# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 18:32:47 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-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]1SC[C@@H]2NC(=N)N[C@H]12
#
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
 ZOF  ZOF  '6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid'  ligand  52  24  .  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_ZOF
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
 ZOF  OAW  O  OH1   0  -0.592  34.8333   -4.8288  32.6252
 ZOF  CAV  C  C     0   0.533  34.6614   -3.5104  32.6101
 ZOF  OAX  O  O     0  -0.450  35.5230   -2.7443  32.2525
 ZOF  CAU  C  CH2   0  -0.551  33.2981   -3.1057  33.0967
 ZOF  CAT  C  CH2   0  -0.429  32.1407   -3.8153  32.3930
 ZOF  CAS  C  CH2   0  -0.424  30.7936   -3.3081  32.8902
 ZOF  CAR  C  CH2   0  -0.428  29.6155   -3.9745  32.1928
 ZOF  CAQ  C  CH2   0  -0.279  28.2839   -3.4602  32.7285
 ZOF  NAO  N  NH1   0  -0.629  27.1317   -4.0174  32.0561
 ZOF  CAN  C  C     0   0.541  26.5986   -5.2103  32.3597
 ZOF  OAP  O  O     0  -0.509  27.0394   -5.9274  33.2504
 ZOF  CAM  C  CH2   0  -0.571  25.3920   -5.6164  31.5392
 ZOF  CAL  C  CH2   0  -0.428  25.5607   -6.9978  30.9144
 ZOF  CAK  C  CH2   0  -0.416  26.6436   -7.0443  29.8442
 ZOF  CAI  C  CH2   0  -0.431  26.7490   -8.4202  29.1969
 ZOF  CAH  C  CR15  0  -0.368  27.8318   -8.5144  28.1376
 ZOF  SAG  S  S2    0  -0.023  27.4939   -7.4530  26.6937
 ZOF  CAF  C  CH2   0  -0.571  28.8186   -8.3061  25.8044
 ZOF  CAC  C  CR15  0  -0.066  28.6433   -9.7920  26.1227
 ZOF  CAD  C  CR15  0  -0.054  28.0539   -9.9257  27.5581
 ZOF  NAE  N  NH1   0  -0.661  26.8440  -10.6733  27.3264
 ZOF  CAA  C  C     0   0.565  26.5162  -10.7659  26.0030
 ZOF  NAJ  N  N     0  -0.724  25.4256  -11.1472  25.4531
 ZOF  NAB  N  NH1   0  -0.644  27.6430  -10.4333  25.3017
 ZOF  H1   H  HOH1  0   0.480  35.7218   -5.0509  32.3091
 ZOF  H2   H  HCH2  0   0.259  33.2068   -2.0258  32.9755
 ZOF  H3   H  HCH2  0   0.271  33.2490   -3.3100  34.1715
 ZOF  H4   H  HCH2  0   0.233  32.2045   -4.8934  32.5553
 ZOF  H5   H  HCH2  0   0.231  32.2139   -3.6561  31.3132
 ZOF  H6   H  HCH2  0   0.220  30.7359   -2.2240  32.7456
 ZOF  H7   H  HCH2  0   0.220  30.7210   -3.4744  33.9705
 ZOF  H8   H  HCH2  0   0.225  29.6674   -5.0583  32.3288
 ZOF  H9   H  HCH2  0   0.221  29.6694   -3.7898  31.1157
 ZOF  H10  H  HCH2  0   0.244  28.2338   -2.3762  32.6142
 ZOF  H11  H  HCH2  0   0.237  28.2080   -3.6688  33.7973
 ZOF  H12  H  HNH1  0   0.398  26.7420   -3.4975  31.2880
 ZOF  H13  H  HCH2  0   0.243  25.1738   -4.8794  30.7621
 ZOF  H14  H  HCH2  0   0.271  24.5305   -5.6244  32.2128
 ZOF  H15  H  HCH2  0   0.233  24.6058   -7.2953  30.4734
 ZOF  H16  H  HCH2  0   0.226  25.7770   -7.7290  31.6974
