# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:17:18 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 4-[[4-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyloxymethyl]phenyl]methylamino]-4-oxidanylidene-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)NCc1ccc(COC(=O)N[C@H]2CC(=O)NC2=O)cc1
#
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
 JOW  JOW  '4-[[4-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyloxymethyl]phenyl]methylamino]-4-oxidanylidene-butanoic acid'  ligand  45  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JOW
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
 JOW  C4   C  CR5    0   0.574   6.1758   0.7368   0.8333
 JOW  C14  C  C      0   0.565  -5.1598  -0.4589  -0.1651
 JOW  C5   C  C      0   0.766   3.7263  -1.0242  -0.6345
 JOW  C6   C  CH2    0  -0.244   1.8454  -2.4474  -0.5713
 JOW  C11  C  CR16   0  -0.282  -1.8730  -1.7340  -0.6356
 JOW  C7   C  CR6    0   0.060   0.4105  -2.3553  -0.1550
 JOW  C8   C  CR16   0  -0.279   0.0136  -2.7532   1.1150
 JOW  C9   C  CR16   0  -0.299  -1.3145  -2.6431   1.5071
 JOW  C10  C  CR6    0   0.111  -2.2724  -2.1339   0.6391
 JOW  C12  C  CR16   0  -0.268  -0.5490  -1.8426  -1.0259
 JOW  C13  C  CH2    0  -0.372  -3.7179  -2.0424   1.0626
 JOW  N1   N  NR15   0  -0.678   7.0024   1.8292   0.7925
 JOW  N2   N  NH1    0  -0.657   4.1268   0.2528  -0.4442
 JOW  C3   C  CR15   0  -0.230   5.4980   0.6409  -0.5314
 JOW  N3   N  NH1    0  -0.628  -4.2993  -0.7421   0.8315
 JOW  C1   C  CR5    0   0.549   6.8641   2.6039  -0.3379
 JOW  C2   C  CH2    0  -0.600   5.7508   2.0077  -1.1629
 JOW  O1   O  O      0  -0.419   7.5143   3.5891  -0.5784
 JOW  O2   O  O      0  -0.409   6.0305  -0.0096   1.7658
 JOW  O3   O  O2     0  -0.477   2.4271  -1.1517  -0.3650
 JOW  O4   O  O      0  -0.511   4.4381  -1.9288  -1.0156
 JOW  C15  C  CH2    0  -0.566  -5.6002   0.9851  -0.2464
 JOW  O5   O  O      0  -0.512  -5.5491  -1.3031  -0.9632
 JOW  C16  C  CH2    0  -0.582  -7.1047   1.1270  -0.4199
 JOW  C17  C  C      0   0.417  -7.5883   2.5659  -0.6784
 JOW  O6   O  O      0  -0.608  -6.7387   3.4103  -1.0236
 JOW  O7   O  OC    -1  -0.627  -8.8136   2.7608  -0.5419
 JOW  H1   H  HCH2   0   0.252   2.3729  -3.1954   0.0230
 JOW  H2   H  HCH2   0   0.250   1.9298  -2.7262  -1.6237
 JOW  H3   H  HCR6   0   0.255  -2.6019  -1.3429  -1.3351
 JOW  H4   H  HCR6   0   0.255   0.7447  -3.1526   1.8081
 JOW  H5   H  HCR6   0   0.255  -1.6040  -2.9587   2.5023
 JOW  H6   H  HCR6   0   0.255  -0.2586  -1.5312  -2.0224
 JOW  H7   H  HCH2   0   0.267  -4.3107  -2.7805   0.5220
 JOW  H8   H  HCH2   0   0.267  -3.8052  -2.2848   2.1232
 JOW  H9   H  HNR5   0   0.428   7.6307   2.0744   1.5478
