# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 03:15:42 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-oxidanylidene-propan-2-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(C)=O)C(=O)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
 DV2  DV2  ~{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-oxidanylidene-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_DV2
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
 DV2  CAA  C  CH3   0  -0.775   6.2315   2.8942  -2.6865
 DV2  CAT  C  C     0   0.526   6.3369   1.7434  -1.7177
 DV2  OAD  O  O     0  -0.510   7.3803   1.1193  -1.5680
 DV2  N    N  NH1   0  -0.630   5.2101   1.4490  -1.0502
 DV2  CA   C  CH1   0  -0.201   5.1210   0.3856  -0.0813
 DV2  CB   C  CH3   0  -0.651   5.5798   0.8380   1.3084
 DV2  C    C  C     0   0.572   3.6695  -0.0706  -0.0103
 DV2  O    O  O     0  -0.490   2.7582   0.6680  -0.3623
 DV2  NBD  N  NT    0  -0.470   3.4295  -1.2842   0.5033
 DV2  CAO  C  CH2   0  -0.308   4.3855  -2.3052   0.8988
 DV2  CBA  C  CH1   0   0.005   3.5750  -3.5891   0.7587
 DV2  OAF  O  OH1   0  -0.666   3.4418  -3.9880  -0.5846
 DV2  CAN  C  CH2   0  -0.492   2.2090  -3.1442   1.2529
 DV2  CBC  C  CH1   0  -0.134   2.0611  -1.7166   0.7004
 DV2  CAV  C  C     0   0.246   1.3122  -0.8277   1.6773
 DV2  SAG  S  S1    0  -0.350   2.0384  -0.2447   3.0516
 DV2  NAQ  N  NH1   0  -0.558   0.0448  -0.6351   1.3745
 DV2  CAM  C  CH2   0  -0.326  -0.8921   0.1099   2.1964
 DV2  CAX  C  CR6   0   0.041  -2.1880   0.2891   1.4597
 DV2  CAI  C  CR16  0  -0.266  -3.2242  -0.6264   1.6076
 DV2  CAK  C  CR16  0  -0.291  -4.4095  -0.4761   0.9045
 DV2  CAH  C  CR16  0  -0.265  -2.3623   1.3610   0.5888
 DV2  CAJ  C  CR16  0  -0.292  -3.5415   1.5119  -0.1211
 DV2  CAY  C  CR6   0   0.086  -4.5812   0.5908   0.0220
 DV2  CAZ  C  CR5   0  -0.311  -5.8294   0.7458  -0.7269
 DV2  SAS  S  S2    0   0.225  -6.6103   2.2802  -0.8479
 DV2  CAL  C  CR15  0  -0.222  -7.8405   1.5597  -1.7963
 DV2  NAP  N  N     0  -0.372  -7.6914   0.2937  -2.0086
 DV2  CAW  C  CR5   0   0.324  -6.5576  -0.1895  -1.4137
 DV2  CAB  C  CH3   0  -0.744  -6.2072  -1.6303  -1.5825
 DV2  H1   H  HCH3  0   0.266   6.4033   2.5279  -3.6990
 DV2  H2   H  HCH3  0   0.249   5.2678   3.3995  -2.6640
 DV2  H3   H  HCH3  0   0.264   7.0107   3.6241  -2.4693
 DV2  H4   H  HNH1  0   0.398   4.3822   2.0070  -1.1922
 DV2  H5   H  HCH1  0   0.274   5.7576  -0.4337  -0.4196
 DV2  H6   H  HCH3  0   0.250   6.6184   1.1613   1.2665
 DV2  H7   H  HCH3  0   0.236   4.9699   1.6705   1.6587
 DV2  H8   H  HCH3  0   0.243   5.5039   0.0354   2.0405
