# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:27:51 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: (~{Z})-7-[(1~{R},5~{S})-2-oxidanylidene-5-[(~{E},3~{S})-3-oxidanyloct-1-enyl]cyclopent-3-en-1-yl]hept-5-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](O)\C=C\[C@H]1C=CC(=O)[C@@H]1C\C=C/CCCC(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
 8SU  8SU  '(~{Z})-7-[(1~{R},5~{S})-2-oxidanylidene-5-[(~{E},3~{S})-3-oxidanyloct-1-enyl]cyclopent-3-en-1-yl]hept-5-enoic acid'  ligand  53  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8SU
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
 8SU  O9   O  O      0  -0.414  -2.0168  -4.9247  -0.1369
 8SU  C9   C  CR5    0   0.381  -1.0173  -4.2595  -0.3071
 8SU  C10  C  CR15   0  -0.335   0.3015  -4.7645  -0.7105
 8SU  C11  C  CR15   0  -0.140   1.1175  -3.7380  -0.9565
 8SU  C12  C  CR15   0  -0.384   0.4670  -2.3981  -0.7540
 8SU  C13  C  C1     0  -0.179   1.2926  -1.4780   0.0911
 8SU  C14  C  C1     0  -0.255   1.7714  -0.3143  -0.3339
 8SU  C15  C  CH1    0   0.004   2.6568   0.6132   0.4489
 8SU  C16  C  CH2    0  -0.465   3.9566   0.8541  -0.3243
 8SU  C17  C  CH2    0  -0.413   4.9206   1.8184   0.3549
 8SU  C18  C  CH2    0  -0.407   6.1702   2.0694  -0.4808
 8SU  C19  C  CH2    0  -0.419   7.1777   2.9877   0.2000
 8SU  C20  C  CH3    0  -0.662   8.4229   3.2218  -0.6444
 8SU  O15  O  OH1    0  -0.662   2.8857   0.1780   1.7677
 8SU  C8   C  CR15   0  -0.351  -0.9048  -2.7506  -0.1470
 8SU  C7   C  CH2    0  -0.506  -2.0577  -1.9400  -0.7473
 8SU  C6   C  C1     0  -0.211  -3.3588  -2.0740  -0.0162
 8SU  C5   C  C1     0  -0.207  -3.9310  -1.1441   0.7476
 8SU  C4   C  CH2    0  -0.489  -3.4174   0.2274   1.0559
 8SU  C3   C  CH2    0  -0.403  -4.1887   1.3242   0.3170
 8SU  C2   C  CH2    0  -0.578  -3.7122   2.7161   0.6993
 8SU  C1   C  C      0   0.409  -4.4307   3.8894   0.0105
 8SU  O1   O  OC    -1  -0.633  -3.9007   5.0125   0.1487
 8SU  O2   O  O      0  -0.610  -5.4830   3.6439  -0.6120
 8SU  H1   H  HCR5   0   0.272   0.5339  -5.8145  -0.8230
 8SU  H3   H  HCR5   0   0.282   2.1439  -3.8228  -1.2909
 8SU  H5   H  HCR5   0   0.285   0.3293  -1.9373  -1.7404
 8SU  H6   H  H      0   0.245   1.4930  -1.8200   1.1034
 8SU  H8   H  H      0   0.246   1.5510   0.0109  -1.3485
 8SU  H10  H  HCH1   0   0.236   2.1402   1.5767   0.5434
 8SU  H11  H  HCH2   0   0.224   4.4551  -0.1076  -0.4963
 8SU  H12  H  HCH2   0   0.228   3.6973   1.2388  -1.3156
 8SU  H13  H  HCH2   0   0.212   4.4129   2.7699   0.5479
 8SU  H14  H  HCH2   0   0.213   5.2134   1.4238   1.3319
 8SU  H15  H  HCH2   0   0.207   6.6527   1.1118  -0.7079
 8SU  H16  H  HCH2   0   0.208   5.8846   2.4993  -1.4472
