# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:21:14 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-sulfanylidene-propan-2-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(C)=O)C(=S)N1C[C@H](O)C[C@H]1C(=S)NCc2ccc(cc2)c3scnc3C
#
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
 DV8  DV8  ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-sulfanylidene-propan-2-yl]ethanamide  ligand  56  30  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DV8
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
 DV8  CAA  C  CH3   0  -0.776  -4.8788   2.7406   3.3142
 DV8  CAT  C  C     0   0.527  -5.1069   1.9664   2.0407
 DV8  OAD  O  O     0  -0.510  -6.2227   1.8430   1.5508
 DV8  NAR  N  NH1   0  -0.627  -4.0045   1.4256   1.4964
 DV8  CBB  C  CH1   0  -0.164  -4.0226   0.6713   0.2702
 DV8  CAC  C  CH3   0  -0.638  -3.8335   1.5687  -0.9572
 DV8  CAV  C  C     0   0.228  -2.9220  -0.3764   0.2675
 DV8  SAG  S  S1    0  -0.331  -1.4895  -0.1010   1.0763
 DV8  NBD  N  NT    0  -0.386  -3.1179  -1.4542  -0.4704
 DV8  CAO  C  CH2   0  -0.319  -4.3440  -1.8644  -1.1523
 DV8  CBA  C  CH1   0   0.007  -4.2410  -3.3831  -1.1342
 DV8  OAE  O  OH1   0  -0.664  -4.5201  -3.9142   0.1377
 DV8  CAN  C  CH2   0  -0.489  -2.7648  -3.5903  -1.4218
 DV8  CBC  C  CH1   0  -0.158  -2.0699  -2.4448  -0.6650
 DV8  CAU  C  C     0   0.245  -0.9144  -1.9001  -1.4876
 DV8  SAF  S  S1    0  -0.329  -1.1898  -0.8588  -2.7513
 DV8  NAQ  N  NH1   0  -0.551   0.2565  -2.4191  -1.1703
 DV8  CAM  C  CH2   0  -0.356   1.4970  -2.2094  -1.8796
 DV8  CAX  C  CR6   0   0.090   2.4208  -1.2360  -1.1952
 DV8  CAI  C  CR16  0  -0.288   3.7913  -1.4732  -1.1892
 DV8  CAK  C  CR16  0  -0.297   4.6669  -0.5733  -0.6039
 DV8  CAH  C  CR16  0  -0.264   1.9426  -0.0728  -0.5993
 DV8  CAJ  C  CR16  0  -0.295   2.8160   0.8309  -0.0157
 DV8  CAY  C  CR6   0   0.088   4.1920   0.5939  -0.0040
 DV8  CAZ  C  CR5   0  -0.310   5.1148   1.5477   0.6125
 DV8  SAS  S  S2    0   0.222   6.5974   1.9706  -0.1664
 DV8  CAL  C  CR15  0  -0.223   6.9702   3.0102   1.1413
 DV8  NAP  N  N     0  -0.373   6.0781   3.0477   2.0754
 DV8  CAW  C  CR5   0   0.321   5.0185   2.2266   1.7987
 DV8  CAB  C  CH3   0  -0.747   3.9074   2.1285   2.7907
 DV8  H1   H  HCH3  0   0.266  -5.4916   2.3172   4.1098
 DV8  H2   H  HCH3  0   0.249  -3.8411   2.7440   3.6413
 DV8  H3   H  HCH3  0   0.266  -5.1995   3.7727   3.1723
 DV8  H4   H  HNH1  0   0.393  -3.0998   1.5809   1.9198
 DV8  H5   H  HCH1  0   0.277  -4.9997   0.1931   0.2077
 DV8  H6   H  HCH3  0   0.234  -2.8823   2.0971  -0.8950
