# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:22:43 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: (2~{S})-2-[[(2~{R})-2-[4-[(4-iodophenyl)carbonylamino]butanoylamino]-3-oxidanyl-3-oxidanylidene-propyl]carbamoylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](NC(=O)NC[C@@H](NC(=O)CCCNC(=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
 JX5  JX5  '(2~{S})-2-[[(2~{R})-2-[4-[(4-iodophenyl)carbonylamino]butanoylamino]-3-oxidanyl-3-oxidanylidene-propyl]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_JX5
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
 JX5  O1   O  O     0  -0.484  25.0574  49.0339  43.5220
 JX5  C1   C  C     0   0.499  24.0174  48.7209  44.0839
 JX5  N1   N  NH1   0  -0.640  22.9301  48.2611  43.4462
 JX5  C2   C  CH2   0  -0.315  22.8987  48.0332  42.0159
 JX5  C3   C  CH2   0  -0.437  23.3194  46.6246  41.6048
 JX5  C4   C  CH2   0  -0.567  22.2853  45.5447  41.9253
 JX5  C5   C  C     0   0.551  22.0742  45.3593  43.4101
 JX5  O2   O  O     0  -0.490  22.9394  44.8927  44.1358
 JX5  N2   N  NH1   0  -0.620  20.8751  45.7745  43.8693
 JX5  C6   C  CH1   0  -0.244  20.4271  45.6103  45.2216
 JX5  C7   C  CH2   0  -0.293  19.3162  44.5518  45.3179
 JX5  N3   N  NH1   0  -0.693  18.1658  44.8863  44.5227
 JX5  C8   C  C     0   0.759  17.9869  44.4264  43.2557
 JX5  O3   O  O     0  -0.532  18.7711  43.6695  42.6946
 JX5  N4   N  NH1   0  -0.690  16.8684  44.8741  42.6301
 JX5  C9   C  CH1   0  -0.161  16.6257  44.5139  41.2626
 JX5  C10  C  CH2   0  -0.487  15.2947  45.0972  40.7744
 JX5  C11  C  CH2   0  -0.596  15.2534  46.6168  40.6954
 JX5  C12  C  C     0   0.561  13.8918  47.1348  40.3176
 JX5  O4   O  OH1   0  -0.595  13.8802  48.4605  40.2347
 JX5  O5   O  O     0  -0.441  12.9212  46.4514  40.1082
 JX5  C13  C  C     0   0.538  17.7510  44.9321  40.3286
 JX5  O6   O  OH1   0  -0.588  18.4129  46.0071  40.7384
 JX5  O7   O  O     0  -0.438  17.9715  44.3727  39.2847
 JX5  C14  C  C     0   0.566  20.0114  46.9610  45.7842
 JX5  O8   O  O     0  -0.426  20.1905  48.0135  45.2250
 JX5  O9   O  OH1   0  -0.580  19.4479  46.8443  46.9725
 JX5  C15  C  CR6   0  -0.040  23.8734  48.8501  45.5674
 JX5  C16  C  CR16  0  -0.280  23.3761  47.8074  46.3410
 JX5  C17  C  CR16  0  -0.214  23.2761  47.9327  47.7195
 JX5  C18  C  CR6   0  -0.224  23.6704  49.1196  48.3186
 JX5  I1   I  I     0   0.066  23.5011  49.3328  50.4028
 JX5  C19  C  CR16  0  -0.214  24.1845  50.1662  47.5649
 JX5  C20  C  CR16  0  -0.264  24.2976  50.0187  46.1910
 JX5  H1   H  HNH1  0   0.409  22.0745  48.1415  43.9688
 JX5  H2   H  HCH2  0   0.261  23.5488  48.7619  41.5327
 JX5  H3   H  HCH2  0   0.249  21.8849  48.2390  41.6677