 DV2  H9   H  HCH2  0   0.271   5.2745  -2.3046   0.2681
 DV2  H10  H  HCH2  0   0.250   4.7015  -2.1712   1.9372
 DV2  H11  H  HCH1  0   0.248   3.9955  -4.3867   1.3806
 DV2  H12  H  HOH1  0   0.455   4.3120  -4.2154  -0.9269
 DV2  H13  H  HCH2  0   0.278   1.4006  -3.7976   0.9275
 DV2  H14  H  HCH2  0   0.261   2.2136  -3.1252   2.3437
 DV2  H15  H  HCH1  0   0.288   1.5301  -1.7276  -0.2574
 DV2  H16  H  HNH1  0   0.418  -0.3075  -1.0284   0.5125
 DV2  H17  H  HCH2  0   0.270  -1.0469  -0.4191   3.1401
 DV2  H18  H  HCH2  0   0.270  -0.4467   1.0749   2.4456
 DV2  H19  H  HCR6  0   0.262  -3.1143  -1.4596   2.2908
 DV2  H20  H  HCR6  0   0.265  -5.2132  -1.1840   1.0613
 DV2  H21  H  HCR6  0   0.262  -1.5687   2.0870   0.4596
 DV2  H22  H  HCR6  0   0.260  -3.6479   2.3464  -0.8034
 DV2  H23  H  HCR5  0   0.303  -8.6668   2.1450  -2.1754
 DV2  H24  H  HCH3  0   0.255  -6.7767  -2.2619  -0.8980
 DV2  H25  H  HCH3  0   0.258  -6.4380  -1.9580  -2.5958
 DV2  H26  H  HCH3  0   0.250  -5.1505  -1.8118  -1.3974

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
 DV2  CAA  CAT  single    1.508  0.020  1.508
 DV2  CAT  OAD  double    1.225  0.020  1.225
 DV2  CAT  N    single    1.342  0.020  1.342
 DV2  N    CA   single    1.441  0.020  1.441
 DV2  CB   CA   single    1.532  0.020  1.532
 DV2  CA   C    single    1.523  0.020  1.523
 DV2  C    O    double    1.225  0.020  1.225
 DV2  C    NBD  single    1.339  0.020  1.339
 DV2  CAO  NBD  single    1.454  0.020  1.454
 DV2  CAO  CBA  single    1.525  0.020  1.525
 DV2  NBD  CBC  single    1.449  0.020  1.449
 DV2  OAF  CBA  single    1.408  0.020  1.408
 DV2  CBA  CAN  single    1.519  0.020  1.519
 DV2  CBC  CAV  single    1.518  0.020  1.518
 DV2  CBC  CAN  single    1.538  0.020  1.538
 DV2  SAG  CAV  double    1.660  0.020  1.660
 DV2  CAV  NAQ  single    1.317  0.020  1.317
 DV2  NAQ  CAM  single    1.452  0.020  1.452
 DV2  CAM  CAX  single    1.501  0.020  1.501
 DV2  CAX  CAI  aromatic  1.391  0.020  1.391
 DV2  CAX  CAH  aromatic  1.392  0.020  1.392
 DV2  CAI  CAK  aromatic  1.386  0.020  1.386
 DV2  CAH  CAJ  aromatic  1.385  0.020  1.385
 DV2  CAK  CAY  aromatic  1.395  0.020  1.395
 DV2  CAJ  CAY  aromatic  1.396  0.020  1.396
 DV2  CAY  CAZ  single    1.464  0.020  1.464
 DV2  CAZ  SAS  aromatic  1.726  0.020  1.726
 DV2  CAZ  CAW  aromatic  1.370  0.020  1.370
 DV2  SAS  CAL  aromatic  1.712  0.020  1.712
 DV2  CAW  CAB  single    1.492  0.020  1.492
 DV2  CAW  NAP  aromatic  1.369  0.020  1.369
 DV2  CAL  NAP  aromatic  1.292  0.020  1.292
 DV2  CAA  H1   single    0.970  0.020  1.090
