# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:50:04 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: methyl (3aS,4S,6aR)-4-(5-methoxy-5-oxopentyl)-2-oxohexahydro-1H-thieno[3,4-d]imidazole-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CCCC[C@@H]1SC[C@H]2[C@@H]1NC(=O)N2C(=O)OC
#
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
 Y7Y  Y7Y  'methyl (3aS,4S,6aR)-4-(5-methoxy-5-oxopentyl)-2-oxohexahydro-1H-thieno[3,4-d]imidazole-1-carboxylate'  ligand  41  21  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y7Y
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
 Y7Y  CAU  C  CH3   0  -0.424   8.4157   0.3629  -0.3796
 Y7Y  OAT  O  O2    0  -0.457   7.1411  -0.2503  -0.5672
 Y7Y  CAR  C  C     0   0.601   6.0909   0.3267   0.0060
 Y7Y  OAS  O  O     0  -0.454   6.1704   1.3278   0.6735
 Y7Y  CAQ  C  CH2   0  -0.582   4.8209  -0.4233  -0.2915
 Y7Y  CAP  C  CH2   0  -0.419   3.5912   0.1667   0.3791
 Y7Y  CAO  C  CH2   0  -0.418   2.3374  -0.6365   0.0592
 Y7Y  CAM  C  CH2   0  -0.429   1.0924  -0.0484   0.7121
 Y7Y  CAC  C  CH1   0  -0.367  -0.1489  -0.8969   0.5092
 Y7Y  SAB  S  S2    0  -0.012  -0.6547  -1.0277  -1.2359
 Y7Y  CAA  C  CH2   0  -0.565  -2.2053  -1.7822  -0.6876
 Y7Y  CAE  C  CR15  0  -0.086  -2.6551  -0.9937   0.5469
 Y7Y  CAD  C  CR15  0  -0.049  -1.4023  -0.3851   1.2301
 Y7Y  NAF  N  NR15  0  -0.659  -1.6174   1.0251   1.0650
 Y7Y  CAG  C  CR5   0   0.700  -2.7829   1.3761   0.4948
 Y7Y  OAN  O  O     0  -0.477  -3.1754   2.4996   0.2773
 Y7Y  NAH  N  NR5   0  -0.598  -3.4535   0.1764   0.2109
 Y7Y  CAV  C  C     0   0.786  -4.7508   0.0094  -0.2036
 Y7Y  OAW  O  O     0  -0.492  -5.2449  -1.0873  -0.3286
 Y7Y  OAX  O  O2    0  -0.451  -5.3747   1.1456  -0.4384
 Y7Y  CAY  C  CH3   0  -0.420  -6.7331   1.0548  -0.8694
 Y7Y  H1   H  HCH3  0   0.237   8.6951   0.3921   0.6736
 Y7Y  H2   H  HCH3  0   0.250   9.1271  -0.2532  -0.9216
 Y7Y  H3   H  HCH3  0   0.237   8.4360   1.3751  -0.7836
 Y7Y  H4   H  HCH2  0   0.275   4.6905  -0.4479  -1.3782
 Y7Y  H5   H  HCH2  0   0.274   4.9592  -1.4665   0.0093
 Y7Y  H6   H  HCH2  0   0.229   3.7372   0.1938   1.4621
 Y7Y  H7   H  HCH2  0   0.229   3.4522   1.2024   0.0582
 Y7Y  H8   H  HCH2  0   0.224   2.2000  -0.6776  -1.0261
 Y7Y  H9   H  HCH2  0   0.224   2.4686  -1.6718   0.3905
 Y7Y  H10  H  HCH2  0   0.246   1.2617   0.0471   1.7900
 Y7Y  H11  H  HCH2  0   0.235   0.9234   0.9619   0.3298
 Y7Y  H12  H  HCH1  0   0.284   0.0467  -1.9109   0.8743
 Y7Y  H13  H  HCH2  0   0.298  -2.9383  -1.7688  -1.4909
 Y7Y  H14  H  HCH2  0   0.283  -2.0281  -2.8227  -0.4110
 Y7Y  H15  H  HCR5  0   0.304  -3.2057  -1.6418   1.2283
 Y7Y  H16  H  HCR5  0   0.293  -1.3456  -0.6507   2.2890
 Y7Y  H17  H  HNR5  0   0.415  -0.9983   1.7267   1.4363
 Y7Y  H18  H  HCH3  0   0.241  -6.8196   0.5059  -1.8063
 Y7Y  H19  H  HCH3  0   0.242  -7.3612   0.5835  -0.1144
 Y7Y  H20  H  HCH3  0   0.254  -7.0605   2.0791  -1.0200

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
 Y7Y  CAU  OAT  single  1.427  0.020  1.427
