# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:09:44 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanethioyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
#   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(=O)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
 DV5  DV5  (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanethioyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide  ligand  56  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DV5
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
 DV5  CAA  C  CH3   0  -0.775   8.5821   1.6846  -0.7767
 DV5  CAT  C  C     0   0.525   7.7591   0.6591  -0.0385
 DV5  OAD  O  O     0  -0.509   8.2633  -0.3426   0.4538
 DV5  NAR  N  NH1   0  -0.626   6.4424   0.9192   0.0186
 DV5  CBB  C  CH1   0  -0.162   5.4947   0.0540   0.6692
 DV5  CAC  C  CH3   0  -0.639   5.2959   0.4267   2.1425
 DV5  CAV  C  C     0   0.226   4.1410   0.1220  -0.0202
 DV5  SAG  S  S1    0  -0.340   3.6361   1.5290  -0.7602
 DV5  N    N  NT    0  -0.391   3.3634  -0.9406   0.0799
 DV5  CD2  C  CH2   0  -0.316   3.7161  -2.2526   0.6223
 DV5  CG   C  CH1   0   0.004   2.7342  -3.1841  -0.0762
 DV5  OD1  O  OH1   0  -0.664   3.1112  -3.4404  -1.4067
 DV5  CB   C  CH2   0  -0.501   1.4722  -2.3413  -0.1008
 DV5  CA   C  CH1   0  -0.193   1.9817  -0.9180  -0.3784
 DV5  C    C  C     0   0.558   1.1662   0.0907   0.4238
 DV5  O    O  O     0  -0.472   1.3860   0.2765   1.6081
 DV5  NAQ  N  NH1   0  -0.628   0.1496   0.6367  -0.2597
 DV5  CAM  C  CH2   0  -0.339  -0.8216   1.5353   0.3106
 DV5  CAX  C  CR6   0   0.086  -2.2355   1.0231   0.1968
 DV5  CAI  C  CR16  0  -0.274  -2.5355  -0.3274   0.3535
 DV5  CAK  C  CR16  0  -0.292  -3.8429  -0.7772   0.2817
 DV5  CAH  C  CR16  0  -0.290  -3.2820   1.9102  -0.0299
 DV5  CAJ  C  CR16  0  -0.291  -4.5942   1.4669  -0.0907
 DV5  CAY  C  CR6   0   0.083  -4.8952   0.1128   0.0554
 DV5  CAZ  C  CR5   0  -0.311  -6.2775  -0.3618  -0.0210
 DV5  SAS  S  S2    0   0.221  -6.8853  -1.5062   1.1209
 DV5  CAL  C  CR15  0  -0.222  -8.4027  -1.4662   0.3289
 DV5  NAP  N  N     0  -0.373  -8.4611  -0.6765  -0.6920
 DV5  CAW  C  CR5   0   0.321  -7.2687  -0.0407  -0.9105
 DV5  CAB  C  CH3   0  -0.745  -7.1496   0.8894  -2.0716
 DV5  H1   H  HCH3  0   0.267   8.9836   1.2333  -1.6847
 DV5  H2   H  HCH3  0   0.249   8.0209   2.5741  -1.0569
 DV5  H3   H  HCH3  0   0.264   9.4291   1.9861  -0.1620
 DV5  H4   H  HNH1  0   0.393   6.0752   1.7722  -0.3799
 DV5  H5   H  HCH1  0   0.277   5.8930  -0.9582   0.6146
 DV5  H6   H  HCH3  0   0.237   4.9496   1.4564   2.2279
