# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 17:10:55 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]oxycarbonylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](OC(=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
 C68  C68  '(2~{S})-2-[[(2~{S})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]oxycarbonylamino]pentanedioic acid'  ligand  40  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_C68
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
 C68  OE1  O  OH1   0  -0.595  -4.9066  -2.3408   1.4679
 C68  CD   C  C     0   0.554  -4.6690  -1.0599   1.2074
 C68  OE2  O  O     0  -0.443  -5.3846  -0.1662   1.5849
 C68  CG   C  CH2   0  -0.577  -3.4156  -0.8817   0.3961
 C68  CB   C  CH2   0  -0.464  -3.1117   0.5769   0.0939
 C68  CA   C  CH1   0  -0.202  -1.8639   0.7165  -0.7817
 C68  C    C  C     0   0.550  -1.6508   2.1686  -1.1947
 C68  OXT  O  OH1   0  -0.589  -2.5889   2.5711  -2.0381
 C68  O    O  O     0  -0.427  -0.7501   2.8616  -0.8019
 C68  N    N  NH1   0  -0.662  -0.7094   0.2138  -0.0906
 C68  CAR  C  C     0   0.774   0.4416  -0.0019  -0.7569
 C68  OAF  O  O     0  -0.508   0.5622   0.0227  -1.9627
 C68  OAN  O  O2    0  -0.481   1.4439  -0.2688   0.0887
 C68  CAU  C  CH1   0  -0.082   2.7158  -0.5012  -0.4844
 C68  CAQ  C  C     0   0.529   2.7115  -1.8468  -1.1873
 C68  OAI  O  O     0  -0.430   1.8800  -2.6984  -1.0171
 C68  OAE  O  OH1   0  -0.589   3.7643  -1.9713  -1.9787
 C68  CAL  C  CH2   0  -0.449   3.7443  -0.4904   0.6428
 C68  CAS  C  CH1   0  -0.237   3.7573   0.7954   1.4748
 C68  CAB  C  CH3   0  -0.653   4.8250   0.6827   2.5583
 C68  CAA  C  CH3   0  -0.666   3.9921   2.0365   0.6205
 C68  H1   H  HOH1  0   0.480  -5.7188  -2.4273   1.9891
 C68  H2   H  HCH2  0   0.289  -2.5914  -1.3592   0.9325
 C68  H3   H  HCH2  0   0.288  -3.5272  -1.4475  -0.5345
 C68  H4   H  HCH2  0   0.275  -3.9559   1.0276  -0.4265
 C68  H5   H  HCH2  0   0.260  -2.9744   1.1402   1.0208
 C68  H6   H  HCH1  0   0.298  -2.0171   0.1325  -1.6938
 C68  H7   H  HOH1  0   0.487  -2.4512   3.4999  -2.2788
 C68  H8   H  HNH1  0   0.407  -0.6603   0.3535   0.9082
 C68  H9   H  HCH1  0   0.283   2.9575   0.2768  -1.2145
 C68  H10  H  HOH1  0   0.488   3.7805  -2.8510  -2.3857
 C68  H11  H  HCH2  0   0.251   3.5745  -1.3475   1.3018
 C68  H12  H  HCH2  0   0.249   4.7309  -0.6330   0.1927
 C68  H13  H  HCH1  0   0.231   2.7872   0.8961   1.9706
 C68  H14  H  HCH3  0   0.230   4.8193   1.5628   3.2023
 C68  H15  H  HCH3  0   0.228   4.6661  -0.1926   3.1906
 C68  H16  H  HCH3  0   0.216   5.8221   0.5991   2.1193
 C68  H17  H  HCH3  0   0.227   3.1977   2.2009  -0.1095
 C68  H18  H  HCH3  0   0.235   4.0407   2.9303   1.2442