 JOW  H10  H  HNH1   0   0.410   3.4684   0.9136  -0.0589
 JOW  H11  H  HCR5   0   0.332   6.0407  -0.1253  -1.0901
 JOW  H12  H  HNH1   0   0.399  -4.0018   0.0070   1.4352
 JOW  H13  H  HCH2   0   0.311   6.0213   1.9614  -2.2159
 JOW  H14  H  HCH2   0   0.313   4.8780   2.6601  -1.0737
 JOW  H15  H  HCH2   0   0.238  -5.2636   1.5445   0.6291
 JOW  H16  H  HCH2   0   0.257  -5.0904   1.4287  -1.1057
 JOW  H17  H  HCH2   0   0.236  -7.4356   0.5077  -1.2598
 JOW  H18  H  HCH2   0   0.226  -7.6245   0.7311   0.4573

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
 JOW  O1   C1   double    1.205  0.020  1.205
 JOW  N1   C1   single    1.377  0.020  1.377
 JOW  N1   C4   single    1.371  0.020  1.371
 JOW  C1   C2   single    1.509  0.020  1.509
 JOW  C4   O2   double    1.203  0.020  1.203
 JOW  C4   C3   single    1.527  0.020  1.527
 JOW  C2   C3   single    1.527  0.020  1.527
 JOW  C3   N2   single    1.428  0.020  1.428
 JOW  O4   C5   double    1.213  0.020  1.213
 JOW  N2   C5   single    1.352  0.020  1.352
 JOW  C5   O3   single    1.333  0.020  1.333
 JOW  C9   C8   aromatic  1.389  0.020  1.389
 JOW  C9   C10  aromatic  1.389  0.020  1.389
 JOW  C8   C7   aromatic  1.389  0.020  1.389
 JOW  C13  N3   single    1.443  0.020  1.443
 JOW  C13  C10  single    1.509  0.020  1.509
 JOW  O5   C14  double    1.225  0.020  1.225
 JOW  N3   C14  single    1.347  0.020  1.347
 JOW  C10  C11  aromatic  1.394  0.020  1.394
 JOW  O3   C6   single    1.435  0.020  1.435
 JOW  C7   C6   single    1.497  0.020  1.497
 JOW  C7   C12  aromatic  1.394  0.020  1.394
 JOW  C14  C15  single    1.512  0.020  1.512
 JOW  C11  C12  aromatic  1.385  0.020  1.385
 JOW  C15  C16  single    1.521  0.020  1.521
 JOW  C16  C17  single    1.540  0.020  1.540
 JOW  O6   C17  deloc     1.247  0.020  1.247
 JOW  C17  O7   deloc     1.248  0.020  1.248
 JOW  C6   H1   single    0.970  0.020  1.090
 JOW  C6   H2   single    0.970  0.020  1.090
 JOW  C11  H3   single    0.930  0.020  1.080
 JOW  C8   H4   single    0.930  0.020  1.080
 JOW  C9   H5   single    0.930  0.020  1.080
 JOW  C12  H6   single    0.930  0.020  1.080
 JOW  C13  H7   single    0.970  0.020  1.090
 JOW  C13  H8   single    0.970  0.020  1.090
 JOW  N1   H9   single    0.860  0.020  1.020
 JOW  N2   H10  single    0.860  0.020  1.020
 JOW  C3   H11  single    0.970  0.020  1.090
 JOW  N3   H12  single    0.860  0.020  1.020
 JOW  C2   H13  single    0.970  0.020  1.090
 JOW  C2   H14  single    0.970  0.020  1.090
 JOW  C15  H15  single    0.970  0.020  1.090
 JOW  C15  H16  single    0.970  0.020  1.090
 JOW  C16  H17  single    0.970  0.020  1.090
 JOW  C16  H18  single    0.970  0.020  1.090

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
