# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 09:32:50 2020
#   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  51  24  .  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_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  OC    -1  -0.634  -11.1772   0.0439   0.6085
 ZOF  CAV  C  C      0   0.410  -10.0849   0.6326   0.4599
 ZOF  OAX  O  O      0  -0.610   -9.9219   1.8635   0.3465
 ZOF  CAU  C  CH2    0  -0.582   -8.8380  -0.2681   0.4136
 ZOF  CAT  C  CH2    0  -0.402   -7.5032   0.4422   0.2622
 ZOF  CAS  C  CH2    0  -0.415   -6.3268  -0.5263   0.2216
 ZOF  CAR  C  CH2    0  -0.461   -4.9847   0.1740   0.0548
 ZOF  CAQ  C  CH2    0  -0.240   -3.8297  -0.8134  -0.0003
 ZOF  NAO  N  NH1    0  -0.641   -2.5640  -0.1253  -0.1429
 ZOF  CAN  C  C      0   0.551   -1.4554  -0.6933  -0.6398
 ZOF  OAP  O  O      0  -0.513   -1.4232  -1.8556  -1.0287
 ZOF  CAM  C  CH2    0  -0.569   -0.2374   0.2025  -0.7027
 ZOF  CAL  C  CH2    0  -0.417    0.9930  -0.4540  -0.0856
 ZOF  CAK  C  CH2    0  -0.419    2.2161   0.4520  -0.1360
 ZOF  CAI  C  CH2    0  -0.419    3.4475  -0.2116   0.4679
 ZOF  CAH  C  CH1    0  -0.358    4.6554   0.7026   0.5540
 ZOF  SAG  S  S2     0  -0.029    5.2336   1.2723  -1.0784
 ZOF  CAF  C  CH2    0  -0.572    6.7427   1.9003  -0.2956
 ZOF  CAC  C  CR15   0  -0.043    7.1460   0.8776   0.7772
 ZOF  CAD  C  CR15   0  -0.075    5.8932   0.0560   1.1853
 ZOF  NAE  N  NR15   0  -0.657    6.1752  -1.2500   0.6386
 ZOF  CAA  C  CR5    0   0.563    7.4557  -1.3633   0.1625
 ZOF  NAJ  N  N      0  -0.723    8.0498  -2.3840  -0.3298
 ZOF  NAB  N  NR15   0  -0.650    8.0496  -0.1437   0.3135
 ZOF  H2   H  HCH2   0   0.216   -8.8278  -0.8833   1.3214
 ZOF  H3   H  HCH2   0   0.217   -8.9662  -0.9842  -0.4072
 ZOF  H4   H  HCH2   0   0.203   -7.5044   1.0449  -0.6508
 ZOF  H5   H  HCH2   0   0.203   -7.3618   1.1467   1.0870
 ZOF  H6   H  HCH2   0   0.210   -6.3141  -1.1246   1.1395
 ZOF  H7   H  HCH2   0   0.209   -6.4682  -1.2372  -0.6001
 ZOF  H8   H  HCH2   0   0.226   -4.9903   0.7741  -0.8606
 ZOF  H9   H  HCH2   0   0.223   -4.8332   0.8724   0.8852
 ZOF  H10  H  HCH2   0   0.226   -3.8292  -1.4347   0.9022
 ZOF  H11  H  HCH2   0   0.234   -3.9602  -1.4887  -0.8472
 ZOF  H12  H  HNH1   0   0.396   -2.5012   0.8126   0.2189
 ZOF  H13  H  HCH2   0   0.261   -0.0442   0.4244  -1.7570
 ZOF  H14  H  HCH2   0   0.244   -0.4326   1.1618  -0.2167
 ZOF  H15  H  HCH2   0   0.226    0.7810  -0.7165   0.9555
 ZOF  H16  H  HCH2   0   0.227    1.2099  -1.3907  -0.6046
 ZOF  H17  H  HCH2   0   0.222    2.4165   0.7330  -1.1751
 ZOF  H18  H  HCH2   0   0.220    2.0020   1.3845   0.3968
 ZOF  H19  H  HCH2   0   0.237    3.2100  -0.5476   1.4833
 ZOF  H20  H  HCH2   0   0.232    3.7053  -1.1060  -0.1054
 ZOF  H21  H  HCH1   0   0.272    4.3946   1.5884   1.1444
 ZOF  H22  H  HCH2   0   0.286    7.5222   2.0445  -1.0435