 DV5  H7   H  HCH3  0   0.241   4.5622  -0.2187   2.6252
 DV5  H8   H  HCH3  0   0.252   6.2382   0.3270   2.6789
 DV5  H9   H  HCH2  0   0.283   4.7515  -2.5153   0.4129
 DV5  H10  H  HCH2  0   0.269   3.5658  -2.2744   1.7049
 DV5  H11  H  HCH1  0   0.254   2.6028  -4.1074   0.4975
 DV5  H12  H  HOH1  0   0.457   3.9356  -3.9376  -1.4046
 DV5  H13  H  HCH2  0   0.283   0.7508  -2.6727  -0.8460
 DV5  H14  H  HCH2  0   0.271   0.9936  -2.3964   0.8785
 DV5  H15  H  HCH1  0   0.297   1.9566  -0.6846  -1.4460
 DV5  H16  H  HNH1  0   0.406   0.1014   0.4788  -1.2539
 DV5  H17  H  HCH2  0   0.274  -0.5663   1.6817   1.3606
 DV5  H18  H  HCH2  0   0.267  -0.7455   2.5142  -0.1681
 DV5  H19  H  HCR6  0   0.252  -1.7420  -1.0448   0.5216
 DV5  H20  H  HCR6  0   0.257  -4.0428  -1.8367   0.3884
 DV5  H21  H  HCR6  0   0.257  -3.0766   2.9669  -0.1545
 DV5  H22  H  HCR6  0   0.261  -5.3901   2.1851  -0.2388
 DV5  H23  H  HCR5  0   0.302  -9.2295  -2.0704   0.6761
 DV5  H24  H  HCH3  0   0.254  -7.5665   1.8713  -1.8386
 DV5  H25  H  HCH3  0   0.249  -6.1135   1.0332  -2.3716
 DV5  H26  H  HCH3  0   0.257  -7.7010   0.4974  -2.9257

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
 DV5  NAP  CAL  aromatic  1.292  0.020  1.292
 DV5  NAP  CAW  aromatic  1.369  0.020  1.369
 DV5  CAL  SAS  aromatic  1.712  0.020  1.712
 DV5  CAB  CAW  single    1.492  0.020  1.492
 DV5  CAW  CAZ  aromatic  1.370  0.020  1.370
 DV5  SAS  CAZ  aromatic  1.727  0.020  1.727
 DV5  CAZ  CAY  single    1.463  0.020  1.463
 DV5  CAY  CAK  aromatic  1.397  0.020  1.397
 DV5  CAY  CAJ  aromatic  1.395  0.020  1.395
 DV5  CAK  CAI  aromatic  1.385  0.020  1.385
 DV5  CAJ  CAH  aromatic  1.386  0.020  1.386
 DV5  CAI  CAX  aromatic  1.392  0.020  1.392
 DV5  CAH  CAX  aromatic  1.391  0.020  1.391
 DV5  CAX  CAM  single    1.508  0.020  1.508
 DV5  CAM  NAQ  single    1.441  0.020  1.441
 DV5  NAQ  C    single    1.341  0.020  1.341
 DV5  CB   CA   single    1.537  0.020  1.537
 DV5  CB   CG   single    1.518  0.020  1.518
 DV5  C    O    double    1.219  0.020  1.219
 DV5  C    CA   single    1.525  0.020  1.525
 DV5  CA   N    single    1.456  0.020  1.456
 DV5  CG   OD1  single    1.406  0.020  1.406
 DV5  CG   CD2  single    1.523  0.020  1.523
 DV5  N    CD2  single    1.463  0.020  1.463
 DV5  N    CAV  single    1.320  0.020  1.320
 DV5  SAG  CAV  double    1.668  0.020  1.668
 DV5  CAV  CBB  single    1.521  0.020  1.521
 DV5  CAC  CBB  single    1.533  0.020  1.533
 DV5  CBB  NAR  single    1.439  0.020  1.439
 DV5  NAR  CAT  single    1.343  0.020  1.343
 DV5  OAD  CAT  double    1.225  0.020  1.225
 DV5  CAT  CAA  single    1.508  0.020  1.508
