# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 15:10:57 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (4R,5S)-3-{[(3R,5R)-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
 KE1  KE1  '(4R,5S)-3-{[(3R,5R)-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  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KE1
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
 KE1  C1   C  CR15   0  -0.221   1.1576   1.2553   0.7434
 KE1  C2   C  CR5    0  -0.235   0.7380  -0.2000   0.6386
 KE1  C3   C  CR5    0   0.205   1.7268  -0.9583   1.1582
 KE1  C5   C  CR15   0  -0.093   2.6853   1.1062   0.8629
 KE1  C7   C  C1     0   0.187   2.9850  -0.0489  -1.3805
 KE1  C11  C  CH3    0  -0.689   0.6368   2.1980  -0.3264
 KE1  C1A  C  CH1    0  -0.358  -1.7897  -1.1140   1.5088
 KE1  C2A  C  CH2    0  -0.309  -1.8296   0.0191   2.5269
 KE1  C31  C  C      0   0.364   1.8526  -2.4620   1.2981
 KE1  C4A  C  CH2    0  -0.495  -3.2527  -1.1918   1.0846
 KE1  C5A  C  CH1    0  -0.205  -3.7892   0.2609   1.2874
 KE1  C6   C  CH1    0  -0.406   3.4194   1.0940  -0.5010
 KE1  C61  C  CH1    0   0.050   4.9537   1.0143  -0.3166
 KE1  C62  C  CH3    0  -0.691   5.6863   1.1103  -1.6473
 KE1  C6A  C  C      0   0.542  -4.1306   0.9611  -0.0268
 KE1  C8A  C  CH3    0  -0.523  -5.5402   1.0709  -2.0016
 KE1  C9A  C  CH3    0  -0.528  -6.0432  -0.6013  -0.3230
 KE1  N3A  N  NH1    0  -0.596  -2.7629   1.0033   2.0072
 KE1  N4   N  NR15   0  -0.631   2.7892  -0.1697   1.5594
 KE1  N7A  N  NT     0  -0.446  -5.1898   0.4977  -0.7191
 KE1  O31  O  OC    -1  -0.597   3.0285  -2.8798   1.3354
 KE1  O32  O  O      0  -0.559   0.8080  -3.1283   1.3452
 KE1  O62  O  OH1    0  -0.655   5.4149   1.9894   0.5912
 KE1  O6A  O  O      0  -0.496  -3.4550   1.9055  -0.4181
 KE1  O7   O  O      0  -0.391   2.4562   0.0703  -2.4615
 KE1  S21  S  S2     0  -0.027  -0.8113  -0.7003   0.0212
 KE1  H1   H  HCR5   0   0.241   0.8032   1.6372   1.7141
 KE1  H4   H  HCR5   0   0.250   3.1121   1.9136   1.4573
 KE1  H5   H  H      0   0.190   3.2545  -1.0522  -1.0015
 KE1  H7   H  HCH3   0   0.243  -0.4526   2.2290  -0.2928
 KE1  H8   H  HCH3   0   0.230   1.0027   3.2132  -0.1645
 KE1  H9   H  HCH3   0   0.227   0.9184   1.8910  -1.3322
 KE1  H10  H  HCH1   0   0.280  -1.4064  -2.0472   1.9176
 KE1  H11  H  HCH2   0   0.232  -2.2026  -0.3858   3.4748
 KE1  H12  H  HCH2   0   0.252  -0.8569   0.4662   2.7327
 KE1  H13  H  HCH2   0   0.262  -3.3867  -1.5680   0.0683
 KE1  H14  H  HCH2   0   0.267  -3.7835  -1.8800   1.7452
 KE1  H15  H  HCH1   0   0.266  -4.6958   0.2192   1.8990
 KE1  H16  H  HCH1   0   0.260   3.1894   2.0299  -1.0205
