# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:46:17 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (2R,3S)-N~1~-[(1S)-1-benzyl-2-(methylamino)-2-oxoethyl]-N~4~-hydroxy-2-(2-methylpropyl)-3-[(thiophen-2-ylsulfanyl)methyl]butanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(C)C)[C@H](CSc2sccc2)C(=O)NO
#
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
 DSX  DSX  (2R,3S)-N~1~-[(1S)-1-benzyl-2-(methylamino)-2-oxoethyl]-N~4~-hydroxy-2-(2-methylpropyl)-3-[(thiophen-2-ylsulfanyl)methyl]butanediamide  ligand  63  32  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DSX
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
 DSX  C1    C  CR16  0  -0.279  -3.2791  -1.5344  -3.1367
 DSX  C2    C  CR16  0  -0.225  -2.7435  -2.3682  -2.1654
 DSX  C3    C  CR16  0  -0.327  -2.8487  -2.0305  -0.8225
 DSX  C4    C  CR6   0   0.154  -3.4851  -0.8557  -0.4308
 DSX  C5    C  CR16  0  -0.299  -4.0054  -0.0186  -1.4157
 DSX  C6    C  CR16  0  -0.239  -3.9072  -0.3541  -2.7583
 DSX  C10   C  CH2   0  -0.577  -3.6249  -0.4929   1.0227
 DSX  C13   C  CH1   0  -0.149  -2.5761   0.5223   1.4944
 DSX  C14   C  C     0   0.529  -2.9606   1.0324   2.8850
 DSX  O15   O  O     0  -0.494  -3.7204   1.9827   3.0061
 DSX  N16   N  NH1   0  -0.615  -2.4775   0.3422   3.9212
 DSX  C17   C  CH3   0  -0.512  -2.8003   0.6731   5.2894
 DSX  N18   N  NH1   0  -0.658  -1.2588  -0.0665   1.4588
 DSX  C19   C  C     0   0.555  -0.1547   0.6804   1.6481
 DSX  O20   O  O     0  -0.472  -0.2157   1.8781   1.8771
 DSX  C21   C  CH1   0  -0.360   1.1707  -0.0600   1.5819
 DSX  C22   C  CH2   0  -0.411   1.8432   0.0756   2.9604
 DSX  C23   C  CH1   0  -0.251   2.9024  -0.9639   3.3426
 DSX  C24   C  CH3   0  -0.649   3.4574  -0.6123   4.7204
 DSX  C25   C  CH3   0  -0.659   2.3474  -2.3842   3.3393
 DSX  C27   C  CH1   0  -0.389   1.9877   0.5349   0.4178
 DSX  C28   C  CH2   0  -0.584   1.1977   0.4267  -0.8856
 DSX  S29   S  S2    0   0.081   2.1091   1.2374  -2.2319
 DSX  C30   C  CR5   0  -0.315   1.0563   0.9124  -3.5875
 DSX  S31   S  S2    0   0.238  -0.5924   0.4394  -3.3994
 DSX  C32   C  CR15  0  -0.468  -0.8308   0.4075  -5.0991
 DSX  C33   C  CR15  0  -0.182   0.3012   0.7526  -5.7699
 DSX  C34   C  CR15  0  -0.215   1.3931   1.0378  -4.9060
 DSX  C35   C  C     0   0.545   3.2994  -0.2127   0.2413
 DSX  O36   O  O     0  -0.460   3.3421  -1.3936  -0.0501
 DSX  N37   N  NH1   0  -0.371   4.3818   0.5536   0.4455
 DSX  O38   O  OH1   0  -0.536   5.6244   0.0635   0.1933
 DSX  H1    H  HCR6  0   0.258  -3.2101  -1.8047  -4.1828
 DSX  H2    H  HCR6  0   0.255  -2.2513  -3.2885  -2.4521
 DSX  H3    H  HCR6  0   0.250  -2.4499  -2.7030  -0.0705
 DSX  H5    H  HCR6  0   0.249  -4.5071   0.8983  -1.1273
 DSX  H6    H  HCR6  0   0.258  -4.3298   0.3014  -3.5091
 DSX  H101  H  HCH2  0   0.274  -3.5659  -1.3897   1.6454
 DSX  H102  H  HCH2  0   0.286  -4.6112  -0.0593   1.1974
 DSX  H13   H  HCH1  0   0.285  -2.6048   1.3918   0.8321
