# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 17:31:58 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (3S)-3-({[3-({[2-({[5-(methylsulfonyl)thiophen-2-yl]carbonyl}amino)ethyl]disulfanyl}methyl)phenyl]sulfonyl}amino)-4-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H](CC(O)=O)N[S](=O)(=O)c1cccc(CSSCCNC(=O)c2sc(cc2)[S](C)(=O)=O)c1
#
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
 160  160  '(3S)-3-({[3-({[2-({[5-(methylsulfonyl)thiophen-2-yl]carbonyl}amino)ethyl]disulfanyl}methyl)phenyl]sulfonyl}amino)-4-oxopentanoic acid'  ligand  58  35  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_160
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
 160  O35   O  O      0  -0.467   3.7750  -2.3635  -2.3208
 160  C18   C  C      0   0.559   4.0765  -1.9947  -1.1969
 160  C19   C  CR5    0  -0.306   5.2782  -1.1435  -0.9968
 160  S20   S  S2     0   0.339   5.5152  -0.1356   0.3733
 160  C21   C  CR5    0  -0.437   7.0177   0.3944  -0.2459
 160  S24   S  S      0   1.216   7.9652   1.5732   0.6448
 160  O33   O  OS     0  -0.653   9.3723   1.3181   0.3651
 160  O34   O  OS     0  -0.663   7.4791   1.5399   2.0203
 160  C25   C  CH3    0  -0.783   7.5132   3.1294  -0.0805
 160  C22   C  CR15   0  -0.126   7.3298  -0.1713  -1.4478
 160  C23   C  CR15   0  -0.166   6.3169  -1.0521  -1.8831
 160  N17   N  NH1    0  -0.654   3.3837  -2.3197  -0.0949
 160  C16   C  CH2    0  -0.271   2.1701  -3.1052  -0.1429
 160  C15   C  CH2    0  -0.577   0.9538  -2.2515  -0.4722
 160  S14   S  S2     0  -0.027  -0.5798  -3.2250  -0.4981
 160  S13   S  S2     0  -0.026  -0.8592  -3.6780   1.4802
 160  C12   C  CH2    0  -0.668  -1.7473  -2.2030   2.1046
 160  C8    C  CR6    0   0.170  -3.0724  -2.0134   1.4448
 160  C9    C  CR16   0  -0.270  -4.1718  -2.7777   1.8260
 160  C10   C  CR16   0  -0.232  -5.3964  -2.6274   1.1939
 160  C11   C  CR16   0  -0.234  -5.5475  -1.7019   0.1733
 160  C7    C  CR16   0  -0.286  -3.2166  -1.0913   0.4144
 160  C6    C  CR6    0  -0.191  -4.4511  -0.9406  -0.2024
 160  S5    S  S      0   1.381  -4.6660   0.3286  -1.4214
 160  O27   O  OS     0  -0.650  -3.3481   0.7047  -1.9031
 160  O28   O  OS     0  -0.659  -5.6887  -0.1055  -2.3587
 160  N4    N  NC1    0  -0.707  -5.2948   1.6367  -0.6452
 160  C3    C  CH1    0  -0.223  -4.5317   2.2967   0.4020
 160  C2    C  C      0   0.405  -4.6720   1.6126   1.7559
 160  O26   O  O      0  -0.387  -5.6686   0.9889   2.0379
 160  C1    C  CH3    0  -0.770  -3.5226   1.7973   2.7016
 160  C29   C  CH2    0  -0.574  -5.0242   3.7377   0.5350
 160  C30   C  C      0   0.426  -4.7159   4.5926  -0.7139
 160  O31   O  OC    -1  -0.611  -5.5844   5.4234  -1.0396
 160  O32   O  O      0  -0.598  -3.6137   4.4026  -1.2582
 160  H251  H  HCH3   0   0.297   6.4453   3.2881   0.0493
 160  H252  H  HCH3   0   0.317   8.0738   3.9050   0.4409
 160  H253  H  HCH3   0   0.300   7.7723   3.1249  -1.1363
 160  H22   H  HCR5   0   0.303   8.2371   0.0348  -1.9969
 160  H23   H  HCR5   0   0.289   6.3581  -1.6113  -2.8060
 160  H17   H  HNH1   0   0.413   3.7307  -2.0679   0.8165
 160  H161  H  HCH2   0   0.265   2.0453  -3.5675   0.8352
 160  H162  H  HCH2   0   0.260   2.2730  -3.9059  -0.8751
 160  H151  H  HCH2   0   0.296   1.0308  -1.8327  -1.4778
 160  H152  H  HCH2   0   0.284   0.8496  -1.4207   0.2265
 160  H121  H  HCH2   0   0.299  -1.1047  -1.3300   1.9922
 160  H122  H  HCH2   0   0.315  -1.8570  -2.3974   3.1736