 JOW  O2   C4   C3   126.88  3.000
 JOW  C3   C4   N1   106.93  3.000
 JOW  O2   C4   N1   126.18  3.000
 JOW  O5   C14  C15  122.04  3.000
 JOW  C15  C14  N3   115.26  3.000
 JOW  O5   C14  N3   122.69  3.000
 JOW  O4   C5   O3   124.36  3.000
 JOW  O3   C5   N2   110.53  3.000
 JOW  O4   C5   N2   125.10  3.000
 JOW  H2   C6   H1   108.21  3.000
 JOW  H2   C6   O3   109.74  3.000
 JOW  H1   C6   O3   110.16  3.000
 JOW  H2   C6   C7   110.97  3.000
 JOW  H1   C6   C7   110.73  3.000
 JOW  O3   C6   C7   107.04  3.000
 JOW  H3   C11  C12  119.32  3.000
 JOW  H3   C11  C10  120.07  3.000
 JOW  C12  C11  C10  120.60  3.000
 JOW  C12  C7   C8   118.69  3.000
 JOW  C12  C7   C6   120.59  3.000
 JOW  C8   C7   C6   120.71  3.000
 JOW  H4   C8   C9   119.58  3.000
 JOW  H4   C8   C7   119.84  3.000
 JOW  C9   C8   C7   120.58  3.000
 JOW  H5   C9   C10  119.76  3.000
 JOW  H5   C9   C8   119.45  3.000
 JOW  C10  C9   C8   120.79  3.000
 JOW  C13  C10  C9   120.49  3.000
 JOW  C13  C10  C11  120.90  3.000
 JOW  C9   C10  C11  118.60  3.000
 JOW  H6   C12  C7   119.73  3.000
 JOW  H6   C12  C11  119.53  3.000
 JOW  C7   C12  C11  120.74  3.000
 JOW  H8   C13  H7   106.74  3.000
 JOW  H8   C13  N3   108.88  3.000
 JOW  H7   C13  N3   108.15  3.000
 JOW  H8   C13  C10  109.63  3.000
 JOW  H7   C13  C10  109.92  3.000
 JOW  N3   C13  C10  113.30  3.000
 JOW  H9   N1   C1   122.57  3.000
 JOW  H9   N1   C4   123.03  3.000
 JOW  C1   N1   C4   114.34  3.000
 JOW  H10  N2   C3   118.16  3.000
 JOW  H10  N2   C5   118.62  3.000
 JOW  C3   N2   C5   122.19  3.000
 JOW  H11  C3   C2   109.52  3.000
 JOW  H11  C3   N2   108.52  3.000
 JOW  C2   C3   N2   115.31  3.000
 JOW  H11  C3   C4   106.30  3.000
 JOW  N2   C3   C4   112.88  3.000
 JOW  C2   C3   C4   103.89  3.000
 JOW  H12  N3   C13  117.08  3.000
 JOW  H12  N3   C14  118.42  3.000
 JOW  C13  N3   C14  124.43  3.000
 JOW  O1   C1   C2   127.76  3.000
 JOW  C2   C1   N1   107.49  3.000
 JOW  O1   C1   N1   124.73  3.000
 JOW  H14  C2   H13  107.62  3.000
 JOW  H14  C2   C1   107.98  3.000
 JOW  H13  C2   C1   111.25  3.000
 JOW  H14  C2   C3   111.62  3.000
 JOW  H13  C2   C3   113.79  3.000
 JOW  C1   C2   C3   104.47  3.000
 JOW  C6   O3   C5   116.89  3.000
 JOW  H16  C15  H15  106.17  3.000
 JOW  H16  C15  C16  109.50  3.000
 JOW  H15  C15  C16  110.40  3.000
 JOW  H16  C15  C14  107.10  3.000
 JOW  H15  C15  C14  110.87  3.000
 JOW  C16  C15  C14  112.54  3.000
 JOW  H18  C16  H17  105.47  3.000
 JOW  H18  C16  C17  108.88  3.000
 JOW  H17  C16  C17  107.75  3.000
 JOW  H18  C16  C15  110.18  3.000
 JOW  H17  C16  C15  109.49  3.000
 JOW  C17  C16  C15  114.64  3.000
 JOW  O7   C17  O6   126.41  3.000
 JOW  O7   C17  C16  115.84  3.000