 ZOF  H17  H  HCH2  0   0.223  27.6143   -6.7740  30.2734
 ZOF  H18  H  HCH2  0   0.221  26.4265   -6.2900  29.0809
 ZOF  H19  H  HCH2  0   0.229  25.7813   -8.6890  28.7629
 ZOF  H20  H  HCH2  0   0.244  26.9626   -9.1651  29.9720
 ZOF  H21  H  HCR5  0   0.275  28.7846   -8.1877  28.5684
 ZOF  H22  H  HCH2  0   0.275  29.7880   -7.9527  26.1608
 ZOF  H23  H  HCH2  0   0.289  28.7572   -8.1013  24.7357
 ZOF  H24  H  HCR5  0   0.271  29.6073  -10.2989  26.0314
 ZOF  H25  H  HCR5  0   0.271  28.7253  -10.4726  28.2247
 ZOF  H26  H  HNH1  0   0.396  26.1389  -10.7667  28.0371
 ZOF  H27  H  H     0   0.317  24.7284  -11.3605  26.1563
 ZOF  H28  H  HNH1  0   0.386  27.5493  -10.1842  24.3309

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
 ZOF  NAB  CAA  single  1.368  0.020  1.368
 ZOF  NAB  CAC  single  1.444  0.020  1.444
 ZOF  NAJ  CAA  double  1.280  0.020  1.280
 ZOF  CAF  CAC  single  1.530  0.020  1.530
 ZOF  CAF  SAG  single  1.809  0.020  1.809
 ZOF  CAA  NAE  single  1.367  0.020  1.367
 ZOF  CAC  CAD  single  1.557  0.020  1.557
 ZOF  SAG  CAH  single  1.824  0.020  1.824
 ZOF  NAE  CAD  single  1.441  0.020  1.441
 ZOF  CAD  CAH  single  1.542  0.020  1.542
 ZOF  CAH  CAI  single  1.518  0.020  1.518
 ZOF  CAI  CAK  single  1.524  0.020  1.524
 ZOF  CAK  CAL  single  1.523  0.020  1.523
 ZOF  CAL  CAM  single  1.526  0.020  1.526
 ZOF  CAM  CAN  single  1.515  0.020  1.515
 ZOF  OAX  CAV  double  1.207  0.020  1.207
 ZOF  NAO  CAN  single  1.341  0.020  1.341
 ZOF  NAO  CAQ  single  1.446  0.020  1.446
 ZOF  CAR  CAQ  single  1.525  0.020  1.525
 ZOF  CAR  CAS  single  1.523  0.020  1.523
 ZOF  CAN  OAP  double  1.225  0.020  1.225
 ZOF  CAT  CAS  single  1.523  0.020  1.523
 ZOF  CAT  CAU  single  1.529  0.020  1.529
 ZOF  CAV  CAU  single  1.503  0.020  1.503
 ZOF  CAV  OAW  single  1.330  0.020  1.330
 ZOF  OAW  H1   single  0.850  0.020  0.980
 ZOF  CAU  H2   single  0.970  0.020  1.090
 ZOF  CAU  H3   single  0.970  0.020  1.090
 ZOF  CAT  H4   single  0.970  0.020  1.090
 ZOF  CAT  H5   single  0.970  0.020  1.090
 ZOF  CAS  H6   single  0.970  0.020  1.090
 ZOF  CAS  H7   single  0.970  0.020  1.090
 ZOF  CAR  H8   single  0.970  0.020  1.090
 ZOF  CAR  H9   single  0.970  0.020  1.090
 ZOF  CAQ  H10  single  0.970  0.020  1.090
 ZOF  CAQ  H11  single  0.970  0.020  1.090
 ZOF  NAO  H12  single  0.860  0.020  1.020
 ZOF  CAM  H13  single  0.970  0.020  1.090
 ZOF  CAM  H14  single  0.970  0.020  1.090
 ZOF  CAL  H15  single  0.970  0.020  1.090
 ZOF  CAL  H16  single  0.970  0.020  1.090
 ZOF  CAK  H17  single  0.970  0.020  1.090
 ZOF  CAK  H18  single  0.970  0.020  1.090
 ZOF  CAI  H19  single  0.970  0.020  1.090
 ZOF  CAI  H20  single  0.970  0.020  1.090
 ZOF  CAH  H21  single  0.970  0.020  1.090
 ZOF  CAF  H22  single  0.970  0.020  1.090