 DV5  CAA  H1   single    0.970  0.020  1.090
 DV5  CAA  H2   single    0.970  0.020  1.090
 DV5  CAA  H3   single    0.970  0.020  1.090
 DV5  NAR  H4   single    0.860  0.020  1.020
 DV5  CBB  H5   single    0.970  0.020  1.090
 DV5  CAC  H6   single    0.970  0.020  1.090
 DV5  CAC  H7   single    0.970  0.020  1.090
 DV5  CAC  H8   single    0.970  0.020  1.090
 DV5  CD2  H9   single    0.970  0.020  1.090
 DV5  CD2  H10  single    0.970  0.020  1.090
 DV5  CG   H11  single    0.970  0.020  1.090
 DV5  OD1  H12  single    0.850  0.020  0.980
 DV5  CB   H13  single    0.970  0.020  1.090
 DV5  CB   H14  single    0.970  0.020  1.090
 DV5  CA   H15  single    0.970  0.020  1.090
 DV5  NAQ  H16  single    0.860  0.020  1.020
 DV5  CAM  H17  single    0.970  0.020  1.090
 DV5  CAM  H18  single    0.970  0.020  1.090
 DV5  CAI  H19  single    0.930  0.020  1.080
 DV5  CAK  H20  single    0.930  0.020  1.080
 DV5  CAH  H21  single    0.930  0.020  1.080
 DV5  CAJ  H22  single    0.930  0.020  1.080
 DV5  CAL  H23  single    0.930  0.020  1.080
 DV5  CAB  H24  single    0.970  0.020  1.090
 DV5  CAB  H25  single    0.970  0.020  1.090
 DV5  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
 DV5  H3   CAA  H2   108.67  3.000
 DV5  H3   CAA  H1   107.35  3.000
 DV5  H2   CAA  H1   108.28  3.000
 DV5  H3   CAA  CAT  109.65  3.000
 DV5  H2   CAA  CAT  113.60  3.000
 DV5  H1   CAA  CAT  109.09  3.000
 DV5  NAR  CAT  OAD  123.01  3.000
 DV5  OAD  CAT  CAA  121.89  3.000
 DV5  NAR  CAT  CAA  115.09  3.000
 DV5  H4   NAR  CBB  116.53  3.000
 DV5  H4   NAR  CAT  120.18  3.000
 DV5  CBB  NAR  CAT  123.26  3.000
 DV5  H5   CBB  CAV  110.14  3.000
 DV5  H5   CBB  CAC  108.76  3.000
 DV5  CAV  CBB  CAC  108.02  3.000
 DV5  H5   CBB  NAR  107.18  3.000
 DV5  CAC  CBB  NAR  111.96  3.000
 DV5  CAV  CBB  NAR  110.76  3.000
 DV5  H8   CAC  H7   108.07  3.000
 DV5  H8   CAC  H6   108.84  3.000
 DV5  H7   CAC  H6   108.12  3.000
 DV5  H8   CAC  CBB  109.81  3.000
 DV5  H7   CAC  CBB  111.66  3.000
 DV5  H6   CAC  CBB  110.26  3.000
 DV5  N    CAV  SAG  122.28  3.000
 DV5  SAG  CAV  CBB  120.55  3.000
 DV5  N    CAV  CBB  116.99  3.000
 DV5  CA   N    CD2  111.07  3.000
 DV5  CD2  N    CAV  127.43  3.000
 DV5  CA   N    CAV  121.50  3.000
 DV5  H10  CD2  H9   108.44  3.000
 DV5  H10  CD2  CG   110.69  3.000
 DV5  H9   CD2  CG   112.17  3.000
 DV5  H10  CD2  N    110.61  3.000
 DV5  H9   CD2  N    111.99  3.000
 DV5  CG   CD2  N    102.89  3.000
 DV5  H11  CG   CB   112.15  3.000
 DV5  H11  CG   OD1  111.97  3.000
 DV5  CB   CG   OD1  107.99  3.000
 DV5  H11  CG   CD2  110.65  3.000
