# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 03:50:31 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)N[C@@H](CCC(O)=O)C(O)=O)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
 D6E  D6E  '(2~{S})-2-[[(2~{S})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoylamino]pentanedioic acid'  ligand  38  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D6E
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
 D6E  OE1  O  O      0  -0.611   5.4021   0.3335   1.6157
 D6E  CD   C  C      0   0.409   4.8394   1.2941   1.0534
 D6E  OE2  O  OC    -1  -0.635   5.2204   2.4844   1.0734
 D6E  CG   C  CH2    0  -0.573   3.5472   1.0145   0.2663
 D6E  CB   C  CH2    0  -0.447   3.1872  -0.4522   0.0906
 D6E  CA   C  CH1    0  -0.173   1.9254  -0.6823  -0.7432
 D6E  C    C  C      0   0.400   1.7466  -2.1946  -1.0179
 D6E  O    O  O     -1  -0.604   0.9052  -2.8104  -0.3394
 D6E  OXT  O  OC     0  -0.626   2.5051  -2.6732  -1.8876
 D6E  N    N  NH1    0  -0.674   0.7932  -0.0824  -0.0728
 D6E  CAR  C  C      0   0.747  -0.4288  -0.0791  -0.6769
 D6E  OAF  O  O      0  -0.567  -0.5671  -0.2611  -1.8834
 D6E  NAN  N  NH1    0  -0.669  -1.4821   0.1465   0.1561
 D6E  CAU  C  CH1    0  -0.192  -2.7638   0.5317  -0.3830
 D6E  CAQ  C  C      0   0.407  -2.7636   1.9302  -1.0482
 D6E  OAI  O  O      0  -0.601  -1.7874   2.6721  -0.8402
 D6E  OAE  O  OC    -1  -0.624  -3.7779   2.1948  -1.7273
 D6E  CAL  C  CH2    0  -0.439  -3.8188   0.4829   0.7231
 D6E  CAS  C  CH1    0  -0.218  -3.9347  -0.8517   1.4621
 D6E  CAB  C  CH3    0  -0.651  -5.0051  -0.7574   2.5449
 D6E  CAA  C  CH3    0  -0.661  -4.2279  -2.0125   0.5184
 D6E  H2   H  HCH2   0   0.224   2.7290   1.5472   0.7632
 D6E  H3   H  HCH2   0   0.212   3.6341   1.4887  -0.7179
 D6E  H4   H  HCH2   0   0.222   4.0104  -0.9752  -0.3985
 D6E  H5   H  HCH2   0   0.206   3.0638  -0.9294   1.0689
 D6E  H6   H  HCH1   0   0.212   2.0636  -0.1792  -1.7049
 D6E  H8   H  HNH1   0   0.365   0.7896  -0.1949   0.9301
 D6E  H9   H  HNH1   0   0.366  -1.2611   0.5384   1.0591
 D6E  H10  H  HCH1   0   0.226  -3.0390  -0.1952  -1.1506
 D6E  H12  H  HCH2   0   0.217  -3.6091   1.2731   1.4557
 D6E  H13  H  HCH2   0   0.222  -4.7856   0.7332   0.2780
 D6E  H14  H  HCH1   0   0.211  -2.9770  -1.0541   1.9531
 D6E  H15  H  HCH3   0   0.221  -4.8039   0.0622   3.2376
 D6E  H16  H  HCH3   0   0.210  -5.9918  -0.5850   2.1077
 D6E  H17  H  HCH3   0   0.222  -5.0597  -1.6785   3.1280
 D6E  H18  H  HCH3   0   0.230  -3.4268  -2.1626  -0.2067
 D6E  H19  H  HCH3   0   0.223  -4.3428  -2.9458   1.0729
 D6E  H20  H  HCH3   0   0.209  -5.1537  -1.8435  -0.0380

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
 D6E  O    C    deloc   1.244  0.020  1.244
 D6E  OE1  CD   deloc   1.247  0.020  1.247
 D6E  OXT  C    deloc   1.249  0.020  1.249
 D6E  C    CA   single  1.547  0.020  1.547
 D6E  CD   OE2  deloc   1.250  0.020  1.250
 D6E  CD   CG   single  1.539  0.020  1.539
 D6E  CG   CB   single  1.520  0.020  1.520
 D6E  CB   CA   single  1.530  0.020  1.530
 D6E  CA   N    single  1.446  0.020  1.446
 D6E  OAF  CAR  double  1.228  0.020  1.228
 D6E  N    CAR  single  1.363  0.020  1.363
 D6E  CAB  CAS  single  1.526  0.020  1.526
 D6E  CAR  NAN  single  1.362  0.020  1.362
 D6E  CAL  CAS  single  1.530  0.020  1.530
 D6E  CAL  CAU  single  1.529  0.020  1.529
 D6E  CAS  CAA  single  1.524  0.020  1.524
 D6E  NAN  CAU  single  1.443  0.020  1.443
 D6E  CAU  CAQ  single  1.549  0.020  1.549
 D6E  CAQ  OAI  deloc   1.244  0.020  1.244
 D6E  CAQ  OAE  deloc   1.249  0.020  1.249
 D6E  CG   H2   single  0.970  0.020  1.090
 D6E  CG   H3   single  0.970  0.020  1.090
 D6E  CB   H4   single  0.970  0.020  1.090
 D6E  CB   H5   single  0.970  0.020  1.090
 D6E  CA   H6   single  0.970  0.020  1.090
 D6E  N    H8   single  0.890  0.020  1.040
