# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:56:47 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C=O)[C@@H]1N=C([C@@H](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
 MXR  MXR  '(2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid'  ligand  52  26  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MXR
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
 MXR  C1   C  C1     0   0.185   5.1451   0.7472   0.3707
 MXR  C2   C  CR15   0  -0.461   0.9756   0.2275   1.1246
 MXR  C3   C  CH1    0  -0.413   4.4948  -0.5538  -0.0125
 MXR  C4   C  CR15   0  -0.094   2.9642  -0.4779   0.0576
 MXR  C5   C  CR5    0   0.147   1.3821   1.0812  -0.0504
 MXR  O6   O  O      0  -0.383   6.0858   0.8523   1.1204
 MXR  C7   C  CH1    0   0.052   4.9480  -0.9246  -1.4535
 MXR  O8   O  OH1    0  -0.654   4.3589  -2.1392  -1.8616
 MXR  C9   C  CH3    0  -0.698   6.4618  -0.9801  -1.5977
 MXR  N10  N  N      0  -0.357   2.4453   0.6984  -0.6286
 MXR  C11  C  C      0   0.379   0.6081   2.3163  -0.4943
 MXR  O12  O  O      0  -0.579  -0.2091   2.7492   0.3413
 MXR  O13  O  OC    -1  -0.582   0.8774   2.7782  -1.6131
 MXR  S14  S  S2     0  -0.004  -0.2492  -1.0331   0.6040
 MXR  C15  C  CR15   0  -0.379  -1.8094  -0.1200   0.5440
 MXR  C16  C  CH2    0  -0.477  -2.9470  -1.0669   0.1635
 MXR  C17  C  CR15   0  -0.209  -4.1970  -0.4149   0.8360
 MXR  C18  C  CR15   0  -0.247   2.2974  -0.4827   1.4503
 MXR  N19  N  NR15   0  -0.593  -3.7163   0.6701   1.6841
 MXR  C20  C  CH3    0  -0.682   3.0475   0.2778   2.5358
 MXR  C21  C  CH2    0  -0.291  -2.2933   0.4440   1.8765
 MXR  C22  C  C      0   0.537  -5.1755   0.1159  -0.2068
 MXR  N23  N  NT     0  -0.442  -5.9746  -0.7805  -0.8121
 MXR  O24  O  O      0  -0.500  -5.1951   1.3119  -0.4781
 MXR  C25  C  CH3    0  -0.526  -6.9700  -0.3536  -1.7743
 MXR  C26  C  CH3    0  -0.537  -5.9980  -2.1976  -0.5094
 MXR  H1   H  H      0   0.200   4.7190   1.6384  -0.1231
 MXR  H3   H  HCR5   0   0.293   0.5657   0.7886   1.9628
 MXR  H4   H  HCH1   0   0.264   4.8580  -1.3331   0.6683
 MXR  H5   H  HCR5   0   0.264   2.5940  -1.3540  -0.4875
 MXR  H8   H  HCH1   0   0.238   4.5518  -0.1669  -2.1352
 MXR  H9   H  HOH1   0   0.446   4.7283  -2.8491  -1.3246
 MXR  H10  H  HCH3   0   0.228   6.9026  -1.6796  -0.8832
 MXR  H11  H  HCH3   0   0.247   6.7265  -1.3071  -2.6032
 MXR  H12  H  HCH3   0   0.236   6.9258  -0.0070  -1.4408
 MXR  H16  H  HCR5   0   0.285  -1.7351   0.6876  -0.1846
 MXR  H17  H  HCH2   0   0.268  -3.0459  -1.1807  -0.9163
 MXR  H18  H  HCH2   0   0.254  -2.7802  -2.0622   0.5831
 MXR  H19  H  HCR5   0   0.272  -4.6964  -1.1610   1.4590