 DV5  OD1  CG   CD2  111.87  3.000
 DV5  CB   CG   CD2  101.76  3.000
 DV5  H12  OD1  CG   108.76  3.000
 DV5  H14  CB   H13  107.95  3.000
 DV5  H14  CB   CA   110.74  3.000
 DV5  H13  CB   CA   112.20  3.000
 DV5  H14  CB   CG   108.79  3.000
 DV5  H13  CB   CG   113.14  3.000
 DV5  CA   CB   CG   103.98  3.000
 DV5  H15  CA   C    111.12  3.000
 DV5  H15  CA   CB   111.50  3.000
 DV5  C    CA   CB   109.89  3.000
 DV5  H15  CA   N    109.42  3.000
 DV5  C    CA   N    110.61  3.000
 DV5  CB   CA   N    104.08  3.000
 DV5  NAQ  C    O    124.74  3.000
 DV5  O    C    CA   121.04  3.000
 DV5  NAQ  C    CA   113.98  3.000
 DV5  H16  NAQ  CAM  117.12  3.000
 DV5  H16  NAQ  C    118.38  3.000
 DV5  CAM  NAQ  C    124.27  3.000
 DV5  H18  CAM  H17  106.58  3.000
 DV5  H18  CAM  CAX  109.67  3.000
 DV5  H17  CAM  CAX  109.74  3.000
 DV5  H18  CAM  NAQ  109.79  3.000
 DV5  H17  CAM  NAQ  107.88  3.000
 DV5  CAX  CAM  NAQ  112.97  3.000
 DV5  CAH  CAX  CAI  118.36  3.000
 DV5  CAH  CAX  CAM  120.08  3.000
 DV5  CAI  CAX  CAM  121.53  3.000
 DV5  H19  CAI  CAK  118.99  3.000
 DV5  H19  CAI  CAX  120.15  3.000
 DV5  CAK  CAI  CAX  120.85  3.000
 DV5  H20  CAK  CAY  120.01  3.000
 DV5  H20  CAK  CAI  119.13  3.000
 DV5  CAY  CAK  CAI  120.85  3.000
 DV5  H21  CAH  CAJ  119.09  3.000
 DV5  H21  CAH  CAX  119.88  3.000
 DV5  CAJ  CAH  CAX  121.03  3.000
 DV5  H22  CAJ  CAY  120.00  3.000
 DV5  H22  CAJ  CAH  119.33  3.000
 DV5  CAY  CAJ  CAH  120.67  3.000
 DV5  CAZ  CAY  CAJ  120.87  3.000
 DV5  CAJ  CAY  CAK  118.23  3.000
 DV5  CAZ  CAY  CAK  120.90  3.000
 DV5  CAW  CAZ  SAS  109.27  3.000
 DV5  SAS  CAZ  CAY  120.85  3.000
 DV5  CAW  CAZ  CAY  129.89  3.000
 DV5  CAL  SAS  CAZ   89.46  3.000
 DV5  H23  CAL  NAP  124.10  3.000
 DV5  H23  CAL  SAS  121.07  3.000
 DV5  NAP  CAL  SAS  114.82  3.000
 DV5  CAW  NAP  CAL  111.76  3.000
 DV5  CAB  CAW  NAP  118.89  3.000
 DV5  CAB  CAW  CAZ  126.41  3.000
 DV5  NAP  CAW  CAZ  114.69  3.000
 DV5  H26  CAB  H25  108.26  3.000
 DV5  H26  CAB  H24  107.31  3.000
 DV5  H25  CAB  H24  107.67  3.000
 DV5  H26  CAB  CAW  110.20  3.000
 DV5  H25  CAB  CAW  111.88  3.000
 DV5  H24  CAB  CAW  111.34  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
 DV5  CONST_01  CAY  CAK  CAI  CAX     0.00   0.0  0
 DV5  CONST_02  CAY  CAJ  CAH  CAX     0.00   0.0  0
 DV5  CONST_03  CAZ  CAY  CAK  CAI   180.00   0.0  0
 DV5  CONST_04  CAJ  CAY  CAK  CAI     0.00   0.0  0
 DV5  CONST_05  CAJ  CAH  CAX  CAI     0.00   0.0  0
 DV5  CONST_08  CAH  CAJ  CAY  CAK     0.00   0.0  0
 DV5  CONST_09  CAH  CAX  CAI  CAK     0.00   0.0  0
 DV5  CONST_10  CAZ  CAY  CAJ  CAH   180.00   0.0  0
