# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 13:36:01 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: (4~{R})-5-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-[[(6~{S})-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-yl]sulfanyl]-4-methyl-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C(O)=O)C1=N[C@@H]([C@@H](S[C@H]2Cn3cnc[n+]3C2)[C@@H]1C)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
 OEN  OEN  '(4~{R})-5-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-[[(6~{S})-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-yl]sulfanyl]-4-methyl-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid'  ligand  44  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OEN
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
 OEN  N    N  NR5    1  -0.200  -28.0390  -18.6013   -0.9891
 OEN  O    O  OC    -1  -0.585  -26.4419  -20.5796   -4.3380
 OEN  C1   C  CR15   0  -0.209  -26.7709  -19.1159   -6.2084
 OEN  C10  C  CR5    0   0.283  -28.0661  -19.3228   -8.0257
 OEN  C11  C  CH1    0  -0.489  -28.4820  -19.6010   -9.4420
 OEN  C12  C  CH1    0   0.071  -27.8553  -18.6208  -10.4580
 OEN  C13  C  CH3    0  -0.685  -28.0941  -17.1688  -10.0840
 OEN  C14  C  C      0   0.464  -28.1857  -21.0881   -9.7647
 OEN  C2   C  CR15   0  -0.399  -28.2079  -18.8801   -5.7291
 OEN  C3   C  CH1    0  -0.468  -27.6776  -17.8718   -3.1490
 OEN  C4   C  CH2    0  -0.251  -28.3915  -18.9727   -2.3558
 OEN  C5   C  CR15   0   0.175  -27.9968  -19.1008    0.2320
 OEN  C6   C  CR15   0   0.177  -27.3693  -17.0904    0.3643
 OEN  C7   C  CH2    0  -0.252  -27.6562  -16.6628   -2.2021
 OEN  C8   C  CR15   0  -0.316  -29.0188  -18.7134   -7.0200
 OEN  C9   C  CH3    0  -0.659  -30.4020  -19.3426   -6.9493
 OEN  N1   N  N      0  -0.431  -27.5806  -18.1793    1.0919
 OEN  N2   N  NR5    0  -0.200  -27.6421  -17.3301   -0.9056
 OEN  N3   N  N      0  -0.366  -26.8892  -19.5340   -7.6017
 OEN  O1   O  OH1    0  -0.697  -26.4792  -18.8337  -10.6201
 OEN  O2   O  O      0  -0.599  -27.1556  -21.3306  -10.4446
 OEN  O3   O  OC    -1  -0.575  -28.9758  -21.9238   -9.3071
 OEN  S    S  S2     0   0.028  -28.4876  -17.4194   -4.6924
 OEN  H2   H  HCR5   0   0.241  -26.2091  -18.1713   -6.1960
 OEN  H4   H  HCH1   0   0.243  -29.5644  -19.4650   -9.5114
 OEN  H5   H  HCH1   0   0.179  -28.3876  -18.8070  -11.4069
 OEN  H6   H  HCH3   0   0.220  -29.1594  -16.9727   -9.9548
 OEN  H7   H  HCH3   0   0.221  -27.5853  -16.9044   -9.1547
 OEN  H8   H  HCH3   0   0.233  -27.7263  -16.5022  -10.8658
 OEN  H9   H  HCR5   0   0.291  -28.5686  -19.7589   -5.1914
 OEN  H10  H  HCH1   0   0.340  -26.6536  -18.1891   -3.3440
 OEN  H11  H  HCH2   0   0.308  -29.4752  -18.9330   -2.4630
 OEN  H12  H  HCH2   0   0.332  -28.0140  -19.9616   -2.5946
 OEN  H13  H  HCR5   0   0.348  -28.2645  -20.1200    0.4611
 OEN  H14  H  HCR5   0   0.348  -27.0190  -16.1347    0.7211
 OEN  H15  H  HCH2   0   0.332  -26.7711  -16.0428   -2.3123
 OEN  H16  H  HCH2   0   0.314  -28.5540  -16.0470   -2.2691
 OEN  H17  H  HCR5   0   0.267  -29.1303  -17.6513   -7.2826
 OEN  H18  H  HCH3   0   0.237  -30.9676  -18.9128   -6.1219
 OEN  H19  H  HCH3   0   0.238  -30.9753  -19.1706   -7.8599
 OEN  H20  H  HCH3   0   0.228  -30.3341  -20.4192   -6.7884
 OEN  H23  H  HOH1   0   0.435  -26.4211  -19.8173  -10.6450