 JX5  H4   H  HCH2  0   0.246  24.2794  46.3754  42.0614
 JX5  H5   H  HCH2  0   0.255  23.4796  46.6218  40.5249
 JX5  H6   H  HCH2  0   0.232  21.3454  45.7783  41.4184
 JX5  H7   H  HCH2  0   0.285  22.6272  44.5895  41.5220
 JX5  H8   H  HNH1  0   0.395  20.1954  46.0919  43.1966
 JX5  H9   H  HCH1  0   0.318  21.2709  45.2551  45.8223
 JX5  H10  H  HCH2  0   0.278  19.0130  44.4161  46.3547
 JX5  H11  H  HCH2  0   0.278  19.7292  43.6031  44.9805
 JX5  H12  H  HNH1  0   0.402  17.4512  45.4567  44.9448
 JX5  H13  H  HNH1  0   0.403  16.2529  45.5286  43.0850
 JX5  H14  H  HCH1  0   0.298  16.5452  43.4278  41.1669
 JX5  H15  H  HCH2  0   0.274  14.5171  44.7307  41.4470
 JX5  H16  H  HCH2  0   0.272  15.0811  44.6695  39.7947
 JX5  H17  H  HCH2  0   0.291  15.9634  46.9979  39.9564
 JX5  H18  H  HCH2  0   0.284  15.5389  47.0886  41.6404
 JX5  H19  H  HOH1  0   0.481  12.9962  48.7696  39.9870
 JX5  H20  H  HOH1  0   0.482  19.0620  46.2610  40.0651
 JX5  H21  H  HOH1  0   0.492  19.2097  47.7162  47.3237
 JX5  H22  H  HCR6  0   0.285  23.1067  46.8645  45.8821
 JX5  H23  H  HCR6  0   0.284  22.9033  47.1042  48.3060
 JX5  H24  H  HCR6  0   0.285  24.5022  51.0888  48.0306
 JX5  H25  H  HCR6  0   0.273  24.7071  50.8323  45.6064

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
 JX5  O7   C13  double    1.205  0.020  1.205
 JX5  O5   C12  double    1.205  0.020  1.205
 JX5  C13  O6   single    1.327  0.020  1.327
 JX5  C13  C9   single    1.521  0.020  1.521
 JX5  C12  O4   single    1.328  0.020  1.328
 JX5  C12  C11  single    1.505  0.020  1.505
 JX5  C11  C10  single    1.522  0.020  1.522
 JX5  C10  C9   single    1.533  0.020  1.533
 JX5  C9   N4   single    1.435  0.020  1.435
 JX5  C4   C3   single    1.529  0.020  1.529
 JX5  C4   C5   single    1.511  0.020  1.511
 JX5  C3   C2   single    1.526  0.020  1.526
 JX5  C2   N1   single    1.449  0.020  1.449
 JX5  O3   C8   double    1.226  0.020  1.226
 JX5  N4   C8   single    1.358  0.020  1.358
 JX5  C8   N3   single    1.360  0.020  1.360
 JX5  C5   N2   single    1.350  0.020  1.350
 JX5  C5   O2   double    1.222  0.020  1.222
 JX5  N2   C6   single    1.434  0.020  1.434
 JX5  N1   C1   single    1.342  0.020  1.342
 JX5  O1   C1   double    1.223  0.020  1.223
 JX5  N3   C7   single    1.438  0.020  1.438
 JX5  C1   C15  single    1.496  0.020  1.496
 JX5  O8   C14  double    1.205  0.020  1.205
 JX5  C6   C7   single    1.537  0.020  1.537
 JX5  C6   C14  single    1.521  0.020  1.521
 JX5  C14  O9   single    1.320  0.020  1.320
 JX5  C15  C20  aromatic  1.391  0.020  1.391
 JX5  C15  C16  aromatic  1.390  0.020  1.390
 JX5  C20  C19  aromatic  1.386  0.020  1.386
 JX5  C16  C17  aromatic  1.388  0.020  1.388