 ZOF  CAF  H23  single  0.970  0.020  1.090
 ZOF  CAC  H24  single  0.970  0.020  1.090
 ZOF  CAD  H25  single  0.970  0.020  1.090
 ZOF  NAE  H26  single  0.890  0.020  1.040
 ZOF  NAJ  H27  single  0.890  0.020  1.040
 ZOF  NAB  H28  single  0.890  0.020  1.040

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
 ZOF  H1   OAW  CAV  110.02  3.000
 ZOF  CAU  CAV  OAX  124.92  3.000
 ZOF  CAU  CAV  OAW  112.37  3.000
 ZOF  OAX  CAV  OAW  122.71  3.000
 ZOF  H3   CAU  H2   106.86  3.000
 ZOF  H3   CAU  CAT  109.34  3.000
 ZOF  H2   CAU  CAT  110.18  3.000
 ZOF  H3   CAU  CAV  107.94  3.000
 ZOF  H2   CAU  CAV  107.86  3.000
 ZOF  CAT  CAU  CAV  114.37  3.000
 ZOF  H5   CAT  H4   106.65  3.000
 ZOF  H5   CAT  CAS  109.45  3.000
 ZOF  H4   CAT  CAS  109.38  3.000
 ZOF  H5   CAT  CAU  109.64  3.000
 ZOF  H4   CAT  CAU  110.21  3.000
 ZOF  CAS  CAT  CAU  111.39  3.000
 ZOF  H7   CAS  H6   106.08  3.000
 ZOF  H7   CAS  CAR  109.52  3.000
 ZOF  H6   CAS  CAR  109.39  3.000
 ZOF  H7   CAS  CAT  109.27  3.000
 ZOF  H6   CAS  CAT  109.46  3.000
 ZOF  CAR  CAS  CAT  112.90  3.000
 ZOF  H9   CAR  H8   106.70  3.000
 ZOF  H9   CAR  CAQ  109.39  3.000
 ZOF  H8   CAR  CAQ  109.40  3.000
 ZOF  H9   CAR  CAS  109.81  3.000
 ZOF  H8   CAR  CAS  109.88  3.000
 ZOF  CAQ  CAR  CAS  111.54  3.000
 ZOF  H11  CAQ  H10  106.81  3.000
 ZOF  H11  CAQ  NAO  109.04  3.000
 ZOF  H10  CAQ  NAO  107.31  3.000
 ZOF  H11  CAQ  CAR  109.90  3.000
 ZOF  H10  CAQ  CAR  109.78  3.000
 ZOF  NAO  CAQ  CAR  113.74  3.000
 ZOF  H12  NAO  CAN  118.58  3.000
 ZOF  H12  NAO  CAQ  117.69  3.000
 ZOF  CAN  NAO  CAQ  123.66  3.000
 ZOF  CAM  CAN  OAP  121.56  3.000
 ZOF  OAP  CAN  NAO  122.82  3.000
 ZOF  CAM  CAN  NAO  115.62  3.000
 ZOF  H14  CAM  H13  106.60  3.000
 ZOF  H14  CAM  CAL  109.44  3.000
 ZOF  H13  CAM  CAL  109.96  3.000
 ZOF  H14  CAM  CAN  107.21  3.000
 ZOF  H13  CAM  CAN  111.31  3.000
 ZOF  CAL  CAM  CAN  112.12  3.000
 ZOF  H16  CAL  H15  106.25  3.000
 ZOF  H16  CAL  CAK  110.01  3.000
 ZOF  H15  CAL  CAK  109.23  3.000
 ZOF  H16  CAL  CAM  109.52  3.000
 ZOF  H15  CAL  CAM  108.37  3.000
 ZOF  CAK  CAL  CAM  113.21  3.000
 ZOF  H18  CAK  H17  106.19  3.000
 ZOF  H18  CAK  CAI  109.86  3.000
 ZOF  H17  CAK  CAI  109.15  3.000
 ZOF  H18  CAK  CAL  109.13  3.000
 ZOF  H17  CAK  CAL  110.32  3.000
 ZOF  CAI  CAK  CAL  112.03  3.000
 ZOF  H20  CAI  H19  106.62  3.000
 ZOF  H20  CAI  CAH  108.20  3.000
 ZOF  H19  CAI  CAH  109.81  3.000
 ZOF  H20  CAI  CAK  109.07  3.000
 ZOF  H19  CAI  CAK  109.22  3.000
 ZOF  CAH  CAI  CAK  113.68  3.000
 ZOF  H21  CAH  CAD  107.19  3.000
 ZOF  H21  CAH  SAG  107.39  3.000
 ZOF  CAD  CAH  SAG  105.18  3.000
 ZOF  H21  CAH  CAI  109.12  3.000
 ZOF  CAD  CAH  CAI  114.96  3.000
 ZOF  SAG  CAH  CAI  112.60  3.000
 ZOF  CAF  SAG  CAH   88.80  3.000