 160  H9    H  HCR6   0   0.269  -4.0676  -3.5015   2.6250
 160  H10   H  HCR6   0   0.272  -6.2399  -3.2312   1.5002
 160  H11   H  HCR6   0   0.282  -6.5067  -1.5825  -0.3122
 160  H7    H  HCR6   0   0.284  -2.3668  -0.4989   0.1009
 160  H4    H  HNC1   0   0.407  -6.2782   1.5129  -0.4237
 160  H3    H  HCH1   0   0.283  -3.4839   2.3393   0.1004
 160  H11A  H  HCH3   0   0.266  -3.7845   1.5100   3.7174
 160  H12   H  HCH3   0   0.265  -2.6902   1.1738   2.3634
 160  H13   H  HCH3   0   0.265  -3.1583   2.8252   2.6928
 160  H291  H  HCH2   0   0.233  -6.0936   3.7441   0.7592
 160  H292  H  HCH2   0   0.256  -4.5275   4.2069   1.3918

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
 160  O35  C18   double    1.221  0.020  1.221
 160  C18  C19   single    1.486  0.020  1.486
 160  C18  N17   single    1.342  0.020  1.342
 160  C19  S20   aromatic  1.717  0.020  1.717
 160  C19  C23   aromatic  1.369  0.020  1.369
 160  S20  C21   aromatic  1.709  0.020  1.709
 160  C21  S24   single    1.755  0.020  1.755
 160  C21  C22   aromatic  1.365  0.020  1.365
 160  S24  O33   double    1.457  0.020  1.457
 160  S24  O34   double    1.459  0.020  1.459
 160  S24  C25   single    1.775  0.020  1.775
 160  C25  H251  single    0.970  0.020  1.090
 160  C25  H252  single    0.970  0.020  1.090
 160  C25  H253  single    0.970  0.020  1.090
 160  C22  C23   aromatic  1.411  0.020  1.411
 160  C22  H22   single    0.930  0.020  1.080
 160  C23  H23   single    0.930  0.020  1.080
 160  N17  C16   single    1.446  0.020  1.446
 160  N17  H17   single    0.860  0.020  1.020
 160  C16  C15   single    1.522  0.020  1.522
 160  C16  H161  single    0.970  0.020  1.090
 160  C16  H162  single    0.970  0.020  1.090
 160  C15  S14   single    1.817  0.020  1.817
 160  C15  H151  single    0.970  0.020  1.090
 160  C15  H152  single    0.970  0.020  1.090
 160  S14  S13   single    2.049  0.020  2.049
 160  S13  C12   single    1.831  0.020  1.831
 160  C12  C8    single    1.492  0.020  1.492
 160  C12  H121  single    0.970  0.020  1.090
 160  C12  H122  single    0.970  0.020  1.090
 160  C8   C9    aromatic  1.392  0.020  1.392
 160  C8   C7    aromatic  1.390  0.020  1.390
 160  C9   C10   aromatic  1.386  0.020  1.386
 160  C9   H9    single    0.930  0.020  1.080
 160  C10  C11   aromatic  1.386  0.020  1.386
 160  C10  H10   single    0.930  0.020  1.080
 160  C11  C6    aromatic  1.387  0.020  1.387
 160  C11  H11   single    0.930  0.020  1.080
 160  C7   C6    aromatic  1.388  0.020  1.388
 160  C7   H7    single    0.930  0.020  1.080
 160  C6   S5    single    1.773  0.020  1.773
 160  S5   O27   double    1.453  0.020  1.453
 160  S5   O28   double    1.454  0.020  1.454
 160  S5   N4    single    1.646  0.020  1.646
 160  N4   C3    single    1.454  0.020  1.454
 160  N4   H4    single    0.890  0.020  1.040
 160  C3   C2    single    1.523  0.020  1.523
 160  C3   C29   single    1.529  0.020  1.529
 160  C3   H3    single    0.970  0.020  1.090
 160  C2   O26   double    1.209  0.020  1.209
 160  C2   C1    single    1.500  0.020  1.500
 160  C1   H11A  single    0.970  0.020  1.090
 160  C1   H12   single    0.970  0.020  1.090
 160  C1   H13   single    0.970  0.020  1.090
 160  C29  C30   single    1.545  0.020  1.545
 160  C29  H291  single    0.970  0.020  1.090
 160  C29  H292  single    0.970  0.020  1.090
 160  C30  O31   deloc     1.245  0.020  1.245
 160  C30  O32   deloc     1.244  0.020  1.244

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