 MXR  H20  H  HCR5   0   0.256   2.1391  -1.5075   1.7947
 MXR  H21  H  HNR5   0   0.350  -3.8476   1.5425   1.1846
 MXR  H23  H  HCH3   0   0.250   2.4556   0.2969   3.4518
 MXR  H24  H  HCH3   0   0.242   3.9990  -0.1958   2.7758
 MXR  H25  H  HCH3   0   0.228   3.2407   1.3160   2.2580
 MXR  H26  H  HCH2   0   0.218  -2.1291  -0.2935   2.6693
 MXR  H27  H  HCH2   0   0.254  -1.7902   1.3674   2.1572
 MXR  H28  H  HCH3   0   0.242  -6.7480  -0.7603  -2.7627
 MXR  H29  H  HCH3   0   0.242  -7.9560  -0.7117  -1.4734
 MXR  H30  H  HCH3   0   0.259  -7.0005   0.7283  -1.8406
 MXR  H31  H  HCH3   0   0.249  -6.7612  -2.4384   0.2342
 MXR  H32  H  HCH3   0   0.257  -6.2302  -2.7467  -1.4210
 MXR  H33  H  HCH3   0   0.265  -5.0396  -2.5645  -0.1560

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
 MXR  C26  N23  single  1.449  0.020  1.449
 MXR  O12  C11  deloc   1.246  0.020  1.246
 MXR  C25  N23  single  1.449  0.020  1.449
 MXR  O13  C11  deloc   1.240  0.020  1.240
 MXR  N23  C22  single  1.345  0.020  1.345
 MXR  C11  C5   single  1.524  0.020  1.524
 MXR  C22  C17  single  1.525  0.020  1.525
 MXR  C22  O24  double  1.226  0.020  1.226
 MXR  C17  C16  single  1.562  0.020  1.562
 MXR  C17  N19  single  1.459  0.020  1.459
 MXR  C5   N10  double  1.269  0.020  1.269
 MXR  C5   C2   single  1.508  0.020  1.508
 MXR  N10  C4   single  1.457  0.020  1.457
 MXR  C16  C15  single  1.528  0.020  1.528
 MXR  N19  C21  single  1.454  0.020  1.454
 MXR  C2   S14  single  1.833  0.020  1.833
 MXR  C2   C18  single  1.535  0.020  1.535
 MXR  O6   C1   double  1.207  0.020  1.207
 MXR  S14  C15  single  1.809  0.020  1.809
 MXR  C1   C3   single  1.504  0.020  1.504
 MXR  C15  C21  single  1.526  0.020  1.526
 MXR  C4   C18  single  1.544  0.020  1.544
 MXR  C4   C3   single  1.534  0.020  1.534
 MXR  C18  C20  single  1.523  0.020  1.523
 MXR  C3   C7   single  1.555  0.020  1.555
 MXR  C7   C9   single  1.522  0.020  1.522
 MXR  C7   O8   single  1.410  0.020  1.410
 MXR  C1   H1   single  0.930  0.020  1.080
 MXR  C2   H3   single  0.970  0.020  1.090
 MXR  C3   H4   single  0.970  0.020  1.090
 MXR  C4   H5   single  0.970  0.020  1.090
 MXR  C7   H8   single  0.970  0.020  1.090
 MXR  O8   H9   single  0.850  0.020  0.980
 MXR  C9   H10  single  0.970  0.020  1.090
 MXR  C9   H11  single  0.970  0.020  1.090
 MXR  C9   H12  single  0.970  0.020  1.090
 MXR  C15  H16  single  0.970  0.020  1.090
 MXR  C16  H17  single  0.970  0.020  1.090
 MXR  C16  H18  single  0.970  0.020  1.090
 MXR  C17  H19  single  0.970  0.020  1.090
 MXR  C18  H20  single  0.970  0.020  1.090
