# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun  7 00:56:03 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C=O)[C@@H]1NC(=C(S[C@@H]2CN[C@@H](C2)C(=O)N(C)C)[C@@H]1C)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
 MER  MER  '(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid'  ligand  52  26  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MER
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
 MER  C1    C  C1     0   0.181   3.7672  -0.3242   1.3633
 MER  C2    C  CR5    0  -0.107   0.9216  -0.2096   0.0097
 MER  C3    C  CH1    0  -0.365   4.1399  -0.8252  -0.0048
 MER  C4    C  CR15   0  -0.085   3.0131  -0.5524  -1.0284
 MER  C5    C  CR5    0   0.201   1.4447   0.9931  -0.3024
 MER  O6    O  O      0  -0.453   3.7126  -1.0065   2.3607
 MER  C7    C  CH1    0   0.036   5.4506  -0.1375  -0.4524
 MER  O8    O  OH1    0  -0.656   5.8373  -0.5747  -1.7375
 MER  C9    C  CH3    0  -0.679   6.5760  -0.3278   0.5546
 MER  N10   N  NR15   0  -0.637   2.6484   0.8588  -0.9720
 MER  C11   C  C      0   0.384   0.9243   2.3933  -0.0584
 MER  O12   O  OC    -1  -0.642   1.2499   3.2208  -0.9343
 MER  O13   O  O      0  -0.609   0.2399   2.5882   0.9564
 MER  S14   S  S2     0   0.032  -0.4963  -0.5343   0.9707
 MER  C15   C  CH1    0  -0.413  -1.6530  -1.0990  -0.3120
 MER  C16   C  CH2    0  -0.442  -3.0361  -1.3776   0.2794
 MER  C17   C  CH1    0  -0.231  -4.0143  -1.0039  -0.8794
 MER  C18   C  CR15   0  -0.278   1.6918  -1.2885  -0.7340
 MER  N19   N  NH1    0  -0.614  -3.2120  -0.4764  -1.9735
 MER  C20   C  CH3    0  -0.714   1.7944  -2.6456  -0.0610
 MER  C21   C  CH2    0  -0.266  -1.9459  -0.0617  -1.3932
 MER  C22   C  C      0   0.554  -5.0133   0.0458  -0.3931
 MER  N23   N  NT     0  -0.476  -5.9877  -0.3729   0.4454
 MER  O24   O  O      0  -0.514  -4.8993   1.2153  -0.7297
 MER  C25   C  CH3    0  -0.541  -6.1662  -1.7291   0.9155
 MER  C26   C  CH3    0  -0.495  -6.9033   0.5750   1.0435
 MER  H1    H  H      0   0.233   3.5840   0.7625   1.4223
 MER  H3    H  HCH1   0   0.262   4.3214  -1.9033   0.0650
 MER  H4    H  HCR5   0   0.257   3.3932  -0.8152  -2.0151
 MER  H7    H  HCH1   0   0.278   5.2522   0.9332  -0.5577
 MER  HO8   H  HOH1   0   0.429   6.0829  -1.5046  -1.6791
 MER  H9    H  HCH3   0   0.200   6.7707  -1.3869   0.7400
 MER  H9A   H  HCH3   0   0.191   7.4948   0.1291   0.1865
 MER  H9B   H  HCH3   0   0.288   6.3446   0.1386   1.5131
 MER  HN10  H  HNR5   0   0.274   2.8238   1.4632  -1.7574
 MER  H15   H  HCH1   0   0.277  -1.2645  -2.0094  -0.7774
 MER  H16   H  HCH2   0   0.276  -3.1489  -2.4155   0.5896
 MER  H16A  H  HCH2   0   0.237  -3.2138  -0.7570   1.1626
 MER  H17   H  HCH1   0   0.302  -4.5470  -1.8861  -1.2370
 MER  H18   H  HCR5   0   0.279   1.1838  -1.4494  -1.6972
 MER  HN19  H  HNH1   0   0.345  -3.0409  -1.2244  -2.6329
 MER  H20   H  HCH3   0   0.265   0.8022  -3.0852   0.0476
 MER  H20A  H  HCH3   0   0.190   2.3929  -3.3333  -0.6608
 MER  H20B  H  HCH3   0   0.283   2.2338  -2.5931   0.9335
 MER  H21   H  HCH2   0   0.235  -2.0409   0.9280  -0.9378
 MER  H21A  H  HCH2   0   0.211  -1.1673  -0.0036  -2.1537
 MER  H25   H  HCH3   0   0.238  -5.8787  -1.8223   1.9656
 MER  H25A  H  HCH3   0   0.245  -7.2170  -2.0110   0.8297
 MER  H25B  H  HCH3   0   0.263  -5.5913  -2.4495   0.3447
 MER  H26   H  HCH3   0   0.260  -7.9322   0.3382   0.7657
 MER  H26A  H  HCH3   0   0.251  -6.8308   0.5347   2.1327
 MER  H26B  H  HCH3   0   0.260  -6.6774   1.5840   0.7171

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
 MER  C1   O6    double  1.210  0.020  1.210
 MER  C1   C3    single  1.504  0.020  1.504
