# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 21:34:12 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 6-({5-[(3aS,4S,5S,6aR)-5-oxido-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCNC(=O)CCCC[C@H]1[C@H]2NC(=O)N[C@H]2C[S@]1=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
 ZOE  ZOE  '6-({5-[(3aS,4S,5S,6aR)-5-oxido-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid'  ligand  52  25  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZOE
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
 ZOE  OAD  O  O     0  -0.760  -2.2772  -4.5634  -20.7879
 ZOE  SAY  S  S3    0   0.747  -2.0213  -5.8411  -20.0264
 ZOE  CAO  C  CH2   0  -0.622  -3.6451  -6.5847  -19.6398
 ZOE  CAV  C  CR15  0  -0.051  -3.4967  -8.1091  -19.6987
 ZOE  NAQ  N  NR15  0  -0.655  -3.3099  -8.7489  -18.4228
 ZOE  CAU  C  CR5   0   0.642  -2.0042  -9.0323  -18.1661
 ZOE  OAC  O  O     0  -0.511  -1.5458  -9.4697  -17.1256
 ZOE  NAR  N  NR15  0  -0.658  -1.2950  -8.7310  -19.2988
 ZOE  CAX  C  CR15  0  -0.121  -2.1644  -8.4410  -20.4200
 ZOE  CAW  C  CH1   0  -0.413  -1.7121  -7.2187  -21.2012
 ZOE  CAN  C  CH2   0  -0.419  -0.2774  -7.2737  -21.6981
 ZOE  CAJ  C  CH2   0  -0.441   0.1189  -6.0621  -22.5330
 ZOE  CAI  C  CH2   0  -0.426   1.4737  -6.2332  -23.2111
 ZOE  CAM  C  CH2   0  -0.564   1.9605  -4.9489  -23.8919
 ZOE  CAT  C  C     0   0.516   0.9188  -4.4570  -24.8727
 ZOE  OAB  O  O     0  -0.504   0.6804  -5.0562  -25.9145
 ZOE  NAP  N  NH1   0  -0.614   0.2499  -3.3556  -24.4891
 ZOE  CAK  C  CH2   0  -0.287  -0.9795  -2.9053  -25.1055
 ZOE  CAG  C  CH2   0  -0.436  -2.1980  -3.6369  -24.5524
 ZOE  CAF  C  CH2   0  -0.427  -3.5121  -3.1055  -25.1047
 ZOE  CAH  C  CH2   0  -0.434  -4.7110  -3.8205  -24.4931
 ZOE  CAL  C  CH2   0  -0.555  -6.0574  -3.2734  -24.9648
 ZOE  CAS  C  C     0   0.526  -6.2759  -3.3671  -26.4502
 ZOE  OAA  O  OH1   0  -0.592  -6.0648  -4.5952  -26.9155
 ZOE  OAE  O  O     0  -0.449  -6.6184  -2.4519  -27.1587
 ZOE  H2   H  HCH2  0   0.307  -3.9984  -6.2239  -18.6749
 ZOE  H3   H  HCH2  0   0.301  -4.3144  -6.2209  -20.4221
 ZOE  H4   H  HCR5  0   0.299  -4.3501  -8.5331  -20.2263
 ZOE  H5   H  HNR5  0   0.404  -3.9687  -8.6346  -17.6696
 ZOE  H6   H  HNR5  0   0.405  -0.4133  -9.1959  -19.4487
 ZOE  H7   H  HCR5  0   0.301  -2.2658  -9.2993  -21.0909
 ZOE  H8   H  HCH1  0   0.303  -2.3987  -7.0510  -22.0395
 ZOE  H9   H  HCH2  0   0.248  -0.1769  -8.1788  -22.3070
 ZOE  H10  H  HCH2  0   0.241   0.4111  -7.3853  -20.8560
 ZOE  H11  H  HCH2  0   0.226   0.1301  -5.1645  -21.9098
 ZOE  H12  H  HCH2  0   0.236  -0.6538  -5.8962  -23.2882
 ZOE  H13  H  HCH2  0   0.229   1.4154  -7.0390  -23.9471
 ZOE  H14  H  HCH2  0   0.235   2.2226  -6.5377  -22.4753
 ZOE  H15  H  HCH2  0   0.265   2.8916  -5.1433  -24.4273