 MXR  N19  H21  single  0.890  0.020  1.040
 MXR  C20  H23  single  0.970  0.020  1.090
 MXR  C20  H24  single  0.970  0.020  1.090
 MXR  C20  H25  single  0.970  0.020  1.090
 MXR  C21  H26  single  0.970  0.020  1.090
 MXR  C21  H27  single  0.970  0.020  1.090
 MXR  C25  H28  single  0.970  0.020  1.090
 MXR  C25  H29  single  0.970  0.020  1.090
 MXR  C25  H30  single  0.970  0.020  1.090
 MXR  C26  H31  single  0.970  0.020  1.090
 MXR  C26  H32  single  0.970  0.020  1.090
 MXR  C26  H33  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
 MXR  H1   C1   O6   120.53  3.000
 MXR  H1   C1   C3   114.66  3.000
 MXR  O6   C1   C3   124.77  3.000
 MXR  H3   C2   C18  113.53  3.000
 MXR  H3   C2   S14  108.75  3.000
 MXR  C18  C2   S14  108.50  3.000
 MXR  H3   C2   C5   114.18  3.000
 MXR  C18  C2   C5   101.25  3.000
 MXR  S14  C2   C5   110.37  3.000
 MXR  H4   C3   C7   108.01  3.000
 MXR  H4   C3   C4   109.71  3.000
 MXR  C7   C3   C4   110.17  3.000
 MXR  H4   C3   C1   108.26  3.000
 MXR  C7   C3   C1   108.44  3.000
 MXR  C4   C3   C1   112.15  3.000
 MXR  H5   C4   C18  107.46  3.000
 MXR  H5   C4   N10  106.90  3.000
 MXR  C18  C4   N10  105.86  3.000
 MXR  H5   C4   C3   105.95  3.000
 MXR  C18  C4   C3   118.16  3.000
 MXR  N10  C4   C3   111.94  3.000
 MXR  C11  C5   N10  122.50  3.000
 MXR  N10  C5   C2   114.20  3.000
 MXR  C11  C5   C2   123.29  3.000
 MXR  H8   C7   C9   109.07  3.000
 MXR  H8   C7   O8   105.37  3.000
 MXR  C9   C7   O8   110.90  3.000
 MXR  H8   C7   C3   107.86  3.000
 MXR  O8   C7   C3   110.59  3.000
 MXR  C9   C7   C3   112.73  3.000
 MXR  H9   O8   C7   108.25  3.000
 MXR  H12  C9   H11  107.30  3.000
 MXR  H12  C9   H10  107.81  3.000
 MXR  H11  C9   H10  108.25  3.000
 MXR  H12  C9   C7   112.17  3.000
 MXR  H11  C9   C7   109.87  3.000
 MXR  H10  C9   C7   111.27  3.000
 MXR  C5   N10  C4   109.10  3.000
 MXR  O13  C11  O12  128.17  3.000
 MXR  O13  C11  C5   117.03  3.000
 MXR  O12  C11  C5   114.79  3.000
 MXR  C15  S14  C2   103.80  3.000
 MXR  H16  C15  C21  109.36  3.000
 MXR  H16  C15  C16  110.08  3.000
 MXR  C21  C15  C16  102.15  3.000
 MXR  H16  C15  S14  109.72  3.000
 MXR  C21  C15  S14  115.54  3.000
 MXR  C16  C15  S14  109.73  3.000
 MXR  H18  C16  H17  107.39  3.000
 MXR  H18  C16  C17  109.70  3.000
 MXR  H17  C16  C17  113.41  3.000
 MXR  H18  C16  C15  110.79  3.000
 MXR  H17  C16  C15  112.26  3.000
 MXR  C17  C16  C15  103.29  3.000
 MXR  H19  C17  C22  109.52  3.000
 MXR  H19  C17  N19  109.09  3.000
 MXR  C22  C17  N19  110.49  3.000
 MXR  H19  C17  C16  109.03  3.000
 MXR  N19  C17  C16  107.28  3.000
 MXR  C22  C17  C16  111.37  3.000