 160  N17   C18  C19   116.47  3.000
 160  N17   C18  O35   123.75  3.000
 160  C19   C18  O35   119.78  3.000
 160  C23   C19  S20   111.88  3.000
 160  C23   C19  C18   124.39  3.000
 160  S20   C19  C18   123.72  3.000
 160  C21   S20  C19    90.82  3.000
 160  C22   C21  S24   127.01  3.000
 160  C22   C21  S20   113.05  3.000
 160  S24   C21  S20   119.93  3.000
 160  C25   S24  O34   108.68  3.000
 160  C25   S24  O33   108.72  3.000
 160  O34   S24  O33   119.91  3.000
 160  C25   S24  C21   104.12  3.000
 160  O34   S24  C21   106.45  3.000
 160  O33   S24  C21   107.83  3.000
 160  H253  C25  H252  110.18  3.000
 160  H253  C25  H251  110.52  3.000
 160  H252  C25  H251  110.14  3.000
 160  H253  C25  S24   109.42  3.000
 160  H252  C25  S24   107.30  3.000
 160  H251  C25  S24   109.22  3.000
 160  H22   C22  C23   124.41  3.000
 160  H22   C22  C21   124.11  3.000
 160  C23   C22  C21   111.49  3.000
 160  H23   C23  C22   124.02  3.000
 160  H23   C23  C19   123.21  3.000
 160  C22   C23  C19   112.75  3.000
 160  H17   N17  C16   117.06  3.000
 160  H17   N17  C18   120.31  3.000
 160  C16   N17  C18   122.52  3.000
 160  H162  C16  H161  107.60  3.000
 160  H162  C16  C15   110.01  3.000
 160  H161  C16  C15   109.93  3.000
 160  H162  C16  N17   110.00  3.000
 160  H161  C16  N17   107.27  3.000
 160  C15   C16  N17   111.91  3.000
 160  H152  C15  H151  107.73  3.000
 160  H152  C15  S14   109.68  3.000
 160  H151  C15  S14   104.59  3.000
 160  H152  C15  C16   111.41  3.000
 160  H151  C15  C16   110.97  3.000
 160  S14   C15  C16   112.15  3.000
 160  S13   S14  C15   102.70  3.000
 160  C12   S13  S14   102.55  3.000
 160  H122  C12  H121  107.62  3.000
 160  H122  C12  C8    111.49  3.000
 160  H121  C12  C8    112.10  3.000
 160  H122  C12  S13   103.83  3.000
 160  H121  C12  S13   108.90  3.000
 160  C8    C12  S13   112.47  3.000
 160  C7    C8   C9    119.02  3.000
 160  C7    C8   C12   120.27  3.000
 160  C9    C8   C12   120.69  3.000
 160  H9    C9   C10   119.59  3.000
 160  H9    C9   C8    119.53  3.000
 160  C10   C9   C8    120.88  3.000
 160  H10   C10  C11   119.75  3.000
 160  H10   C10  C9    119.95  3.000
 160  C11   C10  C9    120.30  3.000
 160  H11   C11  C6    121.26  3.000
 160  H11   C11  C10   120.06  3.000
 160  C6    C11  C10   118.68  3.000
 160  H7    C7   C6    120.68  3.000
 160  H7    C7   C8    119.75  3.000
 160  C6    C7   C8    119.57  3.000
 160  S5    C6   C7    119.41  3.000
 160  S5    C6   C11   118.91  3.000
 160  C7    C6   C11   121.55  3.000
 160  N4    S5   O28   105.83  3.000
 160  N4    S5   O27   107.29  3.000
 160  O28   S5   O27   120.12  3.000
 160  N4    S5   C6    106.92  3.000
 160  O28   S5   C6    108.35  3.000
 160  O27   S5   C6    107.66  3.000
 160  H4    N4   C3    113.98  3.000
 160  H4    N4   S5    112.08  3.000
 160  C3    N4   S5    119.99  3.000
 160  H3    C3   C29   107.25  3.000
 160  H3    C3   C2    110.59  3.000
 160  C29   C3   C2    108.44  3.000
 160  H3    C3   N4    108.82  3.000
 160  C29   C3   N4    108.75  3.000
 160  C2    C3   N4    112.82  3.000
 160  C1    C2   O26   123.24  3.000
 160  C1    C2   C3    115.75  3.000
 160  O26   C2   C3    120.99  3.000
 160  H13   C1   H12   106.30  3.000
 160  H13   C1   H11A  109.68  3.000
 160  H12   C1   H11A  108.76  3.000
 160  H13   C1   C2    111.53  3.000
 160  H12   C1   C2    108.55  3.000
 160  H11A  C1   C2    111.82  3.000
