# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 00:44:02 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (2~{S},3~{S})-2-azanyl-4-(2-hydroxy-2-oxoethylamino)-3-oxidanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H](O)CNCC(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
 5KC  5KC  "(2S,3S)-2-azanyl-4-(2-hydroxy-2-oxoethylamino)-3-oxidanyl-butanoic acid"  ligand  23  13  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5KC
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
 5KC  N    N  NH2    0  -0.818   1.4572  -31.4171  -12.5977
 5KC  CA   C  CH1    0  -0.237   2.2053  -31.4009  -13.8529
 5KC  C    C  C      0   0.405   1.9969  -30.0561  -14.5963
 5KC  O    O  O      0  -0.599   1.2109  -29.2336  -14.0854
 5KC  CB   C  CH1    0   0.051   1.6935  -32.6137  -14.6488
 5KC  OG1  O  OH1    0  -0.686   0.3115  -32.4568  -14.8833
 5KC  CG2  C  CH2    0  -0.274   2.3856  -32.9204  -15.9656
 5KC  OXT  O  OC    -1  -0.600   2.6564  -29.8954  -15.6422
 5KC  CAH  C  CH2    0  -0.392   4.4821  -33.6182  -16.9482
 5KC  CAI  C  C      0   0.385   5.7579  -34.4442  -16.6794
 5KC  NAL  N  NH1    0  -0.602   3.7655  -33.2868  -15.7386
 5KC  OAJ  O  O      0  -0.615   6.6063  -34.4540  -17.5918
 5KC  OAK  O  OC    -1  -0.603   5.8121  -35.0597  -15.5955
 5KC  H1   H  HNH2   0   0.338   1.9220  -32.0015  -11.9154
 5KC  H2   H  HNH2   0   0.342   1.4013  -30.4808  -12.2228
 5KC  H4   H  HCH1   0   0.204   3.2860  -31.5278  -13.7042
 5KC  H5   H  HCH1   0   0.172   1.8600  -33.4926  -13.9970
 5KC  HG1  H  HOH1   0   0.430  -0.0251  -32.1002  -14.0473
 5KC  H6   H  HCH2   0   0.217   2.3488  -32.0473  -16.6170
 5KC  H7   H  HCH2   0   0.174   1.8203  -33.7216  -16.4749
 5KC  H9   H  HCH2   0   0.204   4.7481  -32.7042  -17.4889
 5KC  H10  H  HCH2   0   0.181   3.8646  -34.2069  -17.6534
 5KC  HAL  H  HNH1   0   0.322   3.8169  -34.0929  -15.1273

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
 5KC  OAJ  CAI  deloc   1.246  0.020  1.246
 5KC  CAI  CAH  single  1.543  0.020  1.543
 5KC  CAI  OAK  deloc   1.248  0.020  1.248
 5KC  CAH  NAL  single  1.444  0.020  1.444
 5KC  CG2  NAL  single  1.446  0.020  1.446
 5KC  CG2  CB   single  1.519  0.020  1.519
 5KC  OG1  CB   single  1.411  0.020  1.411
 5KC  O    C    deloc   1.247  0.020  1.247
 5KC  CB   CA   single  1.538  0.020  1.538
 5KC  OXT  C    deloc   1.247  0.020  1.247
 5KC  C    CA   single  1.551  0.020  1.551
 5KC  CA   N    single  1.461  0.020  1.461
 5KC  N    H1   single  0.890  0.020  1.040
 5KC  N    H2   single  0.890  0.020  1.040
 5KC  CA   H4   single  0.970  0.020  1.090
 5KC  CB   H5   single  0.970  0.020  1.090
 5KC  OG1  HG1  single  0.850  0.020  0.980