 8SU  H17  H  HCH2   0   0.211   6.7000   3.9460   0.4265
 8SU  H18  H  HCH2   0   0.210   7.4620   2.5557   1.1643
 8SU  H19  H  HCH3   0   0.215   8.9328   2.2809  -0.8611
 8SU  H20  H  HCH3   0   0.216   8.1691   3.6847  -1.6001
 8SU  H21  H  HCH3   0   0.226   9.1355   3.8758  -0.1406
 8SU  H22  H  HOH1   0   0.445   3.4531  -0.6006   1.7368
 8SU  H23  H  HCR5   0   0.293  -0.8686  -2.5603   0.9337
 8SU  H24  H  HCH2   0   0.249  -1.7425  -0.8946  -0.7754
 8SU  H25  H  HCH2   0   0.248  -2.1953  -2.2430  -1.7903
 8SU  H26  H  H      0   0.234  -3.8715  -3.0223  -0.1296
 8SU  H27  H  H      0   0.228  -4.8930  -1.3867   1.1916
 8SU  H28  H  HCH2   0   0.226  -3.5070   0.3980   2.1344
 8SU  H29  H  HCH2   0   0.220  -2.3528   0.3139   0.8246
 8SU  H30  H  HCH2   0   0.209  -4.0771   1.1713  -0.7604
 8SU  H31  H  HCH2   0   0.209  -5.2561   1.2252   0.5294
 8SU  H32  H  HCH2   0   0.221  -3.8187   2.8472   1.7838
 8SU  H33  H  HCH2   0   0.213  -2.6367   2.8036   0.5101

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
 8SU  O15  C15  single  1.407  0.020  1.407
 8SU  C20  C19  single  1.523  0.020  1.523
 8SU  C17  C16  single  1.523  0.020  1.523
 8SU  C17  C18  single  1.524  0.020  1.524
 8SU  C15  C16  single  1.531  0.020  1.531
 8SU  C15  C14  single  1.502  0.020  1.502
 8SU  C19  C18  single  1.524  0.020  1.524
 8SU  C14  C13  double  1.328  0.020  1.328
 8SU  C13  C12  single  1.497  0.020  1.497
 8SU  O2   C1   deloc   1.247  0.020  1.247
 8SU  C1   C2   single  1.539  0.020  1.539
 8SU  C1   O1   deloc   1.250  0.020  1.250
 8SU  C11  C12  single  1.503  0.020  1.503
 8SU  C11  C10  double  1.334  0.020  1.334
 8SU  C12  C8   single  1.541  0.020  1.541
 8SU  C2   C3   single  1.520  0.020  1.520
 8SU  C3   C4   single  1.531  0.020  1.531
 8SU  C10  C9   single  1.469  0.020  1.469
 8SU  C8   C7   single  1.532  0.020  1.532
 8SU  C8   C9   single  1.522  0.020  1.522
 8SU  C7   C6   single  1.498  0.020  1.498
 8SU  C4   C5   single  1.497  0.020  1.497
 8SU  C9   O9   double  1.213  0.020  1.213
 8SU  C6   C5   double  1.332  0.020  1.332
 8SU  C10  H1   single  0.930  0.020  1.080
 8SU  C11  H3   single  0.930  0.020  1.080
 8SU  C12  H5   single  0.970  0.020  1.090
 8SU  C13  H6   single  0.930  0.020  1.080
 8SU  C14  H8   single  0.930  0.020  1.080
 8SU  C15  H10  single  0.970  0.020  1.090
 8SU  C16  H11  single  0.970  0.020  1.090
 8SU  C16  H12  single  0.970  0.020  1.090
 8SU  C17  H13  single  0.970  0.020  1.090
 8SU  C17  H14  single  0.970  0.020  1.090
 8SU  C18  H15  single  0.970  0.020  1.090
 8SU  C18  H16  single  0.970  0.020  1.090
 8SU  C19  H17  single  0.970  0.020  1.090
 8SU  C19  H18  single  0.970  0.020  1.090
 8SU  C20  H19  single  0.970  0.020  1.090
