# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 10:05:53 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (4S)-4-amino-5-oxohexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@@H](N)CCC(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
 MKE  MKE  '(4S)-4-amino-5-oxohexanoic acid'  ligand  20  10  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MKE
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
 MKE  N     N  NH2    0  -0.777   1.2523  -1.9067   0.0172
 MKE  CA    C  CH1    0  -0.202   1.1965  -0.5185  -0.3844
 MKE  CB    C  CH2    0  -0.416  -0.0706   0.1517   0.1700
 MKE  CG    C  CH2    0  -0.579  -1.3427  -0.4268  -0.4261
 MKE  CD    C  C      0   0.411  -2.6544   0.2118   0.0624
 MKE  OE1   O  OC    -1  -0.633  -3.7037  -0.2747  -0.4100
 MKE  OE2   O  O      0  -0.609  -2.5797   1.1548   0.8747
 MKE  C     C  C      0   0.380   2.3993   0.3143   0.0379
 MKE  O     O  O      0  -0.406   3.0791   0.0104   0.9938
 MKE  CMK   C  CH3    0  -0.779   2.7008   1.5223  -0.8047
 MKE  HN1   H  HNH2   0   0.347   2.0640  -2.3551  -0.3893
 MKE  HN2   H  HNH2   0   0.338   1.3754  -1.9665   1.0211
 MKE  HA    H  HCH1   0   0.241   1.1414  -0.4788  -1.4792
 MKE  HB1   H  HCH2   0   0.219  -0.0738   0.0428   1.2590
 MKE  HB2   H  HCH2   0   0.227  -0.0355   1.2261  -0.0230
 MKE  HG1   H  HCH2   0   0.220  -1.3052  -0.3298  -1.5177
 MKE  HG2   H  HCH2   0   0.229  -1.3833  -1.5031  -0.2379
 MKE  HMK1  H  HCH3   0   0.260   3.2917   2.2582  -0.2628
 MKE  HMK2  H  HCH3   0   0.273   3.2780   1.1930  -1.6734
 MKE  HMK3  H  HCH3   0   0.255   1.7961   1.9901  -1.1919

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
 MKE  N    CA    single  1.446  0.020  1.446
 MKE  N    HN1   single  0.890  0.020  1.040
 MKE  N    HN2   single  0.890  0.020  1.040
 MKE  CA   CB    single  1.537  0.020  1.537
 MKE  CA   C     single  1.523  0.020  1.523
 MKE  CA   HA    single  0.970  0.020  1.090
 MKE  CB   CG    single  1.519  0.020  1.519
 MKE  CB   HB1   single  0.970  0.020  1.090
 MKE  CB   HB2   single  0.970  0.020  1.090
 MKE  CG   CD    single  1.539  0.020  1.539
 MKE  CG   HG1   single  0.970  0.020  1.090
 MKE  CG   HG2   single  0.970  0.020  1.090
 MKE  CD   OE1   deloc   1.249  0.020  1.249
 MKE  CD   OE2   deloc   1.247  0.020  1.247
 MKE  C    O     double  1.212  0.020  1.212
 MKE  C    CMK   single  1.503  0.020  1.503
 MKE  CMK  HMK1  single  0.970  0.020  1.090
 MKE  CMK  HMK2  single  0.970  0.020  1.090
 MKE  CMK  HMK3  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
 MKE  HN2   N    HN1   105.92  3.000
 MKE  HN2   N    CA    109.67  3.000
 MKE  HN1   N    CA    110.15  3.000
 MKE  HA    CA   C     107.26  3.000
 MKE  HA    CA   CB    107.63  3.000
 MKE  C     CA   CB    108.22  3.000
 MKE  HA    CA   N     108.29  3.000
 MKE  C     CA   N     114.68  3.000
 MKE  CB    CA   N     110.50  3.000
 MKE  HB2   CB   HB1   105.89  3.000
 MKE  HB2   CB   CG    109.40  3.000
 MKE  HB1   CB   CG    110.49  3.000
 MKE  HB2   CB   CA    109.80  3.000
 MKE  HB1   CB   CA    108.54  3.000
 MKE  CG    CB   CA    112.50  3.000
 MKE  HG2   CG   HG1   105.05  3.000
 MKE  HG2   CG   CD    108.80  3.000
 MKE  HG1   CG   CD    107.97  3.000
 MKE  HG2   CG   CB    109.78  3.000
 MKE  HG1   CG   CB    109.16  3.000
 MKE  CD    CG   CB    115.54  3.000
 MKE  OE2   CD   OE1   126.24  3.000
 MKE  OE2   CD   CG    118.01  3.000
 MKE  OE1   CD   CG    115.74  3.000
 MKE  CMK   C    O     122.09  3.000
 MKE  CMK   C    CA    116.26  3.000
 MKE  O     C    CA    121.65  3.000
 MKE  HMK3  CMK  HMK2  106.57  3.000
 MKE  HMK3  CMK  HMK1  109.72  3.000
 MKE  HMK2  CMK  HMK1  108.22  3.000
 MKE  HMK3  CMK  C     112.19  3.000
 MKE  HMK2  CMK  C     108.00  3.000
 MKE  HMK1  CMK  C     111.91  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
 MKE  Var_01  CD    CG   CB  CA  -178.95  30.0  3
 MKE  Var_02  OE1   CD   CG  CB  -178.95  30.0  3
 MKE  Var_03  HMK1  CMK  C   CA   158.05  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
 MKE  chir_01  CA  N  CB  C  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
 MKE  plan-1  CA   0.020
 MKE  plan-1  C    0.020
 MKE  plan-1  O    0.020
 MKE  plan-1  CMK  0.020
 MKE  plan-2  CG   0.020
 MKE  plan-2  CD   0.020
 MKE  plan-2  OE1  0.020
 MKE  plan-2  OE2  0.020