 5KC  CG2  H6   single  0.970  0.020  1.090
 5KC  CG2  H7   single  0.970  0.020  1.090
 5KC  CAH  H9   single  0.970  0.020  1.090
 5KC  CAH  H10  single  0.970  0.020  1.090
 5KC  NAL  HAL  single  0.890  0.020  1.040

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
 5KC  H2   N    H1   108.10  3.000
 5KC  H2   N    CA   109.69  3.000
 5KC  H1   N    CA   110.52  3.000
 5KC  H4   CA   CB   107.84  3.000
 5KC  H4   CA   C    107.30  3.000
 5KC  CB   CA   C    113.02  3.000
 5KC  H4   CA   N    112.71  3.000
 5KC  C    CA   N    110.65  3.000
 5KC  CB   CA   N    105.39  3.000
 5KC  OXT  C    O    126.31  3.000
 5KC  OXT  C    CA   116.28  3.000
 5KC  O    C    CA   117.40  3.000
 5KC  H5   CB   CG2  106.36  3.000
 5KC  H5   CB   OG1  109.49  3.000
 5KC  CG2  CB   OG1  108.95  3.000
 5KC  H5   CB   CA   105.75  3.000
 5KC  OG1  CB   CA   108.93  3.000
 5KC  CG2  CB   CA   117.13  3.000
 5KC  HG1  OG1  CB   103.75  3.000
 5KC  H7   CG2  H6   106.74  3.000
 5KC  H7   CG2  NAL  112.14  3.000
 5KC  H6   CG2  NAL  109.22  3.000
 5KC  H7   CG2  CB   108.23  3.000
 5KC  H6   CG2  CB   109.94  3.000
 5KC  NAL  CG2  CB   110.49  3.000
 5KC  H10  CAH  H9   105.36  3.000
 5KC  H10  CAH  NAL  112.26  3.000
 5KC  H9   CAH  NAL  110.04  3.000
 5KC  H10  CAH  CAI  106.70  3.000
 5KC  H9   CAH  CAI  109.39  3.000
 5KC  NAL  CAH  CAI  112.77  3.000
 5KC  OAK  CAI  OAJ  127.07  3.000
 5KC  OAK  CAI  CAH  116.82  3.000
 5KC  OAJ  CAI  CAH  116.08  3.000
 5KC  HAL  NAL  CAH  107.32  3.000
 5KC  HAL  NAL  CG2  110.18  3.000
 5KC  CAH  NAL  CG2  113.59  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
 5KC  Var_01  CAH  NAL  CG2  CB    178.88  30.0  3
 5KC  Var_02  CAI  CAH  NAL  CG2  -160.62  30.0  1
 5KC  Var_03  OAJ  CAI  CAH  NAL  -160.93  30.0  2
 5KC  Var_04  OAK  CAI  CAH  NAL    21.15  30.0  2
 5KC  Var_05  HAL  NAL  CG2  CB     58.45  30.0  3
 5KC  Var_06  H9   CAH  NAL  CG2    76.95  30.0  1
 5KC  Var_07  H10  CAH  NAL  CG2   -40.05  30.0  1
 5KC  Var_08  H6   CG2  NAL  CAH   -60.08  30.0  1
 5KC  Var_09  H7   CG2  NAL  CAH    58.04  30.0  1
 5KC  Var_10  HAL  NAL  CAH  CAI   -38.59  30.0  3
 5KC  Var_11  H9   CAH  CAI  OAJ   -38.13  30.0  3
 5KC  Var_12  H10  CAH  CAI  OAJ    75.37  30.0  3
 5KC  Var_13  H9   CAH  CAI  OAK   143.95  30.0  3
 5KC  Var_14  H10  CAH  CAI  OAK  -102.55  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
 5KC  chir_01  CA  CB   C   N    negativ
 5KC  chir_02  CB  OG1  CA  CG2  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
 5KC  plan-1  CA   0.020
 5KC  plan-1  C    0.020
 5KC  plan-1  O    0.020
 5KC  plan-1  OXT  0.020
 5KC  plan-2  CAH  0.020
 5KC  plan-2  CAI  0.020
 5KC  plan-2  OAJ  0.020
 5KC  plan-2  OAK  0.020