 C68  H19  H  HCH3  0   0.219   4.9358   1.9640   0.0741

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
 C68  O    C    double  1.202  0.020  1.202
 C68  OE2  CD   double  1.206  0.020  1.206
 C68  OXT  C    single  1.324  0.020  1.324
 C68  C    CA   single  1.525  0.020  1.525
 C68  CD   OE1  single  1.329  0.020  1.329
 C68  CD   CG   single  1.504  0.020  1.504
 C68  CG   CB   single  1.520  0.020  1.520
 C68  CB   CA   single  1.531  0.020  1.531
 C68  CA   N    single  1.436  0.020  1.436
 C68  OAF  CAR  double  1.212  0.020  1.212
 C68  N    CAR  single  1.347  0.020  1.347
 C68  CAB  CAS  single  1.525  0.020  1.525
 C68  CAR  OAN  single  1.338  0.020  1.338
 C68  CAL  CAS  single  1.532  0.020  1.532
 C68  CAL  CAU  single  1.526  0.020  1.526
 C68  CAS  CAA  single  1.525  0.020  1.525
 C68  OAN  CAU  single  1.414  0.020  1.414
 C68  CAU  CAQ  single  1.518  0.020  1.518
 C68  CAQ  OAI  double  1.202  0.020  1.202
 C68  CAQ  OAE  single  1.323  0.020  1.323
 C68  OE1  H1   single  0.850  0.020  0.980
 C68  CG   H2   single  0.970  0.020  1.090
 C68  CG   H3   single  0.970  0.020  1.090
 C68  CB   H4   single  0.970  0.020  1.090
 C68  CB   H5   single  0.970  0.020  1.090
 C68  CA   H6   single  0.970  0.020  1.090
 C68  OXT  H7   single  0.850  0.020  0.980
 C68  N    H8   single  0.890  0.020  1.040
 C68  CAU  H9   single  0.970  0.020  1.090
 C68  OAE  H10  single  0.850  0.020  0.980
 C68  CAL  H11  single  0.970  0.020  1.090
 C68  CAL  H12  single  0.970  0.020  1.090
 C68  CAS  H13  single  0.970  0.020  1.090
 C68  CAB  H14  single  0.970  0.020  1.090
 C68  CAB  H15  single  0.970  0.020  1.090
 C68  CAB  H16  single  0.970  0.020  1.090
 C68  CAA  H17  single  0.970  0.020  1.090
 C68  CAA  H18  single  0.970  0.020  1.090
 C68  CAA  H19  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
 C68  H1   OE1  CD   109.96  3.000
 C68  CG   CD   OE2  125.17  3.000
 C68  CG   CD   OE1  111.66  3.000
 C68  OE2  CD   OE1  123.17  3.000
 C68  H3   CG   H2   105.56  3.000
 C68  H3   CG   CB   110.32  3.000
 C68  H2   CG   CB   111.47  3.000
 C68  H3   CG   CD   108.20  3.000
 C68  H2   CG   CD   108.18  3.000
 C68  CB   CG   CD   112.80  3.000
 C68  H5   CB   H4   106.81  3.000
 C68  H5   CB   CA   109.61  3.000
 C68  H4   CB   CA   108.70  3.000
 C68  H5   CB   CG   110.54  3.000
 C68  H4   CB   CG   109.70  3.000
 C68  CA   CB   CG   111.36  3.000
 C68  H6   CA   N    109.08  3.000
 C68  H6   CA   C    107.59  3.000
 C68  N    CA   C    110.56  3.000
 C68  H6   CA   CB   108.31  3.000
 C68  N    CA   CB   110.37  3.000
 C68  C    CA   CB   110.84  3.000
 C68  O    C    OXT  124.30  3.000
 C68  OXT  C    CA   111.28  3.000
