# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:36:27 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2~{R},3~{S})-2-azanyl-4-methyl-3-oxidanyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](O)[C@@H](N)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
 KJW  KJW  '(2~{R},3~{S})-2-azanyl-4-methyl-3-oxidanyl-pentanoic acid'  D-peptide  22  10  .  2022-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KJW
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
 KJW  CB    C  CH1    0   0.100  -16.4126  19.5669  -4.1512
 KJW  CA    C  CH1    0  -0.248  -17.0661  18.7761  -2.9963
 KJW  CG    C  CH1    0  -0.243  -16.6006  21.0892  -4.1400
 KJW  CD2   C  CH3    0  -0.671  -15.7049  21.7977  -3.1278
 KJW  CD1   C  CH3    0  -0.666  -18.0542  21.5210  -3.9722
 KJW  OE    O  OH1    0  -0.698  -16.9320  19.0732  -5.3684
 KJW  C     C  C      0   0.408  -16.3751  19.0044  -1.6338
 KJW  O     O  O      0  -0.603  -15.2428  18.4913  -1.5101
 KJW  N     N  NH2    0  -0.816  -17.0402  17.3682  -3.4091
 KJW  OXT   O  OC    -1  -0.606  -16.9975  19.6609  -0.7748
 KJW  HB3   H  HCH1   0   0.168  -15.3275  19.3696  -4.1034
 KJW  HA    H  HCH1   0   0.217  -18.1175  19.0669  -2.9265
 KJW  HG    H  HCH1   0   0.215  -16.2717  21.4185  -5.1330
 KJW  HD23  H  HCH3   0   0.223  -15.7322  22.8766  -3.2900
 KJW  HD21  H  HCH3   0   0.224  -16.0269  21.6125  -2.1040
 KJW  HD22  H  HCH3   0   0.217  -14.6648  21.4783  -3.2182
 KJW  HD12  H  HCH3   0   0.222  -18.7178  20.9983  -4.6620
 KJW  HD13  H  HCH3   0   0.211  -18.4111  21.3374  -2.9571
 KJW  HD11  H  HCH3   0   0.223  -18.1586  22.5906  -4.1629
 KJW  HE    H  HOH1   0   0.430  -17.1219  18.1389  -5.1600
 KJW  H     H  HNH2   0   0.339  -16.1321  16.9835  -3.1703
 KJW  H2    H  HNH2   0   0.354  -17.7200  16.8381  -2.8793

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
 KJW  OE   CB    single  1.412  0.020  1.412
 KJW  CG   CD2   single  1.526  0.020  1.526
 KJW  CG   CB    single  1.534  0.020  1.534
 KJW  CG   CD1   single  1.526  0.020  1.526
 KJW  CB   CA    single  1.521  0.033  1.521
 KJW  N    CA    single  1.458  0.019  1.458
 KJW  CA   C     single  1.525  0.021  1.525
 KJW  C    O     deloc   1.231  0.020  1.231
 KJW  C    OXT   deloc   1.247  0.020  1.247
 KJW  CB   HB3   single  0.970  0.020  1.090
 KJW  CA   HA    single  0.970  0.020  0.970
 KJW  CG   HG    single  0.970  0.020  1.090
 KJW  CD2  HD23  single  0.970  0.020  1.090
 KJW  CD2  HD21  single  0.970  0.020  1.090
 KJW  CD2  HD22  single  0.970  0.020  1.090
 KJW  CD1  HD12  single  0.970  0.020  1.090
 KJW  CD1  HD13  single  0.970  0.020  1.090
 KJW  CD1  HD11  single  0.970  0.020  1.090
 KJW  OE   HE    single  0.850  0.020  0.980
 KJW  N    H     single  0.860  0.020  0.860
 KJW  N    H2    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
 KJW  HB3   CB   OE    109.65  3.000
 KJW  HB3   CB   CG    107.31  3.000
 KJW  OE    CB   CG    107.94  3.000
 KJW  HB3   CB   CA    106.98  3.000
 KJW  CG    CB   CA    116.80  3.000
 KJW  OE    CB   CA    108.05  3.000
 KJW  HA    CA   N     110.00  3.000
 KJW  HA    CA   C     110.00  3.000
 KJW  N     CA   C     111.00  2.800
 KJW  HA    CA   CB    109.00  3.000
 KJW  C     CA   CB    110.50  1.500
 KJW  N     CA   CB    110.40  1.500
 KJW  HG    CG   CD1   107.48  3.000
 KJW  HG    CG   CD2   106.57  3.000
 KJW  CD1   CG   CD2   110.78  3.000
 KJW  HG    CG   CB    104.76  3.000
 KJW  CD1   CG   CB    113.48  3.000
 KJW  CD2   CG   CB    113.18  3.000
 KJW  HD22  CD2  HD21  108.05  3.000
 KJW  HD22  CD2  HD23  107.50  3.000
 KJW  HD21  CD2  HD23  107.49  3.000
 KJW  HD22  CD2  CG    111.62  3.000
 KJW  HD21  CD2  CG    111.78  3.000
 KJW  HD23  CD2  CG    110.22  3.000
 KJW  HD11  CD1  HD13  107.22  3.000
 KJW  HD11  CD1  HD12  107.52  3.000
 KJW  HD13  CD1  HD12  107.98  3.000
 KJW  HD11  CD1  CG    110.44  3.000
 KJW  HD13  CD1  CG    111.48  3.000
 KJW  HD12  CD1  CG    111.99  3.000
 KJW  HE    OE   CB    102.84  3.000
 KJW  OXT   C    O     126.88  3.000
 KJW  OXT   C    CA    120.80  1.700
 KJW  O     C    CA    120.80  1.700
 KJW  H2    N    H     106.23  3.000
 KJW  H2    N    CA    110.09  3.000
 KJW  H     N    CA    114.00  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
 KJW  Var_01  HD23  CD2  CG  CB  169.10  30.0  3
 KJW  Var_02  HD12  CD1  CG  CB  -49.27  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
 KJW  chir_01  CB  OE  CG  CA  negativ
 KJW  chir_02  CA  N   CB  C   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
 KJW  plan-1  CA   0.020
 KJW  plan-1  C    0.020
 KJW  plan-1  O    0.020
 KJW  plan-1  OXT  0.020