 DV2  CAA  H2   single    0.970  0.020  1.090
 DV2  CAA  H3   single    0.970  0.020  1.090
 DV2  N    H4   single    0.860  0.020  1.020
 DV2  CA   H5   single    0.970  0.020  1.090
 DV2  CB   H6   single    0.970  0.020  1.090
 DV2  CB   H7   single    0.970  0.020  1.090
 DV2  CB   H8   single    0.970  0.020  1.090
 DV2  CAO  H9   single    0.970  0.020  1.090
 DV2  CAO  H10  single    0.970  0.020  1.090
 DV2  CBA  H11  single    0.970  0.020  1.090
 DV2  OAF  H12  single    0.850  0.020  0.980
 DV2  CAN  H13  single    0.970  0.020  1.090
 DV2  CAN  H14  single    0.970  0.020  1.090
 DV2  CBC  H15  single    0.970  0.020  1.090
 DV2  NAQ  H16  single    0.860  0.020  1.020
 DV2  CAM  H17  single    0.970  0.020  1.090
 DV2  CAM  H18  single    0.970  0.020  1.090
 DV2  CAI  H19  single    0.930  0.020  1.080
 DV2  CAK  H20  single    0.930  0.020  1.080
 DV2  CAH  H21  single    0.930  0.020  1.080
 DV2  CAJ  H22  single    0.930  0.020  1.080
 DV2  CAL  H23  single    0.930  0.020  1.080
 DV2  CAB  H24  single    0.970  0.020  1.090
 DV2  CAB  H25  single    0.970  0.020  1.090
 DV2  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
 DV2  H3   CAA  H2   108.55  3.000
 DV2  H3   CAA  H1   107.31  3.000
 DV2  H2   CAA  H1   108.34  3.000
 DV2  H3   CAA  CAT  109.46  3.000
 DV2  H2   CAA  CAT  113.76  3.000
 DV2  H1   CAA  CAT  109.22  3.000
 DV2  N    CAT  OAD  122.85  3.000
 DV2  N    CAT  CAA  115.35  3.000
 DV2  OAD  CAT  CAA  121.80  3.000
 DV2  H4   N    CA   116.88  3.000
 DV2  H4   N    CAT  119.85  3.000
 DV2  CA   N    CAT  123.23  3.000
 DV2  H5   CA   C    110.21  3.000
 DV2  H5   CA   CB   109.16  3.000
 DV2  C    CA   CB   109.37  3.000
 DV2  H5   CA   N    108.03  3.000
 DV2  C    CA   N    108.13  3.000
 DV2  CB   CA   N    111.93  3.000
 DV2  H8   CB   H7   107.93  3.000
 DV2  H8   CB   H6   108.14  3.000
 DV2  H7   CB   H6   108.62  3.000
 DV2  H8   CB   CA   111.80  3.000
 DV2  H7   CB   CA   110.46  3.000
 DV2  H6   CB   CA   109.79  3.000
 DV2  NBD  C    O    121.55  3.000
 DV2  NBD  C    CA   117.38  3.000
 DV2  O    C    CA   121.00  3.000
 DV2  CBC  NBD  CAO  112.00  3.000
 DV2  CBC  NBD  C    119.46  3.000
 DV2  CAO  NBD  C    128.53  3.000
 DV2  H10  CAO  H9   108.28  3.000
 DV2  H10  CAO  CBA  110.12  3.000
 DV2  H9   CAO  CBA  112.39  3.000
 DV2  H10  CAO  NBD  111.24  3.000
 DV2  H9   CAO  NBD  112.24  3.000
 DV2  CBA  CAO  NBD  102.53  3.000
 DV2  H11  CBA  CAN  111.95  3.000
 DV2  H11  CBA  OAF  111.83  3.000
 DV2  CAN  CBA  OAF  107.96  3.000
 DV2  H11  CBA  CAO  110.91  3.000
 DV2  CAN  CBA  CAO  101.62  3.000
 DV2  OAF  CBA  CAO  112.12  3.000