 ZOF  H23  H  HCH2   0   0.272    6.5367   2.8664   0.1681
 ZOF  H24  H  HCR5   0   0.270    7.5706   1.4119   1.6301
 ZOF  H25  H  HCR5   0   0.277    5.7676   0.0160   2.2718
 ZOF  H26  H  HNR5   0   0.394    5.7263  -2.0617   1.0290
 ZOF  H27  H  H      0   0.317    7.4245  -3.1806  -0.3487
 ZOF  H28  H  HNR5   0   0.387    8.8551   0.0903  -0.2422

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  1.365  0.020  1.365
 ZOF  NAB  CAC  single  1.440  0.020  1.440
 ZOF  NAJ  CAA  double  1.279  0.020  1.279
 ZOF  CAF  CAC  single  1.536  0.020  1.536
 ZOF  CAF  SAG  single  1.812  0.020  1.812
 ZOF  CAA  NAE  single  1.371  0.020  1.371
 ZOF  CAC  CAD  single  1.553  0.020  1.553
 ZOF  SAG  CAH  single  1.823  0.020  1.823
 ZOF  NAE  CAD  single  1.444  0.020  1.444
 ZOF  CAD  CAH  single  1.533  0.020  1.533
 ZOF  CAH  CAI  single  1.517  0.020  1.517
 ZOF  CAI  CAK  single  1.524  0.020  1.524
 ZOF  CAK  CAL  single  1.523  0.020  1.523
 ZOF  CAL  CAM  single  1.525  0.020  1.525
 ZOF  CAM  CAN  single  1.513  0.020  1.513
 ZOF  OAX  CAV  deloc   1.247  0.020  1.247
 ZOF  NAO  CAN  single  1.341  0.020  1.341
 ZOF  NAO  CAQ  single  1.448  0.020  1.448
 ZOF  CAR  CAQ  single  1.521  0.020  1.521
 ZOF  CAR  CAS  single  1.523  0.020  1.523
 ZOF  CAN  OAP  double  1.226  0.020  1.226
 ZOF  CAT  CAS  single  1.524  0.020  1.524
 ZOF  CAT  CAU  single  1.520  0.020  1.520
 ZOF  CAV  CAU  single  1.539  0.020  1.539
 ZOF  CAV  OAW  deloc   1.250  0.020  1.250
 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  CAU  CAV  OAX  117.98  3.000
 ZOF  CAU  CAV  OAW  115.85  3.000
 ZOF  OAX  CAV  OAW  126.17  3.000
 ZOF  H3   CAU  H2   104.74  3.000
 ZOF  H3   CAU  CAT  109.47  3.000
 ZOF  H2   CAU  CAT  109.67  3.000
 ZOF  H3   CAU  CAV  108.06  3.000
 ZOF  H2   CAU  CAV  108.11  3.000
 ZOF  CAT  CAU  CAV  116.17  3.000
 ZOF  H5   CAT  H4   105.94  3.000
 ZOF  H5   CAT  CAS  109.24  3.000
 ZOF  H4   CAT  CAS  109.19  3.000
 ZOF  H5   CAT  CAU  109.85  3.000
 ZOF  H4   CAT  CAU  109.86  3.000
 ZOF  CAS  CAT  CAU  112.55  3.000
 ZOF  H7   CAS  H6   105.99  3.000
 ZOF  H7   CAS  CAR  109.26  3.000
 ZOF  H6   CAS  CAR  109.43  3.000
 ZOF  H7   CAS  CAT  109.43  3.000
 ZOF  H6   CAS  CAT  109.49  3.000
 ZOF  CAR  CAS  CAT  113.01  3.000
 ZOF  H9   CAR  H8   106.57  3.000
 ZOF  H9   CAR  CAQ  109.65  3.000
 ZOF  H8   CAR  CAQ  109.24  3.000
 ZOF  H9   CAR  CAS  109.39  3.000
 ZOF  H8   CAR  CAS  109.83  3.000
 ZOF  CAQ  CAR  CAS  112.01  3.000
 ZOF  H11  CAQ  H10  106.77  3.000
 ZOF  H11  CAQ  NAO  108.81  3.000
 ZOF  H10  CAQ  NAO  110.51  3.000
 ZOF  H11  CAQ  CAR  109.83  3.000
 ZOF  H10  CAQ  CAR  109.80  3.000
 ZOF  NAO  CAQ  CAR  111.04  3.000
 ZOF  H12  NAO  CAN  118.42  3.000
 ZOF  H12  NAO  CAQ  117.50  3.000
 ZOF  CAN  NAO  CAQ  123.91  3.000
 ZOF  CAM  CAN  OAP  121.79  3.000
 ZOF  OAP  CAN  NAO  122.74  3.000
 ZOF  CAM  CAN  NAO  115.47  3.000
