# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 06:54:39 2020
#   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  51  25  .  2021-08-25  2021-08-25  
;
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  -0.779    4.2524  -2.8338   0.6810
 ZOE  SAY  S  S3     0   0.745    4.9858  -1.5140   0.7380
 ZOE  CAO  C  CH2    0  -0.591    6.6774  -1.7750   0.1226
 ZOE  CAV  C  CR15   0  -0.135    7.0851  -0.4240  -0.4166
 ZOE  NAQ  N  NR15   0  -0.654    7.2290   0.5544   0.6422
 ZOE  CAU  C  CR5    0   0.641    6.6884   1.7625   0.2909
 ZOE  OAC  O  O      0  -0.510    6.8208   2.8151   0.8893
 ZOE  NAR  N  NR15   0  -0.654    5.9737   1.5596  -0.8498
 ZOE  CAX  C  CR15   0  -0.034    5.8940   0.1700  -1.2117
 ZOE  CAW  C  CH1    0  -0.447    4.5998  -0.5648  -0.7925
 ZOE  CAN  C  CH2    0  -0.432    3.3751   0.3163  -0.6184
 ZOE  CAJ  C  CH2    0  -0.421    2.0856  -0.4569  -0.3650
 ZOE  CAI  C  CH2    0  -0.417    0.8815   0.4706  -0.2744
 ZOE  CAM  C  CH2    0  -0.577   -0.4118  -0.2913  -0.0166
 ZOE  CAT  C  C      0   0.556   -1.6008   0.6224   0.1983
 ZOE  OAB  O  O      0  -0.510   -1.5054   1.6689   0.8286
 ZOE  NAP  N  NH1    0  -0.642   -2.7600   0.1862  -0.3177
 ZOE  CAK  C  CH2    0  -0.244   -4.0219   0.8833  -0.1866
 ZOE  CAG  C  CH2    0  -0.455   -5.1925  -0.0877  -0.1679
 ZOE  CAF  C  CH2    0  -0.416   -6.5284   0.6349  -0.0516
 ZOE  CAH  C  CH2    0  -0.402   -7.7199  -0.3152  -0.0277
 ZOE  CAL  C  CH2    0  -0.581   -9.0471   0.4162   0.0858
 ZOE  CAS  C  C      0   0.410  -10.3076  -0.4663   0.1177
 ZOE  OAA  O  OC    -1  -0.634  -11.3917   0.1369   0.2697
 ZOE  OAE  O  O      0  -0.610  -10.1630  -1.6977  -0.0132
 ZOE  H2   H  HCH2   0   0.310    7.3182  -2.1338   0.9272
 ZOE  H3   H  HCH2   0   0.301    6.6251  -2.5301  -0.6646
 ZOE  H4   H  HCR5   0   0.301    7.9868  -0.4989  -1.0306
 ZOE  H5   H  HNR5   0   0.404    8.0456   0.5418   1.2335
 ZOE  H6   H  HNR5   0   0.405    5.3131   2.2456  -1.1764
 ZOE  H7   H  HCR5   0   0.298    6.0303   0.0410  -2.2847
 ZOE  H8   H  HCH1   0   0.309    4.3996  -1.3496  -1.5296
 ZOE  H9   H  HCH2   0   0.241    3.5421   1.0296   0.1940
 ZOE  H10  H  HCH2   0   0.251    3.2549   0.9122  -1.5295
 ZOE  H11  H  HCH2   0   0.224    1.9363  -1.1865  -1.1672
 ZOE  H12  H  HCH2   0   0.225    2.1617  -1.0350   0.5606
 ZOE  H13  H  HCH2   0   0.227    1.0417   1.1964   0.5256
 ZOE  H14  H  HCH2   0   0.226    0.7924   1.0448  -1.2020
 ZOE  H15  H  HCH2   0   0.248   -0.6017  -0.9972  -0.8292
 ZOE  H16  H  HCH2   0   0.265   -0.3036  -0.8971   0.8901
 ZOE  H17  H  HNH1   0   0.395   -2.7479  -0.6491  -0.8810
 ZOE  H18  H  HCH2   0   0.236   -4.0052   1.4606   0.7382
 ZOE  H19  H  HCH2   0   0.226   -4.1489   1.5999  -1.0055
 ZOE  H20  H  HCH2   0   0.222   -5.1841  -0.6930  -1.0810
 ZOE  H21  H  HCH2   0   0.224   -5.0725  -0.7827   0.6689
 ZOE  H22  H  HCH2   0   0.209   -6.5315   1.2479   0.8569
 ZOE  H23  H  HCH2   0   0.209   -6.6370   1.3347  -0.8877
 ZOE  H24  H  HCH2   0   0.203   -7.7095  -0.9285  -0.9335
