# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 04:01:18 2022
#   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  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_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  -0.499  24.6109  49.0399  43.2846
 JX5  C1   C  C      0   0.483  23.6407  48.6680  43.9384
 JX5  N1   N  NH1    0  -0.662  22.5678  48.0649  43.4191
 JX5  C2   C  CH2    0  -0.317  22.4912  47.7408  42.0105
 JX5  C3   C  CH2    0  -0.434  23.1785  46.4250  41.6434
 JX5  C4   C  CH2    0  -0.571  22.3559  45.1797  41.9818
 JX5  C5   C  C      0   0.516  22.0566  45.0660  43.4619
 JX5  O2   O  O      0  -0.519  22.9293  44.7425  44.2650
 JX5  N2   N  NH1    0  -0.642  20.7976  45.3643  43.8051
 JX5  C6   C  CH1    0  -0.258  20.3146  45.3975  45.1628
 JX5  C7   C  CH2    0  -0.283  19.3169  44.2670  45.4366
 JX5  N3   N  NH1    0  -0.669  18.0672  44.4391  44.7303
 JX5  C8   C  C      0   0.691  17.9140  44.0382  43.4319
 JX5  O3   O  O      0  -0.537  18.5737  43.1353  42.9319
 JX5  N4   N  NH1    0  -0.657  16.9076  44.6734  42.7544
 JX5  C9   C  CH1    0  -0.206  17.0053  44.7510  41.3097
 JX5  C10  C  CH2    0  -0.422  15.7316  45.3692  40.7257
 JX5  C11  C  CH2    0  -0.602  15.4959  46.8284  41.0912
 JX5  C12  C  C      0   0.416  14.2258  47.4679  40.4894
 JX5  O4   O  OC    -1  -0.624  14.0461  48.6722  40.7665
 JX5  O5   O  O      0  -0.602  13.4896  46.7495  39.7850
 JX5  C13  C  C      0   0.442  18.2678  45.5148  40.8289
 JX5  O6   O  OC    -1  -0.602  18.9213  46.1564  41.6868
 JX5  O7   O  O      0  -0.589  18.5122  45.4393  39.6138
 JX5  C14  C  C      0   0.456  19.7383  46.7950  45.5193
 JX5  O8   O  O      0  -0.575  20.2166  47.7805  44.9145
 JX5  O9   O  OC    -1  -0.574  18.8651  46.8262  46.4006
 JX5  C15  C  CR6    0  -0.031  23.5957  48.8973  45.4179
 JX5  C16  C  CR16   0  -0.267  23.1777  47.9076  46.3008
 JX5  C17  C  CR16   0  -0.219  23.1811  48.1326  47.6705
 JX5  C18  C  CR6    0  -0.225  23.5954  49.3655  48.1509
 JX5  I1   I  I      0   0.055  23.5865  49.7252  50.2232
 JX5  C19  C  CR16   0  -0.216  24.0246  50.3644  47.2878
 JX5  C20  C  CR16   0  -0.268  24.0365  50.1163  45.9237
 JX5  H1   H  HNH1   0   0.440  21.7402  47.8820  44.0054
 JX5  H2   H  HCH2   0   0.243  22.9294  48.5541  41.4300
 JX5  H3   H  HCH2   0   0.239  21.4349  47.6935  41.7386
 JX5  H4   H  HCH2   0   0.234  24.1589  46.3765  42.1215
 JX5  H5   H  HCH2   0   0.239  23.3614  46.4219  40.5664
 JX5  H6   H  HCH2   0   0.247  21.4348  45.1941  41.3967
 JX5  H7   H  HCH2   0   0.254  22.9144  44.2908  41.6810
 JX5  H8   H  HNH1   0   0.429  20.1465  45.6358  43.0681
 JX5  H9   H  HCH1   0   0.260  21.1747  45.2339  45.8203
 JX5  H10  H  HCH2   0   0.236  19.1094  44.2207  46.5050
 JX5  H11  H  HCH2   0   0.242  19.7567  43.3110  45.1568
 JX5  H12  H  HNH1   0   0.376  17.5613  45.2626  45.0206
 JX5  H13  H  HNH1   0   0.370  16.5906  45.5300  43.1832
 JX5  H14  H  HCH1   0   0.235  17.0734  43.7305  40.9259
 JX5  H15  H  HCH2   0   0.212  14.8774  44.7660  41.0438
 JX5  H16  H  HCH2   0   0.215  15.7833  45.2726  39.6407
