KRZ  O3   C8   double    1.227  0.020  1.227
 KRZ  N4   C8   single    1.364  0.020  1.364
 KRZ  C8   N3   single    1.353  0.020  1.353
 KRZ  C2   N1   single    1.446  0.020  1.446
 KRZ  N2   C4   single    1.342  0.020  1.342
 KRZ  N2   C5   single    1.440  0.020  1.440
 KRZ  C4   O2   double    1.224  0.020  1.224
 KRZ  C6   C5   single    1.531  0.020  1.531
 KRZ  C6   C7   single    1.526  0.020  1.526
 KRZ  N3   C7   single    1.442  0.020  1.442
 KRZ  C5   C14  single    1.522  0.020  1.522
 KRZ  N1   C1   single    1.342  0.020  1.342
 KRZ  O1   C1   double    1.224  0.020  1.224
 KRZ  C1   C15  single    1.496  0.020  1.496
 KRZ  C14  O9   double    1.203  0.020  1.203
 KRZ  C14  O8   single    1.326  0.020  1.326
 KRZ  C15  C20  aromatic  1.392  0.020  1.392
 KRZ  C15  C16  aromatic  1.392  0.020  1.392
 KRZ  C20  C19  aromatic  1.388  0.020  1.388
 KRZ  C16  C17  aromatic  1.386  0.020  1.386
 KRZ  C19  C18  aromatic  1.387  0.020  1.387
 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    0.860  0.020  1.020
 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    0.860  0.020  1.020
 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  O5   H19  single    0.850  0.020  0.980
 KRZ  O7   H20  single    0.850  0.020  0.980
 KRZ  O8   H21  single    0.850  0.020  0.980
 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   115.95  3.000
 KRZ  C15  C1   O1   120.93  3.000
 KRZ  N1   C1   O1   123.11  3.000
 KRZ  H1   N1   C2   117.51  3.000
 KRZ  H1   N1   C1   119.52  3.000
 KRZ  C2   N1   C1   122.97  3.000
 KRZ  H3   C2   H2   107.10  3.000
 KRZ  H3   C2   C3   110.21  3.000
 KRZ  H2   C2   C3   109.57  3.000
 KRZ  H3   C2   N1   107.57  3.000
 KRZ  H2   C2   N1   109.67  3.000
 KRZ  C3   C2   N1   112.56  3.000
 KRZ  H5   C3   H4   106.49  3.000
 KRZ  H5   C3   C4   111.34  3.000
 KRZ  H4   C3   C4   107.96  3.000
 KRZ  H5   C3   C2   110.51  3.000
 KRZ  H4   C3   C2   108.88  3.000
 KRZ  C4   C3   C2   111.48  3.000
 KRZ  N2   C4   O2   121.55  3.000
 KRZ  O2   C4   C3   122.39  3.000
 KRZ  N2   C4   C3   116.05  3.000
 KRZ  H6   N2   C5   119.02  3.000
 KRZ  H6   N2   C4   119.78  3.000
 KRZ  C5   N2   C4   121.02  3.000
 KRZ  H7   C5   C14  108.84  3.000
 KRZ  H7   C5   C6   108.96  3.000
 KRZ  C14  C5   C6   110.38  3.000
 KRZ  H7   C5   N2   109.69  3.000
 KRZ  C14  C5   N2   109.89  3.000
 KRZ  C6   C5   N2   109.07  3.000
 KRZ  H9   C6   H8   106.97  3.000
 KRZ  H9   C6   C7   108.33  3.000
 KRZ  H8   C6   C7   109.29  3.000
 KRZ  H9   C6   C5   109.54  3.000
 KRZ  H8   C6   C5   107.54  3.000
 KRZ  C7   C6   C5   114.90  3.000
 KRZ  H11  C7   H10  105.96  3.000
 KRZ  H11  C7   N3   107.32  3.000
 KRZ  H10  C7   N3   109.61  3.000
 KRZ  H11  C7   C6   110.92  3.000
 KRZ  H10  C7   C6   108.08  3.000
 KRZ  N3   C7   C6   114.61  3.000
 KRZ  H12  N3   C8   119.43  3.000
 KRZ  H12  N3   C7   117.87  3.000
 KRZ  C8   N3   C7   122.33  3.000
 KRZ  N4   C8   O3   121.34  3.000
 KRZ  N4   C8   N3   115.44  3.000
 KRZ  O3   C8   N3   123.22  3.000
 KRZ  H13  N4   C9   117.67  3.000