 DV8  H7   H  HCH3  0   0.243  -3.8364   0.9910  -1.8811
 DV8  H8   H  HCH3  0   0.250  -4.6402   2.2990  -1.0047
 DV8  H9   H  HCH2  0   0.285  -5.2380  -1.4989  -0.6529
 DV8  H10  H  HCH2  0   0.266  -4.3427  -1.4957  -2.1810
 DV8  H11  H  HCH1  0   0.254  -4.8732  -3.8236  -1.9123
 DV8  H12  H  HOH1  0   0.456  -5.4486  -3.7610   0.3402
 DV8  H13  H  HCH2  0   0.284  -2.3984  -4.5659  -1.1061
 DV8  H14  H  HCH2  0   0.268  -2.5967  -3.4927  -2.4948
 DV8  H15  H  HCH1  0   0.301  -1.7086  -2.7765   0.3130
 DV8  H16  H  HNH1  0   0.420   0.3069  -3.0067  -0.3497
 DV8  H17  H  HCH2  0   0.283   1.9889  -3.1765  -1.9888
 DV8  H18  H  HCH2  0   0.275   1.2488  -1.8526  -2.8801
 DV8  H19  H  HCR6  0   0.259   4.1836  -2.3776  -1.6387
 DV8  H20  H  HCR6  0   0.257   5.7272  -0.7951  -0.5970
 DV8  H21  H  HCR6  0   0.260   0.8804   0.1392  -0.5887
 DV8  H22  H  HCR6  0   0.259   2.4222   1.7426   0.4140
 DV8  H23  H  HCR5  0   0.302   7.8901   3.5782   1.1588
 DV8  H24  H  HCH3  0   0.255   3.1845   2.9360   2.6607
 DV8  H25  H  HCH3  0   0.249   3.3677   1.1870   2.7066
 DV8  H26  H  HCH3  0   0.258   4.3023   2.2054   3.8030

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
 DV8  NAP  CAL  aromatic  1.292  0.020  1.292
 DV8  NAP  CAW  aromatic  1.369  0.020  1.369
 DV8  CAL  SAS  aromatic  1.712  0.020  1.712
 DV8  CAB  CAW  single    1.493  0.020  1.493
 DV8  CAW  CAZ  aromatic  1.370  0.020  1.370
 DV8  SAS  CAZ  aromatic  1.727  0.020  1.727
 DV8  CAZ  CAY  single    1.463  0.020  1.463
 DV8  CAY  CAJ  aromatic  1.396  0.020  1.396
 DV8  CAY  CAK  aromatic  1.396  0.020  1.396
 DV8  CAJ  CAH  aromatic  1.386  0.020  1.386
 DV8  CAK  CAI  aromatic  1.385  0.020  1.385
 DV8  CAH  CAX  aromatic  1.392  0.020  1.392
 DV8  CAI  CAX  aromatic  1.391  0.020  1.391
 DV8  CAX  CAM  single    1.506  0.020  1.506
 DV8  CAM  NAQ  single    1.444  0.020  1.444
 DV8  NAQ  CAU  single    1.320  0.020  1.320
 DV8  CAN  CBC  single    1.539  0.020  1.539
 DV8  CAN  CBA  single    1.518  0.020  1.518
 DV8  CAU  SAF  double    1.660  0.020  1.660
 DV8  CAU  CBC  single    1.519  0.020  1.519
 DV8  CBC  NBD  single    1.455  0.020  1.455
 DV8  CBA  OAE  single    1.406  0.020  1.406
 DV8  CBA  CAO  single    1.522  0.020  1.522
 DV8  NBD  CAO  single    1.462  0.020  1.462
 DV8  NBD  CAV  single    1.321  0.020  1.321
 DV8  SAG  CAV  double    1.668  0.020  1.668
 DV8  CAV  CBB  single    1.520  0.020  1.520
 DV8  CBB  CAC  single    1.532  0.020  1.532
 DV8  CBB  NAR  single    1.440  0.020  1.440
 DV8  NAR  CAT  single    1.343  0.020  1.343