 JX5  H17  H  HCH2   0   0.222  16.3518  47.4375  40.7816
 JX5  H18  H  HCH2   0   0.213  15.4375  46.9565  42.1785
 JX5  H22  H  HCR6   0   0.281  22.8791  46.9348  45.9333
 JX5  H23  H  HCR6   0   0.280  22.8651  47.3461  48.3422
 JX5  H24  H  HCR6   0   0.280  24.3518  51.3253  47.6608
 JX5  H25  H  HCR6   0   0.265  24.3803  50.8911  45.2506

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  deloc     1.242  0.020  1.242
 JX5  O5   C12  deloc     1.247  0.020  1.247
 JX5  C13  O6   deloc     1.255  0.020  1.255
 JX5  C13  C9   single    1.552  0.020  1.552
 JX5  C12  O4   deloc     1.249  0.020  1.249
 JX5  C12  C11  single    1.544  0.020  1.544
 JX5  C11  C10  single    1.523  0.020  1.523
 JX5  C10  C9   single    1.531  0.020  1.531
 JX5  C9   N4   single    1.450  0.020  1.450
 JX5  C4   C3   single    1.530  0.020  1.530
 JX5  C4   C5   single    1.514  0.020  1.514
 JX5  C3   C2   single    1.529  0.020  1.529
 JX5  C2   N1   single    1.447  0.020  1.447
 JX5  O3   C8   double    1.225  0.020  1.225
 JX5  N4   C8   single    1.369  0.020  1.369
 JX5  C8   N3   single    1.367  0.020  1.367
 JX5  C5   N2   single    1.339  0.020  1.339
 JX5  C5   O2   double    1.229  0.020  1.229
 JX5  N2   C6   single    1.441  0.020  1.441
 JX5  N1   C1   single    1.336  0.020  1.336
 JX5  O1   C1   double    1.228  0.020  1.228
 JX5  N3   C7   single    1.446  0.020  1.446
 JX5  C1   C15  single    1.498  0.020  1.498
 JX5  O8   C14  deloc     1.251  0.020  1.251
 JX5  C6   C7   single    1.532  0.020  1.532
 JX5  C6   C14  single    1.553  0.020  1.553
 JX5  C14  O9   deloc     1.241  0.020  1.241
 JX5  C15  C20  aromatic  1.391  0.020  1.391
 JX5  C15  C16  aromatic  1.391  0.020  1.391
 JX5  C20  C19  aromatic  1.387  0.020  1.387
 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    2.103  0.020  2.103
 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    0.890  0.020  1.040
 JX5  N4   H13  single    0.890  0.020  1.040
 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  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   115.40  3.000
 JX5  C15  C1   O1   120.22  3.000
 JX5  N1   C1   O1   124.37  3.000
 JX5  H1   N1   C2   118.13  3.000
 JX5  H1   N1   C1   120.26  3.000
 JX5  C2   N1   C1   121.46  3.000
 JX5  H3   C2   H2   106.76  3.000
 JX5  H3   C2   C3   109.74  3.000
 JX5  H2   C2   C3   109.46  3.000
 JX5  H3   C2   N1   107.66  3.000
 JX5  H2   C2   N1   109.25  3.000
 JX5  C3   C2   N1   113.74  3.000
 JX5  H5   C3   H4   106.34  3.000
 JX5  H5   C3   C4   107.80  3.000
 JX5  H4   C3   C4   110.46  3.000
 JX5  H5   C3   C2   108.33  3.000
 JX5  H4   C3   C2   109.67  3.000
 JX5  C4   C3   C2   113.92  3.000
 JX5  H7   C4   H6   107.14  3.000
 JX5  H7   C4   C5   108.01  3.000
 JX5  H6   C4   C5   110.99  3.000
 JX5  H7   C4   C3   109.06  3.000
 JX5  H6   C4   C3   108.93  3.000
 JX5  C5   C4   C3   112.55  3.000
 JX5  N2   C5   O2   123.98  3.000
 JX5  O2   C5   C4   121.19  3.000
 JX5  N2   C5   C4   114.82  3.000
 JX5  H8   N2   C6   117.42  3.000
 JX5  H8   N2   C5   118.31  3.000
