# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 02:17:04 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: (2~{S},3~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-3-methyl-2,3-dihydro-1~{H}-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H]([C@@H]1NC(=C(S[C@@H]2CN[C@@H](C2)C(=O)Nc3cccc(c3)C(O)=O)[C@@H]1C)C(O)=O)C(O)=O
#
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
 LHT  LHT  '(2~{S},3~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-3-methyl-2,3-dihydro-1~{H}-pyrrole-5-carboxylic acid'  ligand  61  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LHT
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
 LHT  C11  C  CR16  0  -0.280   -7.0339  15.7815  -19.3629
 LHT  C18  C  CR15  0  -0.118  -11.8323   6.2370  -16.9065
 LHT  C6   C  CH1   0  -0.146   -7.5965  10.7668  -15.1317
 LHT  C5   C  CH2   0  -0.250   -9.5770  11.4429  -13.9782
 LHT  O5   O  O     0  -0.415  -11.5668   7.7966  -12.5358
 LHT  C16  C  CR5   0   0.263  -11.4977   6.9747  -14.7701
 LHT  C4   C  CH1   0  -0.383   -9.8019  10.0122  -14.4512
 LHT  O4   O  OH1   0  -0.596  -11.5934   5.5945  -12.9093
 LHT  C3   C  CR5   0  -0.194  -11.4994   8.1051  -15.5043
 LHT  C2   C  CR15  0  -0.224  -11.3546   7.7012  -16.9569
 LHT  C15  C  CH2   0  -0.463   -8.7762   9.8603  -15.5717
 LHT  C1   C  CH3   0  -0.688  -11.9889   8.6082  -17.9935
 LHT  C12  C  CR6   0  -0.067   -6.4339  14.5401  -19.5436
 LHT  C19  C  CH1   0  -0.394  -13.3489   6.0456  -17.1619
 LHT  C10  C  CR16  0  -0.229   -7.7896  16.0077  -18.2239
 LHT  C21  C  CH1   0   0.032  -13.7537   4.5612  -17.3602
 LHT  C22  C  CH3   0  -0.683  -13.1588   3.9910  -18.6363
 LHT  C20  C  C     0   0.562  -14.2388   6.7265  -16.1448
 LHT  C7   C  C     0   0.505   -7.1051  11.5436  -16.3500
 LHT  C8   C  CR6   0   0.410   -7.3463  13.7614  -17.4536
 LHT  C9   C  CR16  0  -0.338   -7.9456  15.0109  -17.2780
 LHT  C13  C  C     0   0.539   -5.6298  14.3274  -20.7758
 LHT  C14  C  CR16  0  -0.341   -6.5843  13.5280  -18.5970
 LHT  O7   O  O     0  -0.434  -14.8650   7.7386  -16.3418
 LHT  S1   S  S2    0   0.011  -11.5259   9.7663  -14.9717
 LHT  N1   N  NH1   0  -0.642   -8.1332  11.5082  -14.0157
 LHT  O1   O  O     0  -0.469   -6.3873  10.9998  -17.1712
 LHT  N2   N  NH1   0  -0.740   -7.5599  12.8149  -16.4490
 LHT  O2   O  O     0  -0.438   -5.4947  15.1622  -21.6380
 LHT  O3   O  OH1   0  -0.593   -5.0726  13.1267  -20.8372
 LHT  N3   N  NR15  0  -0.637  -11.4091   5.8443  -15.5666
 LHT  O8   O  OH1   0  -0.666  -13.3643   3.7164  -16.2967
 LHT  H1   H  HCR6  0   0.267   -6.9123  16.5626  -20.1000
 LHT  H2   H  HCR5  0   0.270  -11.3037   5.6497  -17.6580
 LHT  H3   H  HCH1  0   0.271   -6.7425  10.1599  -14.8153
 LHT  H4   H  HOH1  0   0.484  -14.9275   6.5073  -14.3890