 KRZ  H13  N4   C8   119.18  3.000
 KRZ  C9   N4   C8   118.95  3.000
 KRZ  H14  C9   C13  105.74  3.000
 KRZ  H14  C9   C10  106.59  3.000
 KRZ  C13  C9   C10  110.01  3.000
 KRZ  H14  C9   N4   111.20  3.000
 KRZ  C10  C9   N4   110.72  3.000
 KRZ  C13  C9   N4   112.32  3.000
 KRZ  H16  C10  H15  106.26  3.000
 KRZ  H16  C10  C11  110.24  3.000
 KRZ  H15  C10  C11  110.16  3.000
 KRZ  H16  C10  C9   107.74  3.000
 KRZ  H15  C10  C9   107.19  3.000
 KRZ  C11  C10  C9   114.84  3.000
 KRZ  H18  C11  H17  105.34  3.000
 KRZ  H18  C11  C12  107.95  3.000
 KRZ  H17  C11  C12  107.45  3.000
 KRZ  H18  C11  C10  111.72  3.000
 KRZ  H17  C11  C10  111.55  3.000
 KRZ  C12  C11  C10  112.45  3.000
 KRZ  O5   C12  O4   123.13  3.000
 KRZ  O5   C12  C11  111.59  3.000
 KRZ  O4   C12  C11  125.28  3.000
 KRZ  H19  O5   C12  109.97  3.000
 KRZ  O7   C13  O6   123.70  3.000
 KRZ  O7   C13  C9   113.81  3.000
 KRZ  O6   C13  C9   122.39  3.000
 KRZ  H20  O7   C13  109.68  3.000
 KRZ  O9   C14  O8   123.98  3.000
 KRZ  O8   C14  C5   111.82  3.000
 KRZ  O9   C14  C5   124.13  3.000
 KRZ  H21  O8   C14  110.23  3.000
 KRZ  C20  C15  C16  119.19  3.000
 KRZ  C16  C15  C1   118.35  3.000
 KRZ  C20  C15  C1   122.42  3.000
 KRZ  H22  C16  C17  119.19  3.000
 KRZ  H22  C16  C15  120.04  3.000
 KRZ  C17  C16  C15  120.76  3.000
 KRZ  H23  C17  C18  121.24  3.000
 KRZ  H23  C17  C16  119.64  3.000
 KRZ  C18  C17  C16  119.12  3.000
 KRZ  C19  C18  I1   119.48  3.000
 KRZ  I1   C18  C17  119.46  3.000
 KRZ  C19  C18  C17  121.06  3.000
 KRZ  H24  C19  C20  119.54  3.000
 KRZ  H24  C19  C18  121.29  3.000
 KRZ  C20  C19  C18  119.17  3.000
 KRZ  H25  C20  C19  118.26  3.000
 KRZ  H25  C20  C15  121.03  3.000
 KRZ  C19  C20  C15  120.67  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_18  C5   N2   C4   C3    180.00   0.0  0
 KRZ  CONST_19  C5   N2   C4   O2      0.00   0.0  0
 KRZ  CONST_20  O3   C8   N3   C7      0.00   0.0  0
 KRZ  CONST_21  C9   N4   C8   O3      0.00   0.0  0
 KRZ  CONST_22  N4   C8   N3   C7    180.00   0.0  0
 KRZ  CONST_23  C9   N4   C8   N3    180.00   0.0  0
 KRZ  CONST_24  H6   N2   C4   C3      0.00   0.0  0
 KRZ  CONST_26  H12  N3   C8   O3    180.00   0.0  0
 KRZ  CONST_27  H21  O8   C14  C5    180.00   0.0  0
 KRZ  CONST_28  H20  O7   C13  C9    180.00   0.0  0
 KRZ  CONST_29  H19  O5   C12  C11   180.00   0.0  0
 KRZ  Var_01    C20  C15  C1   O1   -148.14  30.0  2
 KRZ  Var_02    C3   C2   N1   C1     81.34  30.0  1
 KRZ  Var_03    C4   C3   C2   N1     59.73  30.0  2
 KRZ  Var_04    N2   C4   C3   C2   -144.27  30.0  3
 KRZ  Var_05    N3   C7   C6   C5     53.35  30.0  3
 KRZ  Var_06    C8   N3   C7   C6     77.33  30.0  1
 KRZ  Var_07    C12  C11  C10  C9   -175.84  30.0  1
 KRZ  Var_08    O4   C12  C11  C10    -1.23  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-2  H19  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-3  H20  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-4  H21  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