 DV2  H12  OAF  CBA  108.71  3.000
 DV2  H14  CAN  H13  108.20  3.000
 DV2  H14  CAN  CBC  110.09  3.000
 DV2  H13  CAN  CBC  112.22  3.000
 DV2  H14  CAN  CBA  109.06  3.000
 DV2  H13  CAN  CBA  113.23  3.000
 DV2  CBC  CAN  CBA  103.97  3.000
 DV2  H15  CBC  CAV  109.23  3.000
 DV2  H15  CBC  CAN  110.58  3.000
 DV2  CAV  CBC  CAN  111.08  3.000
 DV2  H15  CBC  NBD  110.00  3.000
 DV2  CAN  CBC  NBD  103.60  3.000
 DV2  CAV  CBC  NBD  112.26  3.000
 DV2  NAQ  CAV  SAG  124.04  3.000
 DV2  NAQ  CAV  CBC  114.35  3.000
 DV2  SAG  CAV  CBC  121.50  3.000
 DV2  H16  NAQ  CAM  117.22  3.000
 DV2  H16  NAQ  CAV  118.33  3.000
 DV2  CAM  NAQ  CAV  124.45  3.000
 DV2  H18  CAM  H17  106.78  3.000
 DV2  H18  CAM  CAX  111.02  3.000
 DV2  H17  CAM  CAX  111.05  3.000
 DV2  H18  CAM  NAQ  108.63  3.000
 DV2  H17  CAM  NAQ  109.38  3.000
 DV2  CAX  CAM  NAQ  109.90  3.000
 DV2  CAH  CAX  CAI  118.69  3.000
 DV2  CAH  CAX  CAM  120.47  3.000
 DV2  CAI  CAX  CAM  120.82  3.000
 DV2  H19  CAI  CAK  119.34  3.000
 DV2  H19  CAI  CAX  119.86  3.000
 DV2  CAK  CAI  CAX  120.79  3.000
 DV2  H20  CAK  CAY  120.02  3.000
 DV2  H20  CAK  CAI  119.38  3.000
 DV2  CAY  CAK  CAI  120.59  3.000
 DV2  H21  CAH  CAJ  119.32  3.000
 DV2  H21  CAH  CAX  119.92  3.000
 DV2  CAJ  CAH  CAX  120.75  3.000
 DV2  H22  CAJ  CAY  119.98  3.000
 DV2  H22  CAJ  CAH  119.38  3.000
 DV2  CAY  CAJ  CAH  120.64  3.000
 DV2  CAZ  CAY  CAJ  120.83  3.000
 DV2  CAZ  CAY  CAK  120.63  3.000
 DV2  CAJ  CAY  CAK  118.53  3.000
 DV2  CAW  CAZ  SAS  109.35  3.000
 DV2  CAW  CAZ  CAY  129.60  3.000
 DV2  SAS  CAZ  CAY  121.05  3.000
 DV2  CAL  SAS  CAZ   89.42  3.000
 DV2  H23  CAL  NAP  124.11  3.000
 DV2  H23  CAL  SAS  121.04  3.000
 DV2  NAP  CAL  SAS  114.85  3.000
 DV2  CAW  NAP  CAL  111.72  3.000
 DV2  CAB  CAW  NAP  119.09  3.000
 DV2  NAP  CAW  CAZ  114.66  3.000
 DV2  CAB  CAW  CAZ  126.23  3.000
 DV2  H26  CAB  H25  108.28  3.000
 DV2  H26  CAB  H24  107.67  3.000
 DV2  H25  CAB  H24  107.37  3.000
 DV2  H26  CAB  CAW  111.70  3.000
 DV2  H25  CAB  CAW  110.23  3.000
 DV2  H24  CAB  CAW  111.41  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
 DV2  CONST_01  CAY  CAK  CAI  CAX    0.00   0.0  0
 DV2  CONST_02  CAY  CAJ  CAH  CAX    0.00   0.0  0
 DV2  CONST_03  CAJ  CAH  CAX  CAI    0.00   0.0  0
 DV2  CONST_04  CAJ  CAY  CAK  CAI    0.00   0.0  0
 DV2  CONST_05  CAZ  CAY  CAK  CAI  180.00   0.0  0
 DV2  CONST_06  CAH  CAX  CAI  CAK    0.00   0.0  0
 DV2  CONST_07  CAH  CAJ  CAY  CAK    0.00   0.0  0
 DV2  CONST_10  CAZ  CAY  CAJ  CAH  180.00   0.0  0
 DV2  CONST_13  CAL  SAS  CAZ  CAY  180.00   0.0  0
