# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 18:56:56 2021
#   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  53  26  .  2021-08-12  2022-11-17
;
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  -0.238  25.7903  10.2210   7.5152
 KE1  C2   C  CR5   0  -0.174  26.4923  10.3369   6.1716
 KE1  C3   C  CR5   0   0.272  25.9042  11.3148   5.4603
 KE1  C5   C  CR15  0  -0.108  24.4688  10.9822   7.2494
 KE1  C7   C  C1    0   0.214  22.3217  10.9394   6.0589
 KE1  C11  C  CH3   0  -0.685  25.6843   8.8122   8.0715
 KE1  C1A  C  CH1   0  -0.361  29.2506  10.3248   6.3269
 KE1  C2A  C  CH2   0  -0.272  29.4355  10.2880   7.8498
 KE1  C31  C  C     0   0.470  26.2796  11.9388   4.1709
 KE1  C4A  C  CH2   0  -0.433  30.5841   9.7985   5.7577
 KE1  C5A  C  CH1   0  -0.271  31.3980   9.3862   6.9818
 KE1  C6   C  CH1   0  -0.389  23.2562  10.1020   6.9006
 KE1  C61  C  CH1   0   0.049  22.4854   9.5286   8.1034
 KE1  C62  C  CH3   0  -0.712  22.0415  10.5664   9.1266
 KE1  C6A  C  C     0   0.571  31.1700   7.9104   7.3409
 KE1  C8A  C  CH3   0  -0.548  32.9893   8.0604   9.0342
 KE1  C9A  C  CH3   0  -0.523  31.6176   6.0517   8.8207
 KE1  N3A  N  NH1   0  -0.600  30.8828  10.2932   8.0033
 KE1  N4   N  NR15  0  -0.668  24.7514  11.8048   6.0618
 KE1  N7A  N  NT    0  -0.447  31.8919   7.3984   8.3600
 KE1  O31  O  OH1   0  -0.575  27.4174  11.5008   3.6650
 KE1  O32  O  O     0  -0.436  25.6009  12.7957   3.6577
 KE1  O62  O  OH1   0  -0.669  21.3748   8.8486   7.5493
 KE1  O6A  O  O     0  -0.494  30.3222   7.2445   6.7590
 KE1  O7   O  O     0  -0.383  21.8380  10.5900   5.0117
 KE1  S21  S  S2    0   0.018  27.8487   9.3221   5.7284
 KE1  H1   H  HCR5  0   0.266  26.3850  10.8044   8.2311
 KE1  H4   H  HCR5  0   0.272  24.2316  11.6422   8.0834
 KE1  H5   H  H     0   0.179  22.0656  11.9242   6.4918
 KE1  H7   H  HCH3  0   0.239  25.2269   8.8183   9.0602
 KE1  H8   H  HCH3  0   0.232  25.1087   8.1483   7.4253
 KE1  H9   H  HCH3  0   0.251  26.6792   8.3807   8.1762
 KE1  H10  H  HCH1  0   0.289  29.0722  11.3424   5.9833
 KE1  H11  H  HCH2  0   0.243  28.9939  11.1581   8.3394
 KE1  H12  H  HCH2  0   0.222  28.9517   9.3947   8.2660
 KE1  H13  H  HCH2  0   0.259  30.4624   8.9904   5.0393
 KE1  H14  H  HCH2  0   0.263  31.0987  10.6095   5.2431
 KE1  H15  H  HCH1  0   0.277  32.4602   9.5755   6.8097
 KE1  H16  H  HCH1  0   0.266  23.5864   9.2619   6.2797
 KE1  H17  H  HCH1  0   0.232  23.1432   8.8181   8.6154
 KE1  H18  H  HCH3  0   0.246  21.4513  10.0818   9.9071
 KE1  H19  H  HCH3  0   0.235  22.8914  11.0343   9.6222
 KE1  H20  H  HCH3  0   0.233  21.4267  11.3533   8.6875
 KE1  H21  H  HCH3  0   0.258  33.8533   7.3956   9.0707
 KE1  H22  H  HCH3  0   0.263  33.3023   8.9631   8.5214
 KE1  H23  H  HCH3  0   0.245  32.7220   8.3208  10.0607
 KE1  H24  H  HCH3  0   0.244  31.8475   5.9855   9.8833
 KE1  H25  H  HCH3  0   0.251  30.5703   5.7978   8.6830