 LHT  H5   H  HCH2  0   0.207  -10.0902  12.1516  -14.6468
 LHT  H6   H  HCH2  0   0.254   -9.9513  11.6140  -12.9682
 LHT  H7   H  HCH1  0   0.293   -9.5910   9.3216  -13.6348
 LHT  H8   H  HOH1  0   0.492  -11.6349   5.5409  -11.9424
 LHT  H9   H  HCR5  0   0.264  -10.2750   7.6661  -17.1675
 LHT  H10  H  HCH2  0   0.274   -8.4626   8.8292  -15.7228
 LHT  H11  H  HCH2  0   0.257   -9.2097  10.2121  -16.5111
 LHT  H12  H  HCH3  0   0.238  -11.8648   8.1933  -18.9950
 LHT  H13  H  HCH3  0   0.235  -13.0513   8.7671  -17.8170
 LHT  H14  H  HCH3  0   0.243  -11.5029   9.5835  -17.9805
 LHT  H15  H  HCH1  0   0.288  -13.5711   6.5359  -18.1127
 LHT  H16  H  HCR6  0   0.270   -8.2623  16.9680  -18.0679
 LHT  H17  H  HCH1  0   0.237  -14.8462   4.5414  -17.4750
 LHT  H18  H  HCH3  0   0.248  -13.5765   3.0043  -18.8361
 LHT  H19  H  HCH3  0   0.234  -13.3919   4.6297  -19.4879
 LHT  H20  H  HCH3  0   0.234  -12.0750   3.8855  -18.5769
 LHT  H21  H  HCR6  0   0.280   -8.5398  15.2036  -16.3925
 LHT  H22  H  HCR6  0   0.292   -6.1171  12.5693  -18.7455
 LHT  H23  H  HNH1  0   0.371   -7.6892  12.3738  -13.7515
 LHT  H25  H  HNH1  0   0.407   -8.1292  13.1347  -15.6796
 LHT  H26  H  HOH1  0   0.489   -4.5627  13.0419  -21.6566
 LHT  H27  H  HNR5  0   0.372  -11.8079   4.9856  -15.2187
 LHT  H28  H  HOH1  0   0.456  -13.9301   3.8970  -15.5391
 LHT  C17  C  C     0   0.477  -11.5525   6.8626  -13.2968
 LHT  O6   O  OH1   0  -0.601  -14.3206   6.0554  -14.9955

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
 LHT  O2   C13  double    1.208  0.020  1.208
 LHT  O3   C13  single    1.325  0.020  1.325
 LHT  C13  C12  single    1.487  0.020  1.487
 LHT  C1   C2   single    1.516  0.020  1.516
 LHT  C12  C11  aromatic  1.391  0.020  1.391
 LHT  C12  C14  aromatic  1.394  0.020  1.394
 LHT  C11  C10  aromatic  1.386  0.020  1.386
 LHT  S1   C3   single    1.745  0.020  1.745
 LHT  S1   C4   single    1.818  0.020  1.818
 LHT  C14  C8   aromatic  1.394  0.020  1.394
 LHT  O1   C7   double    1.219  0.020  1.219
 LHT  C22  C21  single    1.519  0.020  1.519
 LHT  C10  C9   aromatic  1.383  0.020  1.383
 LHT  O7   C20  double    1.206  0.020  1.206
 LHT  C2   C3   single    1.515  0.020  1.515
 LHT  C2   C18  single    1.541  0.020  1.541
 LHT  C3   C16  double    1.348  0.020  1.348
 LHT  C19  C21  single    1.551  0.020  1.551
 LHT  C19  C20  single    1.513  0.020  1.513
 LHT  C19  C18  single    1.550  0.020  1.550
 LHT  C8   C9   aromatic  1.397  0.020  1.397
 LHT  C8   N2   single    1.397  0.020  1.397
 LHT  C21  O8   single    1.413  0.020  1.413
 LHT  C7   N2   single    1.354  0.020  1.354
 LHT  C7   C6   single    1.526  0.020  1.526
 LHT  C15  C4   single    1.527  0.020  1.527