 ZOE  H16  H  HCH2  0   0.245   2.1724  -4.1934  -23.1319
 ZOE  H17  H  HNH1  0   0.396   0.4644  -2.9722  -23.5830
 ZOE  H18  H  HCH2  0   0.239  -0.9073  -3.0389  -26.1852
 ZOE  H19  H  HCH2  0   0.243  -1.0698  -1.8329  -24.9239
 ZOE  H20  H  HCH2  0   0.233  -2.2001  -3.5642  -23.4604
 ZOE  H21  H  HCH2  0   0.222  -2.1085  -4.7023  -24.7823
 ZOE  H22  H  HCH2  0   0.221  -3.5197  -3.2174  -26.1946
 ZOE  H23  H  HCH2  0   0.219  -3.5895  -2.0310  -24.9074
 ZOE  H24  H  HCH2  0   0.239  -4.6705  -3.7186  -23.4056
 ZOE  H25  H  HCH2  0   0.230  -4.6463  -4.8921  -24.6955
 ZOE  H26  H  HCH2  0   0.258  -6.1665  -2.2276  -24.6758
 ZOE  H27  H  HCH2  0   0.282  -6.8658  -3.8251  -24.4750
 ZOE  H28  H  HOH1  0   0.479  -6.2185  -4.6162  -27.8719

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
 ZOE  OAE  CAS  double  1.207  0.020  1.207
 ZOE  CAS  OAA  single  1.330  0.020  1.330
 ZOE  CAS  CAL  single  1.504  0.020  1.504
 ZOE  CAL  CAH  single  1.528  0.020  1.528
 ZOE  CAH  CAF  single  1.524  0.020  1.524
 ZOE  CAF  CAG  single  1.521  0.020  1.521
 ZOE  CAK  CAG  single  1.525  0.020  1.525
 ZOE  CAK  NAP  single  1.447  0.020  1.447
 ZOE  OAB  CAT  double  1.225  0.020  1.225
 ZOE  CAT  NAP  single  1.345  0.020  1.345
 ZOE  CAT  CAM  single  1.513  0.020  1.513
 ZOE  CAM  CAI  single  1.533  0.020  1.533
 ZOE  CAI  CAJ  single  1.525  0.020  1.525
 ZOE  CAJ  CAN  single  1.524  0.020  1.524
 ZOE  CAN  CAW  single  1.519  0.020  1.519
 ZOE  CAW  CAX  single  1.520  0.020  1.520
 ZOE  CAW  SAY  single  1.837  0.020  1.837
 ZOE  NAR  CAX  single  1.448  0.020  1.448
 ZOE  NAR  CAU  single  1.370  0.020  1.370
 ZOE  CAX  CAV  single  1.551  0.020  1.551
 ZOE  OAD  SAY  double  1.509  0.020  1.509
 ZOE  SAY  CAO  single  1.827  0.020  1.827
 ZOE  CAU  OAC  double  1.218  0.020  1.218
 ZOE  CAU  NAQ  single  1.361  0.020  1.361
 ZOE  CAV  CAO  single  1.533  0.020  1.533
 ZOE  CAV  NAQ  single  1.439  0.020  1.439
 ZOE  CAO  H2   single  0.970  0.020  1.090
 ZOE  CAO  H3   single  0.970  0.020  1.090
 ZOE  CAV  H4   single  0.970  0.020  1.090
 ZOE  NAQ  H5   single  0.890  0.020  1.040
 ZOE  NAR  H6   single  0.890  0.020  1.040
 ZOE  CAX  H7   single  0.970  0.020  1.090
 ZOE  CAW  H8   single  0.970  0.020  1.090
 ZOE  CAN  H9   single  0.970  0.020  1.090
 ZOE  CAN  H10  single  0.970  0.020  1.090
 ZOE  CAJ  H11  single  0.970  0.020  1.090
 ZOE  CAJ  H12  single  0.970  0.020  1.090
 ZOE  CAI  H13  single  0.970  0.020  1.090
 ZOE  CAI  H14  single  0.970  0.020  1.090
 ZOE  CAM  H15  single  0.970  0.020  1.090
 ZOE  CAM  H16  single  0.970  0.020  1.090
 ZOE  NAP  H17  single  0.860  0.020  1.020
 ZOE  CAK  H18  single  0.970  0.020  1.090
 ZOE  CAK  H19  single  0.970  0.020  1.090
 ZOE  CAG  H20  single  0.970  0.020  1.090
 ZOE  CAG  H21  single  0.970  0.020  1.090