 JX5  C19  C18  aromatic  1.388  0.020  1.388
 JX5  C17  C18  aromatic  1.387  0.020  1.387
 JX5  C18  I1   single    2.102  0.020  2.102
 JX5  N1   H1   single    0.860  0.020  1.020
 JX5  C2   H2   single    0.970  0.020  1.090
 JX5  C2   H3   single    0.970  0.020  1.090
 JX5  C3   H4   single    0.970  0.020  1.090
 JX5  C3   H5   single    0.970  0.020  1.090
 JX5  C4   H6   single    0.970  0.020  1.090
 JX5  C4   H7   single    0.970  0.020  1.090
 JX5  N2   H8   single    0.860  0.020  1.020
 JX5  C6   H9   single    0.970  0.020  1.090
 JX5  C7   H10  single    0.970  0.020  1.090
 JX5  C7   H11  single    0.970  0.020  1.090
 JX5  N3   H12  single    0.860  0.020  1.020
 JX5  N4   H13  single    0.860  0.020  1.020
 JX5  C9   H14  single    0.970  0.020  1.090
 JX5  C10  H15  single    0.970  0.020  1.090
 JX5  C10  H16  single    0.970  0.020  1.090
 JX5  C11  H17  single    0.970  0.020  1.090
 JX5  C11  H18  single    0.970  0.020  1.090
 JX5  O4   H19  single    0.850  0.020  0.980
 JX5  O6   H20  single    0.850  0.020  0.980
 JX5  O9   H21  single    0.850  0.020  0.980
 JX5  C16  H22  single    0.930  0.020  1.080
 JX5  C17  H23  single    0.930  0.020  1.080
 JX5  C19  H24  single    0.930  0.020  1.080
 JX5  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
 JX5  C15  C1   N1   115.02  3.000
 JX5  C15  C1   O1   121.03  3.000
 JX5  N1   C1   O1   123.95  3.000
 JX5  H1   N1   C2   118.30  3.000
 JX5  H1   N1   C1   118.77  3.000
 JX5  C2   N1   C1   122.74  3.000
 JX5  H3   C2   H2   106.65  3.000
 JX5  H3   C2   C3   110.13  3.000
 JX5  H2   C2   C3   109.47  3.000
 JX5  H3   C2   N1   107.78  3.000
 JX5  H2   C2   N1   108.64  3.000
 JX5  C3   C2   N1   113.90  3.000
 JX5  H5   C3   H4   106.50  3.000
 JX5  H5   C3   C4   107.74  3.000
 JX5  H4   C3   C4   110.23  3.000
 JX5  H5   C3   C2   108.01  3.000
 JX5  H4   C3   C2   109.90  3.000
 JX5  C4   C3   C2   114.13  3.000
 JX5  H7   C4   H6   106.56  3.000
 JX5  H7   C4   C5   107.42  3.000
 JX5  H6   C4   C5   111.21  3.000
 JX5  H7   C4   C3   109.19  3.000
 JX5  H6   C4   C3   109.48  3.000
 JX5  C5   C4   C3   112.77  3.000
 JX5  N2   C5   O2   122.99  3.000
 JX5  O2   C5   C4   122.11  3.000
 JX5  N2   C5   C4   114.88  3.000
 JX5  H8   N2   C6   117.06  3.000
 JX5  H8   N2   C5   117.98  3.000
 JX5  C6   N2   C5   124.28  3.000
 JX5  H9   C6   C14  107.20  3.000
 JX5  H9   C6   C7   107.41  3.000
 JX5  C14  C6   C7   113.00  3.000
 JX5  H9   C6   N2   108.28  3.000
 JX5  C14  C6   N2   109.42  3.000
 JX5  C7   C6   N2   111.32  3.000
 JX5  H11  C7   H10  107.00  3.000
 JX5  H11  C7   N3   109.56  3.000
 JX5  H10  C7   N3   109.44  3.000
 JX5  H11  C7   C6   107.86  3.000