 KE1  H26  H  HCH3  0   0.239  32.2269   5.3129   8.2947
 KE1  H27  H  HNH1  0   0.365  31.1672  10.0535   8.9445
 KE1  H29  H  HNR5  0   0.385  24.7129  12.8059   6.1947
 KE1  H31  H  HOH1  0   0.487  27.5992  11.9628   2.8322
 KE1  H32  H  HOH1  0   0.453  20.8759   8.4528   8.2710

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  double  1.208  0.020  1.208
 KE1  O7   C7   double  1.205  0.020  1.205
 KE1  C4A  C1A  single  1.542  0.020  1.542
 KE1  C4A  C5A  single  1.527  0.020  1.527
 KE1  O31  C31  single  1.320  0.020  1.320
 KE1  C1A  S21  single  1.825  0.020  1.825
 KE1  C1A  C2A  single  1.535  0.020  1.535
 KE1  C31  C3   single  1.481  0.020  1.481
 KE1  S21  C2   single  1.751  0.020  1.751
 KE1  C7   C6   single  1.511  0.020  1.511
 KE1  C5A  N3A  single  1.460  0.020  1.460
 KE1  C5A  C6A  single  1.536  0.020  1.536
 KE1  C2A  N3A  single  1.455  0.020  1.455
 KE1  C3   N4   single  1.390  0.020  1.390
 KE1  C3   C2   double  1.345  0.020  1.345
 KE1  N4   C5   single  1.472  0.020  1.472
 KE1  C6   C5   single  1.538  0.020  1.538
 KE1  C6   C61  single  1.539  0.020  1.539
 KE1  C2   C1   single  1.520  0.020  1.520
 KE1  O62  C61  single  1.415  0.020  1.415
 KE1  O6A  C6A  double  1.225  0.020  1.225
 KE1  C6A  N7A  single  1.350  0.020  1.350
 KE1  C5   C1   single  1.548  0.020  1.548
 KE1  C61  C62  single  1.524  0.020  1.524
 KE1  C1   C11  single  1.518  0.020  1.518
 KE1  N7A  C8A  single  1.448  0.020  1.448
 KE1  N7A  C9A  single  1.450  0.020  1.450
 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  O31  H31  single  0.850  0.020  0.980
 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  106.97  3.000
 KE1  H1   C1   C5   108.23  3.000
 KE1  C11  C1   C5   117.36  3.000
 KE1  H1   C1   C2   106.59  3.000
 KE1  C11  C1   C2   115.26  3.000
 KE1  C5   C1   C2   101.82  3.000
 KE1  S21  C2   C3   128.79  3.000
 KE1  C3   C2   C1   108.72  3.000
 KE1  S21  C2   C1   122.49  3.000
 KE1  N4   C3   C31  116.02  3.000
 KE1  N4   C3   C2   112.98  3.000
 KE1  C31  C3   C2   131.01  3.000
 KE1  H4   C5   N4   108.71  3.000
 KE1  H4   C5   C6   110.40  3.000
 KE1  N4   C5   C6   106.75  3.000
 KE1  H4   C5   C1   110.62  3.000
 KE1  C6   C5   C1   115.50  3.000
 KE1  N4   C5   C1   104.44  3.000
 KE1  H5   C7   O7   120.35  3.000
 KE1  H5   C7   C6   114.75  3.000
 KE1  O7   C7   C6   124.86  3.000
 KE1  H9   C11  H8   107.33  3.000
 KE1  H9   C11  H7   107.36  3.000
 KE1  H8   C11  H7   108.64  3.000
 KE1  H9   C11  C1   109.81  3.000
 KE1  H8   C11  C1   112.61  3.000
 KE1  H7   C11  C1   110.89  3.000
 KE1  H10  C1A  S21  106.51  3.000
 KE1  H10  C1A  C4A  110.13  3.000
 KE1  S21  C1A  C4A  110.84  3.000
 KE1  H10  C1A  C2A  110.81  3.000
 KE1  S21  C1A  C2A  113.89  3.000
 KE1  C4A  C1A  C2A  104.71  3.000
 KE1  H12  C2A  H11  107.47  3.000
 KE1  H12  C2A  N3A  113.65  3.000
 KE1  H11  C2A  N3A  110.61  3.000