 DV5  CONST_13  NAP  CAW  CAZ  CAY   180.00   0.0  0
 DV5  CONST_14  CAL  SAS  CAZ  CAY   180.00   0.0  0
 DV5  CONST_15  CAL  NAP  CAW  CAZ     0.00   0.0  0
 DV5  CONST_16  NAP  CAL  SAS  CAZ     0.00   0.0  0
 DV5  CONST_17  CAW  NAP  CAL  SAS     0.00   0.0  0
 DV5  CONST_18  NAP  CAW  CAZ  SAS     0.00   0.0  0
 DV5  CONST_19  CAW  CAZ  SAS  CAL     0.00   0.0  0
 DV5  CONST_20  CAK  CAI  CAX  CAM   180.00   0.0  0
 DV5  CONST_21  CAJ  CAH  CAX  CAM   180.00   0.0  0
 DV5  CONST_22  CAB  CAW  CAZ  CAY     0.00   0.0  0
 DV5  CONST_23  CAB  CAW  CAZ  SAS   180.00   0.0  0
 DV5  CONST_24  CAB  CAW  NAP  CAL   180.00   0.0  0
 DV5  CONST_25  H20  CAK  CAI  CAX   180.00   0.0  0
 DV5  CONST_26  H22  CAJ  CAH  CAX   180.00   0.0  0
 DV5  CONST_27  H21  CAH  CAX  CAI   180.00   0.0  0
 DV5  CONST_28  H19  CAI  CAX  CAH   180.00   0.0  0
 DV5  CONST_29  H23  CAL  SAS  CAZ   180.00   0.0  0
 DV5  CONST_30  CAM  NAQ  C    CA    180.00   0.0  0
 DV5  CONST_31  H16  NAQ  C    CA      0.00   0.0  0
 DV5  CONST_32  CBB  NAR  CAT  CAA   180.00   0.0  0
 DV5  CONST_33  CBB  NAR  CAT  OAD     0.00   0.0  0
 DV5  CONST_34  CAM  NAQ  C    O       0.00   0.0  0
 DV5  CONST_35  H4   NAR  CAT  CAA     0.00   0.0  0
 DV5  Var_01    CA   N    CD2  CG     24.63  30.0  1
 DV5  Var_02    CAI  CAX  CAM  NAQ    37.90  30.0  2
 DV5  Var_03    H24  CAB  CAW  CAZ  -100.18  30.0  2
 DV5  Var_04    CAX  CAM  NAQ  C    -120.93  30.0  1
 DV5  Var_05    H1   CAA  CAT  OAD    65.86  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
 DV5  chir_01  CBB  CAV  CAC  NAR  positiv
 DV5  chir_02  CG   OD1  CB   CD2  positiv
 DV5  chir_03  CA   N    C    CB   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
 DV5  plan-1  CAY  0.020
 DV5  plan-1  CAZ  0.020
 DV5  plan-1  SAS  0.020
 DV5  plan-1  CAL  0.020
 DV5  plan-1  NAP  0.020
 DV5  plan-1  CAW  0.020
 DV5  plan-1  CAB  0.020
 DV5  plan-1  H23  0.020
 DV5  plan-2  CAM  0.020
 DV5  plan-2  CAX  0.020
 DV5  plan-2  CAI  0.020
 DV5  plan-2  CAK  0.020
 DV5  plan-2  CAH  0.020
 DV5  plan-2  CAJ  0.020
 DV5  plan-2  CAY  0.020
 DV5  plan-2  CAZ  0.020
 DV5  plan-2  H19  0.020
 DV5  plan-2  H20  0.020
 DV5  plan-2  H21  0.020
 DV5  plan-2  H22  0.020
 DV5  plan-3  CA   0.020
 DV5  plan-3  C    0.020
 DV5  plan-3  O    0.020
 DV5  plan-3  NAQ  0.020
 DV5  plan-3  CAM  0.020
 DV5  plan-3  H16  0.020
 DV5  plan-4  CAA  0.020
 DV5  plan-4  CAT  0.020
 DV5  plan-4  OAD  0.020
 DV5  plan-4  NAR  0.020
 DV5  plan-4  CBB  0.020
 DV5  plan-4  H4   0.020
 DV5  plan-5  CBB  0.020
 DV5  plan-5  CAV  0.020
 DV5  plan-5  SAG  0.020
 DV5  plan-5  N    0.020