 Y7Y  OAT  CAR  single  1.328  0.020  1.328
 Y7Y  CAR  OAS  double  1.206  0.020  1.206
 Y7Y  CAR  CAQ  single  1.505  0.020  1.505
 Y7Y  CAP  CAQ  single  1.520  0.020  1.520
 Y7Y  CAP  CAO  single  1.523  0.020  1.523
 Y7Y  CAO  CAM  single  1.524  0.020  1.524
 Y7Y  CAM  CAC  single  1.517  0.020  1.517
 Y7Y  CAC  SAB  single  1.822  0.020  1.822
 Y7Y  CAC  CAD  single  1.534  0.020  1.534
 Y7Y  SAB  CAA  single  1.809  0.020  1.809
 Y7Y  CAD  NAF  single  1.436  0.020  1.436
 Y7Y  CAD  CAE  single  1.551  0.020  1.551
 Y7Y  CAA  CAE  single  1.532  0.020  1.532
 Y7Y  NAF  CAG  single  1.344  0.020  1.344
 Y7Y  CAE  NAH  single  1.456  0.020  1.456
 Y7Y  CAG  NAH  single  1.403  0.020  1.403
 Y7Y  CAG  OAN  double  1.210  0.020  1.210
 Y7Y  NAH  CAV  single  1.372  0.020  1.372
 Y7Y  CAV  OAW  double  1.209  0.020  1.209
 Y7Y  CAV  OAX  single  1.317  0.020  1.317
 Y7Y  CAY  OAX  single  1.428  0.020  1.428
 Y7Y  CAU  H1   single  0.970  0.020  1.090
 Y7Y  CAU  H2   single  0.970  0.020  1.090
 Y7Y  CAU  H3   single  0.970  0.020  1.090
 Y7Y  CAQ  H4   single  0.970  0.020  1.090
 Y7Y  CAQ  H5   single  0.970  0.020  1.090
 Y7Y  CAP  H6   single  0.970  0.020  1.090
 Y7Y  CAP  H7   single  0.970  0.020  1.090
 Y7Y  CAO  H8   single  0.970  0.020  1.090
 Y7Y  CAO  H9   single  0.970  0.020  1.090
 Y7Y  CAM  H10  single  0.970  0.020  1.090
 Y7Y  CAM  H11  single  0.970  0.020  1.090
 Y7Y  CAC  H12  single  0.970  0.020  1.090
 Y7Y  CAA  H13  single  0.970  0.020  1.090
 Y7Y  CAA  H14  single  0.970  0.020  1.090
 Y7Y  CAE  H15  single  0.970  0.020  1.090
 Y7Y  CAD  H16  single  0.970  0.020  1.090
 Y7Y  NAF  H17  single  0.860  0.020  1.020
 Y7Y  CAY  H18  single  0.970  0.020  1.090
 Y7Y  CAY  H19  single  0.970  0.020  1.090
 Y7Y  CAY  H20  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
 Y7Y  H3   CAU  H2   109.24  3.000
 Y7Y  H3   CAU  H1   109.18  3.000
 Y7Y  H2   CAU  H1   109.24  3.000
 Y7Y  H3   CAU  OAT  111.53  3.000
 Y7Y  H2   CAU  OAT  106.00  3.000
 Y7Y  H1   CAU  OAT  111.57  3.000
 Y7Y  CAR  OAT  CAU  117.57  3.000
 Y7Y  CAQ  CAR  OAS  125.37  3.000
 Y7Y  CAQ  CAR  OAT  111.44  3.000
 Y7Y  OAS  CAR  OAT  123.19  3.000
 Y7Y  H5   CAQ  H4   105.45  3.000
 Y7Y  H5   CAQ  CAP  110.55  3.000
 Y7Y  H4   CAQ  CAP  110.51  3.000
 Y7Y  H5   CAQ  CAR  108.31  3.000
 Y7Y  H4   CAQ  CAR  107.94  3.000
 Y7Y  CAP  CAQ  CAR  113.71  3.000
 Y7Y  H7   CAP  H6   106.52  3.000
 Y7Y  H7   CAP  CAO  109.47  3.000
 Y7Y  H6   CAP  CAO  109.34  3.000
 Y7Y  H7   CAP  CAQ  109.94  3.000
 Y7Y  H6   CAP  CAQ  109.80  3.000
 Y7Y  CAO  CAP  CAQ  111.63  3.000
 Y7Y  H9   CAO  H8   106.23  3.000
 Y7Y  H9   CAO  CAM  109.46  3.000
 Y7Y  H8   CAO  CAM  109.67  3.000
 Y7Y  H9   CAO  CAP  109.67  3.000
 Y7Y  H8   CAO  CAP  109.36  3.000
 Y7Y  CAM  CAO  CAP  112.28  3.000
 Y7Y  H11  CAM  H10  106.71  3.000
 Y7Y  H11  CAM  CAC  110.09  3.000
 Y7Y  H10  CAM  CAC  107.87  3.000
 Y7Y  H11  CAM  CAO  109.46  3.000
 Y7Y  H10  CAM  CAO  109.21  3.000
 Y7Y  CAC  CAM  CAO  113.28  3.000
 Y7Y  H12  CAC  CAD  107.35  3.000