 160  H292  C29  H291  106.30  3.000
 160  H292  C29  C30   107.74  3.000
 160  H291  C29  C30   110.98  3.000
 160  H292  C29  C3    109.00  3.000
 160  H291  C29  C3    109.79  3.000
 160  C30   C29  C3    112.77  3.000
 160  O32   C30  O31   127.26  3.000
 160  O32   C30  C29   116.50  3.000
 160  O31   C30  C29   116.20  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
 160  CONST_01  C22   C21  S20  C19     0.00   0.0  0
 160  CONST_02  C21   C22  C23  C19     0.00   0.0  0
 160  CONST_03  C22   C23  C19  S20     0.00   0.0  0
 160  CONST_04  C23   C22  C21  S20     0.00   0.0  0
 160  CONST_05  C23   C19  S20  C21     0.00   0.0  0
 160  CONST_06  C11   C10  C9   C8      0.00   0.0  0
 160  CONST_07  C11   C6   C7   C8      0.00   0.0  0
 160  CONST_08  C6    C7   C8   C9      0.00   0.0  0
 160  CONST_09  C6    C11  C10  C9      0.00   0.0  0
 160  CONST_10  C7    C8   C9   C10     0.00   0.0  0
 160  CONST_11  C7    C6   C11  C10     0.00   0.0  0
 160  CONST_12  C21   S20  C19  C18   180.00   0.0  0
 160  CONST_13  C22   C23  C19  C18   180.00   0.0  0
 160  CONST_14  S24   C21  S20  C19   180.00   0.0  0
 160  CONST_15  C23   C22  C21  S24   180.00   0.0  0
 160  CONST_16  C10   C9   C8   C12   180.00   0.0  0
 160  CONST_17  C6    C7   C8   C12   180.00   0.0  0
 160  CONST_18  S5    C6   C7   C8    180.00   0.0  0
 160  CONST_19  S5    C6   C11  C10   180.00   0.0  0
 160  CONST_20  H22   C22  C23  C19   180.00   0.0  0
 160  CONST_21  H23   C23  C19  S20   180.00   0.0  0
 160  CONST_22  H10   C10  C9   C8    180.00   0.0  0
 160  CONST_23  H7    C7   C8   C9    180.00   0.0  0
 160  CONST_24  H11   C11  C10  C9    180.00   0.0  0
 160  CONST_25  H9    C9   C10  C11   180.00   0.0  0
 160  CONST_26  C16   N17  C18  C19   180.00   0.0  0
 160  CONST_27  H17   N17  C18  C19     0.00   0.0  0
 160  CONST_28  C16   N17  C18  O35     0.00   0.0  0
 160  Var_01    S20   C19  C18  O35   158.19  30.0  2
 160  Var_02    O33   S24  C21  S20   149.55  30.0  2
 160  Var_03    C9    C8   C12  S13    78.32  30.0  2
 160  Var_04    O27   S5   C6   C11  -164.20  30.0  2
 160  Var_05    C8    C12  S13  S14    62.46  30.0  3
 160  Var_06    C3    N4   S5   C6     62.76  30.0  3
 160  Var_07    H251  C25  S24  C21    60.43  30.0  3
 160  Var_08    C15   C16  N17  C18   -82.54  30.0  3
 160  Var_09    S14   C15  C16  N17  -178.74  30.0  3
 160  Var_10    O31   C30  C29  C3    142.92  30.0  3
 160  Var_11    H11A  C1   C2   C3    165.44  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
 160  chir_01  C3  N4  C2  C29  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
 160  plan-1  C18  0.020
 160  plan-1  C19  0.020
 160  plan-1  S20  0.020
 160  plan-1  C21  0.020
 160  plan-1  S24  0.020
 160  plan-1  C22  0.020
 160  plan-1  C23  0.020
 160  plan-1  H22  0.020
 160  plan-1  H23  0.020
 160  plan-2  C12  0.020
 160  plan-2  C8   0.020
 160  plan-2  C9   0.020
 160  plan-2  C10  0.020
 160  plan-2  C11  0.020
 160  plan-2  C7   0.020
 160  plan-2  C6   0.020
 160  plan-2  S5   0.020
 160  plan-2  H9   0.020
 160  plan-2  H10  0.020
 160  plan-2  H11  0.020
 160  plan-2  H7   0.020
 160  plan-3  O35  0.020
 160  plan-3  C18  0.020
 160  plan-3  C19  0.020
 160  plan-3  N17  0.020
 160  plan-3  C16  0.020
 160  plan-3  H17  0.020
 160  plan-4  C3   0.020
 160  plan-4  C2   0.020
 160  plan-4  O26  0.020
 160  plan-4  C1   0.020
 160  plan-5  C29  0.020
 160  plan-5  C30  0.020
 160  plan-5  O31  0.020
 160  plan-5  O32  0.020