 LHT  C15  C6   single    1.551  0.020  1.551
 LHT  C4   C5   single    1.524  0.020  1.524
 LHT  C20  O6   single    1.333  0.020  1.333
 LHT  C18  N3   single    1.459  0.020  1.459
 LHT  C16  N3   single    1.386  0.020  1.386
 LHT  C16  C17  single    1.479  0.020  1.479
 LHT  O5   C17  double    1.205  0.020  1.205
 LHT  C5   N1   single    1.446  0.020  1.446
 LHT  C6   N1   single    1.443  0.020  1.443
 LHT  C17  O4   single    1.327  0.020  1.327
 LHT  C11  H1   single    0.930  0.020  1.080
 LHT  C18  H2   single    0.970  0.020  1.090
 LHT  C6   H3   single    0.970  0.020  1.090
 LHT  O6   H4   single    0.850  0.020  0.980
 LHT  C5   H5   single    0.970  0.020  1.090
 LHT  C5   H6   single    0.970  0.020  1.090
 LHT  C4   H7   single    0.970  0.020  1.090
 LHT  O4   H8   single    0.850  0.020  0.980
 LHT  C2   H9   single    0.970  0.020  1.090
 LHT  C15  H10  single    0.970  0.020  1.090
 LHT  C15  H11  single    0.970  0.020  1.090
 LHT  C1   H12  single    0.970  0.020  1.090
 LHT  C1   H13  single    0.970  0.020  1.090
 LHT  C1   H14  single    0.970  0.020  1.090
 LHT  C19  H15  single    0.970  0.020  1.090
 LHT  C10  H16  single    0.930  0.020  1.080
 LHT  C21  H17  single    0.970  0.020  1.090
 LHT  C22  H18  single    0.970  0.020  1.090
 LHT  C22  H19  single    0.970  0.020  1.090
 LHT  C22  H20  single    0.970  0.020  1.090
 LHT  C9   H21  single    0.930  0.020  1.080
 LHT  C14  H22  single    0.930  0.020  1.080
 LHT  N1   H23  single    0.890  0.020  1.040
 LHT  N2   H25  single    0.860  0.020  1.020
 LHT  O3   H26  single    0.850  0.020  0.980
 LHT  N3   H27  single    0.890  0.020  1.040
 LHT  O8   H28  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
 LHT  H1   C11  C10  120.26  3.000
 LHT  H1   C11  C12  120.53  3.000
 LHT  C10  C11  C12  119.21  3.000
 LHT  H2   C18  N3   110.32  3.000
 LHT  H2   C18  C19  107.11  3.000
 LHT  N3   C18  C19  113.70  3.000
 LHT  H2   C18  C2   109.82  3.000
 LHT  N3   C18  C2   101.29  3.000
 LHT  C19  C18  C2   114.54  3.000
 LHT  H3   C6   N1   110.58  3.000
 LHT  H3   C6   C7   105.17  3.000
 LHT  N1   C6   C7   118.39  3.000
 LHT  H3   C6   C15  110.57  3.000
 LHT  N1   C6   C15  103.69  3.000
 LHT  C7   C6   C15  108.41  3.000
 LHT  H6   C5   H5   107.54  3.000
 LHT  H6   C5   N1   111.08  3.000
 LHT  H5   C5   N1   114.87  3.000
 LHT  H6   C5   C4   112.59  3.000
 LHT  H5   C5   C4   110.30  3.000
 LHT  N1   C5   C4   100.48  3.000
 LHT  N3   C16  C3   111.78  3.000
 LHT  N3   C16  C17  120.88  3.000
 LHT  C3   C16  C17  127.32  3.000
 LHT  H7   C4   S1   108.20  3.000
 LHT  H7   C4   C15  110.90  3.000
 LHT  S1   C4   C15  114.43  3.000
 LHT  H7   C4   C5   109.50  3.000
 LHT  C15  C4   C5   102.83  3.000
 LHT  S1   C4   C5   110.86  3.000