 DSX  HN6   H  HNH1  0   0.399  -1.8694  -0.4407   3.7489
 DSX  H171  H  HCH3  0   0.252  -2.2854  -0.0247   5.9431
 DSX  H172  H  HCH3  0   0.240  -2.4774   1.6830   5.5422
 DSX  H173  H  HCH3  0   0.240  -3.8712   0.5967   5.4793
 DSX  HN8   H  HNH1  0   0.409  -1.1609  -1.0460   1.2409
 DSX  H21   H  HCH1  0   0.274   0.9878  -1.1157   1.3618
 DSX  H221  H  HCH2  0   0.244   2.2663   1.0807   3.0451
 DSX  H222  H  HCH2  0   0.232   1.0610   0.0203   3.7272
 DSX  H23   H  HCH1  0   0.227   3.7380  -0.9245   2.6396
 DSX  H241  H  HCH3  0   0.229   4.2479  -1.3045   5.0141
 DSX  H242  H  HCH3  0   0.227   3.8749   0.3960   4.7367
 DSX  H243  H  HCH3  0   0.216   2.6751  -0.6609   5.4815
 DSX  H251  H  HCH3  0   0.214   1.4911  -2.4704   4.0134
 DSX  H252  H  HCH3  0   0.231   2.0277  -2.7043   2.3474
 DSX  H253  H  HCH3  0   0.231   3.1053  -3.0928   3.6776
 DSX  H27   H  HCH1  0   0.290   2.1708   1.5919   0.6363
 DSX  H281  H  HCH2  0   0.293   1.0283  -0.6212  -1.1384
 DSX  H282  H  HCH2  0   0.300   0.2305   0.9206  -0.7859
 DSX  H32   H  HCR5  0   0.293  -1.7878   0.1204  -5.5062
 DSX  H33   H  HCR5  0   0.269   0.3656   0.7888  -6.8480
 DSX  H34   H  HCR5  0   0.272   2.3801   1.3175  -5.2466
 DSX  HN7   H  HNH1  0   0.420   4.3292   1.5543   0.5721
 DSX  HO8   H  HOH1  0   0.479   5.9834  -0.2197   1.0447

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
 DSX  C1   C2    aromatic  1.388  0.020  1.388
 DSX  C1   C6    aromatic  1.389  0.020  1.389
 DSX  C1   H1    single    0.930  0.020  1.080
 DSX  C2   C3    aromatic  1.389  0.020  1.389
 DSX  C2   H2    single    0.930  0.020  1.080
 DSX  C3   C4    aromatic  1.392  0.020  1.392
 DSX  C3   H3    single    0.930  0.020  1.080
 DSX  C4   C5    aromatic  1.393  0.020  1.393
 DSX  C4   C10   single    1.505  0.020  1.505
 DSX  C5   C6    aromatic  1.387  0.020  1.387
 DSX  C5   H5    single    0.930  0.020  1.080
 DSX  C6   H6    single    0.930  0.020  1.080
 DSX  C10  C13   single    1.534  0.020  1.534
 DSX  C10  H101  single    0.970  0.020  1.090
 DSX  C10  H102  single    0.970  0.020  1.090
 DSX  C13  C14   single    1.530  0.020  1.530
 DSX  C13  N18   single    1.443  0.020  1.443
 DSX  C13  H13   single    0.970  0.020  1.090
 DSX  C14  O15   double    1.223  0.020  1.223
 DSX  C14  N16   single    1.335  0.020  1.335
 DSX  N16  C17   single    1.444  0.020  1.444
 DSX  N16  HN6   single    0.860  0.020  1.020
 DSX  C17  H171  single    0.970  0.020  1.090
 DSX  C17  H172  single    0.970  0.020  1.090
 DSX  C17  H173  single    0.970  0.020  1.090
 DSX  N18  C19   single    1.346  0.020  1.346
 DSX  N18  HN8   single    0.860  0.020  1.020
 DSX  C19  O20   double    1.221  0.020  1.221
 DSX  C19  C21   single    1.520  0.020  1.520
 DSX  C21  C22   single    1.540  0.020  1.540
 DSX  C21  C27   single    1.542  0.020  1.542
 DSX  C21  H21   single    0.970  0.020  1.090
 DSX  C22  C23   single    1.532  0.020  1.532
 DSX  C22  H221  single    0.970  0.020  1.090