 JX5  H10  C7   C6   110.29  3.000
 JX5  N3   C7   C6   112.53  3.000
 JX5  H12  N3   C8   119.26  3.000
 JX5  H12  N3   C7   117.88  3.000
 JX5  C8   N3   C7   122.81  3.000
 JX5  N4   C8   O3   121.32  3.000
 JX5  N4   C8   N3   115.23  3.000
 JX5  O3   C8   N3   123.45  3.000
 JX5  H13  N4   C9   119.36  3.000
 JX5  H13  N4   C8   120.64  3.000
 JX5  C9   N4   C8   119.72  3.000
 JX5  H14  C9   C13  105.89  3.000
 JX5  H14  C9   C10  106.63  3.000
 JX5  C13  C9   C10  110.01  3.000
 JX5  H14  C9   N4   110.20  3.000
 JX5  C10  C9   N4   110.78  3.000
 JX5  C13  C9   N4   113.03  3.000
 JX5  H16  C10  H15  106.40  3.000
 JX5  H16  C10  C11  109.86  3.000
 JX5  H15  C10  C11  110.36  3.000
 JX5  H16  C10  C9   107.88  3.000
 JX5  H15  C10  C9   107.13  3.000
 JX5  C11  C10  C9   114.83  3.000
 JX5  H18  C11  H17  105.31  3.000
 JX5  H18  C11  C12  107.73  3.000
 JX5  H17  C11  C12  107.33  3.000
 JX5  H18  C11  C10  112.24  3.000
 JX5  H17  C11  C10  111.43  3.000
 JX5  C12  C11  C10  112.41  3.000
 JX5  O5   C12  O4   123.23  3.000
 JX5  O4   C12  C11  111.54  3.000
 JX5  O5   C12  C11  125.24  3.000
 JX5  H19  O4   C12  110.02  3.000
 JX5  O7   C13  O6   123.53  3.000
 JX5  O6   C13  C9   113.71  3.000
 JX5  O7   C13  C9   122.68  3.000
 JX5  H20  O6   C13  109.37  3.000
 JX5  O9   C14  O8   123.94  3.000
 JX5  O9   C14  C6   111.78  3.000
 JX5  O8   C14  C6   124.28  3.000
 JX5  H21  O9   C14  110.57  3.000
 JX5  C20  C15  C16  119.32  3.000
 JX5  C16  C15  C1   121.43  3.000
 JX5  C20  C15  C1   119.20  3.000
 JX5  H22  C16  C17  118.80  3.000
 JX5  H22  C16  C15  120.41  3.000
 JX5  C17  C16  C15  120.72  3.000
 JX5  H23  C17  C18  121.29  3.000
 JX5  H23  C17  C16  119.63  3.000
 JX5  C18  C17  C16  119.07  3.000
 JX5  C19  C18  I1   119.45  3.000
 JX5  I1   C18  C17  119.49  3.000
 JX5  C19  C18  C17  121.06  3.000
 JX5  H24  C19  C20  119.58  3.000
 JX5  H24  C19  C18  121.21  3.000
 JX5  C20  C19  C18  119.21  3.000
 JX5  H25  C20  C19  119.08  3.000
 JX5  H25  C20  C15  120.32  3.000
 JX5  C19  C20  C15  120.59  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
 JX5  CONST_01  C18  C19  C20  C15     0.00   0.0  0
 JX5  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 JX5  CONST_03  C19  C20  C15  C16     0.00   0.0  0
 JX5  CONST_04  C19  C18  C17  C16     0.00   0.0  0
 JX5  CONST_05  C20  C15  C16  C17     0.00   0.0  0
 JX5  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 JX5  CONST_07  C19  C20  C15  C1    180.00   0.0  0
 JX5  CONST_08  C17  C16  C15  C1    180.00   0.0  0
 JX5  CONST_09  I1   C18  C17  C16   180.00   0.0  0
 JX5  CONST_10  C20  C19  C18  I1    180.00   0.0  0
 JX5  CONST_11  H24  C19  C20  C15   180.00   0.0  0