 DV8  OAD  CAT  double    1.225  0.020  1.225
 DV8  CAT  CAA  single    1.508  0.020  1.508
 DV8  CAA  H1   single    0.970  0.020  1.090
 DV8  CAA  H2   single    0.970  0.020  1.090
 DV8  CAA  H3   single    0.970  0.020  1.090
 DV8  NAR  H4   single    0.860  0.020  1.020
 DV8  CBB  H5   single    0.970  0.020  1.090
 DV8  CAC  H6   single    0.970  0.020  1.090
 DV8  CAC  H7   single    0.970  0.020  1.090
 DV8  CAC  H8   single    0.970  0.020  1.090
 DV8  CAO  H9   single    0.970  0.020  1.090
 DV8  CAO  H10  single    0.970  0.020  1.090
 DV8  CBA  H11  single    0.970  0.020  1.090
 DV8  OAE  H12  single    0.850  0.020  0.980
 DV8  CAN  H13  single    0.970  0.020  1.090
 DV8  CAN  H14  single    0.970  0.020  1.090
 DV8  CBC  H15  single    0.970  0.020  1.090
 DV8  NAQ  H16  single    0.860  0.020  1.020
 DV8  CAM  H17  single    0.970  0.020  1.090
 DV8  CAM  H18  single    0.970  0.020  1.090
 DV8  CAI  H19  single    0.930  0.020  1.080
 DV8  CAK  H20  single    0.930  0.020  1.080
 DV8  CAH  H21  single    0.930  0.020  1.080
 DV8  CAJ  H22  single    0.930  0.020  1.080
 DV8  CAL  H23  single    0.930  0.020  1.080
 DV8  CAB  H24  single    0.970  0.020  1.090
 DV8  CAB  H25  single    0.970  0.020  1.090
 DV8  CAB  H26  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
 DV8  H3   CAA  H2   108.47  3.000
 DV8  H3   CAA  H1   107.31  3.000
 DV8  H2   CAA  H1   108.54  3.000
 DV8  H3   CAA  CAT  109.37  3.000
 DV8  H2   CAA  CAT  113.57  3.000
 DV8  H1   CAA  CAT  109.39  3.000
 DV8  NAR  CAT  OAD  123.03  3.000
 DV8  OAD  CAT  CAA  121.83  3.000
 DV8  NAR  CAT  CAA  115.14  3.000
 DV8  H4   NAR  CBB  116.65  3.000
 DV8  H4   NAR  CAT  120.19  3.000
 DV8  CBB  NAR  CAT  123.07  3.000
 DV8  H5   CBB  CAV  110.29  3.000
 DV8  H5   CBB  CAC  108.77  3.000
 DV8  CAV  CBB  CAC  108.24  3.000
 DV8  H5   CBB  NAR  106.87  3.000
 DV8  CAC  CBB  NAR  111.95  3.000
 DV8  CAV  CBB  NAR  110.71  3.000
 DV8  H8   CAC  H7   108.44  3.000
 DV8  H8   CAC  H6   108.89  3.000
 DV8  H7   CAC  H6   107.93  3.000
 DV8  H8   CAC  CBB  109.65  3.000
 DV8  H7   CAC  CBB  111.62  3.000
 DV8  H6   CAC  CBB  110.24  3.000
 DV8  NBD  CAV  SAG  122.21  3.000
 DV8  SAG  CAV  CBB  120.49  3.000
 DV8  NBD  CAV  CBB  117.14  3.000
 DV8  CBC  NBD  CAO  110.53  3.000
 DV8  CAO  NBD  CAV  127.88  3.000
 DV8  CBC  NBD  CAV  121.56  3.000
 DV8  H10  CAO  H9   108.66  3.000
 DV8  H10  CAO  CBA  110.35  3.000
 DV8  H9   CAO  CBA  112.67  3.000
 DV8  H10  CAO  NBD  110.10  3.000
 DV8  H9   CAO  NBD  112.40  3.000
 DV8  CBA  CAO  NBD  102.57  3.000
 DV8  H11  CBA  CAN  111.83  3.000