 DSX  C22  H222  single    0.970  0.020  1.090
 DSX  C23  C24   single    1.526  0.020  1.526
 DSX  C23  C25   single    1.525  0.020  1.525
 DSX  C23  H23   single    0.970  0.020  1.090
 DSX  C24  H241  single    0.970  0.020  1.090
 DSX  C24  H242  single    0.970  0.020  1.090
 DSX  C24  H243  single    0.970  0.020  1.090
 DSX  C25  H251  single    0.970  0.020  1.090
 DSX  C25  H252  single    0.970  0.020  1.090
 DSX  C25  H253  single    0.970  0.020  1.090
 DSX  C27  C28   single    1.528  0.020  1.528
 DSX  C27  C35   single    1.520  0.020  1.520
 DSX  C27  H27   single    0.970  0.020  1.090
 DSX  C28  S29   single    1.817  0.020  1.817
 DSX  C28  H281  single    0.970  0.020  1.090
 DSX  C28  H282  single    0.970  0.020  1.090
 DSX  S29  C30   single    1.747  0.020  1.747
 DSX  C30  S31   aromatic  1.725  0.020  1.725
 DSX  C30  C34   aromatic  1.367  0.020  1.367
 DSX  S31  C32   aromatic  1.717  0.020  1.717
 DSX  C32  C33   aromatic  1.360  0.020  1.360
 DSX  C32  H32   single    0.930  0.020  1.080
 DSX  C33  C34   aromatic  1.421  0.020  1.421
 DSX  C33  H33   single    0.930  0.020  1.080
 DSX  C34  H34   single    0.930  0.020  1.080
 DSX  C35  O36   double    1.217  0.020  1.217
 DSX  C35  N37   single    1.342  0.020  1.342
 DSX  N37  O38   single    1.359  0.020  1.359
 DSX  N37  HN7   single    0.860  0.020  1.020
 DSX  O38  HO8   single    0.850  0.020  0.980

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
 DSX  H1    C1   C6    120.26  3.000
 DSX  H1    C1   C2    120.11  3.000
 DSX  C6    C1   C2    119.63  3.000
 DSX  H2    C2   C3    119.83  3.000
 DSX  H2    C2   C1    120.07  3.000
 DSX  C3    C2   C1    120.10  3.000
 DSX  H3    C3   C4    119.74  3.000
 DSX  H3    C3   C2    119.46  3.000
 DSX  C4    C3   C2    120.79  3.000
 DSX  C10   C4   C5    120.22  3.000
 DSX  C10   C4   C3    121.18  3.000
 DSX  C5    C4   C3    118.60  3.000
 DSX  H5    C5   C6    119.64  3.000
 DSX  H5    C5   C4    119.53  3.000
 DSX  C6    C5   C4    120.82  3.000
 DSX  H6    C6   C5    119.81  3.000
 DSX  H6    C6   C1    120.13  3.000
 DSX  C5    C6   C1    120.06  3.000
 DSX  H102  C10  H101  106.47  3.000
 DSX  H102  C10  C13   107.80  3.000
 DSX  H101  C10  C13   109.31  3.000
 DSX  H102  C10  C4    109.54  3.000
 DSX  H101  C10  C4    110.33  3.000
 DSX  C13   C10  C4    113.15  3.000
 DSX  H13   C13  N18   109.47  3.000
 DSX  H13   C13  C14   106.19  3.000
 DSX  N18   C13  C14   112.81  3.000
 DSX  H13   C13  C10   108.79  3.000
 DSX  N18   C13  C10   110.27  3.000
 DSX  C14   C13  C10   109.16  3.000
 DSX  N16   C14  O15   123.34  3.000
 DSX  N16   C14  C13   116.23  3.000
 DSX  O15   C14  C13   120.35  3.000
 DSX  HN6   N16  C17   118.40  3.000
 DSX  HN6   N16  C14   119.20  3.000
 DSX  C17   N16  C14   122.40  3.000
 DSX  H173  C17  H172  108.40  3.000
 DSX  H173  C17  H171  108.41  3.000
 DSX  H172  C17  H171  108.38  3.000
 DSX  H173  C17  N16   111.62  3.000
 DSX  H172  C17  N16   111.45  3.000
