# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:17:08 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (4S,5R)-4-amino-5-hydroxyhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](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
 EKE  EKE  '(4S,5R)-4-amino-5-hydroxyhexanoic acid'  ligand  22  10  .  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_EKE
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
 EKE  N     N  NH2    0  -0.790   1.1835  -1.8296   0.4493
 EKE  CA    C  CH1    0  -0.120   1.1417  -0.5016  -0.1491
 EKE  CB    C  CH2    0  -0.393  -0.1771   0.1748   0.2247
 EKE  CG    C  CH2    0  -0.582  -1.3879  -0.4986  -0.3989
 EKE  CD    C  C      0   0.408  -2.7575   0.0908  -0.0243
 EKE  OE1   O  O      0  -0.611  -2.7888   1.0287   0.7975
 EKE  OE2   O  OC    -1  -0.637  -3.7471  -0.4315  -0.5824
 EKE  C     C  CH1    0   0.042   2.3548   0.3783   0.2107
 EKE  O     O  OH1    0  -0.667   2.2894   1.6374  -0.4380
 EKE  CMK   C  CH3    0  -0.698   3.6855  -0.3040  -0.0825
 EKE  HN1   H  HNH2   0   0.347   1.9828  -2.3504   0.1133
 EKE  HN2   H  HNH2   0   0.333   1.3017  -1.7475   1.4532
 EKE  HA    H  HCH1   0   0.203   1.1650  -0.6456  -1.2394
 EKE  HB1   H  HCH2   0   0.197  -0.2698   0.1770   1.3166
 EKE  HB2   H  HCH2   0   0.212  -0.1460   1.2237  -0.0731
 EKE  HG1   H  HCH2   0   0.211  -1.2967  -0.4713  -1.4914
 EKE  HG2   H  HCH2   0   0.222  -1.3881  -1.5628  -0.1437
 EKE  H     H  HCH1   0   0.206   2.3050   0.6031   1.2831
 EKE  HO    H  HOH1   0   0.438   2.2937   1.4791  -1.3884
 EKE  HMK1  H  HCH3   0   0.237   4.5121   0.3844   0.0977
 EKE  HMK2  H  HCH3   0   0.223   3.8500  -1.1750   0.5510
 EKE  HMK3  H  HCH3   0   0.219   3.7407  -0.6316  -1.1246

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
 EKE  N    CA    single  1.457  0.020  1.457
 EKE  N    HN1   single  0.890  0.020  1.040
 EKE  N    HN2   single  0.890  0.020  1.040
 EKE  CA   CB    single  1.529  0.020  1.529
 EKE  CA   C     single  1.541  0.020  1.541
 EKE  CA   HA    single  0.970  0.020  1.090
 EKE  CB   CG    single  1.519  0.020  1.519
 EKE  CB   HB1   single  0.970  0.020  1.090
 EKE  CB   HB2   single  0.970  0.020  1.090
 EKE  CG   CD    single  1.537  0.020  1.537
 EKE  CG   HG1   single  0.970  0.020  1.090
 EKE  CG   HG2   single  0.970  0.020  1.090
 EKE  CD   OE1   deloc   1.247  0.020  1.247
 EKE  CD   OE2   deloc   1.250  0.020  1.250
 EKE  C    O     single  1.418  0.020  1.418
 EKE  C    CMK   single  1.524  0.020  1.524
 EKE  C    H     single  0.970  0.020  1.090
 EKE  O    HO    single  0.850  0.020  0.980
 EKE  CMK  HMK1  single  0.970  0.020  1.090
 EKE  CMK  HMK2  single  0.970  0.020  1.090
 EKE  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
 EKE  HN2   N    HN1   106.16  3.000
 EKE  HN2   N    CA    109.64  3.000
 EKE  HN1   N    CA    110.82  3.000
 EKE  HA    CA   C     106.83  3.000
 EKE  HA    CA   CB    108.58  3.000
 EKE  C     CA   CB    111.68  3.000
 EKE  HA    CA   N     106.69  3.000
 EKE  C     CA   N     113.69  3.000
 EKE  CB    CA   N     109.12  3.000
 EKE  HB2   CB   HB1   105.82  3.000
 EKE  HB2   CB   CG    109.68  3.000
 EKE  HB1   CB   CG    110.03  3.000
 EKE  HB2   CB   CA    109.51  3.000
 EKE  HB1   CB   CA    108.52  3.000
 EKE  CG    CB   CA    113.02  3.000
 EKE  HG2   CG   HG1   104.86  3.000
 EKE  HG2   CG   CD    108.41  3.000
 EKE  HG1   CG   CD    107.90  3.000
 EKE  HG2   CG   CB    109.60  3.000
 EKE  HG1   CG   CB    109.36  3.000
 EKE  CD    CG   CB    116.10  3.000
 EKE  OE2   CD   OE1   126.04  3.000
 EKE  OE2   CD   CG    115.85  3.000
 EKE  OE1   CD   CG    118.11  3.000
 EKE  H     C    CMK   108.63  3.000
 EKE  H     C    O     105.27  3.000
 EKE  CMK   C    O     110.48  3.000
 EKE  H     C    CA    108.03  3.000
 EKE  CMK   C    CA    112.75  3.000
 EKE  O     C    CA    111.34  3.000
 EKE  HO    O    C     107.77  3.000
 EKE  HMK3  CMK  HMK2  107.87  3.000
 EKE  HMK3  CMK  HMK1  107.95  3.000
 EKE  HMK2  CMK  HMK1  107.10  3.000
 EKE  HMK3  CMK  C     111.19  3.000
 EKE  HMK2  CMK  C     112.21  3.000
 EKE  HMK1  CMK  C     110.33  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
 EKE  Var_01  CD   CG  CB  CA  177.65  30.0  3
 EKE  Var_02  OE1  CD  CG  CB   -3.02  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
 EKE  chir_01  CA  N  CB  C    negativ
 EKE  chir_02  C   O  CA  CMK  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
 EKE  plan-1  CG   0.020
 EKE  plan-1  CD   0.020
 EKE  plan-1  OE1  0.020
 EKE  plan-1  OE2  0.020