 LHT  H8   O4   C17  110.22  3.000
 LHT  S1   C3   C2   123.24  3.000
 LHT  C2   C3   C16  107.38  3.000
 LHT  S1   C3   C16  129.22  3.000
 LHT  H9   C2   C1   107.38  3.000
 LHT  H9   C2   C3   106.61  3.000
 LHT  C1   C2   C3   117.14  3.000
 LHT  H9   C2   C18  106.26  3.000
 LHT  C3   C2   C18  101.09  3.000
 LHT  C1   C2   C18  117.45  3.000
 LHT  H11  C15  H10  107.46  3.000
 LHT  H11  C15  C4   109.41  3.000
 LHT  H10  C15  C4   112.94  3.000
 LHT  H11  C15  C6   110.94  3.000
 LHT  H10  C15  C6   111.95  3.000
 LHT  C4   C15  C6   104.16  3.000
 LHT  H14  C1   H13  107.62  3.000
 LHT  H14  C1   H12  107.49  3.000
 LHT  H13  C1   H12  108.38  3.000
 LHT  H14  C1   C2   109.91  3.000
 LHT  H13  C1   C2   112.63  3.000
 LHT  H12  C1   C2   110.64  3.000
 LHT  C14  C12  C13  121.16  3.000
 LHT  C14  C12  C11  120.89  3.000
 LHT  C13  C12  C11  117.96  3.000
 LHT  H15  C19  C20  105.27  3.000
 LHT  H15  C19  C21  105.37  3.000
 LHT  C20  C19  C21  111.28  3.000
 LHT  H15  C19  C18  106.68  3.000
 LHT  C20  C19  C18  114.15  3.000
 LHT  C21  C19  C18  113.24  3.000
 LHT  H16  C10  C9   119.47  3.000
 LHT  H16  C10  C11  120.13  3.000
 LHT  C9   C10  C11  120.40  3.000
 LHT  H17  C21  O8   109.99  3.000
 LHT  H17  C21  C22  107.15  3.000
 LHT  O8   C21  C22  107.45  3.000
 LHT  H17  C21  C19  106.87  3.000
 LHT  O8   C21  C19  113.83  3.000
 LHT  C22  C21  C19  111.37  3.000
 LHT  H20  C22  H19  108.17  3.000
 LHT  H20  C22  H18  107.65  3.000
 LHT  H19  C22  H18  107.78  3.000
 LHT  H20  C22  C21  112.32  3.000
 LHT  H19  C22  C21  110.65  3.000
 LHT  H18  C22  C21  110.10  3.000
 LHT  O7   C20  C19  124.96  3.000
 LHT  C19  C20  O6   112.89  3.000
 LHT  O7   C20  O6   122.08  3.000
 LHT  N2   C7   O1   124.58  3.000
 LHT  N2   C7   C6   115.35  3.000
 LHT  O1   C7   C6   120.03  3.000
 LHT  N2   C8   C14  124.07  3.000
 LHT  N2   C8   C9   116.76  3.000
 LHT  C14  C8   C9   119.18  3.000
 LHT  H21  C9   C8   119.80  3.000
 LHT  H21  C9   C10  119.51  3.000
 LHT  C8   C9   C10  120.69  3.000
 LHT  O3   C13  O2   123.11  3.000
 LHT  O3   C13  C12  113.29  3.000
 LHT  O2   C13  C12  123.60  3.000
 LHT  H22  C14  C8   119.96  3.000
 LHT  H22  C14  C12  120.40  3.000
 LHT  C8   C14  C12  119.64  3.000
 LHT  C3   S1   C4   101.64  3.000
 LHT  H23  N1   C5   118.15  3.000
 LHT  H23  N1   C6   118.68  3.000
 LHT  C5   N1   C6   111.60  3.000
 LHT  H25  N2   C8   114.83  3.000
 LHT  H25  N2   C7   115.55  3.000
 LHT  C8   N2   C7   129.62  3.000
 LHT  H26  O3   C13  109.86  3.000
 LHT  H27  N3   C16  118.10  3.000
 LHT  H27  N3   C18  115.55  3.000
 LHT  C16  N3   C18  106.84  3.000
 LHT  H28  O8   C21  108.56  3.000
 LHT  O4   C17  C16  111.39  3.000
 LHT  O4   C17  O5   123.79  3.000