 DSX  H171  C17  N16   108.48  3.000
 DSX  HN8   N18  C19   119.32  3.000
 DSX  HN8   N18  C13   119.36  3.000
 DSX  C19   N18  C13   121.24  3.000
 DSX  C21   C19  O20   121.98  3.000
 DSX  C21   C19  N18   116.03  3.000
 DSX  O20   C19  N18   121.98  3.000
 DSX  H21   C21  C27   108.00  3.000
 DSX  H21   C21  C22   109.76  3.000
 DSX  C27   C21  C22   114.24  3.000
 DSX  H21   C21  C19   109.46  3.000
 DSX  C27   C21  C19   107.89  3.000
 DSX  C22   C21  C19   107.40  3.000
 DSX  H222  C22  H221  105.54  3.000
 DSX  H222  C22  C23   106.52  3.000
 DSX  H221  C22  C23   109.67  3.000
 DSX  H222  C22  C21   108.06  3.000
 DSX  H221  C22  C21   108.62  3.000
 DSX  C23   C22  C21   117.74  3.000
 DSX  H23   C23  C25   108.09  3.000
 DSX  H23   C23  C24   107.12  3.000
 DSX  C25   C23  C24   110.42  3.000
 DSX  H23   C23  C22   110.09  3.000
 DSX  C25   C23  C22   112.32  3.000
 DSX  C24   C23  C22   108.68  3.000
 DSX  H243  C24  H242  107.73  3.000
 DSX  H243  C24  H241  107.64  3.000
 DSX  H242  C24  H241  107.75  3.000
 DSX  H243  C24  C23   110.99  3.000
 DSX  H242  C24  C23   111.43  3.000
 DSX  H241  C24  C23   111.12  3.000
 DSX  H253  C25  H252  107.16  3.000
 DSX  H253  C25  H251  107.56  3.000
 DSX  H252  C25  H251  107.95  3.000
 DSX  H253  C25  C23   110.57  3.000
 DSX  H252  C25  C23   112.47  3.000
 DSX  H251  C25  C23   110.93  3.000
 DSX  H27   C27  C35   110.71  3.000
 DSX  H27   C27  C28   108.97  3.000
 DSX  C35   C27  C28   108.19  3.000
 DSX  H27   C27  C21   108.09  3.000
 DSX  C35   C27  C21   110.81  3.000
 DSX  C28   C27  C21   110.05  3.000
 DSX  H282  C28  H281  108.57  3.000
 DSX  H282  C28  S29   108.10  3.000
 DSX  H281  C28  S29   109.56  3.000
 DSX  H282  C28  C27   110.39  3.000
 DSX  H281  C28  C27   110.24  3.000
 DSX  S29   C28  C27   109.95  3.000
 DSX  C30   S29  C28   100.93  3.000
 DSX  C34   C30  S31   111.46  3.000
 DSX  C34   C30  S29   125.67  3.000
 DSX  S31   C30  S29   122.84  3.000
 DSX  C32   S31  C30    91.71  3.000
 DSX  H32   C32  C33   128.28  3.000
 DSX  H32   C32  S31   120.12  3.000
 DSX  C33   C32  S31   111.59  3.000
 DSX  H33   C33  C34   123.64  3.000
 DSX  H33   C33  C32   123.37  3.000
 DSX  C34   C33  C32   112.98  3.000
 DSX  H34   C34  C33   124.19  3.000
 DSX  H34   C34  C30   123.56  3.000
 DSX  C33   C34  C30   112.25  3.000
 DSX  N37   C35  O36   124.21  3.000
 DSX  N37   C35  C27   113.42  3.000
 DSX  O36   C35  C27   122.37  3.000
 DSX  HN7   N37  O38   115.34  3.000
 DSX  HN7   N37  C35   122.88  3.000
 DSX  O38   N37  C35   120.21  3.000
 DSX  HO8   O38  N37   106.36  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
 DSX  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 DSX  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 DSX  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 DSX  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 DSX  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 DSX  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 DSX  CONST_07  C33   C32  S31  C30     0.00   0.0  0