 MER  C1   H1    single  0.930  0.020  1.080
 MER  C5   C2    double  1.348  0.020  1.348
 MER  C2   C18   single  1.520  0.020  1.520
 MER  C2   S14   single  1.743  0.020  1.743
 MER  C4   C3    single  1.547  0.020  1.547
 MER  C3   C7    single  1.546  0.020  1.546
 MER  C3   H3    single  0.970  0.020  1.090
 MER  N10  C4    single  1.459  0.020  1.459
 MER  C4   C18   single  1.541  0.020  1.541
 MER  C4   H4    single  0.970  0.020  1.090
 MER  C11  C5    single  1.514  0.020  1.514
 MER  N10  C5    single  1.384  0.020  1.384
 MER  O8   C7    single  1.411  0.020  1.411
 MER  C7   C9    single  1.522  0.020  1.522
 MER  C7   H7    single  0.970  0.020  1.090
 MER  O8   HO8   single  0.850  0.020  0.980
 MER  C9   H9    single  0.970  0.020  1.090
 MER  C9   H9A   single  0.970  0.020  1.090
 MER  C9   H9B   single  0.970  0.020  1.090
 MER  N10  HN10  single  0.890  0.020  1.040
 MER  O13  C11   deloc   1.239  0.020  1.239
 MER  C11  O12   deloc   1.248  0.020  1.248
 MER  S14  C15   single  1.817  0.020  1.817
 MER  C16  C15   single  1.530  0.020  1.530
 MER  C15  C21   single  1.527  0.020  1.527
 MER  C15  H15   single  0.970  0.020  1.090
 MER  C16  C17   single  1.562  0.020  1.562
 MER  C16  H16   single  0.970  0.020  1.090
 MER  C16  H16A  single  0.970  0.020  1.090
 MER  C22  C17   single  1.528  0.020  1.528
 MER  C17  N19   single  1.456  0.020  1.456
 MER  C17  H17   single  0.970  0.020  1.090
 MER  C18  C20   single  1.518  0.020  1.518
 MER  C18  H18   single  0.970  0.020  1.090
 MER  N19  C21   single  1.453  0.020  1.453
 MER  N19  HN19  single  0.890  0.020  1.040
 MER  C20  H20   single  0.970  0.020  1.090
 MER  C20  H20A  single  0.970  0.020  1.090
 MER  C20  H20B  single  0.970  0.020  1.090
 MER  C21  H21   single  0.970  0.020  1.090
 MER  C21  H21A  single  0.970  0.020  1.090
 MER  N23  C22   single  1.352  0.020  1.352
 MER  O24  C22   double  1.222  0.020  1.222
 MER  C25  N23   single  1.446  0.020  1.446
 MER  N23  C26   single  1.447  0.020  1.447
 MER  C25  H25   single  0.970  0.020  1.090
 MER  C25  H25A  single  0.970  0.020  1.090
 MER  C25  H25B  single  0.970  0.020  1.090
 MER  C26  H26   single  0.970  0.020  1.090
 MER  C26  H26A  single  0.970  0.020  1.090
 MER  C26  H26B  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
 MER  H1    C1   O6    120.25  3.000
 MER  H1    C1   C3    114.70  3.000
 MER  O6    C1   C3    124.99  3.000
 MER  C18   C2   S14   123.34  3.000
 MER  S14   C2   C5    127.54  3.000
 MER  C18   C2   C5    108.87  3.000
 MER  H3    C3   C7    108.40  3.000
 MER  H3    C3   C4    109.66  3.000
 MER  C7    C3   C4    110.34  3.000
 MER  H3    C3   C1    108.12  3.000
 MER  C7    C3   C1    108.98  3.000
 MER  C4    C3   C1    111.27  3.000
 MER  H4    C4   C18   110.91  3.000
 MER  H4    C4   N10   110.83  3.000
 MER  C18   C4   N10   103.91  3.000
 MER  H4    C4   C3    107.62  3.000
 MER  C18   C4   C3    114.46  3.000
 MER  N10   C4   C3    109.10  3.000
 MER  C11   C5   N10   117.83  3.000
 MER  N10   C5   C2    111.28  3.000
 MER  C11   C5   C2    130.88  3.000
 MER  H7    C7   C9    108.67  3.000
 MER  H7    C7   O8    105.38  3.000
 MER  C9    C7   O8    111.17  3.000
 MER  H7    C7   C3    108.02  3.000
 MER  C9    C7   C3    112.31  3.000
 MER  O8    C7   C3    110.98  3.000
 MER  HO8   O8   C7    108.28  3.000
 MER  H9B   C9   H9A   107.23  3.000
 MER  H9B   C9   H9    107.65  3.000
 MER  H9A   C9   H9    108.26  3.000
 MER  H9B   C9   C7    111.78  3.000
 MER  H9A   C9   C7    110.32  3.000
 MER  H9    C9   C7    111.42  3.000
 MER  HN10  N10  C5    118.09  3.000
 MER  HN10  N10  C4    120.48  3.000
 MER  C5    N10  C4    109.27  3.000