 ZOE  CAF  H22  single  0.970  0.020  1.090
 ZOE  CAF  H23  single  0.970  0.020  1.090
 ZOE  CAH  H24  single  0.970  0.020  1.090
 ZOE  CAH  H25  single  0.970  0.020  1.090
 ZOE  CAL  H26  single  0.970  0.020  1.090
 ZOE  CAL  H27  single  0.970  0.020  1.090
 ZOE  OAA  H28  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
 ZOE  CAW  SAY  CAO   88.84  3.000
 ZOE  CAO  SAY  OAD  107.49  3.000
 ZOE  CAW  SAY  OAD  109.93  3.000
 ZOE  H3   CAO  H2   109.00  3.000
 ZOE  H3   CAO  CAV  111.29  3.000
 ZOE  H2   CAO  CAV  113.26  3.000
 ZOE  H3   CAO  SAY  104.93  3.000
 ZOE  H2   CAO  SAY  109.94  3.000
 ZOE  CAV  CAO  SAY  108.09  3.000
 ZOE  H4   CAV  CAX  111.38  3.000
 ZOE  H4   CAV  NAQ  110.98  3.000
 ZOE  CAX  CAV  NAQ  101.87  3.000
 ZOE  H4   CAV  CAO  109.26  3.000
 ZOE  NAQ  CAV  CAO  114.87  3.000
 ZOE  CAX  CAV  CAO  108.29  3.000
 ZOE  H5   NAQ  CAU  120.68  3.000
 ZOE  H5   NAQ  CAV  121.85  3.000
 ZOE  CAU  NAQ  CAV  112.60  3.000
 ZOE  NAR  CAU  OAC  126.19  3.000
 ZOE  OAC  CAU  NAQ  126.66  3.000
 ZOE  NAR  CAU  NAQ  107.15  3.000
 ZOE  H6   NAR  CAX  120.15  3.000
 ZOE  H6   NAR  CAU  118.32  3.000
 ZOE  CAX  NAR  CAU  111.93  3.000
 ZOE  H7   CAX  CAW  110.08  3.000
 ZOE  H7   CAX  NAR  111.92  3.000
 ZOE  CAW  CAX  NAR  112.36  3.000
 ZOE  H7   CAX  CAV  111.93  3.000
 ZOE  NAR  CAX  CAV  101.45  3.000
 ZOE  CAW  CAX  CAV  108.83  3.000
 ZOE  H8   CAW  CAN  110.29  3.000
 ZOE  H8   CAW  CAX  109.25  3.000
 ZOE  CAN  CAW  CAX  114.84  3.000
 ZOE  H8   CAW  SAY  105.60  3.000
 ZOE  CAX  CAW  SAY  102.97  3.000
 ZOE  CAN  CAW  SAY  113.29  3.000
 ZOE  H10  CAN  H9   106.62  3.000
 ZOE  H10  CAN  CAJ  109.84  3.000
 ZOE  H9   CAN  CAJ  109.18  3.000
 ZOE  H10  CAN  CAW  110.27  3.000
 ZOE  H9   CAN  CAW  107.36  3.000
 ZOE  CAJ  CAN  CAW  113.33  3.000
 ZOE  H12  CAJ  H11  106.06  3.000
 ZOE  H12  CAJ  CAI  109.75  3.000
 ZOE  H11  CAJ  CAI  109.67  3.000
 ZOE  H12  CAJ  CAN  108.38  3.000
 ZOE  H11  CAJ  CAN  110.08  3.000
 ZOE  CAI  CAJ  CAN  112.67  3.000
 ZOE  H14  CAI  H13  106.53  3.000
 ZOE  H14  CAI  CAM  108.35  3.000
 ZOE  H13  CAI  CAM  109.60  3.000
 ZOE  H14  CAI  CAJ  109.92  3.000
 ZOE  H13  CAI  CAJ  109.56  3.000
 ZOE  CAM  CAI  CAJ  112.69  3.000
 ZOE  H16  CAM  H15  107.39  3.000
 ZOE  H16  CAM  CAT  111.08  3.000
 ZOE  H15  CAM  CAT  109.11  3.000
 ZOE  H16  CAM  CAI  109.39  3.000
 ZOE  H15  CAM  CAI  109.85  3.000
 ZOE  CAT  CAM  CAI  109.97  3.000
 ZOE  NAP  CAT  OAB  123.12  3.000
 ZOE  NAP  CAT  CAM  115.08  3.000
 ZOE  OAB  CAT  CAM  121.75  3.000
 ZOE  H17  NAP  CAK  116.47  3.000
 ZOE  H17  NAP  CAT  117.56  3.000
 ZOE  CAK  NAP  CAT  123.78  3.000
 ZOE  H19  CAK  H18  106.90  3.000
 ZOE  H19  CAK  CAG  110.17  3.000
 ZOE  H18  CAK  CAG  110.68  3.000
 ZOE  H19  CAK  NAP  107.77  3.000
 ZOE  H18  CAK  NAP  109.11  3.000