 C68  O    C    CA   124.42  3.000
 C68  H7   OXT  C    110.42  3.000
 C68  H8   N    CAR  118.02  3.000
 C68  H8   N    CA   117.81  3.000
 C68  CAR  N    CA   120.31  3.000
 C68  OAN  CAR  OAF  123.93  3.000
 C68  OAN  CAR  N    111.05  3.000
 C68  OAF  CAR  N    125.01  3.000
 C68  CAU  OAN  CAR  116.76  3.000
 C68  H9   CAU  CAL  109.82  3.000
 C68  H9   CAU  CAQ  108.78  3.000
 C68  CAL  CAU  CAQ  110.49  3.000
 C68  H9   CAU  OAN  110.63  3.000
 C68  CAQ  CAU  OAN  109.32  3.000
 C68  CAL  CAU  OAN  107.80  3.000
 C68  OAE  CAQ  OAI  124.64  3.000
 C68  OAE  CAQ  CAU  110.99  3.000
 C68  OAI  CAQ  CAU  124.34  3.000
 C68  H10  OAE  CAQ  110.48  3.000
 C68  H12  CAL  H11  106.60  3.000
 C68  H12  CAL  CAS  108.99  3.000
 C68  H11  CAL  CAS  109.37  3.000
 C68  H12  CAL  CAU  107.64  3.000
 C68  H11  CAL  CAU  109.55  3.000
 C68  CAS  CAL  CAU  114.39  3.000
 C68  H13  CAS  CAA  108.39  3.000
 C68  H13  CAS  CAB  107.80  3.000
 C68  CAA  CAS  CAB  110.51  3.000
 C68  H13  CAS  CAL  108.41  3.000
 C68  CAA  CAS  CAL  112.35  3.000
 C68  CAB  CAS  CAL  109.26  3.000
 C68  H16  CAB  H15  107.71  3.000
 C68  H16  CAB  H14  107.68  3.000
 C68  H15  CAB  H14  107.72  3.000
 C68  H16  CAB  CAS  111.04  3.000
 C68  H15  CAB  CAS  111.65  3.000
 C68  H14  CAB  CAS  110.87  3.000
 C68  H19  CAA  H18  107.56  3.000
 C68  H19  CAA  H17  107.70  3.000
 C68  H18  CAA  H17  106.94  3.000
 C68  H19  CAA  CAS  111.04  3.000
 C68  H18  CAA  CAS  110.70  3.000
 C68  H17  CAA  CAS  112.67  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
 C68  CONST_01  H1   OE1  CD   OE2     0.00   0.0  0
 C68  CONST_02  H7   OXT  C    CA    180.00   0.0  0
 C68  CONST_03  H10  OAE  CAQ  CAU   180.00   0.0  0
 C68  Var_01    CB   CG   CD   OE1  -179.46  30.0  3
 C68  Var_02    CA   CB   CG   CD   -177.60  30.0  3
 C68  Var_03    OAF  CAR  N    CA    -10.44  30.0  2
 C68  Var_04    CAB  CAS  CAL  CAU  -179.81  30.0  3
 C68  Var_05    H14  CAB  CAS  CAL  -176.84  30.0  3
 C68  Var_06    H17  CAA  CAS  CAL    62.84  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
 C68  chir_01  CA   C    CB   N    positiv
 C68  chir_02  CAU  OAN  CAQ  CAL  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
 C68  plan-1  OE1  0.020
 C68  plan-1  CD   0.020
 C68  plan-1  OE2  0.020
 C68  plan-1  CG   0.020
 C68  plan-1  H1   0.020
 C68  plan-2  CA   0.020
 C68  plan-2  C    0.020
 C68  plan-2  OXT  0.020
 C68  plan-2  O    0.020
 C68  plan-2  H7   0.020
 C68  plan-3  CAU  0.020
 C68  plan-3  CAQ  0.020
 C68  plan-3  OAI  0.020
 C68  plan-3  OAE  0.020
 C68  plan-3  H10  0.020
 C68  plan-4  N    0.020
 C68  plan-4  CAR  0.020
 C68  plan-4  OAF  0.020
 C68  plan-4  OAN  0.020

