# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 05:21:17 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C[C@H](O)C(=O)N[C@@H](CC(C)C)C(=O)NCCC(C)C
#
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
 E6D  E6D  'ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate'  ligand  56  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E6D
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
 E6D  C14  C  CH3   0  -0.658  -5.5775  -3.4137   0.9809
 E6D  C13  C  CH1   0  -0.238  -5.8138  -2.2676   0.0010
 E6D  C15  C  CH3   0  -0.650  -7.2814  -1.8523   0.0182
 E6D  C12  C  CH2   0  -0.454  -4.9256  -1.0575   0.2938
 E6D  C11  C  CH2   0  -0.241  -3.4404  -1.3221   0.1004
 E6D  N10  N  NH1   0  -0.640  -2.6814  -0.1097   0.3361
 E6D  C8   C  C     0   0.560  -1.4330   0.0838  -0.1028
 E6D  O9   O  O     0  -0.488  -0.7934  -0.7512  -0.7229
 E6D  C7   C  CH1   0  -0.212  -0.8762   1.4838   0.1797
 E6D  C19  C  CH2   0  -0.444  -1.3397   2.4477  -0.9138
 E6D  C20  C  CH1   0  -0.235  -0.9247   3.9076  -0.7140
 E6D  C22  C  CH3   0  -0.653  -1.4211   4.7383  -1.8934
 E6D  C21  C  CH3   0  -0.664  -1.4428   4.4768   0.6022
 E6D  N6   N  NH1   0  -0.629   0.5621   1.4396   0.2316
 E6D  C4   C  C     0   0.522   1.2018   0.7243   1.1650
 E6D  O5   O  O     0  -0.485   0.6452   0.2355   2.1369
 E6D  C3   C  CH1   0  -0.075   2.6903   0.4972   0.9287
 E6D  O1   O  OH1   0  -0.655   3.3639   0.3230   2.1400
 E6D  C2   C  CH2   0  -0.602   2.8391  -0.7231   0.0158
 E6D  C16  C  C     0   0.606   4.2914  -1.0126  -0.2636
 E6D  O18  O  O     0  -0.457   5.1155  -0.1637  -0.4980
 E6D  O17  O  O2    0  -0.451   4.5510  -2.3090  -0.2522
 E6D  C23  C  CH2   0  -0.185   5.8890  -2.7352  -0.5637
 E6D  H1   H  HCH3  0   0.228  -6.2312  -4.2577   0.7545
 E6D  H2   H  HCH3  0   0.229  -4.5520  -3.7829   0.9533
 E6D  H3   H  HCH3  0   0.214  -5.7901  -3.0961   2.0049
 E6D  H4   H  HCH1  0   0.218  -5.5738  -2.6229  -1.0083
 E6D  H5   H  HCH3  0   0.214  -7.5696  -1.4877   1.0070
 E6D  H6   H  HCH3  0   0.225  -7.4810  -1.0560  -0.7009
 E6D  H7   H  HCH3  0   0.227  -7.9332  -2.6923  -0.2272
 E6D  H8   H  HCH2  0   0.234  -5.2178  -0.2337  -0.3652
 E6D  H9   H  HCH2  0   0.223  -5.1100  -0.7159   1.3194
 E6D  H10  H  HCH2  0   0.234  -3.0934  -2.1166   0.7671
 E6D  H11  H  HCH2  0   0.235  -3.2569  -1.6619  -0.9209
 E6D  H12  H  HNH1  0   0.399  -3.1109   0.6045   0.9026
 E6D  H13  H  HCH1  0   0.275  -1.2532   1.8251   1.1480
 E6D  H14  H  HCH2  0   0.248  -0.9663   2.0887  -1.8790
 E6D  H15  H  HCH2  0   0.247  -2.4308   2.3962  -0.9712
 E6D  H16  H  HCH1  0   0.224   0.1692   3.9663  -0.7032
 E6D  H17  H  HCH3  0   0.216  -2.5117   4.7135  -1.9570
 E6D  H18  H  HCH3  0   0.230  -1.1193   5.7818  -1.7929
 E6D  H19  H  HCH3  0   0.228  -1.0251   4.3669  -2.8401