 LHT  C16  C17  O5   124.82  3.000
 LHT  H4   O6   C20  110.06  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
 LHT  CONST_01  C8   C14  C12  C11    0.00   0.0  0
 LHT  CONST_02  C8   C9   C10  C11    0.00   0.0  0
 LHT  CONST_03  C9   C10  C11  C12    0.00   0.0  0
 LHT  CONST_04  C9   C8   C14  C12    0.00   0.0  0
 LHT  CONST_05  C14  C12  C11  C10    0.00   0.0  0
 LHT  CONST_06  C14  C8   C9   C10    0.00   0.0  0
 LHT  CONST_07  N2   C8   C14  C12  180.00   0.0  0
 LHT  CONST_08  C13  C12  C11  C10  180.00   0.0  0
 LHT  CONST_09  N2   C8   C9   C10  180.00   0.0  0
 LHT  CONST_10  C13  C12  C14  C8   180.00   0.0  0
 LHT  CONST_11  H22  C14  C12  C11  180.00   0.0  0
 LHT  CONST_12  H21  C9   C10  C11  180.00   0.0  0
 LHT  CONST_13  H16  C10  C11  C12  180.00   0.0  0
 LHT  CONST_14  H1   C11  C10  C9   180.00   0.0  0
 LHT  CONST_15  C8   N2   C7   C6   180.00   0.0  0
 LHT  CONST_16  C14  C8   N2   C7     0.00   0.0  0
 LHT  CONST_17  C9   C8   N2   C7   180.00   0.0  0
 LHT  CONST_18  H25  N2   C8   C9     0.00   0.0  0
 LHT  CONST_19  O1   C7   N2   C8     0.00   0.0  0
 LHT  CONST_20  H8   O4   C17  C16  180.00   0.0  0
 LHT  CONST_21  H26  O3   C13  C12  180.00   0.0  0
 LHT  CONST_22  H4   O6   C20  C19  180.00   0.0  0
 LHT  Var_01    C3   C16  N3   C18  -20.24  30.0  1
 LHT  Var_02    C4   C5   N1   C6    36.55  30.0  1
 LHT  Var_03    N3   C16  C3   C2    -1.85  30.0  1
 LHT  Var_04    O2   C13  C12  C11   -1.66  30.0  2

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
 LHT  chir_01  C18  C2   C19  N3   positiv
 LHT  chir_02  C6   N1   C7   C15  positiv
 LHT  chir_03  C4   S1   C5   C15  positiv
 LHT  chir_04  C2   C18  C3   C1   positiv
 LHT  chir_05  C19  C18  C20  C21  positiv
 LHT  chir_06  C21  O8   C19  C22  negativ

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
 LHT  plan-1  C6   0.020
 LHT  plan-1  C7   0.020
 LHT  plan-1  C8   0.020
 LHT  plan-1  O1   0.020
 LHT  plan-1  N2   0.020
 LHT  plan-1  H25  0.020
 LHT  plan-2  C11  0.020
 LHT  plan-2  C12  0.020
 LHT  plan-2  C10  0.020
 LHT  plan-2  C8   0.020
 LHT  plan-2  C9   0.020
 LHT  plan-2  C13  0.020
 LHT  plan-2  C14  0.020
 LHT  plan-2  N2   0.020
 LHT  plan-2  H1   0.020
 LHT  plan-2  H16  0.020
 LHT  plan-2  H21  0.020
 LHT  plan-2  H22  0.020
 LHT  plan-3  C18  0.020
 LHT  plan-3  C16  0.020
 LHT  plan-3  N3   0.020
 LHT  plan-3  H27  0.020
 LHT  plan-4  C19  0.020
 LHT  plan-4  C20  0.020
 LHT  plan-4  O7   0.020
 LHT  plan-4  H4   0.020
 LHT  plan-4  O6   0.020
 LHT  plan-5  C12  0.020
 LHT  plan-5  C13  0.020
 LHT  plan-5  O2   0.020
 LHT  plan-5  O3   0.020
 LHT  plan-5  H26  0.020
 LHT  plan-6  O5   0.020
 LHT  plan-6  C16  0.020
 LHT  plan-6  O4   0.020
 LHT  plan-6  H8   0.020
 LHT  plan-6  C17  0.020