 Y7Y  H12  CAC  SAB  107.61  3.000
 Y7Y  CAD  CAC  SAB  104.32  3.000
 Y7Y  H12  CAC  CAM  109.09  3.000
 Y7Y  CAD  CAC  CAM  114.77  3.000
 Y7Y  SAB  CAC  CAM  113.29  3.000
 Y7Y  CAA  SAB  CAC   88.72  3.000
 Y7Y  H14  CAA  H13  107.96  3.000
 Y7Y  H14  CAA  CAE  109.52  3.000
 Y7Y  H13  CAA  CAE  113.01  3.000
 Y7Y  H14  CAA  SAB  109.59  3.000
 Y7Y  H13  CAA  SAB  110.41  3.000
 Y7Y  CAE  CAA  SAB  106.33  3.000
 Y7Y  H15  CAE  NAH  110.20  3.000
 Y7Y  H15  CAE  CAD  111.47  3.000
 Y7Y  NAH  CAE  CAD  103.25  3.000
 Y7Y  H15  CAE  CAA  110.25  3.000
 Y7Y  NAH  CAE  CAA  112.87  3.000
 Y7Y  CAD  CAE  CAA  108.64  3.000
 Y7Y  H16  CAD  NAF  110.97  3.000
 Y7Y  H16  CAD  CAE  111.91  3.000
 Y7Y  NAF  CAD  CAE  102.34  3.000
 Y7Y  H16  CAD  CAC  109.38  3.000
 Y7Y  CAE  CAD  CAC  108.78  3.000
 Y7Y  NAF  CAD  CAC  113.33  3.000
 Y7Y  H17  NAF  CAG  120.51  3.000
 Y7Y  H17  NAF  CAD  123.36  3.000
 Y7Y  CAG  NAF  CAD  115.79  3.000
 Y7Y  NAH  CAG  OAN  127.05  3.000
 Y7Y  OAN  CAG  NAF  126.88  3.000
 Y7Y  NAH  CAG  NAF  106.08  3.000
 Y7Y  CAV  NAH  CAG  128.10  3.000
 Y7Y  CAV  NAH  CAE  119.37  3.000
 Y7Y  CAG  NAH  CAE  112.23  3.000
 Y7Y  OAX  CAV  OAW  124.77  3.000
 Y7Y  OAX  CAV  NAH  113.37  3.000
 Y7Y  OAW  CAV  NAH  121.87  3.000
 Y7Y  CAY  OAX  CAV  116.71  3.000
 Y7Y  H20  CAY  H19  109.29  3.000
 Y7Y  H20  CAY  H18  109.40  3.000
 Y7Y  H19  CAY  H18  109.41  3.000
 Y7Y  H20  CAY  OAX  105.59  3.000
 Y7Y  H19  CAY  OAX  111.52  3.000
 Y7Y  H18  CAY  OAX  111.54  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
 Y7Y  CONST_01  NAF  CAG  NAH  CAE     0.00   0.0  0
 Y7Y  CONST_02  NAH  CAG  NAF  CAD     0.00   0.0  0
 Y7Y  CONST_03  OAN  CAG  NAH  CAE   180.00   0.0  0
 Y7Y  CONST_04  OAN  CAG  NAF  CAD   180.00   0.0  0
 Y7Y  CONST_05  CAV  NAH  CAG  NAF   180.00   0.0  0
 Y7Y  CONST_06  H17  NAF  CAG  NAH   180.00   0.0  0
 Y7Y  CONST_07  CAV  NAH  CAG  OAN     0.00   0.0  0
 Y7Y  Var_01    CAE  CAA  SAB  CAC    41.29  30.0  1
 Y7Y  Var_02    OAW  CAV  NAH  CAE    -1.73  30.0  2
 Y7Y  Var_03    CAC  CAM  CAO  CAP  -174.97  30.0  3
 Y7Y  Var_04    OAS  CAR  OAT  CAU    -0.38  30.0  3
 Y7Y  Var_05    CAP  CAQ  CAR  OAT   178.05  30.0  3
 Y7Y  Var_06    CAO  CAP  CAQ  CAR  -179.37  30.0  2
 Y7Y  Var_07    CAM  CAO  CAP  CAQ  -179.37  30.0  3
 Y7Y  Var_08    H1   CAU  OAT  CAR    61.29  30.0  3
 Y7Y  Var_09    H18  CAY  OAX  CAV   -60.53  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
 Y7Y  chir_01  CAC  CAM  SAB  CAD  positiv
 Y7Y  chir_02  CAE  NAH  CAA  CAD  negativ
 Y7Y  chir_03  CAD  NAF  CAC  CAE  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
 Y7Y  plan-1  CAE  0.020
 Y7Y  plan-1  CAD  0.020
 Y7Y  plan-1  NAF  0.020
 Y7Y  plan-1  CAG  0.020
 Y7Y  plan-1  OAN  0.020
 Y7Y  plan-1  NAH  0.020
 Y7Y  plan-1  CAV  0.020
 Y7Y  plan-1  H17  0.020
 Y7Y  plan-2  OAT  0.020
 Y7Y  plan-2  CAR  0.020
 Y7Y  plan-2  OAS  0.020
 Y7Y  plan-2  CAQ  0.020
 Y7Y  plan-3  NAH  0.020
 Y7Y  plan-3  CAV  0.020
 Y7Y  plan-3  OAW  0.020
 Y7Y  plan-3  OAX  0.020