 8SU  C20  H20  single  0.970  0.020  1.090
 8SU  C20  H21  single  0.970  0.020  1.090
 8SU  O15  H22  single  0.850  0.020  0.980
 8SU  C8   H23  single  0.970  0.020  1.090
 8SU  C7   H24  single  0.970  0.020  1.090
 8SU  C7   H25  single  0.970  0.020  1.090
 8SU  C6   H26  single  0.930  0.020  1.080
 8SU  C5   H27  single  0.930  0.020  1.080
 8SU  C4   H28  single  0.970  0.020  1.090
 8SU  C4   H29  single  0.970  0.020  1.090
 8SU  C3   H30  single  0.970  0.020  1.090
 8SU  C3   H31  single  0.970  0.020  1.090
 8SU  C2   H32  single  0.970  0.020  1.090
 8SU  C2   H33  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
 8SU  C8   C9   C10  107.67  3.000
 8SU  C8   C9   O9   126.17  3.000
 8SU  C10  C9   O9   126.16  3.000
 8SU  H1   C10  C11  126.62  3.000
 8SU  H1   C10  C9   123.74  3.000
 8SU  C11  C10  C9   109.59  3.000
 8SU  H3   C11  C12  121.44  3.000
 8SU  H3   C11  C10  125.20  3.000
 8SU  C12  C11  C10  113.35  3.000
 8SU  H5   C12  C8   109.78  3.000
 8SU  H5   C12  C13  108.57  3.000
 8SU  C8   C12  C13  114.15  3.000
 8SU  H5   C12  C11  107.91  3.000
 8SU  C8   C12  C11  103.56  3.000
 8SU  C13  C12  C11  112.65  3.000
 8SU  H6   C13  C14  120.48  3.000
 8SU  H6   C13  C12  115.71  3.000
 8SU  C14  C13  C12  123.81  3.000
 8SU  H8   C14  C15  114.88  3.000
 8SU  H8   C14  C13  119.16  3.000
 8SU  C15  C14  C13  125.92  3.000
 8SU  H10  C15  O15  105.51  3.000
 8SU  H10  C15  C16  107.75  3.000
 8SU  O15  C15  C16  112.56  3.000
 8SU  H10  C15  C14  108.03  3.000
 8SU  C16  C15  C14  109.52  3.000
 8SU  O15  C15  C14  113.15  3.000
 8SU  H12  C16  H11  105.89  3.000
 8SU  H12  C16  C17  109.34  3.000
 8SU  H11  C16  C17  109.71  3.000
 8SU  H12  C16  C15  108.15  3.000
 8SU  H11  C16  C15  109.09  3.000
 8SU  C17  C16  C15  114.30  3.000
 8SU  H14  C17  H13  106.26  3.000
 8SU  H14  C17  C18  109.26  3.000
 8SU  H13  C17  C18  109.48  3.000
 8SU  H14  C17  C16  109.84  3.000
 8SU  H13  C17  C16  109.57  3.000
 8SU  C18  C17  C16  112.25  3.000
 8SU  H16  C18  H15  105.95  3.000
 8SU  H16  C18  C19  109.27  3.000
 8SU  H15  C18  C19  109.15  3.000
 8SU  H16  C18  C17  109.55  3.000
 8SU  H15  C18  C17  109.31  3.000
 8SU  C19  C18  C17  113.35  3.000
 8SU  H18  C19  H17  106.06  3.000
 8SU  H18  C19  C20  109.69  3.000
 8SU  H17  C19  C20  109.70  3.000
 8SU  H18  C19  C18  109.12  3.000
 8SU  H17  C19  C18  109.36  3.000
 8SU  C20  C19  C18  112.68  3.000
 8SU  H21  C20  H20  107.58  3.000
 8SU  H21  C20  H19  107.65  3.000
 8SU  H20  C20  H19  107.47  3.000
 8SU  H21  C20  C19  111.74  3.000
 8SU  H20  C20  C19  111.13  3.000
 8SU  H19  C20  C19  111.07  3.000
 8SU  H22  O15  C15  108.39  3.000
 8SU  H23  C8   C7   108.59  3.000
 8SU  H23  C8   C12  108.59  3.000