 KE1  H12  C2A  C1A  110.04  3.000
 KE1  H11  C2A  C1A  112.16  3.000
 KE1  N3A  C2A  C1A  102.97  3.000
 KE1  O32  C31  O31  123.85  3.000
 KE1  O31  C31  C3   114.35  3.000
 KE1  O32  C31  C3   121.77  3.000
 KE1  H14  C4A  H13  107.08  3.000
 KE1  H14  C4A  C5A  109.14  3.000
 KE1  H13  C4A  C5A  112.86  3.000
 KE1  H14  C4A  C1A  109.18  3.000
 KE1  H13  C4A  C1A  113.60  3.000
 KE1  C5A  C4A  C1A  104.90  3.000
 KE1  H15  C5A  N3A  110.22  3.000
 KE1  H15  C5A  C6A  110.35  3.000
 KE1  N3A  C5A  C6A  112.39  3.000
 KE1  H15  C5A  C4A  110.19  3.000
 KE1  C6A  C5A  C4A  111.58  3.000
 KE1  N3A  C5A  C4A  101.84  3.000
 KE1  H16  C6   C61  107.94  3.000
 KE1  H16  C6   C7   107.20  3.000
 KE1  C61  C6   C7   109.39  3.000
 KE1  H16  C6   C5   109.25  3.000
 KE1  C61  C6   C5   115.51  3.000
 KE1  C7   C6   C5   107.26  3.000
 KE1  H17  C61  O62  110.04  3.000
 KE1  H17  C61  C62  107.63  3.000
 KE1  O62  C61  C62  111.20  3.000
 KE1  H17  C61  C6   107.83  3.000
 KE1  C62  C61  C6   114.64  3.000
 KE1  O62  C61  C6   105.43  3.000
 KE1  H20  C62  H19  108.23  3.000
 KE1  H20  C62  H18  107.65  3.000
 KE1  H19  C62  H18  106.68  3.000
 KE1  H20  C62  C61  112.65  3.000
 KE1  H19  C62  C61  111.77  3.000
 KE1  H18  C62  C61  109.59  3.000
 KE1  O6A  C6A  N7A  121.51  3.000
 KE1  N7A  C6A  C5A  117.49  3.000
 KE1  O6A  C6A  C5A  120.93  3.000
 KE1  H23  C8A  H22  108.46  3.000
 KE1  H23  C8A  H21  107.92  3.000
 KE1  H22  C8A  H21  107.13  3.000
 KE1  H23  C8A  N7A  111.17  3.000
 KE1  H22  C8A  N7A  112.28  3.000
 KE1  H21  C8A  N7A  109.70  3.000
 KE1  H26  C9A  H25  108.58  3.000
 KE1  H26  C9A  H24  108.11  3.000
 KE1  H25  C9A  H24  108.24  3.000
 KE1  H26  C9A  N7A  111.69  3.000
 KE1  H25  C9A  N7A  111.06  3.000
 KE1  H24  C9A  N7A  109.06  3.000
 KE1  H27  N3A  C5A  113.85  3.000
 KE1  H27  N3A  C2A  112.13  3.000
 KE1  C5A  N3A  C2A  105.96  3.000
 KE1  H29  N4   C5   116.12  3.000
 KE1  H29  N4   C3   115.96  3.000
 KE1  C5   N4   C3   108.14  3.000
 KE1  C9A  N7A  C8A  114.85  3.000
 KE1  C9A  N7A  C6A  119.41  3.000
 KE1  C8A  N7A  C6A  125.69  3.000
 KE1  H31  O31  C31  109.43  3.000
 KE1  H32  O62  C61  108.11  3.000
 KE1  C1A  S21  C2   101.17  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     0.00   0.0  0
 KE1  CONST_02  C9A  N7A  C6A  C5A   180.00   0.0  0
 KE1  CONST_03  H31  O31  C31  C3    180.00   0.0  0
 KE1  CONST_04  O6A  C6A  N7A  C8A   180.00   0.0  0
 KE1  CONST_05  O6A  C6A  N7A  C9A     0.00   0.0  0
 KE1  Var_01    N4   C3   C2   C1     -7.74  30.0  1
 KE1  Var_02    C5   N4   C3   C2     -5.57  30.0  1
 KE1  Var_03    C5A  N3A  C2A  C1A   -41.79  30.0  1
 KE1  Var_04    O32  C31  C3   C2    178.05  30.0  2
 KE1  Var_05    H21  C8A  N7A  C6A  -129.21  30.0  3
 KE1  Var_06    H24  C9A  N7A  C6A  -149.88  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-3  H31  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

