# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 07:38:19 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  41  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  -0.443   5.4941   0.2070   1.5660
 D6E  CD   C  C     0   0.554   4.7831   1.0995   1.1768
 D6E  OE2  O  OH1   0  -0.596   5.0418   2.3838   1.3988
 D6E  CG   C  CH2   0  -0.576   3.5123   0.9166   0.3946
 D6E  CB   C  CH2   0  -0.465   3.1968  -0.5437   0.1138
 D6E  CA   C  CH1   0  -0.188   1.9255  -0.6915  -0.7269
 D6E  C    C  C     0   0.543   1.7176  -2.1531  -1.1024
 D6E  O    O  O     0  -0.431   0.9073  -2.8796  -0.5901
 D6E  OXT  O  OH1   0  -0.591   2.5640  -2.5340  -2.0486
 D6E  N    N  NH1   0  -0.682   0.7926  -0.1744  -0.0135
 D6E  CAR  C  C     0   0.767  -0.4079  -0.0590  -0.6517
 D6E  OAF  O  O     0  -0.536  -0.5246  -0.2071  -1.8619
 D6E  NAN  N  NH1   0  -0.681  -1.4607   0.2383   0.1530
 D6E  CAU  C  CH1   0  -0.191  -2.7559   0.4821  -0.4112
 D6E  CAQ  C  C     0   0.549  -2.7771   1.7887  -1.1905
 D6E  OAI  O  O     0  -0.437  -1.9728   2.6751  -1.0632
 D6E  OAE  O  OH1   0  -0.592  -3.8154   1.8446  -2.0134
 D6E  CAL  C  CH2   0  -0.450  -3.8230   0.5153   0.6882
 D6E  CAS  C  CH1   0  -0.231  -3.8780  -0.7496   1.5493
 D6E  CAB  C  CH3   0  -0.652  -4.9673  -0.5982   2.6060
 D6E  CAA  C  CH3   0  -0.663  -4.1085  -2.0039   0.7144
 D6E  H1   H  HOH1  0   0.480   5.8619   2.4726   1.9067
 D6E  H2   H  HCH2  0   0.288   2.7014   1.3995   0.9462
 D6E  H3   H  HCH2  0   0.286   3.6024   1.4738  -0.5430
 D6E  H4   H  HCH2  0   0.272   4.0272  -1.0031  -0.4221
 D6E  H5   H  HCH2  0   0.257   3.0820  -1.0961   1.0504
 D6E  H6   H  HCH1  0   0.289   2.0567  -0.1233  -1.6517
 D6E  H7   H  HOH1  0   0.485   2.4444  -3.4745  -2.2495
 D6E  H8   H  HNH1  0   0.396   0.7803  -0.3312   0.9834
 D6E  H9   H  HNH1  0   0.398  -1.2839   0.5713   1.0881
 D6E  H10  H  HCH1  0   0.284  -2.9952  -0.3223  -1.1109
 D6E  H11  H  HOH1  0   0.484  -3.8374   2.6995  -2.4694
 D6E  H12  H  HCH2  0   0.247  -3.6494   1.3825   1.3350
 D6E  H13  H  HCH2  0   0.251  -4.7981   0.6696   0.2188
 D6E  H14  H  HCH1  0   0.223  -2.9205  -0.8583   2.0690
 D6E  H15  H  HCH3  0   0.227  -4.8140   0.2924   3.2180
 D6E  H16  H  HCH3  0   0.216  -5.9535  -0.5167   2.1430
 D6E  H17  H  HCH3  0   0.230  -4.9851  -1.4606   3.2734
 D6E  H18  H  HCH3  0   0.230  -3.2975  -2.1860   0.0075
 D6E  H19  H  HCH3  0   0.233  -4.1818  -2.8856   1.3530
 D6E  H20  H  HCH3  0   0.217  -5.0379  -1.9307   0.1439

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    double  1.203  0.020  1.203
 D6E  OE1  CD   double  1.206  0.020  1.206
 D6E  OXT  C    single  1.325  0.020  1.325
 D6E  C    CA   single  1.523  0.020  1.523
 D6E  CD   OE2  single  1.329  0.020  1.329
 D6E  CD   CG   single  1.503  0.020  1.503
 D6E  CG   CB   single  1.520  0.020  1.520
 D6E  CB   CA   single  1.531  0.020  1.531
 D6E  CA   N    single  1.435  0.020  1.435
 D6E  OAF  CAR  double  1.225  0.020  1.225
 D6E  N    CAR  single  1.364  0.020  1.364
 D6E  CAB  CAS  single  1.525  0.020  1.525
 D6E  CAR  NAN  single  1.358  0.020  1.358
 D6E  CAL  CAS  single  1.531  0.020  1.531
 D6E  CAL  CAU  single  1.532  0.020  1.532
 D6E  CAS  CAA  single  1.524  0.020  1.524
 D6E  NAN  CAU  single  1.434  0.020  1.434
 D6E  CAU  CAQ  single  1.521  0.020  1.521
 D6E  CAQ  OAI  double  1.204  0.020  1.204
 D6E  CAQ  OAE  single  1.326  0.020  1.326
 D6E  OE2  H1   single  0.850  0.020  0.980
 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  OXT  H7   single  0.850  0.020  0.980