 8SU  C7   C8   C12  113.24  3.000
 8SU  H23  C8   C9   106.13  3.000
 8SU  C7   C8   C9   115.33  3.000
 8SU  C12  C8   C9   104.55  3.000
 8SU  H25  C7   H24  106.06  3.000
 8SU  H25  C7   C6   109.33  3.000
 8SU  H24  C7   C6   110.41  3.000
 8SU  H25  C7   C8   108.75  3.000
 8SU  H24  C7   C8   107.42  3.000
 8SU  C6   C7   C8   114.51  3.000
 8SU  H26  C6   C5   117.87  3.000
 8SU  H26  C6   C7   115.97  3.000
 8SU  C5   C6   C7   126.17  3.000
 8SU  H27  C5   C4   115.09  3.000
 8SU  H27  C5   C6   117.28  3.000
 8SU  C4   C5   C6   127.61  3.000
 8SU  H29  C4   H28  106.00  3.000
 8SU  H29  C4   C3   109.38  3.000
 8SU  H28  C4   C3   108.81  3.000
 8SU  H29  C4   C5   111.30  3.000
 8SU  H28  C4   C5   108.51  3.000
 8SU  C3   C4   C5   112.60  3.000
 8SU  H31  C3   H30  106.17  3.000
 8SU  H31  C3   C2   109.89  3.000
 8SU  H30  C3   C2   110.10  3.000
 8SU  H31  C3   C4   109.47  3.000
 8SU  H30  C3   C4   108.89  3.000
 8SU  C2   C3   C4   112.13  3.000
 8SU  H33  C2   H32  104.85  3.000
 8SU  H33  C2   C1   108.68  3.000
 8SU  H32  C2   C1   107.82  3.000
 8SU  H33  C2   C3   109.72  3.000
 8SU  H32  C2   C3   109.11  3.000
 8SU  C1   C2   C3   116.06  3.000
 8SU  O2   C1   O1   126.17  3.000
 8SU  O1   C1   C2   115.96  3.000
 8SU  O2   C1   C2   117.86  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
 8SU  Var_01  C12  C11  C10  C9      0.02  30.0  1
 8SU  Var_02  C8   C9   C10  C11    -7.21  30.0  1
 8SU  Var_03  C15  C14  C13  C12  -176.89   0.0  2
 8SU  Var_04  C5   C6   C7   C8    107.67  30.0  3
 8SU  Var_05  C4   C5   C6   C7     -0.28   0.0  2
 8SU  Var_06  C18  C17  C16  C15  -177.60  30.0  2
 8SU  Var_07  C19  C18  C17  C16  -177.71  30.0  3
 8SU  Var_08  C20  C19  C18  C17   179.68  30.0  2
 8SU  Var_09  C3   C4   C5   C6    106.29  30.0  1
 8SU  Var_10  C2   C3   C4   C5    176.67  30.0  2
 8SU  Var_11  C1   C2   C3   C4   -179.85  30.0  1
 8SU  Var_12  O2   C1   C2   C3     12.40  30.0  2
 8SU  Var_13  H19  C20  C19  C18   -59.44  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
 8SU  chir_01  C12  C13  C11  C8   negativ
 8SU  chir_02  C15  O15  C16  C14  negativ
 8SU  chir_03  C8   C9   C7   C12  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
 8SU  plan-1  O9   0.020
 8SU  plan-1  C9   0.020
 8SU  plan-1  C10  0.020
 8SU  plan-1  C8   0.020
 8SU  plan-2  C2   0.020
 8SU  plan-2  C1   0.020
 8SU  plan-2  O1   0.020
 8SU  plan-2  O2   0.020
 8SU  plan-3  C12  0.020
 8SU  plan-3  C13  0.020
 8SU  plan-3  C14  0.020
 8SU  plan-3  C15  0.020
 8SU  plan-3  H6   0.020
 8SU  plan-3  H8   0.020
 8SU  plan-4  C7   0.020
 8SU  plan-4  C6   0.020
 8SU  plan-4  C5   0.020
 8SU  plan-4  C4   0.020
 8SU  plan-4  H26  0.020
 8SU  plan-4  H27  0.020