 ZOE  H25  H  HCH2   0   0.203   -7.6070  -1.0122   0.8080
 ZOE  H26  H  HCH2   0   0.215   -9.0465   1.0448   0.9843
 ZOE  H27  H  HCH2   0   0.217   -9.1486   1.1212  -0.7484

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  deloc   1.247  0.020  1.247
 ZOE  CAS  OAA  deloc   1.250  0.020  1.250
 ZOE  CAS  CAL  single  1.539  0.020  1.539
 ZOE  CAL  CAH  single  1.520  0.020  1.520
 ZOE  CAH  CAF  single  1.524  0.020  1.524
 ZOE  CAF  CAG  single  1.523  0.020  1.523
 ZOE  CAK  CAG  single  1.521  0.020  1.521
 ZOE  CAK  NAP  single  1.448  0.020  1.448
 ZOE  OAB  CAT  double  1.225  0.020  1.225
 ZOE  CAT  NAP  single  1.342  0.020  1.342
 ZOE  CAT  CAM  single  1.515  0.020  1.515
 ZOE  CAM  CAI  single  1.523  0.020  1.523
 ZOE  CAI  CAJ  single  1.523  0.020  1.523
 ZOE  CAJ  CAN  single  1.525  0.020  1.525
 ZOE  CAN  CAW  single  1.519  0.020  1.519
 ZOE  CAW  CAX  single  1.546  0.020  1.546
 ZOE  CAW  SAY  single  1.842  0.020  1.842
 ZOE  NAR  CAX  single  1.438  0.020  1.438
 ZOE  NAR  CAU  single  1.361  0.020  1.361
 ZOE  CAX  CAV  single  1.550  0.020  1.550
 ZOE  OAD  SAY  double  1.511  0.020  1.511
 ZOE  SAY  CAO  single  1.819  0.020  1.819
 ZOE  CAU  OAC  double  1.218  0.020  1.218
 ZOE  CAU  NAQ  single  1.369  0.020  1.369
 ZOE  CAV  CAO  single  1.511  0.020  1.511
 ZOE  CAV  NAQ  single  1.449  0.020  1.449
 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

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   89.30  3.000
 ZOE  CAO  SAY  OAD  108.26  3.000
 ZOE  CAW  SAY  OAD  108.49  3.000
 ZOE  H3   CAO  H2   109.44  3.000
 ZOE  H3   CAO  CAV  111.96  3.000
 ZOE  H2   CAO  CAV  113.54  3.000
 ZOE  H3   CAO  SAY  107.37  3.000
 ZOE  H2   CAO  SAY  110.15  3.000
 ZOE  CAV  CAO  SAY  104.09  3.000
 ZOE  H4   CAV  CAX  111.83  3.000
 ZOE  H4   CAV  NAQ  112.01  3.000
 ZOE  CAX  CAV  NAQ  101.09  3.000
 ZOE  H4   CAV  CAO  111.21  3.000
 ZOE  NAQ  CAV  CAO  111.71  3.000
 ZOE  CAX  CAV  CAO  108.56  3.000
 ZOE  H5   NAQ  CAU  118.76  3.000
 ZOE  H5   NAQ  CAV  120.04  3.000
 ZOE  CAU  NAQ  CAV  111.66  3.000
 ZOE  NAR  CAU  OAC  126.69  3.000
 ZOE  OAC  CAU  NAQ  126.41  3.000
 ZOE  NAR  CAU  NAQ  106.90  3.000
 ZOE  H6   NAR  CAX  122.71  3.000
 ZOE  H6   NAR  CAU  120.98  3.000
 ZOE  CAX  NAR  CAU  112.58  3.000
 ZOE  H7   CAX  CAW  108.39  3.000
 ZOE  H7   CAX  NAR  110.81  3.000
 ZOE  CAW  CAX  NAR  115.93  3.000
 ZOE  H7   CAX  CAV  111.32  3.000
 ZOE  NAR  CAX  CAV  101.45  3.000
 ZOE  CAW  CAX  CAV  108.78  3.000
 ZOE  H8   CAW  CAN  110.21  3.000
 ZOE  H8   CAW  CAX  108.13  3.000
 ZOE  CAN  CAW  CAX  115.49  3.000
 ZOE  H8   CAW  SAY  103.19  3.000
 ZOE  CAX  CAW  SAY  107.14  3.000
 ZOE  CAN  CAW  SAY  111.88  3.000
 ZOE  H10  CAN  H9   106.25  3.000
 ZOE  H10  CAN  CAJ  108.74  3.000
 ZOE  H9   CAN  CAJ  109.65  3.000
 ZOE  H10  CAN  CAW  107.99  3.000
 ZOE  H9   CAN  CAW  109.90  3.000
 ZOE  CAJ  CAN  CAW  114.01  3.000
 ZOE  H12  CAJ  H11  106.10  3.000
 ZOE  H12  CAJ  CAI  109.07  3.000
 ZOE  H11  CAJ  CAI  109.99  3.000