 KE1  H17  H  HCH1   0   0.225   5.2037   0.0519   0.1444
 KE1  H18  H  HCH3   0   0.230   5.4223   2.0295  -2.1756
 KE1  H19  H  HCH3   0   0.247   6.7645   1.1049  -1.4858
 KE1  H20  H  HCH3   0   0.236   5.4539   0.2715  -2.3045
 KE1  H21  H  HCH3   0   0.240  -5.4612   0.3170  -2.7878
 KE1  H22  H  HCH3   0   0.240  -6.5702   1.4321  -1.9826
 KE1  H23  H  HCH3   0   0.260  -4.8850   1.8995  -2.2466
 KE1  H24  H  HCH3   0   0.252  -7.0859  -0.2786  -0.3353
 KE1  H25  H  HCH3   0   0.244  -5.9426  -1.4366  -1.0194
 KE1  H26  H  HCH3   0   0.264  -5.8241  -0.9670   0.6738
 KE1  H27  H  HNH1   0   0.357  -2.2866   1.5981   1.3384
 KE1  H29  H  HNR5   0   0.365   3.6836  -0.6375   1.5958
 KE1  H32  H  HOH1   0   0.446   5.2819   2.8588   0.1972

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
 KE1  O32  C31  deloc   1.240  0.020  1.240
 KE1  O7   C7   double  1.209  0.020  1.209
 KE1  C4A  C1A  single  1.525  0.020  1.525
 KE1  C4A  C5A  single  1.562  0.020  1.562
 KE1  O31  C31  deloc   1.248  0.020  1.248
 KE1  C1A  S21  single  1.828  0.020  1.828
 KE1  C1A  C2A  single  1.524  0.020  1.524
 KE1  C31  C3   single  1.515  0.020  1.515
 KE1  S21  C2   single  1.741  0.020  1.741
 KE1  C7   C6   single  1.506  0.020  1.506
 KE1  C5A  N3A  single  1.457  0.020  1.457
 KE1  C5A  C6A  single  1.528  0.020  1.528
 KE1  C2A  N3A  single  1.452  0.020  1.452
 KE1  C3   N4   single  1.383  0.020  1.383
 KE1  C3   C2   double  1.350  0.020  1.350
 KE1  N4   C5   single  1.457  0.020  1.457
 KE1  C6   C5   single  1.549  0.020  1.549
 KE1  C6   C61  single  1.547  0.020  1.547
 KE1  C2   C1   single  1.518  0.020  1.518
 KE1  O62  C61  single  1.410  0.020  1.410
 KE1  O6A  C6A  double  1.225  0.020  1.225
 KE1  C6A  N7A  single  1.348  0.020  1.348
 KE1  C5   C1   single  1.540  0.020  1.540
 KE1  C61  C62  single  1.522  0.020  1.522
 KE1  C1   C11  single  1.518  0.020  1.518
 KE1  N7A  C8A  single  1.448  0.020  1.448
 KE1  N7A  C9A  single  1.447  0.020  1.447
 KE1  C1   H1   single  0.970  0.020  1.090
 KE1  C5   H4   single  0.970  0.020  1.090
 KE1  C7   H5   single  0.930  0.020  1.080
 KE1  C11  H7   single  0.970  0.020  1.090
 KE1  C11  H8   single  0.970  0.020  1.090
 KE1  C11  H9   single  0.970  0.020  1.090
 KE1  C1A  H10  single  0.970  0.020  1.090
 KE1  C2A  H11  single  0.970  0.020  1.090
 KE1  C2A  H12  single  0.970  0.020  1.090
 KE1  C4A  H13  single  0.970  0.020  1.090
 KE1  C4A  H14  single  0.970  0.020  1.090
 KE1  C5A  H15  single  0.970  0.020  1.090
 KE1  C6   H16  single  0.970  0.020  1.090
 KE1  C61  H17  single  0.970  0.020  1.090
 KE1  C62  H18  single  0.970  0.020  1.090
