# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 15:21:29 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  37  21  .  2021-08-07  2021-08-07  
;
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  OC    -1  -0.634  -5.1425  -2.0418   1.6240
 C68  CD   C  C      0   0.410  -4.8149  -0.9012   1.2323
 C68  OE2  O  O      0  -0.610  -5.4415   0.1563   1.4435
 C68  CG   C  CH2    0  -0.575  -3.5251  -0.8208   0.3958
 C68  CB   C  CH2    0  -0.446  -3.0232   0.5846   0.1051
 C68  CA   C  CH1    0  -0.193  -1.7891   0.6316  -0.7957
 C68  C    C  C      0   0.407  -1.4371   2.1013  -1.1449
 C68  OXT  O  OC    -1  -0.622  -2.2494   2.6758  -1.8992
 C68  O    O  O      0  -0.593  -0.4112   2.5880  -0.6374
 C68  N    N  NH1    0  -0.657  -0.6942  -0.0661  -0.1555
 C68  CAR  C  C      0   0.757   0.4850  -0.1845  -0.8046
 C68  OAF  O  O      0  -0.539   0.6192  -0.1114  -2.0103
 C68  OAN  O  O2     0  -0.491   1.4808  -0.4232   0.0481
 C68  CAU  C  CH1    0  -0.082   2.7810  -0.6173  -0.4986
 C68  CAQ  C  C      0   0.395   2.9249  -1.9935  -1.1787
 C68  OAI  O  O      0  -0.597   2.0233  -2.8278  -0.9977
 C68  OAE  O  OC    -1  -0.620   3.9766  -2.1390  -1.8337
 C68  CAL  C  CH2    0  -0.441   3.7675  -0.4701   0.6525
 C68  CAS  C  CH1    0  -0.224   3.6584   0.8338   1.4491
 C68  CAB  C  CH3    0  -0.653   4.7694   0.8840   2.4939
 C68  CAA  C  CH3    0  -0.670   3.6992   2.0688   0.5538
 C68  H2   H  HCH2   0   0.218  -2.7525  -1.4120   0.8956
 C68  H3   H  HCH2   0   0.219  -3.7099  -1.3404  -0.5533
 C68  H4   H  HCH2   0   0.226  -3.8101   1.1597  -0.3812
 C68  H5   H  HCH2   0   0.207  -2.8013   1.1055   1.0438
 C68  H6   H  HCH1   0   0.222  -2.0330   0.1111  -1.7274
 C68  H8   H  HNH1   0   0.372  -0.6257   0.0557   0.8441
 C68  H9   H  HCH1   0   0.223   2.9839   0.1602  -1.2412
 C68  H11  H  HCH2   0   0.223   3.6619  -1.3175   1.3392
 C68  H12  H  HCH2   0   0.222   4.7717  -0.5438   0.2251
 C68  H13  H  HCH1   0   0.218   2.7023   0.8353   1.9822
 C68  H14  H  HCH3   0   0.224   4.6855   1.7735   3.1206
 C68  H15  H  HCH3   0   0.222   4.7372   0.0116   3.1491
 C68  H16  H  HCH3   0   0.211   5.7539   0.9049   2.0196
 C68  H17  H  HCH3   0   0.234   2.8192   2.1380  -0.0872
 C68  H18  H  HCH3   0   0.225   3.7326   2.9808   1.1529
 C68  H19  H  HCH3   0   0.211   4.5856   2.0623  -0.0858

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    deloc   1.244  0.020  1.244
 C68  OE2  CD   deloc   1.247  0.020  1.247
 C68  OXT  C    deloc   1.249  0.020  1.249
 C68  C    CA   single  1.551  0.020  1.551
 C68  CD   OE1  deloc   1.250  0.020  1.250
 C68  CD   CG   single  1.539  0.020  1.539
 C68  CG   CB   single  1.520  0.020  1.520
 C68  CB   CA   single  1.529  0.020  1.529
 C68  CA   N    single  1.448  0.020  1.448
 C68  OAF  CAR  double  1.215  0.020  1.215
 C68  N    CAR  single  1.351  0.020  1.351
 C68  CAB  CAS  single  1.526  0.020  1.526
 C68  CAR  OAN  single  1.333  0.020  1.333
 C68  CAL  CAS  single  1.532  0.020  1.532
 C68  CAL  CAU  single  1.523  0.020  1.523
 C68  CAS  CAA  single  1.526  0.020  1.526
 C68  OAN  CAU  single  1.424  0.020  1.424
 C68  CAU  CAQ  single  1.542  0.020  1.542