 OEN  C    C  C      0   0.425  -25.9367  -20.1376   -5.3907
 OEN  O4   O  O      0  -0.594  -24.8189  -20.4096   -5.8573

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
 OEN  O1   C12  single    1.402  0.020  1.402
 OEN  C12  C13  single    1.518  0.020  1.518
 OEN  C12  C11  single    1.545  0.020  1.545
 OEN  O2   C14  deloc     1.258  0.020  1.258
 OEN  C14  C11  single    1.550  0.020  1.550
 OEN  C14  O3   deloc     1.238  0.020  1.238
 OEN  C11  C10  single    1.502  0.020  1.502
 OEN  C10  N3   double    1.269  0.020  1.269
 OEN  C10  C8   single    1.513  0.020  1.513
 OEN  N3   C1   single    1.460  0.020  1.460
 OEN  C9   C8   single    1.521  0.020  1.521
 OEN  C8   C2   single    1.534  0.020  1.534
 OEN  C1   C2   single    1.533  0.020  1.533
 OEN  C1   C    single    1.552  0.020  1.552
 OEN  O4   C    deloc     1.241  0.020  1.241
 OEN  C2   S    single    1.813  0.020  1.813
 OEN  C    O    deloc     1.249  0.020  1.249
 OEN  S    C3   single    1.801  0.020  1.801
 OEN  C3   C4   single    1.533  0.020  1.533
 OEN  C3   C7   single    1.536  0.020  1.536
 OEN  C4   N    single    1.460  0.020  1.460
 OEN  C7   N2   single    1.458  0.020  1.458
 OEN  N    N2   aromatic  1.334  0.020  1.334
 OEN  N    C5   aromatic  1.320  0.020  1.320
 OEN  N2   C6   aromatic  1.321  0.020  1.321
 OEN  C5   N1   aromatic  1.327  0.020  1.327
 OEN  C6   N1   aromatic  1.327  0.020  1.327
 OEN  C1   H2   single    0.970  0.020  1.090
 OEN  C11  H4   single    0.970  0.020  1.090
 OEN  C12  H5   single    0.970  0.020  1.090
 OEN  C13  H6   single    0.970  0.020  1.090
 OEN  C13  H7   single    0.970  0.020  1.090
 OEN  C13  H8   single    0.970  0.020  1.090
 OEN  C2   H9   single    0.970  0.020  1.090
 OEN  C3   H10  single    0.970  0.020  1.090
 OEN  C4   H11  single    0.970  0.020  1.090
 OEN  C4   H12  single    0.970  0.020  1.090
 OEN  C5   H13  single    0.930  0.020  1.080
 OEN  C6   H14  single    0.930  0.020  1.080
 OEN  C7   H15  single    0.970  0.020  1.090
 OEN  C7   H16  single    0.970  0.020  1.090
 OEN  C8   H17  single    0.970  0.020  1.090
 OEN  C9   H18  single    0.970  0.020  1.090
 OEN  C9   H19  single    0.970  0.020  1.090
 OEN  C9   H20  single    0.970  0.020  1.090
 OEN  O1   H23  single    0.850  0.020  0.980

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
 OEN  N2   N    C5   107.05  3.000
 OEN  C5   N    C4   141.05  3.000
 OEN  N2   N    C4   111.89  3.000
 OEN  H2   C1   N3   107.36  3.000
 OEN  H2   C1   C2   110.09  3.000
 OEN  N3   C1   C2   105.46  3.000
 OEN  H2   C1   C    106.57  3.000
 OEN  C2   C1   C    116.13  3.000
 OEN  N3   C1   C    110.97  3.000
 OEN  N3   C10  C8   115.40  3.000
 OEN  C8   C10  C11  121.79  3.000
 OEN  N3   C10  C11  122.76  3.000
 OEN  H4   C11  C14  107.18  3.000
 OEN  H4   C11  C12  106.32  3.000
 OEN  C14  C11  C12  113.22  3.000
 OEN  H4   C11  C10  108.12  3.000
 OEN  C14  C11  C10  108.72  3.000
 OEN  C12  C11  C10  112.97  3.000
 OEN  H5   C12  O1   110.38  3.000
 OEN  H5   C12  C13  107.29  3.000
 OEN  O1   C12  C13  109.16  3.000
 OEN  H5   C12  C11  105.23  3.000
 OEN  C13  C12  C11  112.40  3.000
 OEN  O1   C12  C11  112.21  3.000
 OEN  H8   C13  H7   107.74  3.000
 OEN  H8   C13  H6   107.71  3.000
 OEN  H7   C13  H6   108.11  3.000
 OEN  H8   C13  C12  110.77  3.000