 E6D  H20  H  HCH3  0   0.234  -1.1924   5.5350   0.6898
 E6D  H21  H  HCH3  0   0.218  -2.5302   4.3891   0.6667
 E6D  H22  H  HCH3  0   0.231  -1.0156   3.9723   1.4699
 E6D  H23  H  HNH1  0   0.407   1.0762   1.7502  -0.5789
 E6D  H24  H  HCH1  0   0.271   3.1256   1.3702   0.4359
 E6D  H25  H  HOH1  0   0.446   2.8141  -0.2293   2.7106
 E6D  H26  H  HCH2  0   0.279   2.3469  -1.5929   0.4540
 E6D  H27  H  HCH2  0   0.294   2.3497  -0.5361  -0.9452
 E6D  H28  H  HCH2  0   0.237   6.1588  -2.3909  -1.5638
 E6D  H29  H  HCH2  0   0.237   6.5888  -2.2908   0.1465
 E6D  C24  C  CH3   0  -0.689   5.9213  -4.2418  -0.4841
 E6D  H30  H  HCH3  0   0.240   6.9267  -4.5894  -0.7198
 E6D  H31  H  HCH3  0   0.237   5.6714  -4.5979   0.5153
 E6D  H32  H  HCH3  0   0.237   5.2353  -4.6959  -1.1990

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
 E6D  C23  O17  single  1.438  0.020  1.438
 E6D  O18  C16  double  1.206  0.020  1.206
 E6D  O17  C16  single  1.322  0.020  1.322
 E6D  C16  C2   single  1.507  0.020  1.507
 E6D  C2   C3   single  1.531  0.020  1.531
 E6D  O1   C3   single  1.397  0.020  1.397
 E6D  C3   C4   single  1.524  0.020  1.524
 E6D  C4   O5   double  1.222  0.020  1.222
 E6D  C4   N6   single  1.339  0.020  1.339
 E6D  N6   C7   single  1.440  0.020  1.440
 E6D  C7   C8   single  1.533  0.020  1.533
 E6D  C7   C19  single  1.530  0.020  1.530
 E6D  O9   C8   double  1.221  0.020  1.221
 E6D  C8   N10  single  1.337  0.020  1.337
 E6D  C19  C20  single  1.531  0.020  1.531
 E6D  C22  C20  single  1.526  0.020  1.526
 E6D  C20  C21  single  1.525  0.020  1.525
 E6D  N10  C11  single  1.450  0.020  1.450
 E6D  C12  C11  single  1.521  0.020  1.521
 E6D  C12  C13  single  1.529  0.020  1.529
 E6D  C13  C15  single  1.525  0.020  1.525
 E6D  C13  C14  single  1.526  0.020  1.526
 E6D  C14  H1   single  0.970  0.020  1.090
 E6D  C14  H2   single  0.970  0.020  1.090
 E6D  C14  H3   single  0.970  0.020  1.090
 E6D  C13  H4   single  0.970  0.020  1.090
 E6D  C15  H5   single  0.970  0.020  1.090
 E6D  C15  H6   single  0.970  0.020  1.090
 E6D  C15  H7   single  0.970  0.020  1.090
 E6D  C12  H8   single  0.970  0.020  1.090
 E6D  C12  H9   single  0.970  0.020  1.090
 E6D  C11  H10  single  0.970  0.020  1.090
 E6D  C11  H11  single  0.970  0.020  1.090
 E6D  N10  H12  single  0.860  0.020  1.020
 E6D  C7   H13  single  0.970  0.020  1.090
 E6D  C19  H14  single  0.970  0.020  1.090
 E6D  C19  H15  single  0.970  0.020  1.090
 E6D  C20  H16  single  0.970  0.020  1.090
 E6D  C22  H17  single  0.970  0.020  1.090
 E6D  C22  H18  single  0.970  0.020  1.090
 E6D  C22  H19  single  0.970  0.020  1.090
 E6D  C21  H20  single  0.970  0.020  1.090
 E6D  C21  H21  single  0.970  0.020  1.090
 E6D  C21  H22  single  0.970  0.020  1.090