 C68  CAQ  OAI  deloc   1.242  0.020  1.242
 C68  CAQ  OAE  deloc   1.247  0.020  1.247
 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  N    H8   single  0.890  0.020  1.040
 C68  CAU  H9   single  0.970  0.020  1.090
 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  CG   CD   OE2  117.95  3.000
 C68  CG   CD   OE1  115.95  3.000
 C68  OE2  CD   OE1  126.09  3.000
 C68  H3   CG   H2   104.97  3.000
 C68  H3   CG   CB   109.14  3.000
 C68  H2   CG   CB   110.72  3.000
 C68  H3   CG   CD   107.70  3.000
 C68  H2   CG   CD   108.38  3.000
 C68  CB   CG   CD   115.39  3.000
 C68  H5   CB   H4   106.12  3.000
 C68  H5   CB   CA   109.06  3.000
 C68  H4   CB   CA   107.70  3.000
 C68  H5   CB   CG   110.02  3.000
 C68  H4   CB   CG   109.57  3.000
 C68  CA   CB   CG   114.05  3.000
 C68  H6   CA   N    108.41  3.000
 C68  H6   CA   C    108.03  3.000
 C68  N    CA   C    112.62  3.000
 C68  H6   CA   CB   107.89  3.000
 C68  N    CA   CB   109.58  3.000
 C68  C    CA   CB   110.18  3.000
 C68  O    C    OXT  127.09  3.000
 C68  OXT  C    CA   115.11  3.000
 C68  O    C    CA   117.78  3.000
 C68  H8   N    CAR  115.28  3.000
 C68  H8   N    CA   115.55  3.000
 C68  CAR  N    CA   119.33  3.000
 C68  OAN  CAR  OAF  124.27  3.000
 C68  OAN  CAR  N    111.13  3.000
 C68  OAF  CAR  N    124.59  3.000
 C68  CAU  OAN  CAR  117.47  3.000
 C68  H9   CAU  CAL  108.92  3.000
 C68  H9   CAU  CAQ  108.51  3.000
 C68  CAL  CAU  CAQ  111.05  3.000
 C68  H9   CAU  OAN  109.45  3.000
 C68  CAQ  CAU  OAN  112.11  3.000
 C68  CAL  CAU  OAN  106.75  3.000
 C68  OAE  CAQ  OAI  127.61  3.000
 C68  OAE  CAQ  CAU  114.48  3.000
 C68  OAI  CAQ  CAU  117.88  3.000
 C68  H12  CAL  H11  106.33  3.000
 C68  H12  CAL  CAS  109.02  3.000
 C68  H11  CAL  CAS  108.99  3.000
 C68  H12  CAL  CAU  107.03  3.000
 C68  H11  CAL  CAU  109.66  3.000
 C68  CAS  CAL  CAU  115.42  3.000
 C68  H13  CAS  CAA  107.93  3.000
 C68  H13  CAS  CAB  107.60  3.000
 C68  CAA  CAS  CAB  110.83  3.000
 C68  H13  CAS  CAL  108.46  3.000
 C68  CAA  CAS  CAL  112.45  3.000
 C68  CAB  CAS  CAL  109.41  3.000
 C68  H16  CAB  H15  107.60  3.000
 C68  H16  CAB  H14  107.63  3.000
 C68  H15  CAB  H14  107.73  3.000
 C68  H16  CAB  CAS  111.06  3.000
 C68  H15  CAB  CAS  111.30  3.000
 C68  H14  CAB  CAS  111.35  3.000
 C68  H19  CAA  H18  107.53  3.000
 C68  H19  CAA  H17  108.10  3.000
 C68  H18  CAA  H17  107.10  3.000
 C68  H19  CAA  CAS  111.11  3.000
 C68  H18  CAA  CAS  110.79  3.000
 C68  H17  CAA  CAS  112.00  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  Var_01  CB   CG   CD   OE1  -171.09  30.0  3
 C68  Var_02  CA   CB   CG   CD   -176.57  30.0  3
 C68  Var_03  OAF  CAR  N    CA    -22.66  30.0  2
 C68  Var_04  CAB  CAS  CAL  CAU  -175.80  30.0  3
 C68  Var_05  H14  CAB  CAS  CAL  -176.58  30.0  3
 C68  Var_06  H17  CAA  CAS  CAL    66.83  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
 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-2  CA   0.020
 C68  plan-2  C    0.020
 C68  plan-2  OXT  0.020
 C68  plan-2  O    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-4  N    0.020
 C68  plan-4  CAR  0.020
 C68  plan-4  OAF  0.020
 C68  plan-4  OAN  0.020