 JOW  O6   C17  C16  117.74  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
 JOW  CONST_01  C8   C9   C10  C11     0.00   0.0  0
 JOW  CONST_02  C8   C7   C12  C11     0.00   0.0  0
 JOW  CONST_03  C10  C9   C8   C7      0.00   0.0  0
 JOW  CONST_04  C10  C11  C12  C7      0.00   0.0  0
 JOW  CONST_05  C12  C7   C8   C9      0.00   0.0  0
 JOW  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 JOW  CONST_07  C1   N1   C4   C3      0.00   0.0  0
 JOW  CONST_08  C9   C8   C7   C6    180.00   0.0  0
 JOW  CONST_09  C11  C12  C7   C6    180.00   0.0  0
 JOW  CONST_10  C13  C10  C9   C8    180.00   0.0  0
 JOW  CONST_11  C13  C10  C11  C12   180.00   0.0  0
 JOW  CONST_12  O2   C4   N1   C1    180.00   0.0  0
 JOW  CONST_13  H5   C9   C10  C11   180.00   0.0  0
 JOW  CONST_14  H3   C11  C12  C7    180.00   0.0  0
 JOW  CONST_15  H6   C12  C7   C8    180.00   0.0  0
 JOW  CONST_16  H4   C8   C9   C10   180.00   0.0  0
 JOW  CONST_17  H9   N1   C4   C3    180.00   0.0  0
 JOW  CONST_18  O5   C14  N3   C13     0.00   0.0  0
 JOW  CONST_19  C15  C14  N3   C13   180.00   0.0  0
 JOW  CONST_20  H12  N3   C14  C15     0.00   0.0  0
 JOW  Var_01    C2   C1   N1   C4      2.92  30.0  1
 JOW  Var_02    C3   C2   C1   N1    -12.53  30.0  1
 JOW  Var_03    N3   C13  C10  C11   -51.31  30.0  2
 JOW  Var_04    O3   C6   C7   C8    -96.53  30.0  2
 JOW  Var_05    C10  C13  N3   C14   104.79  30.0  1
 JOW  Var_06    C7   C6   O3   C5    177.84  30.0  3
 JOW  Var_07    O4   C5   N2   C3     -7.40  30.0  2
 JOW  Var_08    C17  C16  C15  C14  -172.97  30.0  3
 JOW  Var_09    C16  C15  C14  N3   -133.25  30.0  3
 JOW  Var_10    O6   C17  C16  C15    15.99  30.0  3

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
 JOW  chir_01  C3  C4  C2  N2  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
 JOW  plan-1  C6   0.020
 JOW  plan-1  C11  0.020
 JOW  plan-1  C7   0.020
 JOW  plan-1  C8   0.020
 JOW  plan-1  C9   0.020
 JOW  plan-1  C10  0.020
 JOW  plan-1  C12  0.020
 JOW  plan-1  C13  0.020
 JOW  plan-1  H3   0.020
 JOW  plan-1  H4   0.020
 JOW  plan-1  H5   0.020
 JOW  plan-1  H6   0.020
 JOW  plan-2  C14  0.020
 JOW  plan-2  C13  0.020
 JOW  plan-2  N3   0.020
 JOW  plan-2  C15  0.020
 JOW  plan-2  O5   0.020
 JOW  plan-2  H12  0.020
 JOW  plan-3  N1   0.020
 JOW  plan-3  C1   0.020
 JOW  plan-3  C2   0.020
 JOW  plan-3  O1   0.020
 JOW  plan-4  C4   0.020
 JOW  plan-4  N1   0.020
 JOW  plan-4  C3   0.020
 JOW  plan-4  C1   0.020
 JOW  plan-4  O2   0.020
 JOW  plan-4  H9   0.020
 JOW  plan-5  C16  0.020
 JOW  plan-5  C17  0.020
 JOW  plan-5  O6   0.020
 JOW  plan-5  O7   0.020
 JOW  plan-6  C5   0.020
 JOW  plan-6  N2   0.020
 JOW  plan-6  O3   0.020
 JOW  plan-6  O4   0.020