 E6D  N6   H23  single  0.860  0.020  1.020
 E6D  C3   H24  single  0.970  0.020  1.090
 E6D  O1   H25  single  0.850  0.020  0.980
 E6D  C2   H26  single  0.970  0.020  1.090
 E6D  C2   H27  single  0.970  0.020  1.090
 E6D  C23  H28  single  0.970  0.020  1.090
 E6D  C23  H29  single  0.970  0.020  1.090
 E6D  C23  C24  single  1.509  0.020  1.509
 E6D  C24  H30  single  0.970  0.020  1.090
 E6D  C24  H31  single  0.970  0.020  1.090
 E6D  C24  H32  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
 E6D  H3   C14  H2   107.77  3.000
 E6D  H3   C14  H1   107.62  3.000
 E6D  H2   C14  H1   107.24  3.000
 E6D  H3   C14  C13  110.68  3.000
 E6D  H2   C14  C13  112.55  3.000
 E6D  H1   C14  C13  110.78  3.000
 E6D  H4   C13  C12  107.79  3.000
 E6D  H4   C13  C15  108.00  3.000
 E6D  C12  C13  C15  109.95  3.000
 E6D  H4   C13  C14  108.29  3.000
 E6D  C15  C13  C14  110.25  3.000
 E6D  C12  C13  C14  112.42  3.000
 E6D  H7   C15  H6   107.71  3.000
 E6D  H7   C15  H5   107.63  3.000
 E6D  H6   C15  H5   107.73  3.000
 E6D  H7   C15  C13  111.26  3.000
 E6D  H6   C15  C13  111.54  3.000
 E6D  H5   C15  C13  110.79  3.000
 E6D  H9   C12  H8   106.48  3.000
 E6D  H9   C12  C11  109.71  3.000
 E6D  H8   C12  C11  108.36  3.000
 E6D  H9   C12  C13  109.15  3.000
 E6D  H8   C12  C13  108.98  3.000
 E6D  C11  C12  C13  113.90  3.000
 E6D  H11  C11  H10  106.90  3.000
 E6D  H11  C11  N10  108.93  3.000
 E6D  H10  C11  N10  110.02  3.000
 E6D  H11  C11  C12  109.71  3.000
 E6D  H10  C11  C12  111.02  3.000
 E6D  N10  C11  C12  110.19  3.000
 E6D  H12  N10  C8   118.67  3.000
 E6D  H12  N10  C11  117.46  3.000
 E6D  C8   N10  C11  123.81  3.000
 E6D  C7   C8   O9   121.86  3.000
 E6D  O9   C8   N10  123.83  3.000
 E6D  C7   C8   N10  114.25  3.000
 E6D  H13  C7   N6   108.78  3.000
 E6D  H13  C7   C19  109.38  3.000
 E6D  N6   C7   C19  110.35  3.000
 E6D  H13  C7   C8   108.84  3.000
 E6D  C19  C7   C8   109.49  3.000
 E6D  N6   C7   C8   109.96  3.000
 E6D  H15  C19  H14  106.16  3.000
 E6D  H15  C19  C20  108.79  3.000
 E6D  H14  C19  C20  109.58  3.000
 E6D  H15  C19  C7   108.07  3.000
 E6D  H14  C19  C7   108.67  3.000
 E6D  C20  C19  C7   115.18  3.000
 E6D  H16  C20  C21  108.10  3.000
 E6D  H16  C20  C22  107.66  3.000
 E6D  C21  C20  C22  110.70  3.000
 E6D  H16  C20  C19  108.85  3.000
 E6D  C21  C20  C19  112.12  3.000
 E6D  C22  C20  C19  109.28  3.000
 E6D  H19  C22  H18  107.76  3.000
 E6D  H19  C22  H17  107.69  3.000
 E6D  H18  C22  H17  107.65  3.000
 E6D  H19  C22  C20  111.55  3.000
 E6D  H18  C22  C20  111.08  3.000
 E6D  H17  C22  C20  110.94  3.000
 E6D  H22  C21  H21  107.79  3.000
 E6D  H22  C21  H20  107.14  3.000
 E6D  H21  C21  H20  107.55  3.000
 E6D  H22  C21  C20  112.39  3.000
 E6D  H21  C21  C20  111.05  3.000