 DV2  CONST_14  NAP  CAW  CAZ  CAY  180.00   0.0  0
 DV2  CONST_15  NAP  CAL  SAS  CAZ    0.00   0.0  0
 DV2  CONST_16  CAL  NAP  CAW  CAZ    0.00   0.0  0
 DV2  CONST_17  NAP  CAW  CAZ  SAS    0.00   0.0  0
 DV2  CONST_18  CAW  NAP  CAL  SAS    0.00   0.0  0
 DV2  CONST_19  CAW  CAZ  SAS  CAL    0.00   0.0  0
 DV2  CONST_20  CAK  CAI  CAX  CAM  180.00   0.0  0
 DV2  CONST_21  CAJ  CAH  CAX  CAM  180.00   0.0  0
 DV2  CONST_22  CAB  CAW  CAZ  CAY    0.00   0.0  0
 DV2  CONST_23  CAB  CAW  CAZ  SAS  180.00   0.0  0
 DV2  CONST_24  CAB  CAW  NAP  CAL  180.00   0.0  0
 DV2  CONST_25  H20  CAK  CAI  CAX  180.00   0.0  0
 DV2  CONST_26  H22  CAJ  CAH  CAX  180.00   0.0  0
 DV2  CONST_27  H21  CAH  CAX  CAI  180.00   0.0  0
 DV2  CONST_28  H19  CAI  CAX  CAH  180.00   0.0  0
 DV2  CONST_29  H23  CAL  SAS  CAZ  180.00   0.0  0
 DV2  CONST_30  CAO  NBD  C    CA     0.00   0.0  0
 DV2  CONST_31  CBC  NBD  C    CA   180.00   0.0  0
 DV2  CONST_32  CAO  NBD  C    O    180.00   0.0  0
 DV2  CONST_33  CBC  NBD  C    O      0.00   0.0  0
 DV2  CONST_34  CA   N    CAT  CAA  180.00   0.0  0
 DV2  CONST_35  CA   N    CAT  OAD    0.00   0.0  0
 DV2  CONST_36  H4   N    CAT  CAA    0.00   0.0  0
 DV2  Var_01    CBC  NBD  CAO  CBA   24.72  30.0  1
 DV2  Var_02    CAI  CAX  CAM  NAQ   92.05  30.0  2
 DV2  Var_03    H24  CAB  CAW  CAZ  100.91  30.0  2
 DV2  Var_04    CAM  NAQ  CAV  CBC  176.20  30.0  2
 DV2  Var_05    CAX  CAM  NAQ  CAV  172.19  30.0  3
 DV2  Var_06    H1   CAA  CAT  OAD   62.92  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
 DV2  chir_01  CA   N    CB   C    negativ
 DV2  chir_02  CBA  OAF  CAO  CAN  negativ
 DV2  chir_03  CBC  NBD  CAV  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
 DV2  plan-1  CAY  0.020
 DV2  plan-1  CAZ  0.020
 DV2  plan-1  SAS  0.020
 DV2  plan-1  CAL  0.020
 DV2  plan-1  NAP  0.020
 DV2  plan-1  CAW  0.020
 DV2  plan-1  CAB  0.020
 DV2  plan-1  H23  0.020
 DV2  plan-2  CAM  0.020
 DV2  plan-2  CAX  0.020
 DV2  plan-2  CAI  0.020
 DV2  plan-2  CAK  0.020
 DV2  plan-2  CAH  0.020
 DV2  plan-2  CAJ  0.020
 DV2  plan-2  CAY  0.020
 DV2  plan-2  CAZ  0.020
 DV2  plan-2  H19  0.020
 DV2  plan-2  H20  0.020
 DV2  plan-2  H21  0.020
 DV2  plan-2  H22  0.020
 DV2  plan-3  CA   0.020
 DV2  plan-3  C    0.020
 DV2  plan-3  O    0.020
 DV2  plan-3  NBD  0.020
 DV2  plan-3  CAO  0.020
 DV2  plan-3  CBC  0.020
 DV2  plan-4  CAA  0.020
 DV2  plan-4  CAT  0.020
 DV2  plan-4  OAD  0.020
 DV2  plan-4  N    0.020
 DV2  plan-4  CA   0.020
 DV2  plan-4  H4   0.020
 DV2  plan-5  CBC  0.020
 DV2  plan-5  CAV  0.020
 DV2  plan-5  SAG  0.020
 DV2  plan-5  NAQ  0.020