 D6E  N    H8   single  0.890  0.020  1.040
 D6E  NAN  H9   single  0.860  0.020  1.020
 D6E  CAU  H10  single  0.970  0.020  1.090
 D6E  OAE  H11  single  0.850  0.020  0.980
 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  111.66  3.000
 D6E  CG   CD   OE1  125.20  3.000
 D6E  OE2  CD   OE1  123.15  3.000
 D6E  H1   OE2  CD   109.94  3.000
 D6E  H3   CG   H2   105.57  3.000
 D6E  H3   CG   CB   110.36  3.000
 D6E  H2   CG   CB   111.32  3.000
 D6E  H3   CG   CD   108.32  3.000
 D6E  H2   CG   CD   108.10  3.000
 D6E  CB   CG   CD   112.86  3.000
 D6E  H5   CB   H4   106.75  3.000
 D6E  H5   CB   CA   109.53  3.000
 D6E  H4   CB   CA   108.78  3.000
 D6E  H5   CB   CG   110.42  3.000
 D6E  H4   CB   CG   109.73  3.000
 D6E  CA   CB   CG   111.50  3.000
 D6E  H6   CA   N    109.14  3.000
 D6E  H6   CA   C    107.85  3.000
 D6E  N    CA   C    111.13  3.000
 D6E  H6   CA   CB   108.34  3.000
 D6E  N    CA   CB   110.34  3.000
 D6E  C    CA   CB   109.95  3.000
 D6E  OXT  C    O    124.10  3.000
 D6E  OXT  C    CA   111.38  3.000
 D6E  O    C    CA   124.50  3.000
 D6E  H7   OXT  C    110.37  3.000
 D6E  H8   N    CAR  117.68  3.000
 D6E  H8   N    CA   116.40  3.000
 D6E  CAR  N    CA   119.51  3.000
 D6E  NAN  CAR  OAF  122.56  3.000
 D6E  NAN  CAR  N    115.05  3.000
 D6E  OAF  CAR  N    122.39  3.000
 D6E  H9   NAN  CAU  117.85  3.000
 D6E  H9   NAN  CAR  119.07  3.000
 D6E  CAU  NAN  CAR  120.30  3.000
 D6E  H10  CAU  CAL  108.84  3.000
 D6E  H10  CAU  CAQ  107.53  3.000
 D6E  CAL  CAU  CAQ  109.83  3.000
 D6E  H10  CAU  NAN  108.94  3.000
 D6E  CAQ  CAU  NAN  111.11  3.000
 D6E  CAL  CAU  NAN  110.51  3.000
 D6E  OAE  CAQ  OAI  123.90  3.000
 D6E  OAE  CAQ  CAU  111.41  3.000
 D6E  OAI  CAQ  CAU  124.68  3.000
 D6E  H11  OAE  CAQ  110.30  3.000
 D6E  H13  CAL  H12  106.45  3.000
 D6E  H13  CAL  CAS  109.03  3.000
 D6E  H12  CAL  CAS  109.12  3.000
 D6E  H13  CAL  CAU  108.43  3.000
 D6E  H12  CAL  CAU  109.29  3.000
 D6E  CAS  CAL  CAU  114.24  3.000
 D6E  H14  CAS  CAA  108.09  3.000
 D6E  H14  CAS  CAB  107.79  3.000
 D6E  CAA  CAS  CAB  110.68  3.000
 D6E  H14  CAS  CAL  108.51  3.000
 D6E  CAA  CAS  CAL  112.16  3.000
 D6E  CAB  CAS  CAL  109.47  3.000
 D6E  H17  CAB  H16  107.67  3.000
 D6E  H17  CAB  H15  107.72  3.000
 D6E  H16  CAB  H15  107.67  3.000
 D6E  H17  CAB  CAS  110.93  3.000
 D6E  H16  CAB  CAS  111.01  3.000
 D6E  H15  CAB  CAS  111.66  3.000
 D6E  H20  CAA  H19  107.60  3.000
 D6E  H20  CAA  H18  107.76  3.000
 D6E  H19  CAA  H18  107.11  3.000
 D6E  H20  CAA  CAS  111.06  3.000
 D6E  H19  CAA  CAS  110.77  3.000
 D6E  H18  CAA  CAS  112.32  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  CONST_01  OAF  CAR  N    CA      0.00   0.0  0
 D6E  CONST_02  CAU  NAN  CAR  OAF     0.00   0.0  0
 D6E  CONST_03  NAN  CAR  N    CA    180.00   0.0  0
 D6E  CONST_04  CAU  NAN  CAR  N     180.00   0.0  0
 D6E  CONST_07  H1   OE2  CD   OE1     0.00   0.0  0
 D6E  CONST_08  H7   OXT  C    CA    180.00   0.0  0
 D6E  CONST_09  H11  OAE  CAQ  CAU   180.00   0.0  0
 D6E  Var_01    CB   CG   CD   OE1    -0.61  30.0  3
 D6E  Var_02    CA   CB   CG   CD   -177.93  30.0  3
 D6E  Var_03    CAB  CAS  CAL  CAU   179.77  30.0  3
 D6E  Var_04    H15  CAB  CAS  CAL   -56.24  30.0  3
 D6E  Var_05    H18  CAA  CAS  CAL    62.43  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-2  H1   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-3  H7   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
 D6E  plan-4  H11  0.020