 KE1  C62  H19  single  0.970  0.020  1.090
 KE1  C62  H20  single  0.970  0.020  1.090
 KE1  C8A  H21  single  0.970  0.020  1.090
 KE1  C8A  H22  single  0.970  0.020  1.090
 KE1  C8A  H23  single  0.970  0.020  1.090
 KE1  C9A  H24  single  0.970  0.020  1.090
 KE1  C9A  H25  single  0.970  0.020  1.090
 KE1  C9A  H26  single  0.970  0.020  1.090
 KE1  N3A  H27  single  0.890  0.020  1.040
 KE1  N4   H29  single  0.890  0.020  1.040
 KE1  O62  H32  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
 KE1  H1   C1   C11  107.18  3.000
 KE1  H1   C1   C5   106.52  3.000
 KE1  C11  C1   C5   117.09  3.000
 KE1  H1   C1   C2   107.71  3.000
 KE1  C11  C1   C2   116.86  3.000
 KE1  C5   C1   C2   100.76  3.000
 KE1  S21  C2   C3   128.81  3.000
 KE1  C3   C2   C1   108.02  3.000
 KE1  S21  C2   C1   123.08  3.000
 KE1  N4   C3   C31  118.39  3.000
 KE1  N4   C3   C2   110.74  3.000
 KE1  C31  C3   C2   130.82  3.000
 KE1  H4   C5   N4   111.11  3.000
 KE1  H4   C5   C6   107.48  3.000
 KE1  N4   C5   C6   112.34  3.000
 KE1  H4   C5   C1   111.06  3.000
 KE1  C6   C5   C1   113.74  3.000
 KE1  N4   C5   C1   101.11  3.000
 KE1  H5   C7   O7   120.15  3.000
 KE1  H5   C7   C6   114.71  3.000
 KE1  O7   C7   C6   124.98  3.000
 KE1  H9   C11  H8   108.22  3.000
 KE1  H9   C11  H7   107.15  3.000
 KE1  H8   C11  H7   107.70  3.000
 KE1  H9   C11  C1   112.78  3.000
 KE1  H8   C11  C1   110.99  3.000
 KE1  H7   C11  C1   109.80  3.000
 KE1  H10  C1A  S21  108.13  3.000
 KE1  H10  C1A  C4A  113.49  3.000
 KE1  S21  C1A  C4A  107.38  3.000
 KE1  H10  C1A  C2A  113.31  3.000
 KE1  S21  C1A  C2A  112.92  3.000
 KE1  C4A  C1A  C2A  101.45  3.000
 KE1  H12  C2A  H11  106.97  3.000
 KE1  H12  C2A  N3A  111.28  3.000
 KE1  H11  C2A  N3A  109.94  3.000
 KE1  H12  C2A  C1A  114.06  3.000
 KE1  H11  C2A  C1A  108.18  3.000
 KE1  N3A  C2A  C1A  106.36  3.000
 KE1  O32  C31  O31  127.77  3.000
 KE1  O31  C31  C3   114.39  3.000
 KE1  O32  C31  C3   117.83  3.000
 KE1  H14  C4A  H13  106.64  3.000
 KE1  H14  C4A  C5A  109.93  3.000
 KE1  H13  C4A  C5A  113.53  3.000
 KE1  H14  C4A  C1A  109.28  3.000
 KE1  H13  C4A  C1A  113.21  3.000
 KE1  C5A  C4A  C1A  104.24  3.000
 KE1  H15  C5A  N3A  109.08  3.000
 KE1  H15  C5A  C6A  108.24  3.000
 KE1  N3A  C5A  C6A  110.42  3.000
 KE1  H15  C5A  C4A  108.77  3.000
 KE1  C6A  C5A  C4A  113.04  3.000
 KE1  N3A  C5A  C4A  107.22  3.000
 KE1  H16  C6   C61  107.99  3.000
 KE1  H16  C6   C7   108.12  3.000
 KE1  C61  C6   C7   108.45  3.000
 KE1  H16  C6   C5   108.15  3.000
 KE1  C61  C6   C5   111.43  3.000
 KE1  C7   C6   C5   112.55  3.000
 KE1  H17  C61  O62  105.18  3.000
