# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 19:01:02 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: (2S)-2-amino-4-(2-chloroethoxy)-4-oxobutanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)OCCCl)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
 0AK  0AK  '(2S)-2-amino-4-(2-chloroethoxy)-4-oxobutanoic acid (non-preferred name)'  L-peptide  21  12  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_0AK
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
 0AK  N     N   NH2    0  -0.807  33.4787   99.3128  28.7523
 0AK  CA    C   CH1    0  -0.219  32.5833  100.3998  29.1182
 0AK  C     C   C      0   0.435  32.2799  100.3812  30.6344
 0AK  O     O   O      0  -0.596  33.1735   99.9498  31.3853
 0AK  CB    C   CH2    0  -0.547  31.2966  100.2811  28.3031
 0AK  CG    C   C      0   0.598  30.2784  101.3556  28.5551
 0AK  OD1   O   O      0  -0.463  29.0910  101.1794  28.6688
 0AK  OD2   O   O2     0  -0.460  30.8299  102.5756  28.5091
 0AK  C1    C   CH2    0  -0.183  30.0044  103.7067  28.7451
 0AK  C2    C   CH2    0  -0.474  29.8199  103.9234  30.2354
 0AK  CL    CL  CL     0  -0.167  28.9101  105.4537  30.4768
 0AK  OXT   O   OC    -1  -0.587  31.1696  100.8408  30.9745
 0AK  HN1   H   HNH2   0   0.333  33.9512   99.5361  27.8856
 0AK  HN2   H   HNH2   0   0.336  34.1957   99.2460  29.4632
 0AK  HA    H   HCH1   0   0.214  33.0317  101.3841  28.9108
 0AK  HBC1  H   HCH2   0   0.259  31.5399  100.3114  27.2342
 0AK  HBC2  H   HCH2   0   0.247  30.8284   99.3146  28.4911
 0AK  H1C1  H   HCH2   0   0.257  30.5331  104.5534  28.3097
 0AK  H1C2  H   HCH2   0   0.243  29.0378  103.6108  28.2485
 0AK  H2C1  H   HCH2   0   0.291  29.2459  103.1266  30.6999
 0AK  H2C2  H   HCH2   0   0.288  30.7746  104.0244  30.7461

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
 0AK  N    CA    single  1.458  0.019  1.458
 0AK  N    HN1   single  0.890  0.020  1.040
 0AK  N    HN2   single  0.890  0.020  1.040
 0AK  CA   C     single  1.525  0.021  1.525
 0AK  CA   CB    single  1.530  0.020  1.530
 0AK  CA   HA    single  0.970  0.020  0.970
 0AK  C    O     deloc   1.231  0.020  1.231
 0AK  C    OXT   deloc   1.249  0.020  1.249
 0AK  CB   CG    single  1.502  0.020  1.502
 0AK  CB   HBC1  single  0.970  0.020  1.090
 0AK  CB   HBC2  single  0.970  0.020  1.090
 0AK  CG   OD1   double  1.206  0.020  1.206
 0AK  CG   OD2   single  1.340  0.020  1.340
 0AK  OD2  C1    single  1.420  0.020  1.420
 0AK  C1   C2    single  1.517  0.020  1.517
 0AK  C1   H1C1  single  0.970  0.020  1.090
 0AK  C1   H1C2  single  0.970  0.020  1.090
 0AK  C2   CL    single  1.797  0.020  1.797
 0AK  C2   H2C1  single  0.970  0.020  1.090
 0AK  C2   H2C2  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
 0AK  HN2   N    HN1   106.59  3.000
 0AK  HN2   N    CA    107.98  3.000
 0AK  HN1   N    CA    109.74  3.000
 0AK  HA    CA   CB    109.00  3.000
 0AK  HA    CA   C     109.00  3.000
 0AK  CB    CA   C     110.10  1.900
 0AK  HA    CA   N     110.00  3.000
 0AK  CB    CA   N     110.50  1.700
 0AK  C     CA   N     111.00  2.800
 0AK  OXT   C    O     126.99  3.000
 0AK  OXT   C    CA    115.91  3.000
 0AK  O     C    CA    120.80  1.700
 0AK  HBC2  CB   HBC1  106.73  3.000
 0AK  HBC2  CB   CG    108.32  3.000
 0AK  HBC1  CB   CG    107.11  3.000
 0AK  HBC2  CB   CA    109.79  3.000
 0AK  HBC1  CB   CA    109.32  3.000
 0AK  CG    CB   CA    115.21  3.000
 0AK  OD2   CG   OD1   122.80  3.000
 0AK  OD2   CG   CB    111.52  3.000
 0AK  OD1   CG   CB    125.38  3.000
 0AK  C1    OD2  CG    118.71  3.000
 0AK  H1C2  C1   H1C1  108.45  3.000
 0AK  H1C2  C1   C2    110.60  3.000
 0AK  H1C1  C1   C2    109.92  3.000
 0AK  H1C2  C1   OD2   111.68  3.000
 0AK  H1C1  C1   OD2   105.70  3.000
 0AK  C2    C1   OD2   110.35  3.000
 0AK  H2C2  C2   H2C1  109.34  3.000
 0AK  H2C2  C2   CL    107.60  3.000
 0AK  H2C1  C2   CL    107.44  3.000
 0AK  H2C2  C2   C1    111.58  3.000
 0AK  H2C1  C2   C1    112.30  3.000
 0AK  CL    C2   C1    108.38  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
 0AK  Var_01  OD1  CG  CB   CA   -137.50  30.0  3
 0AK  Var_02  C2   C1  OD2  CG     81.55  30.0  3
 0AK  Var_03  CL   C2  C1   OD2   174.40  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
 0AK  chir_01  CA  N  C  CB  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
 0AK  plan-1  CA   0.020
 0AK  plan-1  C    0.020
 0AK  plan-1  O    0.020
 0AK  plan-1  OXT  0.020
 0AK  plan-2  CB   0.020
 0AK  plan-2  CG   0.020
 0AK  plan-2  OD1  0.020
 0AK  plan-2  OD2  0.020