 ZOF  H14  CAM  H13  106.37  3.000
 ZOF  H14  CAM  CAL  110.00  3.000
 ZOF  H13  CAM  CAL  109.55  3.000
 ZOF  H14  CAM  CAN  110.94  3.000
 ZOF  H13  CAM  CAN  107.59  3.000
 ZOF  CAL  CAM  CAN  112.19  3.000
 ZOF  H16  CAL  H15  106.54  3.000
 ZOF  H16  CAL  CAK  109.56  3.000
 ZOF  H15  CAL  CAK  109.25  3.000
 ZOF  H16  CAL  CAM  109.69  3.000
 ZOF  H15  CAL  CAM  109.39  3.000
 ZOF  CAK  CAL  CAM  112.24  3.000
 ZOF  H18  CAK  H17  106.20  3.000
 ZOF  H18  CAK  CAI  109.64  3.000
 ZOF  H17  CAK  CAI  109.87  3.000
 ZOF  H18  CAK  CAL  109.48  3.000
 ZOF  H17  CAK  CAL  109.34  3.000
 ZOF  CAI  CAK  CAL  112.14  3.000
 ZOF  H20  CAI  H19  106.63  3.000
 ZOF  H20  CAI  CAH  109.57  3.000
 ZOF  H19  CAI  CAH  107.74  3.000
 ZOF  H20  CAI  CAK  109.82  3.000
 ZOF  H19  CAI  CAK  109.01  3.000
 ZOF  CAH  CAI  CAK  113.80  3.000
 ZOF  H21  CAH  CAD  108.13  3.000
 ZOF  H21  CAH  SAG  107.78  3.000
 ZOF  CAD  CAH  SAG  104.15  3.000
 ZOF  H21  CAH  CAI  109.15  3.000
 ZOF  CAD  CAH  CAI  114.34  3.000
 ZOF  SAG  CAH  CAI  112.95  3.000
 ZOF  CAF  SAG  CAH   89.18  3.000
 ZOF  H23  CAF  H22  108.03  3.000
 ZOF  H23  CAF  CAC  110.02  3.000
 ZOF  H22  CAF  CAC  112.30  3.000
 ZOF  H23  CAF  SAG  109.46  3.000
 ZOF  H22  CAF  SAG  110.18  3.000
 ZOF  CAC  CAF  SAG  106.83  3.000
 ZOF  H24  CAC  NAB  110.75  3.000
 ZOF  H24  CAC  CAD  111.54  3.000
 ZOF  NAB  CAC  CAD  102.45  3.000
 ZOF  H24  CAC  CAF  108.76  3.000
 ZOF  CAD  CAC  CAF  108.91  3.000
 ZOF  NAB  CAC  CAF  114.33  3.000
 ZOF  H25  CAD  NAE  111.43  3.000
 ZOF  H25  CAD  CAC  111.89  3.000
 ZOF  NAE  CAD  CAC  102.80  3.000
 ZOF  H25  CAD  CAH  109.37  3.000
 ZOF  NAE  CAD  CAH  112.55  3.000
 ZOF  CAC  CAD  CAH  108.67  3.000
 ZOF  H26  NAE  CAA  119.00  3.000
 ZOF  H26  NAE  CAD  119.71  3.000
 ZOF  CAA  NAE  CAD  112.88  3.000
 ZOF  NAB  CAA  NAJ  123.60  3.000
 ZOF  NAJ  CAA  NAE  129.29  3.000
 ZOF  NAB  CAA  NAE  107.10  3.000
 ZOF  H27  NAJ  CAA  110.36  3.000
 ZOF  H28  NAB  CAA  119.67  3.000
 ZOF  H28  NAB  CAC  121.01  3.000
 ZOF  CAA  NAB  CAC  113.35  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_02  NAB  CAA  NAE  CAD     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_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  Var_01    CAC  CAF  SAG  CAH    38.79  30.0  1
 ZOF  Var_02    CAH  CAI  CAK  CAL  -174.66  30.0  2
 ZOF  Var_03    CAT  CAU  CAV  OAW  -178.77  30.0  3
 ZOF  Var_04    CAS  CAT  CAU  CAV  -179.83  30.0  2
 ZOF  Var_05    CAR  CAS  CAT  CAU   179.37  30.0  3
 ZOF  Var_06    CAQ  CAR  CAS  CAT  -179.29  30.0  2
 ZOF  Var_07    NAO  CAQ  CAR  CAS  -179.31  30.0  3
 ZOF  Var_08    CAN  NAO  CAQ  CAR  -157.59  30.0  2
 ZOF  Var_09    CAL  CAM  CAN  NAO   129.96  30.0  2
 ZOF  Var_10    CAK  CAL  CAM  CAN  -179.44  30.0  1
 ZOF  Var_11    CAI  CAK  CAL  CAM  -179.40  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

