# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 01:34:19 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  21  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   1.2214  -1.8671  -0.0131
 MKE  CA    C  CH1   0  -0.207   1.1923  -0.4728  -0.3919
 MKE  CB    C  CH2   0  -0.431  -0.0644   0.2052   0.1724
 MKE  CG    C  CH2   0  -0.574  -1.3272  -0.3994  -0.4158
 MKE  CD    C  C     0   0.549  -2.5899   0.2127   0.1202
 MKE  OE1   O  OH1   0  -0.597  -3.6709  -0.3080  -0.4536
 MKE  OE2   O  O     0  -0.446  -2.6451   1.0696   0.9674
 MKE  C     C  C     0   0.381   2.4081   0.3365   0.0491
 MKE  O     O  O     0  -0.399   3.0823  -0.0042   0.9952
 MKE  CMK   C  CH3   0  -0.779   2.7257   1.5586  -0.7647
 MKE  HN1   H  HNH2  0   0.353   1.9944  -2.3354  -0.4687
 MKE  HN2   H  HNH2  0   0.342   1.3921  -1.9487   0.9823
 MKE  HA    H  HCH1  0   0.254   1.1414  -0.4139  -1.4855
 MKE  HB1   H  HCH2  0   0.243  -0.0633   0.1018   1.2610
 MKE  HB2   H  HCH2  0   0.250  -0.0368   1.2764  -0.0371
 MKE  HG1   H  HCH2  0   0.277  -1.3295  -0.2909  -1.5050
 MKE  HG2   H  HCH2  0   0.287  -1.3556  -1.4758  -0.2287
 MKE  HE1   H  HOH1  0   0.478  -4.4692   0.1016  -0.0882
 MKE  HMK1  H  HCH3  0   0.263   3.3335   2.2691  -0.2082
 MKE  HMK2  H  HCH3  0   0.276   3.2898   1.2407  -1.6461
 MKE  HMK3  H  HCH3  0   0.257   1.8275   2.0536  -1.1331

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  1.445  0.020  1.445
 MKE  N    HN1   single  0.890  0.020  1.040
 MKE  N    HN2   single  0.890  0.020  1.040
 MKE  CA   CB    single  1.535  0.020  1.535
 MKE  CA   C     single  1.526  0.020  1.526
 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  1.502  0.020  1.502
 MKE  CG   HG1   single  0.970  0.020  1.090
 MKE  CG   HG2   single  0.970  0.020  1.090
 MKE  CD   OE1   single  1.330  0.020  1.330
 MKE  CD   OE2   double  1.206  0.020  1.206
 MKE  OE1  HE1   single  0.850  0.020  0.980
 MKE  C    O     double  1.211  0.020  1.211
 MKE  C    CMK   single  1.502  0.020  1.502
 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   106.03  3.000
 MKE  HN2   N    CA    109.80  3.000
 MKE  HN1   N    CA    110.11  3.000
 MKE  HA    CA   C     107.27  3.000
 MKE  HA    CA   CB    107.75  3.000
 MKE  C     CA   CB    108.17  3.000
 MKE  HA    CA   N     108.32  3.000
 MKE  C     CA   N     114.83  3.000
 MKE  CB    CA   N     110.25  3.000
 MKE  HB2   CB   HB1   106.49  3.000
 MKE  HB2   CB   CG    109.71  3.000
 MKE  HB1   CB   CG    110.41  3.000
 MKE  HB2   CB   CA    110.00  3.000
 MKE  HB1   CB   CA    108.86  3.000
 MKE  CG    CB   CA    111.25  3.000
 MKE  HG2   CG   HG1   105.54  3.000
 MKE  HG2   CG   CD    108.57  3.000
 MKE  HG1   CG   CD    108.24  3.000
 MKE  HG2   CG   CB    110.32  3.000
 MKE  HG1   CG   CB    110.35  3.000
 MKE  CD    CG   CB    113.49  3.000
 MKE  OE2   CD   OE1   122.95  3.000
 MKE  OE2   CD   CG    125.35  3.000
 MKE  OE1   CD   CG    111.70  3.000
 MKE  HE1   OE1  CD    109.97  3.000
 MKE  CMK   C    O     122.31  3.000
 MKE  CMK   C    CA    116.32  3.000
 MKE  O     C    CA    121.36  3.000
 MKE  HMK3  CMK  HMK2  106.55  3.000
 MKE  HMK3  CMK  HMK1  109.68  3.000
 MKE  HMK2  CMK  HMK1  108.29  3.000
 MKE  HMK3  CMK  C     112.24  3.000
 MKE  HMK2  CMK  C     108.01  3.000
 MKE  HMK1  CMK  C     111.85  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  CONST_01  HE1   OE1  CD  CG  180.00   0.0  0
 MKE  Var_01    CD    CG   CB  CA  179.03  30.0  3
 MKE  Var_02    OE1   CD   CG  CB  177.71  30.0  3
 MKE  Var_03    HMK1  CMK  C   CA  158.56  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
 MKE  plan-2  HE1  0.020