 ZOE  CAG  CAK  NAP  112.03  3.000
 ZOE  H21  CAG  H20  105.94  3.000
 ZOE  H21  CAG  CAF  109.55  3.000
 ZOE  H20  CAG  CAF  109.72  3.000
 ZOE  H21  CAG  CAK  109.01  3.000
 ZOE  H20  CAG  CAK  109.36  3.000
 ZOE  CAF  CAG  CAK  113.01  3.000
 ZOE  H23  CAF  H22  106.20  3.000
 ZOE  H23  CAF  CAH  109.41  3.000
 ZOE  H22  CAF  CAH  110.23  3.000
 ZOE  H23  CAF  CAG  109.77  3.000
 ZOE  H22  CAF  CAG  109.36  3.000
 ZOE  CAH  CAF  CAG  111.72  3.000
 ZOE  H25  CAH  H24  105.88  3.000
 ZOE  H25  CAH  CAL  110.26  3.000
 ZOE  H24  CAH  CAL  107.84  3.000
 ZOE  H25  CAH  CAF  109.83  3.000
 ZOE  H24  CAH  CAF  109.05  3.000
 ZOE  CAL  CAH  CAF  113.66  3.000
 ZOE  H27  CAL  H26  106.92  3.000
 ZOE  H27  CAL  CAS  107.65  3.000
 ZOE  H26  CAL  CAS  107.87  3.000
 ZOE  H27  CAL  CAH  109.40  3.000
 ZOE  H26  CAL  CAH  110.47  3.000
 ZOE  CAS  CAL  CAH  114.23  3.000
 ZOE  OAE  CAS  OAA  122.66  3.000
 ZOE  OAA  CAS  CAL  112.33  3.000
 ZOE  OAE  CAS  CAL  125.00  3.000
 ZOE  H28  OAA  CAS  109.89  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
 ZOE  CONST_01  NAR  CAU  NAQ  CAV     0.00   0.0  0
 ZOE  CONST_02  CAX  NAR  CAU  NAQ     0.00   0.0  0
 ZOE  CONST_03  OAC  CAU  NAQ  CAV   180.00   0.0  0
 ZOE  CONST_04  CAX  NAR  CAU  OAC   180.00   0.0  0
 ZOE  CONST_08  CAK  NAP  CAT  OAB     0.00   0.0  0
 ZOE  CONST_09  H17  NAP  CAT  CAM     0.00   0.0  0
 ZOE  CONST_10  H28  OAA  CAS  CAL   180.00   0.0  0
 ZOE  Var_01    CAW  SAY  CAO  CAV    34.79  30.0  1
 ZOE  Var_02    CAI  CAJ  CAN  CAW  -170.63  30.0  2
 ZOE  Var_03    CAM  CAI  CAJ  CAN  -172.17  30.0  1
 ZOE  Var_04    CAT  CAM  CAI  CAJ   -55.45  30.0  2
 ZOE  Var_05    OAB  CAT  CAM  CAI   -69.99  30.0  2
 ZOE  Var_06    CAG  CAK  NAP  CAT    82.50  30.0  2
 ZOE  Var_07    CAF  CAG  CAK  NAP   175.48  30.0  3
 ZOE  Var_08    CAH  CAF  CAG  CAK  -177.82  30.0  2
 ZOE  Var_09    CAL  CAH  CAF  CAG   177.10  30.0  1
 ZOE  Var_10    CAS  CAL  CAH  CAF    60.01  30.0  2
 ZOE  Var_11    OAE  CAS  CAL  CAH  -128.72  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
 ZOE  chir_02  CAV  CAX  CAO  NAQ  positiv
 ZOE  chir_03  CAX  NAR  CAW  CAV  positiv
 ZOE  chir_04  CAW  SAY  CAX  CAN  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
 ZOE  plan-1  CAM  0.020
 ZOE  plan-1  CAT  0.020
 ZOE  plan-1  OAB  0.020
 ZOE  plan-1  NAP  0.020
 ZOE  plan-1  CAK  0.020
 ZOE  plan-1  H17  0.020
 ZOE  plan-2  OAD  0.020
 ZOE  plan-2  SAY  0.020
 ZOE  plan-2  CAO  0.020
 ZOE  plan-2  CAW  0.020
 ZOE  plan-3  CAV  0.020
 ZOE  plan-3  NAQ  0.020
 ZOE  plan-3  CAU  0.020
 ZOE  plan-3  OAC  0.020
 ZOE  plan-3  NAR  0.020
 ZOE  plan-3  CAX  0.020
 ZOE  plan-3  H5   0.020
 ZOE  plan-3  H6   0.020
 ZOE  plan-4  CAL  0.020
 ZOE  plan-4  CAS  0.020
 ZOE  plan-4  OAA  0.020
 ZOE  plan-4  OAE  0.020
 ZOE  plan-4  H28  0.020