 DV8  H11  CBA  OAE  112.10  3.000
 DV8  CAN  CBA  OAE  108.22  3.000
 DV8  H11  CBA  CAO  110.72  3.000
 DV8  OAE  CBA  CAO  111.97  3.000
 DV8  CAN  CBA  CAO  101.51  3.000
 DV8  H12  OAE  CBA  108.76  3.000
 DV8  H14  CAN  H13  108.28  3.000
 DV8  H14  CAN  CBC  110.35  3.000
 DV8  H13  CAN  CBC  111.86  3.000
 DV8  H14  CAN  CBA  108.91  3.000
 DV8  H13  CAN  CBA  113.23  3.000
 DV8  CBC  CAN  CBA  104.15  3.000
 DV8  H15  CBC  CAU  109.97  3.000
 DV8  H15  CBC  CAN  111.29  3.000
 DV8  CAU  CBC  CAN  110.12  3.000
 DV8  H15  CBC  NBD  108.95  3.000
 DV8  CAU  CBC  NBD  112.09  3.000
 DV8  CAN  CBC  NBD  104.31  3.000
 DV8  NAQ  CAU  SAF  125.23  3.000
 DV8  SAF  CAU  CBC  120.71  3.000
 DV8  NAQ  CAU  CBC  113.81  3.000
 DV8  H16  NAQ  CAM  116.13  3.000
 DV8  H16  NAQ  CAU  117.92  3.000
 DV8  CAM  NAQ  CAU  125.95  3.000
 DV8  H18  CAM  H17  107.51  3.000
 DV8  H18  CAM  CAX  110.17  3.000
 DV8  H17  CAM  CAX  109.99  3.000
 DV8  H18  CAM  NAQ  107.61  3.000
 DV8  H17  CAM  NAQ  107.94  3.000
 DV8  CAX  CAM  NAQ  113.42  3.000
 DV8  CAH  CAX  CAI  118.64  3.000
 DV8  CAI  CAX  CAM  119.74  3.000
 DV8  CAH  CAX  CAM  121.59  3.000
 DV8  H19  CAI  CAK  119.26  3.000
 DV8  H19  CAI  CAX  119.82  3.000
 DV8  CAK  CAI  CAX  120.92  3.000
 DV8  H20  CAK  CAY  120.11  3.000
 DV8  H20  CAK  CAI  119.23  3.000
 DV8  CAY  CAK  CAI  120.65  3.000
 DV8  H21  CAH  CAJ  119.10  3.000
 DV8  H21  CAH  CAX  120.31  3.000
 DV8  CAJ  CAH  CAX  120.59  3.000
 DV8  H22  CAJ  CAY  119.89  3.000
 DV8  H22  CAJ  CAH  119.16  3.000
 DV8  CAY  CAJ  CAH  120.93  3.000
 DV8  CAZ  CAY  CAJ  120.95  3.000
 DV8  CAJ  CAY  CAK  118.28  3.000
 DV8  CAZ  CAY  CAK  120.77  3.000
 DV8  CAW  CAZ  SAS  109.23  3.000
 DV8  SAS  CAZ  CAY  120.72  3.000
 DV8  CAW  CAZ  CAY  130.05  3.000
 DV8  CAL  SAS  CAZ   89.50  3.000
 DV8  H23  CAL  NAP  124.08  3.000
 DV8  H23  CAL  SAS  121.11  3.000
 DV8  NAP  CAL  SAS  114.80  3.000
 DV8  CAW  NAP  CAL  111.77  3.000
 DV8  CAB  CAW  NAP  118.77  3.000
 DV8  CAB  CAW  CAZ  126.52  3.000
 DV8  NAP  CAW  CAZ  114.70  3.000
 DV8  H26  CAB  H25  108.22  3.000
 DV8  H26  CAB  H24  107.37  3.000
 DV8  H25  CAB  H24  107.60  3.000
 DV8  H26  CAB  CAW  110.06  3.000
 DV8  H25  CAB  CAW  111.99  3.000
 DV8  H24  CAB  CAW  111.42  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
 DV8  CONST_01  CAY  CAJ  CAH  CAX    0.00   0.0  0
 DV8  CONST_02  CAY  CAK  CAI  CAX    0.00   0.0  0
 DV8  CONST_03  CAZ  CAY  CAK  CAI  180.00   0.0  0
 DV8  CONST_04  CAJ  CAY  CAK  CAI    0.00   0.0  0
 DV8  CONST_05  CAJ  CAH  CAX  CAI    0.00   0.0  0
