# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:11:13 2021
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{S},3~{R})-2-azanyl-3-methyl-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H](C)[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
 SKJ  SKJ  '(2~{S},3~{R})-2-azanyl-3-methyl-hexanoic acid'  L-peptide  25  10  .  2022-08-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SKJ
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
 SKJ  N    N  NH2   0  -0.794   4.1325  -29.4253  8.2774
 SKJ  CA   C  CH1   0  -0.172   4.4080  -30.8471  8.3215
 SKJ  C    C  C     0   0.532   4.8611  -31.3004  6.9490
 SKJ  O    O  O     0  -0.440   4.6975  -30.6839  5.9264
 SKJ  CB   C  CH1   0  -0.248   3.1328  -31.6008  8.7776
 SKJ  CG1  C  CH3   0  -0.665   3.4169  -33.0294  9.2292
 SKJ  CG2  C  CH2   0  -0.408   2.0176  -31.5351  7.7321
 SKJ  OXT  O  OH1   0  -0.589   5.4772  -32.4770  6.9920
 SKJ  CAA  C  CH3   0  -0.659  -0.4510  -31.7650  7.2189
 SKJ  CAB  C  CH2   0  -0.426   0.6326  -31.8551  8.2848
 SKJ  H1   H  HNH2  0   0.351   3.8897  -29.1164  9.2102
 SKJ  H2   H  HNH2  0   0.351   4.9668  -28.9113  8.0240
 SKJ  H4   H  HCH1  0   0.249   5.2092  -31.1087  9.0292
 SKJ  H5   H  HCH1  0   0.235   2.7982  -31.0480  9.6644
 SKJ  H6   H  HCH3  0   0.228   4.2245  -33.0640  9.9622
 SKJ  H7   H  HCH3  0   0.233   2.5354  -33.4630  9.7010
 SKJ  H8   H  HCH3  0   0.224   3.6915  -33.6775  8.3967
 SKJ  H9   H  HCH2  0   0.208   2.2423  -32.2313  6.9147
 SKJ  H10  H  HCH2  0   0.226   1.9980  -30.5339  7.2932
 SKJ  HXT  H  HOH1  0   0.478   5.7188  -32.7544  6.0954
 SKJ  H12  H  HCH3  0   0.226  -1.4376  -31.9798  7.6312
 SKJ  H13  H  HCH3  0   0.216  -0.4884  -30.7677  6.7763
 SKJ  H14  H  HCH3  0   0.216  -0.2682  -32.4756  6.4109
 SKJ  H15  H  HCH2  0   0.213   0.4029  -31.1624  9.1005
 SKJ  H16  H  HCH2  0   0.217   0.6220  -32.8559  8.7249

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
 SKJ  O    C    double  1.231  0.020  1.231
 SKJ  OXT  C    single  1.329  0.020  1.329
 SKJ  C    CA   single  1.525  0.021  1.525
 SKJ  CAA  CAB  single  1.523  0.020  1.523
 SKJ  CG2  CAB  single  1.525  0.020  1.525
 SKJ  CG2  CB   single  1.530  0.020  1.530
 SKJ  N    CA   single  1.458  0.019  1.458
 SKJ  CA   CB   single  1.521  0.033  1.521
 SKJ  CB   CG1  single  1.525  0.020  1.525
 SKJ  N    H1   single  0.890  0.020  1.040
 SKJ  N    H2   single  0.890  0.020  1.040
 SKJ  CA   H4   single  0.970  0.020  1.090
 SKJ  CB   H5   single  0.970  0.020  1.090
 SKJ  CG1  H6   single  0.970  0.020  1.090
 SKJ  CG1  H7   single  0.970  0.020  1.090
 SKJ  CG1  H8   single  0.970  0.020  1.090
 SKJ  CG2  H9   single  0.970  0.020  1.090
 SKJ  CG2  H10  single  0.970  0.020  1.090
 SKJ  OXT  HXT  single  0.850  0.020  0.980
 SKJ  CAA  H12  single  0.970  0.020  1.090
 SKJ  CAA  H13  single  0.970  0.020  1.090
 SKJ  CAA  H14  single  0.970  0.020  1.090
 SKJ  CAB  H15  single  0.970  0.020  1.090
 SKJ  CAB  H16  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
 SKJ  H2   N    H1   105.87  3.000
 SKJ  H2   N    CA   110.44  3.000
 SKJ  H1   N    CA   108.49  3.000
 SKJ  H4   CA   CB   107.11  3.000
 SKJ  H4   CA   C    107.08  3.000
 SKJ  CB   CA   C    110.50  1.500
 SKJ  H4   CA   N    113.03  3.000
 SKJ  CB   CA   N    110.40  1.500
 SKJ  C    CA   N    111.00  2.800
 SKJ  OXT  C    O    122.90  3.000
 SKJ  OXT  C    CA   120.80  1.700
 SKJ  O    C    CA   120.80  1.700
 SKJ  H5   CB   CG2  107.96  3.000
 SKJ  H5   CB   CG1  106.82  3.000
 SKJ  CG2  CB   CG1  112.23  3.000
 SKJ  H5   CB   CA   104.11  3.000
 SKJ  CG1  CB   CA   112.92  3.000
 SKJ  CG2  CB   CA   112.19  3.000
 SKJ  H8   CG1  H7   107.33  3.000
 SKJ  H8   CG1  H6   107.91  3.000
 SKJ  H7   CG1  H6   107.18  3.000
 SKJ  H8   CG1  CB   112.19  3.000
 SKJ  H7   CG1  CB   110.50  3.000
 SKJ  H6   CG1  CB   111.50  3.000
 SKJ  H10  CG2  H9   106.60  3.000
 SKJ  H10  CG2  CAB  108.75  3.000
 SKJ  H9   CG2  CAB  108.84  3.000
 SKJ  H10  CG2  CB   109.07  3.000
 SKJ  H9   CG2  CB   109.43  3.000
 SKJ  CAB  CG2  CB   113.90  3.000
 SKJ  HXT  OXT  C    109.82  3.000
 SKJ  H14  CAA  H13  107.49  3.000
 SKJ  H14  CAA  H12  107.65  3.000
 SKJ  H13  CAA  H12  107.59  3.000
 SKJ  H14  CAA  CAB  111.13  3.000
 SKJ  H13  CAA  CAB  111.23  3.000
 SKJ  H12  CAA  CAB  111.56  3.000
 SKJ  H16  CAB  H15  106.10  3.000
 SKJ  H16  CAB  CAA  109.21  3.000
 SKJ  H15  CAB  CAA  109.57  3.000
 SKJ  H16  CAB  CG2  110.28  3.000
 SKJ  H15  CAB  CG2  109.14  3.000
 SKJ  CAA  CAB  CG2  112.34  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
 SKJ  CONST_01  HXT  OXT  C    CA    180.00   0.0  0
 SKJ  Var_01    CAA  CAB  CG2  CB    179.39  30.0  3
 SKJ  Var_02    H12  CAA  CAB  CG2  -179.05  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
 SKJ  chir_01  CA  C    N   CB   negativ
 SKJ  chir_02  CB  CG2  CA  CG1  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
 SKJ  plan-1  CA   0.020
 SKJ  plan-1  C    0.020
 SKJ  plan-1  O    0.020
 SKJ  plan-1  OXT  0.020
 SKJ  plan-1  HXT  0.020