 E6D  H20  C21  C20  110.70  3.000
 E6D  H23  N6   C4   118.76  3.000
 E6D  H23  N6   C7   118.08  3.000
 E6D  C4   N6   C7   121.26  3.000
 E6D  C3   C4   O5   120.56  3.000
 E6D  O5   C4   N6   123.41  3.000
 E6D  C3   C4   N6   115.99  3.000
 E6D  H24  C3   C2   109.21  3.000
 E6D  H24  C3   O1   107.37  3.000
 E6D  C2   C3   O1   111.76  3.000
 E6D  H24  C3   C4   109.87  3.000
 E6D  O1   C3   C4   110.80  3.000
 E6D  C2   C3   C4   107.82  3.000
 E6D  H25  O1   C3   108.00  3.000
 E6D  H27  C2   H26  106.68  3.000
 E6D  H27  C2   C16  107.52  3.000
 E6D  H26  C2   C16  110.85  3.000
 E6D  H27  C2   C3   110.11  3.000
 E6D  H26  C2   C3   110.61  3.000
 E6D  C16  C2   C3   110.93  3.000
 E6D  O17  C16  O18  123.88  3.000
 E6D  O17  C16  C2   112.09  3.000
 E6D  O18  C16  C2   124.01  3.000
 E6D  C23  O17  C16  118.12  3.000
 E6D  C24  C23  H29  111.00  3.000
 E6D  C24  C23  H28  110.97  3.000
 E6D  H29  C23  H28  108.01  3.000
 E6D  C24  C23  O17  107.72  3.000
 E6D  H29  C23  O17  109.56  3.000
 E6D  H28  C23  O17  109.57  3.000
 E6D  H32  C24  H31  108.73  3.000
 E6D  H32  C24  H30  107.82  3.000
 E6D  H31  C24  H30  107.80  3.000
 E6D  H32  C24  C23  111.59  3.000
 E6D  H31  C24  C23  111.69  3.000
 E6D  H30  C24  C23  109.07  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
 E6D  CONST_01  C7   C8   N10  C11   180.00   0.0  0
 E6D  CONST_02  O9   C8   N10  C11     0.00   0.0  0
 E6D  CONST_03  C3   C4   N6   C7    180.00   0.0  0
 E6D  CONST_04  O5   C4   N6   C7      0.00   0.0  0
 E6D  CONST_05  H12  N10  C8   O9    180.00   0.0  0
 E6D  CONST_06  H23  N6   C4   O5    180.00   0.0  0
 E6D  Var_01    C11  C12  C13  C14    65.20  30.0  2
 E6D  Var_02    N10  C11  C12  C13   177.27  30.0  3
 E6D  Var_03    C8   N10  C11  C12  -160.71  30.0  2
 E6D  Var_04    C22  C20  C19  C7    178.46  30.0  3
 E6D  Var_05    O18  C16  C2   C3    -41.66  30.0  1
 E6D  Var_06    C24  C23  O17  C16  -179.94  30.0  1
 E6D  Var_07    H5   C15  C13  C14    61.95  30.0  3
 E6D  Var_08    H1   C14  C13  C15    56.33  30.0  3
 E6D  Var_09    H17  C22  C20  C19    61.71  30.0  3
 E6D  Var_10    H20  C21  C20  C19  -176.16  30.0  3
 E6D  Var_11    H30  C24  C23  O17   179.83  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
 E6D  chir_01  C7  N6  C8  C19  positiv
 E6D  chir_02  C3  O1  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
 E6D  plan-1  C11  0.020
 E6D  plan-1  N10  0.020
 E6D  plan-1  C8   0.020
 E6D  plan-1  O9   0.020
 E6D  plan-1  C7   0.020
 E6D  plan-1  H12  0.020
 E6D  plan-2  C7   0.020
 E6D  plan-2  N6   0.020
 E6D  plan-2  C4   0.020
 E6D  plan-2  O5   0.020
 E6D  plan-2  C3   0.020
 E6D  plan-2  H23  0.020
 E6D  plan-3  C2   0.020
 E6D  plan-3  C16  0.020
 E6D  plan-3  O18  0.020
 E6D  plan-3  O17  0.020