 MER  O13   C11  O12   127.90  3.000
 MER  O12   C11  C5    114.24  3.000
 MER  O13   C11  C5    117.86  3.000
 MER  C15   S14  C2    100.75  3.000
 MER  H15   C15  C21   109.41  3.000
 MER  H15   C15  C16   109.51  3.000
 MER  C21   C15  C16   102.95  3.000
 MER  H15   C15  S14   109.45  3.000
 MER  C21   C15  S14   114.26  3.000
 MER  C16   C15  S14   111.06  3.000
 MER  H16A  C16  H16   107.08  3.000
 MER  H16A  C16  C17   111.20  3.000
 MER  H16   C16  C17   111.99  3.000
 MER  H16A  C16  C15   110.83  3.000
 MER  H16   C16  C15   112.17  3.000
 MER  C17   C16  C15   103.64  3.000
 MER  H17   C17  C22   109.91  3.000
 MER  H17   C17  N19   108.41  3.000
 MER  C22   C17  N19   110.51  3.000
 MER  H17   C17  C16   110.83  3.000
 MER  N19   C17  C16   107.41  3.000
 MER  C22   C17  C16   109.74  3.000
 MER  H18   C18  C20   106.76  3.000
 MER  H18   C18  C4    107.36  3.000
 MER  C20   C18  C4    116.98  3.000
 MER  H18   C18  C2    107.34  3.000
 MER  C20   C18  C2    116.86  3.000
 MER  C4    C18  C2    100.89  3.000
 MER  HN19  N19  C21   108.89  3.000
 MER  HN19  N19  C17   108.37  3.000
 MER  C21   N19  C17   106.47  3.000
 MER  H20B  C20  H20A  108.12  3.000
 MER  H20B  C20  H20   107.20  3.000
 MER  H20A  C20  H20   107.44  3.000
 MER  H20B  C20  C18   112.90  3.000
 MER  H20A  C20  C18   110.90  3.000
 MER  H20   C20  C18   110.06  3.000
 MER  H21A  C21  H21   107.73  3.000
 MER  H21A  C21  N19   111.04  3.000
 MER  H21   C21  N19   110.42  3.000
 MER  H21A  C21  C15   113.16  3.000
 MER  H21   C21  C15   109.67  3.000
 MER  N19   C21  C15   104.83  3.000
 MER  O24   C22  N23   122.30  3.000
 MER  O24   C22  C17   120.57  3.000
 MER  N23   C22  C17   117.11  3.000
 MER  C26   N23  C25   113.69  3.000
 MER  C26   N23  C22   120.62  3.000
 MER  C25   N23  C22   125.52  3.000
 MER  H25B  C25  H25A  107.31  3.000
 MER  H25B  C25  H25   108.05  3.000
 MER  H25A  C25  H25   107.88  3.000
 MER  H25B  C25  N23   112.73  3.000
 MER  H25A  C25  N23   109.60  3.000
 MER  H25   C25  N23   111.08  3.000
 MER  H26B  C26  H26A  108.71  3.000
 MER  H26B  C26  H26   108.76  3.000
 MER  H26A  C26  H26   107.96  3.000
 MER  H26B  C26  N23   110.69  3.000
 MER  H26A  C26  N23   110.24  3.000
 MER  H26   C26  N23   110.42  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
 MER  CONST_01  C25  N23  C22  C17    0.00   0.0  0
 MER  CONST_02  C26  N23  C22  C17  180.00   0.0  0
 MER  CONST_03  C25  N23  C22  O24  180.00   0.0  0
 MER  CONST_04  C26  N23  C22  O24    0.00   0.0  0
 MER  Var_01    C4   N10  C5   C2    -4.49  30.0  1
 MER  Var_02    C18  C2   C5   N10  -11.62  30.0  1
 MER  Var_03    C17  N19  C21  C15   36.48  30.0  1
 MER  Var_04    O13  C11  C5   C2    31.59  30.0  2
 MER  Var_05    H25  C25  N23  C22  107.14  30.0  3
 MER  Var_06    H26  C26  N23  C22  120.62  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
 MER  chir_01  C3   C1   C4   C7   negativ
 MER  chir_02  C4   N10  C3   C18  negativ
 MER  chir_03  C7   O8   C3   C9   negativ
 MER  chir_04  C15  S14  C16  C21  negativ
 MER  chir_05  C17  N19  C16  C22  negativ
 MER  chir_06  C18  C20  C4   C2   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
 MER  plan-1  C17   0.020
 MER  plan-1  C22   0.020
 MER  plan-1  N23   0.020
 MER  plan-1  O24   0.020
 MER  plan-1  C25   0.020
 MER  plan-1  C26   0.020
 MER  plan-2  C4    0.020
 MER  plan-2  C5    0.020
 MER  plan-2  N10   0.020
 MER  plan-2  HN10  0.020
 MER  plan-3  C5    0.020
 MER  plan-3  C11   0.020
 MER  plan-3  O12   0.020
 MER  plan-3  O13   0.020
 MER  plan-4  C1    0.020
 MER  plan-4  C3    0.020
 MER  plan-4  O6    0.020
 MER  plan-4  H1    0.020