 JX5  C6   N2   C5   124.18  3.000
 JX5  H9   C6   C14  106.74  3.000
 JX5  H9   C6   C7   107.10  3.000
 JX5  C14  C6   C7   112.41  3.000
 JX5  H9   C6   N2   107.40  3.000
 JX5  C14  C6   N2   111.18  3.000
 JX5  C7   C6   N2   111.68  3.000
 JX5  H11  C7   H10  106.95  3.000
 JX5  H11  C7   N3   109.15  3.000
 JX5  H10  C7   N3   108.64  3.000
 JX5  H11  C7   C6   109.80  3.000
 JX5  H10  C7   C6   109.30  3.000
 JX5  N3   C7   C6   112.81  3.000
 JX5  H12  N3   C8   117.14  3.000
 JX5  H12  N3   C7   112.95  3.000
 JX5  C8   N3   C7   121.72  3.000
 JX5  N4   C8   O3   122.40  3.000
 JX5  N4   C8   N3   114.59  3.000
 JX5  O3   C8   N3   122.91  3.000
 JX5  H13  N4   C9   113.52  3.000
 JX5  H13  N4   C8   114.48  3.000
 JX5  C9   N4   C8   117.92  3.000
 JX5  H14  C9   C13  107.47  3.000
 JX5  H14  C9   C10  107.16  3.000
 JX5  C13  C9   C10  111.09  3.000
 JX5  H14  C9   N4   107.71  3.000
 JX5  C10  C9   N4   110.21  3.000
 JX5  C13  C9   N4   112.94  3.000
 JX5  H16  C10  H15  106.12  3.000
 JX5  H16  C10  C11  109.34  3.000
 JX5  H15  C10  C11  109.76  3.000
 JX5  H16  C10  C9   107.71  3.000
 JX5  H15  C10  C9   108.43  3.000
 JX5  C11  C10  C9   115.09  3.000
 JX5  H18  C11  H17  104.89  3.000
 JX5  H18  C11  C12  107.12  3.000
 JX5  H17  C11  C12  107.60  3.000
 JX5  H18  C11  C10  111.00  3.000
 JX5  H17  C11  C10  110.13  3.000
 JX5  C12  C11  C10  115.51  3.000
 JX5  O5   C12  O4   126.60  3.000
 JX5  O4   C12  C11  115.55  3.000
 JX5  O5   C12  C11  117.85  3.000
 JX5  O7   C13  O6   126.70  3.000
 JX5  O6   C13  C9   117.61  3.000
 JX5  O7   C13  C9   115.68  3.000
 JX5  O9   C14  O8   126.33  3.000
 JX5  O9   C14  C6   116.53  3.000
 JX5  O8   C14  C6   117.12  3.000
 JX5  C20  C15  C16  119.20  3.000
 JX5  C16  C15  C1   121.82  3.000
 JX5  C20  C15  C1   118.93  3.000
 JX5  H22  C16  C17  118.79  3.000
 JX5  H22  C16  C15  120.48  3.000
 JX5  C17  C16  C15  120.69  3.000
 JX5  H23  C17  C18  121.25  3.000
 JX5  H23  C17  C16  119.62  3.000
 JX5  C18  C17  C16  119.12  3.000
 JX5  C19  C18  I1   119.40  3.000
 JX5  I1   C18  C17  119.48  3.000
 JX5  C19  C18  C17  121.12  3.000
 JX5  H24  C19  C20  119.72  3.000
 JX5  H24  C19  C18  121.23  3.000
 JX5  C20  C19  C18  119.05  3.000
 JX5  H25  C20  C19  119.10  3.000
 JX5  H25  C20  C15  120.11  3.000
 JX5  C19  C20  C15  120.78  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_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  Var_01    C20  C15  C1   O1    41.59  30.0  2
 JX5  Var_02    C3   C2   N1   C1    83.44  30.0  1
 JX5  Var_03    C4   C3   C2   N1    78.43  30.0  1
 JX5  Var_04    C5   C4   C3   C2   -60.60  30.0  1
 JX5  Var_05    N2   C5   C4   C3   105.21  30.0  3
 JX5  Var_06    C8   N3   C7   C6    83.83  30.0  2
 JX5  Var_07    C12  C11  C10  C9   179.08  30.0  1
 JX5  Var_08    O5   C12  C11  C10    1.34  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-3  C9   0.020
 JX5  plan-3  C13  0.020
 JX5  plan-3  O6   0.020
 JX5  plan-3  O7   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-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