 DV8  CONST_08  CAH  CAJ  CAY  CAK    0.00   0.0  0
 DV8  CONST_09  CAH  CAX  CAI  CAK    0.00   0.0  0
 DV8  CONST_10  CAZ  CAY  CAJ  CAH  180.00   0.0  0
 DV8  CONST_13  NAP  CAW  CAZ  CAY  180.00   0.0  0
 DV8  CONST_14  CAL  SAS  CAZ  CAY  180.00   0.0  0
 DV8  CONST_15  CAL  NAP  CAW  CAZ    0.00   0.0  0
 DV8  CONST_16  NAP  CAL  SAS  CAZ    0.00   0.0  0
 DV8  CONST_17  CAW  NAP  CAL  SAS    0.00   0.0  0
 DV8  CONST_18  NAP  CAW  CAZ  SAS    0.00   0.0  0
 DV8  CONST_19  CAW  CAZ  SAS  CAL    0.00   0.0  0
 DV8  CONST_20  CAJ  CAH  CAX  CAM  180.00   0.0  0
 DV8  CONST_21  CAK  CAI  CAX  CAM  180.00   0.0  0
 DV8  CONST_22  CAB  CAW  CAZ  CAY    0.00   0.0  0
 DV8  CONST_23  CAB  CAW  CAZ  SAS  180.00   0.0  0
 DV8  CONST_24  CAB  CAW  NAP  CAL  180.00   0.0  0
 DV8  CONST_25  H22  CAJ  CAH  CAX  180.00   0.0  0
 DV8  CONST_26  H20  CAK  CAI  CAX  180.00   0.0  0
 DV8  CONST_27  H21  CAH  CAX  CAI  180.00   0.0  0
 DV8  CONST_28  H19  CAI  CAX  CAH  180.00   0.0  0
 DV8  CONST_29  H23  CAL  SAS  CAZ  180.00   0.0  0
 DV8  CONST_30  CBB  NAR  CAT  CAA  180.00   0.0  0
 DV8  CONST_31  CBB  NAR  CAT  OAD    0.00   0.0  0
 DV8  CONST_32  H4   NAR  CAT  CAA    0.00   0.0  0
 DV8  Var_01    CBC  NBD  CAO  CBA   28.59  30.0  1
 DV8  Var_02    CAH  CAX  CAM  NAQ  -40.73  30.0  2
 DV8  Var_03    H24  CAB  CAW  CAZ  -97.11  30.0  2
 DV8  Var_04    CAM  NAQ  CAU  CBC  172.40  30.0  1
 DV8  Var_05    CAX  CAM  NAQ  CAU  102.91  30.0  1
 DV8  Var_06    H1   CAA  CAT  OAD   57.18  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
 DV8  chir_01  CBB  CAV  CAC  NAR  positiv
 DV8  chir_02  CBA  OAE  CAN  CAO  positiv
 DV8  chir_03  CBC  NBD  CAU  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
 DV8  plan-1  CAY  0.020
 DV8  plan-1  CAZ  0.020
 DV8  plan-1  SAS  0.020
 DV8  plan-1  CAL  0.020
 DV8  plan-1  NAP  0.020
 DV8  plan-1  CAW  0.020
 DV8  plan-1  CAB  0.020
 DV8  plan-1  H23  0.020
 DV8  plan-2  CAM  0.020
 DV8  plan-2  CAX  0.020
 DV8  plan-2  CAI  0.020
 DV8  plan-2  CAK  0.020
 DV8  plan-2  CAH  0.020
 DV8  plan-2  CAJ  0.020
 DV8  plan-2  CAY  0.020
 DV8  plan-2  CAZ  0.020
 DV8  plan-2  H19  0.020
 DV8  plan-2  H20  0.020
 DV8  plan-2  H21  0.020
 DV8  plan-2  H22  0.020
 DV8  plan-3  CAA  0.020
 DV8  plan-3  CAT  0.020
 DV8  plan-3  OAD  0.020
 DV8  plan-3  NAR  0.020
 DV8  plan-3  CBB  0.020
 DV8  plan-3  H4   0.020
 DV8  plan-4  CBC  0.020
 DV8  plan-4  CAU  0.020
 DV8  plan-4  SAF  0.020
 DV8  plan-4  NAQ  0.020
 DV8  plan-5  CBB  0.020
 DV8  plan-5  CAV  0.020
 DV8  plan-5  SAG  0.020
 DV8  plan-5  NBD  0.020