 KE1  H17  C61  C62  108.26  3.000
 KE1  O62  C61  C62  111.22  3.000
 KE1  H17  C61  C6   108.75  3.000
 KE1  C62  C61  C6   111.70  3.000
 KE1  O62  C61  C6   111.44  3.000
 KE1  H20  C62  H19  107.23  3.000
 KE1  H20  C62  H18  107.71  3.000
 KE1  H19  C62  H18  108.34  3.000
 KE1  H20  C62  C61  112.07  3.000
 KE1  H19  C62  C61  110.26  3.000
 KE1  H18  C62  C61  111.07  3.000
 KE1  O6A  C6A  N7A  122.30  3.000
 KE1  N7A  C6A  C5A  117.39  3.000
 KE1  O6A  C6A  C5A  120.31  3.000
 KE1  H23  C8A  H22  108.74  3.000
 KE1  H23  C8A  H21  108.73  3.000
 KE1  H22  C8A  H21  108.01  3.000
 KE1  H23  C8A  N7A  110.88  3.000
 KE1  H22  C8A  N7A  110.12  3.000
 KE1  H21  C8A  N7A  110.30  3.000
 KE1  H26  C9A  H25  108.04  3.000
 KE1  H26  C9A  H24  107.65  3.000
 KE1  H25  C9A  H24  107.88  3.000
 KE1  H26  C9A  N7A  112.87  3.000
 KE1  H25  C9A  N7A  110.61  3.000
 KE1  H24  C9A  N7A  109.63  3.000
 KE1  H27  N3A  C5A  107.70  3.000
 KE1  H27  N3A  C2A  109.37  3.000
 KE1  C5A  N3A  C2A  106.51  3.000
 KE1  H29  N4   C5   119.07  3.000
 KE1  H29  N4   C3   115.26  3.000
 KE1  C5   N4   C3   107.81  3.000
 KE1  C9A  N7A  C8A  113.61  3.000
 KE1  C9A  N7A  C6A  125.75  3.000
 KE1  C8A  N7A  C6A  120.62  3.000
 KE1  H32  O62  C61  108.39  3.000
 KE1  C1A  S21  C2   104.64  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
 KE1  CONST_01  C8A  N7A  C6A  C5A  180.00   0.0  0
 KE1  CONST_02  C9A  N7A  C6A  C5A    0.00   0.0  0
 KE1  CONST_03  O6A  C6A  N7A  C8A    0.00   0.0  0
 KE1  CONST_04  O6A  C6A  N7A  C9A  180.00   0.0  0
 KE1  Var_01    N4   C3   C2   C1    -2.11  30.0  1
 KE1  Var_02    C5   N4   C3   C2   -20.09  30.0  1
 KE1  Var_03    C5A  N3A  C2A  C1A   33.12  30.0  1
 KE1  Var_04    O32  C31  C3   C2   -25.18  30.0  2
 KE1  Var_05    H21  C8A  N7A  C6A  117.58  30.0  3
 KE1  Var_06    H24  C9A  N7A  C6A  126.87  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
 KE1  chir_01  C1   C2   C5   C11  negativ
 KE1  chir_02  C5   N4   C1   C6   positiv
 KE1  chir_03  C1A  S21  C4A  C2A  positiv
 KE1  chir_04  C5A  N3A  C4A  C6A  positiv
 KE1  chir_05  C6   C7   C5   C61  negativ
 KE1  chir_06  C61  O62  C6   C62  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
 KE1  plan-1  C5A  0.020
 KE1  plan-1  C6A  0.020
 KE1  plan-1  C8A  0.020
 KE1  plan-1  C9A  0.020
 KE1  plan-1  N7A  0.020
 KE1  plan-1  O6A  0.020
 KE1  plan-2  C3   0.020
 KE1  plan-2  C5   0.020
 KE1  plan-2  N4   0.020
 KE1  plan-2  H29  0.020
 KE1  plan-3  C3   0.020
 KE1  plan-3  C31  0.020
 KE1  plan-3  O31  0.020
 KE1  plan-3  O32  0.020
 KE1  plan-4  C7   0.020
 KE1  plan-4  C6   0.020
 KE1  plan-4  O7   0.020
 KE1  plan-4  H5   0.020