 JX5  CONST_12  H23  C17  C16  C15   180.00   0.0  0
 JX5  CONST_13  H25  C20  C15  C16   180.00   0.0  0
 JX5  CONST_14  H22  C16  C17  C18   180.00   0.0  0
 JX5  CONST_15  C15  C1   N1   C2    180.00   0.0  0
 JX5  CONST_16  H1   N1   C1   C15     0.00   0.0  0
 JX5  CONST_17  C2   N1   C1   O1      0.00   0.0  0
 JX5  CONST_18  C6   N2   C5   C4    180.00   0.0  0
 JX5  CONST_19  C6   N2   C5   O2      0.00   0.0  0
 JX5  CONST_20  O3   C8   N3   C7      0.00   0.0  0
 JX5  CONST_21  C9   N4   C8   O3      0.00   0.0  0
 JX5  CONST_22  N4   C8   N3   C7    180.00   0.0  0
 JX5  CONST_23  C9   N4   C8   N3    180.00   0.0  0
 JX5  CONST_24  H8   N2   C5   C4      0.00   0.0  0
 JX5  CONST_25  H13  N4   C8   O3    180.00   0.0  0
 JX5  CONST_26  H12  N3   C8   O3    180.00   0.0  0
 JX5  CONST_27  H21  O9   C14  C6    180.00   0.0  0
 JX5  CONST_28  H20  O6   C13  C9    180.00   0.0  0
 JX5  CONST_29  H19  O4   C12  C11   180.00   0.0  0
 JX5  Var_01    C20  C15  C1   O1     45.98  30.0  2
 JX5  Var_02    C3   C2   N1   C1     90.13  30.0  1
 JX5  Var_03    C4   C3   C2   N1     72.80  30.0  1
 JX5  Var_04    C5   C4   C3   C2    -65.56  30.0  2
 JX5  Var_05    N2   C5   C4   C3    110.45  30.0  3
 JX5  Var_06    C8   N3   C7   C6     94.58  30.0  2
 JX5  Var_07    C12  C11  C10  C9   -175.40  30.0  1
 JX5  Var_08    O5   C12  C11  C10     0.71  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
 JX5  chir_01  C6  N2  C7   C14  positiv
 JX5  chir_02  C9  N4  C13  C10  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
 JX5  plan-1  C1   0.020
 JX5  plan-1  C15  0.020
 JX5  plan-1  C16  0.020
 JX5  plan-1  C17  0.020
 JX5  plan-1  C18  0.020
 JX5  plan-1  I1   0.020
 JX5  plan-1  C19  0.020
 JX5  plan-1  C20  0.020
 JX5  plan-1  H22  0.020
 JX5  plan-1  H23  0.020
 JX5  plan-1  H24  0.020
 JX5  plan-1  H25  0.020
 JX5  plan-2  C11  0.020
 JX5  plan-2  C12  0.020
 JX5  plan-2  O4   0.020
 JX5  plan-2  O5   0.020
 JX5  plan-2  H19  0.020
 JX5  plan-3  C9   0.020
 JX5  plan-3  C13  0.020
 JX5  plan-3  O6   0.020
 JX5  plan-3  O7   0.020
 JX5  plan-3  H20  0.020
 JX5  plan-4  C6   0.020
 JX5  plan-4  C14  0.020
 JX5  plan-4  O8   0.020
 JX5  plan-4  O9   0.020
 JX5  plan-4  H21  0.020
 JX5  plan-5  O1   0.020
 JX5  plan-5  C1   0.020
 JX5  plan-5  N1   0.020
 JX5  plan-5  C2   0.020
 JX5  plan-5  C15  0.020
 JX5  plan-5  H1   0.020
 JX5  plan-6  C4   0.020
 JX5  plan-6  C5   0.020
 JX5  plan-6  O2   0.020
 JX5  plan-6  N2   0.020
 JX5  plan-6  C6   0.020
 JX5  plan-6  H8   0.020
 JX5  plan-7  C7   0.020
 JX5  plan-7  N3   0.020
 JX5  plan-7  C8   0.020
 JX5  plan-7  O3   0.020
 JX5  plan-7  N4   0.020
 JX5  plan-7  C9   0.020
 JX5  plan-7  H12  0.020
 JX5  plan-7  H13  0.020