 MXR  H20  C18  C20  108.36  3.000
 MXR  H20  C18  C4   110.47  3.000
 MXR  C20  C18  C4   115.38  3.000
 MXR  H20  C18  C2   112.09  3.000
 MXR  C20  C18  C2   110.13  3.000
 MXR  C4   C18  C2   100.31  3.000
 MXR  H21  N19  C21  109.01  3.000
 MXR  H21  N19  C17  108.12  3.000
 MXR  C21  N19  C17  106.49  3.000
 MXR  H25  C20  H24  108.35  3.000
 MXR  H25  C20  H23  107.04  3.000
 MXR  H24  C20  H23  107.24  3.000
 MXR  H25  C20  C18  112.37  3.000
 MXR  H24  C20  C18  111.72  3.000
 MXR  H23  C20  C18  109.88  3.000
 MXR  H27  C21  H26  108.39  3.000
 MXR  H27  C21  N19  110.77  3.000
 MXR  H26  C21  N19  110.32  3.000
 MXR  H27  C21  C15  113.09  3.000
 MXR  H26  C21  C15  109.62  3.000
 MXR  N19  C21  C15  104.62  3.000
 MXR  O24  C22  N23  122.75  3.000
 MXR  O24  C22  C17  120.05  3.000
 MXR  N23  C22  C17  117.19  3.000
 MXR  C26  N23  C25  114.57  3.000
 MXR  C25  N23  C22  120.71  3.000
 MXR  C26  N23  C22  124.56  3.000
 MXR  H30  C25  H29  108.59  3.000
 MXR  H30  C25  H28  108.79  3.000
 MXR  H29  C25  H28  108.13  3.000
 MXR  H30  C25  N23  110.73  3.000
 MXR  H29  C25  N23  109.93  3.000
 MXR  H28  C25  N23  110.60  3.000
 MXR  H33  C26  H32  106.88  3.000
 MXR  H33  C26  H31  108.71  3.000
 MXR  H32  C26  H31  108.04  3.000
 MXR  H33  C26  N23  112.60  3.000
 MXR  H32  C26  N23  108.76  3.000
 MXR  H31  C26  N23  111.65  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
 MXR  CONST_01  C26  N23  C22  C17    0.00   0.0  0
 MXR  CONST_02  C25  N23  C22  C17  180.00   0.0  0
 MXR  CONST_03  C26  N23  C22  O24  180.00   0.0  0
 MXR  CONST_04  C25  N23  C22  O24    0.00   0.0  0
 MXR  Var_01    C17  N19  C21  C15   36.08  30.0  1
 MXR  Var_02    C11  C5   N10  C4   178.09  30.0  1
 MXR  Var_03    O12  C11  C5   C2    15.13  30.0  2
 MXR  Var_04    H31  C26  N23  C22   93.47  30.0  3
 MXR  Var_05    H28  C25  N23  C22  116.20  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
 MXR  chir_01  C2   C5   S14  C18  negativ
 MXR  chir_02  C3   C7   C4   C1   positiv
 MXR  chir_03  C4   N10  C3   C18  negativ
 MXR  chir_04  C7   O8   C3   C9   negativ
 MXR  chir_05  C15  S14  C21  C16  positiv
 MXR  chir_06  C17  N19  C22  C16  negativ
 MXR  chir_07  C18  C2   C4   C20  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
 MXR  plan-1  C17  0.020
 MXR  plan-1  C22  0.020
 MXR  plan-1  N23  0.020
 MXR  plan-1  O24  0.020
 MXR  plan-1  C25  0.020
 MXR  plan-1  C26  0.020
 MXR  plan-2  C5   0.020
 MXR  plan-2  C11  0.020
 MXR  plan-2  O12  0.020
 MXR  plan-2  O13  0.020
 MXR  plan-3  C1   0.020
 MXR  plan-3  C3   0.020
 MXR  plan-3  O6   0.020
 MXR  plan-3  H1   0.020