 ZOF  H23  CAF  H22  108.01  3.000
 ZOF  H23  CAF  CAC  112.34  3.000
 ZOF  H22  CAF  CAC  110.38  3.000
 ZOF  H23  CAF  SAG  110.62  3.000
 ZOF  H22  CAF  SAG  109.70  3.000
 ZOF  CAC  CAF  SAG  105.78  3.000
 ZOF  H24  CAC  NAB  110.94  3.000
 ZOF  H24  CAC  CAD  111.78  3.000
 ZOF  NAB  CAC  CAD  102.92  3.000
 ZOF  H24  CAC  CAF  109.40  3.000
 ZOF  CAD  CAC  CAF  108.57  3.000
 ZOF  NAB  CAC  CAF  113.11  3.000
 ZOF  H25  CAD  NAE  110.75  3.000
 ZOF  H25  CAD  CAC  111.88  3.000
 ZOF  NAE  CAD  CAC  102.36  3.000
 ZOF  H25  CAD  CAH  108.50  3.000
 ZOF  NAE  CAD  CAH  114.48  3.000
 ZOF  CAC  CAD  CAH  108.81  3.000
 ZOF  H26  NAE  CAA  120.66  3.000
 ZOF  H26  NAE  CAD  121.56  3.000
 ZOF  CAA  NAE  CAD  113.10  3.000
 ZOF  NAB  CAA  NAJ  123.65  3.000
 ZOF  NAJ  CAA  NAE  129.85  3.000
 ZOF  NAB  CAA  NAE  106.40  3.000
 ZOF  H27  NAJ  CAA  110.55  3.000
 ZOF  H28  NAB  CAA  118.53  3.000
 ZOF  H28  NAB  CAC  120.19  3.000
 ZOF  CAA  NAB  CAC  112.77  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
 ZOF  CONST_01  NAE  CAA  NAB  CAC     0.00   0.0  0
 ZOF  CONST_03  NAJ  CAA  NAB  CAC   180.00   0.0  0
 ZOF  CONST_04  NAJ  CAA  NAE  CAD   180.00   0.0  0
 ZOF  CONST_06  H26  NAE  CAA  NAB   180.00   0.0  0
 ZOF  CONST_07  H27  NAJ  CAA  NAE     0.00   0.0  0
 ZOF  CONST_08  CAM  CAN  NAO  CAQ   180.00   0.0  0
 ZOF  CONST_09  OAP  CAN  NAO  CAQ     0.00   0.0  0
 ZOF  CONST_10  H12  NAO  CAN  OAP   180.00   0.0  0
 ZOF  CONST_11  H1   OAW  CAV  OAX     0.00   0.0  0
 ZOF  Var_01    CAC  CAF  SAG  CAH    43.04  30.0  1
 ZOF  Var_02    CAH  CAI  CAK  CAL  -179.16  30.0  1
 ZOF  Var_03    CAT  CAU  CAV  OAW   -52.39  30.0  3
 ZOF  Var_04    CAS  CAT  CAU  CAV  -177.31  30.0  2
 ZOF  Var_05    CAR  CAS  CAT  CAU   178.94  30.0  3
 ZOF  Var_06    CAQ  CAR  CAS  CAT   179.12  30.0  1
 ZOF  Var_07    NAO  CAQ  CAR  CAS   177.34  30.0  3
 ZOF  Var_08    CAN  NAO  CAQ  CAR    82.72  30.0  2
 ZOF  Var_09    CAL  CAM  CAN  NAO   127.27  30.0  2
 ZOF  Var_10    CAK  CAL  CAM  CAN   -67.49  30.0  1
 ZOF  Var_11    CAI  CAK  CAL  CAM  -177.57  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
 ZOF  chir_01  CAH  SAG  CAD  CAI  positiv
 ZOF  chir_02  CAC  NAB  CAD  CAF  positiv
 ZOF  chir_03  CAD  NAE  CAH  CAC  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
 ZOF  plan-1  CAQ  0.020
 ZOF  plan-1  NAO  0.020
 ZOF  plan-1  CAN  0.020
 ZOF  plan-1  OAP  0.020
 ZOF  plan-1  CAM  0.020
 ZOF  plan-1  H12  0.020
 ZOF  plan-2  CAC  0.020
 ZOF  plan-2  CAD  0.020
 ZOF  plan-2  NAE  0.020
 ZOF  plan-2  CAA  0.020
 ZOF  plan-2  NAJ  0.020
 ZOF  plan-2  NAB  0.020
 ZOF  plan-2  H26  0.020
 ZOF  plan-2  H27  0.020
 ZOF  plan-2  H28  0.020
 ZOF  plan-3  OAW  0.020
 ZOF  plan-3  CAV  0.020
 ZOF  plan-3  OAX  0.020
 ZOF  plan-3  CAU  0.020
 ZOF  plan-3  H1   0.020