 DSX  CONST_08  C32   C33  C34  C30     0.00   0.0  0
 DSX  CONST_09  C33   C34  C30  S31     0.00   0.0  0
 DSX  CONST_10  C34   C33  C32  S31     0.00   0.0  0
 DSX  CONST_11  C34   C30  S31  C32     0.00   0.0  0
 DSX  CONST_12  C10   C4   C3   C2    180.00   0.0  0
 DSX  CONST_13  C10   C4   C5   C6    180.00   0.0  0
 DSX  CONST_14  C32   S31  C30  S29   180.00   0.0  0
 DSX  CONST_15  C33   C34  C30  S29   180.00   0.0  0
 DSX  CONST_16  H3    C3   C2   C1    180.00   0.0  0
 DSX  CONST_17  H5    C5   C6   C1    180.00   0.0  0
 DSX  CONST_18  H6    C6   C1   C2    180.00   0.0  0
 DSX  CONST_19  H1    C1   C2   C3    180.00   0.0  0
 DSX  CONST_20  H2    C2   C3   C4    180.00   0.0  0
 DSX  CONST_21  H32   C32  S31  C30   180.00   0.0  0
 DSX  CONST_22  H33   C33  C34  C30   180.00   0.0  0
 DSX  CONST_23  H34   C34  C30  S31   180.00   0.0  0
 DSX  CONST_24  C17   N16  C14  C13   180.00   0.0  0
 DSX  CONST_25  O20   C19  N18  C13     0.00   0.0  0
 DSX  CONST_26  C21   C19  N18  C13   180.00   0.0  0
 DSX  CONST_27  C17   N16  C14  O15     0.00   0.0  0
 DSX  CONST_28  O38   N37  C35  C27   180.00   0.0  0
 DSX  CONST_29  O38   N37  C35  O36     0.00   0.0  0
 DSX  CONST_30  HN6   N16  C14  C13     0.00   0.0  0
 DSX  CONST_31  HN8   N18  C19  O20   180.00   0.0  0
 DSX  CONST_32  HN7   N37  C35  C27     0.00   0.0  0
 DSX  Var_01    C13   C10  C4   C3     99.43  30.0  2
 DSX  Var_02    S31   C30  S29  C28    17.83  30.0  2
 DSX  Var_03    H281  C28  S29  C30    56.14  30.0  3
 DSX  Var_04    C24   C23  C22  C21   178.37  30.0  3
 DSX  Var_05    H171  C17  N16  C14  -179.69  30.0  3
 DSX  Var_06    H241  C24  C23  C22  -177.55  30.0  3
 DSX  Var_07    H251  C25  C23  C22   -57.07  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
 DSX  chir_01  C13  C10  C14  N18  negativ
 DSX  chir_02  C21  C19  C22  C27  positiv
 DSX  chir_03  C27  C21  C28  C35  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
 DSX  plan-1  S29  0.020
 DSX  plan-1  C30  0.020
 DSX  plan-1  S31  0.020
 DSX  plan-1  C32  0.020
 DSX  plan-1  C33  0.020
 DSX  plan-1  C34  0.020
 DSX  plan-1  H32  0.020
 DSX  plan-1  H33  0.020
 DSX  plan-1  H34  0.020
 DSX  plan-2  C1   0.020
 DSX  plan-2  C2   0.020
 DSX  plan-2  C3   0.020
 DSX  plan-2  C4   0.020
 DSX  plan-2  C5   0.020
 DSX  plan-2  C6   0.020
 DSX  plan-2  C10  0.020
 DSX  plan-2  H1   0.020
 DSX  plan-2  H2   0.020
 DSX  plan-2  H3   0.020
 DSX  plan-2  H5   0.020
 DSX  plan-2  H6   0.020
 DSX  plan-3  C13  0.020
 DSX  plan-3  C14  0.020
 DSX  plan-3  O15  0.020
 DSX  plan-3  N16  0.020
 DSX  plan-3  C17  0.020
 DSX  plan-3  HN6  0.020
 DSX  plan-4  C13  0.020
 DSX  plan-4  N18  0.020
 DSX  plan-4  C19  0.020
 DSX  plan-4  O20  0.020
 DSX  plan-4  C21  0.020
 DSX  plan-4  HN8  0.020
 DSX  plan-5  C27  0.020
 DSX  plan-5  C35  0.020
 DSX  plan-5  O36  0.020
 DSX  plan-5  N37  0.020
 DSX  plan-5  O38  0.020
 DSX  plan-5  HN7  0.020