 D6E  NAN  H9   single  0.890  0.020  1.040
 D6E  CAU  H10  single  0.970  0.020  1.090
 D6E  CAL  H12  single  0.970  0.020  1.090
 D6E  CAL  H13  single  0.970  0.020  1.090
 D6E  CAS  H14  single  0.970  0.020  1.090
 D6E  CAB  H15  single  0.970  0.020  1.090
 D6E  CAB  H16  single  0.970  0.020  1.090
 D6E  CAB  H17  single  0.970  0.020  1.090
 D6E  CAA  H18  single  0.970  0.020  1.090
 D6E  CAA  H19  single  0.970  0.020  1.090
 D6E  CAA  H20  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
 D6E  CG   CD   OE2  115.92  3.000
 D6E  CG   CD   OE1  118.01  3.000
 D6E  OE2  CD   OE1  126.07  3.000
 D6E  H3   CG   H2   104.84  3.000
 D6E  H3   CG   CB   109.41  3.000
 D6E  H2   CG   CB   110.16  3.000
 D6E  H3   CG   CD   108.31  3.000
 D6E  H2   CG   CD   107.87  3.000
 D6E  CB   CG   CD   115.67  3.000
 D6E  H5   CB   H4   106.05  3.000
 D6E  H5   CB   CA   109.16  3.000
 D6E  H4   CB   CA   107.81  3.000
 D6E  H5   CB   CG   110.10  3.000
 D6E  H4   CB   CG   109.61  3.000
 D6E  CA   CB   CG   113.79  3.000
 D6E  H6   CA   N    108.40  3.000
 D6E  H6   CA   C    107.94  3.000
 D6E  N    CA   C    113.41  3.000
 D6E  H6   CA   CB   107.80  3.000
 D6E  N    CA   CB   109.31  3.000
 D6E  C    CA   CB   109.82  3.000
 D6E  OXT  C    O    126.92  3.000
 D6E  OXT  C    CA   115.33  3.000
 D6E  O    C    CA   117.71  3.000
 D6E  H8   N    CAR  115.95  3.000
 D6E  H8   N    CA   114.66  3.000
 D6E  CAR  N    CA   119.83  3.000
 D6E  NAN  CAR  OAF  122.58  3.000
 D6E  NAN  CAR  N    115.00  3.000
 D6E  OAF  CAR  N    122.41  3.000
 D6E  H9   NAN  CAU  115.17  3.000
 D6E  H9   NAN  CAR  116.26  3.000
 D6E  CAU  NAN  CAR  120.18  3.000
 D6E  H10  CAU  CAL  108.26  3.000
 D6E  H10  CAU  CAQ  107.40  3.000
 D6E  CAL  CAU  CAQ  109.85  3.000
 D6E  H10  CAU  NAN  107.98  3.000
 D6E  CAQ  CAU  NAN  113.67  3.000
 D6E  CAL  CAU  NAN  109.51  3.000
 D6E  OAE  CAQ  OAI  127.02  3.000
 D6E  OAE  CAQ  CAU  115.13  3.000
 D6E  OAI  CAQ  CAU  117.84  3.000
 D6E  H13  CAL  H12  106.01  3.000
 D6E  H13  CAL  CAS  109.23  3.000
 D6E  H12  CAL  CAS  108.66  3.000
 D6E  H13  CAL  CAU  107.95  3.000
 D6E  H12  CAL  CAU  109.14  3.000
 D6E  CAS  CAL  CAU  115.43  3.000
 D6E  H14  CAS  CAA  107.76  3.000
 D6E  H14  CAS  CAB  107.87  3.000
 D6E  CAA  CAS  CAB  110.58  3.000
 D6E  H14  CAS  CAL  108.16  3.000
 D6E  CAA  CAS  CAL  112.32  3.000
 D6E  CAB  CAS  CAL  110.01  3.000
 D6E  H17  CAB  H16  107.56  3.000
 D6E  H17  CAB  H15  107.69  3.000
 D6E  H16  CAB  H15  107.56  3.000
 D6E  H17  CAB  CAS  111.23  3.000
 D6E  H16  CAB  CAS  111.06  3.000
 D6E  H15  CAB  CAS  111.55  3.000
 D6E  H20  CAA  H19  107.55  3.000
 D6E  H20  CAA  H18  107.75  3.000
 D6E  H19  CAA  H18  107.30  3.000
 D6E  H20  CAA  CAS  111.11  3.000
 D6E  H19  CAA  CAS  110.91  3.000
 D6E  H18  CAA  CAS  112.03  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
 D6E  Var_01  CB   CG   CD   OE1    -8.25  30.0  3
 D6E  Var_02  CA   CB   CG   CD   -177.77  30.0  3
 D6E  Var_03  CAB  CAS  CAL  CAU   179.28  30.0  3
 D6E  Var_04  H15  CAB  CAS  CAL   -56.05  30.0  3
 D6E  Var_05  H18  CAA  CAS  CAL    62.27  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
 D6E  chir_01  CA   C    CB   N    positiv
 D6E  chir_02  CAU  NAN  CAL  CAQ  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
 D6E  plan-1  CA   0.020
 D6E  plan-1  N    0.020
 D6E  plan-1  CAR  0.020
 D6E  plan-1  OAF  0.020
 D6E  plan-1  NAN  0.020
 D6E  plan-1  CAU  0.020
 D6E  plan-1  H8   0.020
 D6E  plan-1  H9   0.020
 D6E  plan-2  OE1  0.020
 D6E  plan-2  CD   0.020
 D6E  plan-2  OE2  0.020
 D6E  plan-2  CG   0.020
 D6E  plan-3  CA   0.020
 D6E  plan-3  C    0.020
 D6E  plan-3  O    0.020
 D6E  plan-3  OXT  0.020
 D6E  plan-4  CAU  0.020
 D6E  plan-4  CAQ  0.020
 D6E  plan-4  OAI  0.020
 D6E  plan-4  OAE  0.020