 ZOE  H12  CAJ  CAN  110.47  3.000
 ZOE  H11  CAJ  CAN  109.36  3.000
 ZOE  CAI  CAJ  CAN  111.70  3.000
 ZOE  H14  CAI  H13  106.50  3.000
 ZOE  H14  CAI  CAM  109.68  3.000
 ZOE  H13  CAI  CAM  109.45  3.000
 ZOE  H14  CAI  CAJ  109.49  3.000
 ZOE  H13  CAI  CAJ  109.42  3.000
 ZOE  CAM  CAI  CAJ  112.14  3.000
 ZOE  H16  CAM  H15  105.98  3.000
 ZOE  H16  CAM  CAT  107.07  3.000
 ZOE  H15  CAM  CAT  111.01  3.000
 ZOE  H16  CAM  CAI  109.44  3.000
 ZOE  H15  CAM  CAI  110.16  3.000
 ZOE  CAT  CAM  CAI  112.88  3.000
 ZOE  NAP  CAT  OAB  122.87  3.000
 ZOE  NAP  CAT  CAM  115.31  3.000
 ZOE  OAB  CAT  CAM  121.80  3.000
 ZOE  H17  NAP  CAK  117.41  3.000
 ZOE  H17  NAP  CAT  118.31  3.000
 ZOE  CAK  NAP  CAT  124.18  3.000
 ZOE  H19  CAK  H18  106.83  3.000
 ZOE  H19  CAK  CAG  109.73  3.000
 ZOE  H18  CAK  CAG  109.83  3.000
 ZOE  H19  CAK  NAP  110.39  3.000
 ZOE  H18  CAK  NAP  108.57  3.000
 ZOE  CAG  CAK  NAP  111.38  3.000
 ZOE  H21  CAG  H20  106.59  3.000
 ZOE  H21  CAG  CAF  109.82  3.000
 ZOE  H20  CAG  CAF  109.41  3.000
 ZOE  H21  CAG  CAK  109.30  3.000
 ZOE  H20  CAG  CAK  109.67  3.000
 ZOE  CAF  CAG  CAK  111.91  3.000
 ZOE  H23  CAF  H22  105.96  3.000
 ZOE  H23  CAF  CAH  109.43  3.000
 ZOE  H22  CAF  CAH  109.47  3.000
 ZOE  H23  CAF  CAG  109.37  3.000
 ZOE  H22  CAF  CAG  109.34  3.000
 ZOE  CAH  CAF  CAG  113.03  3.000
 ZOE  H25  CAH  H24  105.92  3.000
 ZOE  H25  CAH  CAL  109.86  3.000
 ZOE  H24  CAH  CAL  109.88  3.000
 ZOE  H25  CAH  CAF  109.17  3.000
 ZOE  H24  CAH  CAF  109.21  3.000
 ZOE  CAL  CAH  CAF  112.58  3.000
 ZOE  H27  CAL  H26  104.76  3.000
 ZOE  H27  CAL  CAS  107.97  3.000
 ZOE  H26  CAL  CAS  108.19  3.000
 ZOE  H27  CAL  CAH  109.47  3.000
 ZOE  H26  CAL  CAH  109.67  3.000
 ZOE  CAS  CAL  CAH  116.16  3.000
 ZOE  OAE  CAS  OAA  126.16  3.000
 ZOE  OAA  CAS  CAL  115.86  3.000
 ZOE  OAE  CAS  CAL  117.98  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_05  H6   NAR  CAU  NAQ   180.00   0.0  0
 ZOE  CONST_07  CAK  NAP  CAT  CAM   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  Var_01    CAW  SAY  CAO  CAV    43.98  30.0  1
 ZOE  Var_02    CAI  CAJ  CAN  CAW  -176.88  30.0  1
 ZOE  Var_03    CAM  CAI  CAJ  CAN  -179.80  30.0  2
 ZOE  Var_04    CAT  CAM  CAI  CAJ   174.93  30.0  2
 ZOE  Var_05    OAB  CAT  CAM  CAI   -38.70  30.0  1
 ZOE  Var_06    CAG  CAK  NAP  CAT  -149.38  30.0  1
 ZOE  Var_07    CAF  CAG  CAK  NAP  -179.13  30.0  3
 ZOE  Var_08    CAH  CAF  CAG  CAK  -179.89  30.0  1
 ZOE  Var_09    CAL  CAH  CAF  CAG  -179.89  30.0  1
 ZOE  Var_10    CAS  CAL  CAH  CAF  -179.97  30.0  1
 ZOE  Var_11    OAE  CAS  CAL  CAH    -3.28  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
 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  CAV  0.020
 ZOE  plan-2  NAQ  0.020
 ZOE  plan-2  CAU  0.020
 ZOE  plan-2  OAC  0.020
 ZOE  plan-2  NAR  0.020
 ZOE  plan-2  CAX  0.020
 ZOE  plan-2  H5   0.020
 ZOE  plan-2  H6   0.020
 ZOE  plan-3  CAL  0.020
 ZOE  plan-3  CAS  0.020
 ZOE  plan-3  OAA  0.020
 ZOE  plan-3  OAE  0.020