 OEN  H7   C13  C12  111.59  3.000
 OEN  H6   C13  C12  110.77  3.000
 OEN  O3   C14  O2   126.33  3.000
 OEN  O3   C14  C11  116.66  3.000
 OEN  O2   C14  C11  117.00  3.000
 OEN  H9   C2   S    108.42  3.000
 OEN  H9   C2   C8   109.12  3.000
 OEN  S    C2   C8   108.19  3.000
 OEN  H9   C2   C1   109.87  3.000
 OEN  S    C2   C1   116.57  3.000
 OEN  C8   C2   C1   104.43  3.000
 OEN  H10  C3   S    110.03  3.000
 OEN  H10  C3   C7   109.05  3.000
 OEN  S    C3   C7   109.69  3.000
 OEN  H10  C3   C4   108.73  3.000
 OEN  C7   C3   C4   104.64  3.000
 OEN  S    C3   C4   114.48  3.000
 OEN  H12  C4   H11  110.95  3.000
 OEN  H12  C4   C3   112.24  3.000
 OEN  H11  C4   C3   112.71  3.000
 OEN  H12  C4   N    110.73  3.000
 OEN  H11  C4   N    108.85  3.000
 OEN  C3   C4   N    100.91  3.000
 OEN  H13  C5   N1   126.61  3.000
 OEN  H13  C5   N    123.11  3.000
 OEN  N1   C5   N    110.28  3.000
 OEN  H14  C6   N2   123.09  3.000
 OEN  H14  C6   N1   126.69  3.000
 OEN  N2   C6   N1   110.21  3.000
 OEN  H16  C7   H15  110.02  3.000
 OEN  H16  C7   N2   108.71  3.000
 OEN  H15  C7   N2   110.10  3.000
 OEN  H16  C7   C3   113.27  3.000
 OEN  H15  C7   C3   113.46  3.000
 OEN  N2   C7   C3   100.84  3.000
 OEN  H17  C8   C9   108.56  3.000
 OEN  H17  C8   C2   111.08  3.000
 OEN  C9   C8   C2   113.37  3.000
 OEN  H17  C8   C10  107.10  3.000
 OEN  C2   C8   C10  100.53  3.000
 OEN  C9   C8   C10  115.90  3.000
 OEN  H20  C9   H19  108.17  3.000
 OEN  H20  C9   H18  108.02  3.000
 OEN  H19  C9   H18  107.39  3.000
 OEN  H20  C9   C8   111.01  3.000
 OEN  H19  C9   C8   111.98  3.000
 OEN  H18  C9   C8   110.11  3.000
 OEN  C6   N1   C5   105.33  3.000
 OEN  C7   N2   C6   140.69  3.000
 OEN  C6   N2   N    107.13  3.000
 OEN  C7   N2   N    112.18  3.000
 OEN  C10  N3   C1   110.28  3.000
 OEN  H23  O1   C12  102.26  3.000
 OEN  C3   S    C2   102.61  3.000
 OEN  O4   C    C1   115.48  3.000
 OEN  O4   C    O    127.14  3.000
 OEN  C1   C    O    117.37  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
 OEN  CONST_01  N1   C6   N2  N     0.00   0.0  0
 OEN  CONST_02  C6   N1   C5  N     0.00   0.0  0
 OEN  CONST_03  C6   N2   N   C5    0.00   0.0  0
 OEN  CONST_04  N2   C6   N1  C5    0.00   0.0  0
 OEN  CONST_05  N2   N    C5  N1    0.00   0.0  0
 OEN  CONST_06  H14  C6   N2  N   180.00   0.0  0
 OEN  CONST_07  H13  C5   N   C4    0.00   0.0  0
 OEN  Var_01    C3   C7   N2  N   -18.26  30.0  1
 OEN  Var_02    C8   C10  N3  C1   -0.01  30.0  1
 OEN  Var_03    N2   N    C4  C3   19.14  30.0  1

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
 OEN  chir_01  C1   N3   C2   C    negativ
 OEN  chir_02  C11  C12  C14  C10  negativ
 OEN  chir_03  C12  O1   C11  C13  negativ
 OEN  chir_04  C2   S    C8   C1   negativ
 OEN  chir_05  C3   S    C4   C7   positiv
 OEN  chir_06  C8   C2   C9   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
 OEN  plan-1  C11  0.020
 OEN  plan-1  C14  0.020
 OEN  plan-1  O2   0.020
 OEN  plan-1  O3   0.020
 OEN  plan-2  N    0.020
 OEN  plan-2  C4   0.020
 OEN  plan-2  C5   0.020
 OEN  plan-2  C6   0.020
 OEN  plan-2  C7   0.020
 OEN  plan-2  N1   0.020
 OEN  plan-2  N2   0.020
 OEN  plan-2  H13  0.020
 OEN  plan-2  H14  0.020
 OEN  plan-3  O    0.020
 OEN  plan-3  C1   0.020
 OEN  plan-3  C    0.020
 OEN  plan-3  O4   0.020

