# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:43:57 2021
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{S},3~{S})-2-azanyl-3,4-dimethyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[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
 SKG  SKG  '(2~{S},3~{S})-2-azanyl-3,4-dimethyl-pentanoic 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_SKG
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
 SKG  N    N  NH2   0  -0.796  7.7345  -29.6444  -40.1906
 SKG  CA   C  CH1   0  -0.163  8.0089  -31.0613  -40.3406
 SKG  C    C  C     0   0.536  8.6069  -31.2903  -41.7147
 SKG  O    O  O     0  -0.436  8.2941  -30.6955  -42.7148
 SKG  CB   C  CH1   0  -0.245  6.7071  -31.8680  -40.1144
 SKG  CG   C  CH1   0  -0.229  6.9284  -33.3971  -40.0617
 SKG  CD1  C  CH3   0  -0.658  5.9802  -34.0298  -39.0437
 SKG  CD2  C  CH3   0  -0.669  6.7784  -34.1119  -41.4043
 SKG  OXT  O  OH1   0  -0.595  9.5452  -32.2337  -41.6988
 SKG  CAE  C  CH3   0  -0.661  5.5714  -31.4569  -41.0444
 SKG  H1   H  HNH2  0   0.351  7.3165  -29.4930  -39.2804
 SKG  H2   H  HNH2  0   0.352  8.6026  -29.1229  -40.1796
 SKG  H4   H  HCH1  0   0.244  8.7327  -31.4357  -39.6035
 SKG  H5   H  HCH1  0   0.238  6.4103  -31.5715  -39.1001
 SKG  H6   H  HCH1  0   0.225  7.9486  -33.5720  -39.7026
 SKG  H7   H  HCH3  0   0.226  6.1573  -33.6403  -38.0398
 SKG  H8   H  HCH3  0   0.217  4.9357  -33.8330  -39.2973
 SKG  H9   H  HCH3  0   0.226  6.1086  -35.1130  -39.0063
 SKG  H10  H  HCH3  0   0.231  7.0816  -35.1554  -41.3036
 SKG  H11  H  HCH3  0   0.220  5.7409  -34.1082  -41.7431
 SKG  H12  H  HCH3  0   0.226  7.3828  -33.6790  -42.2005
 SKG  HXT  H  HOH1  0   0.476  9.8863  -32.3757  -42.5949
 SKG  H14  H  HCH3  0   0.226  4.6468  -31.9611  -40.7593
 SKG  H15  H  HCH3  0   0.235  5.3905  -30.3848  -40.9892
 SKG  H16  H  HCH3  0   0.224  5.7697  -31.7055  -42.0867

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
 SKG  O    C    double  1.231  0.020  1.231
 SKG  OXT  C    single  1.331  0.020  1.331
 SKG  C    CA   single  1.525  0.021  1.525
 SKG  CD2  CG   single  1.528  0.020  1.528
 SKG  CAE  CB   single  1.524  0.020  1.524
 SKG  CA   N    single  1.458  0.019  1.458
 SKG  CA   CB   single  1.521  0.033  1.521
 SKG  CB   CG   single  1.546  0.020  1.546
 SKG  CG   CD1  single  1.528  0.020  1.528
 SKG  N    H1   single  0.890  0.020  1.040
 SKG  N    H2   single  0.890  0.020  1.040
 SKG  CA   H4   single  0.970  0.020  1.090
 SKG  CB   H5   single  0.970  0.020  1.090
 SKG  CG   H6   single  0.970  0.020  1.090
 SKG  CD1  H7   single  0.970  0.020  1.090
 SKG  CD1  H8   single  0.970  0.020  1.090
 SKG  CD1  H9   single  0.970  0.020  1.090
 SKG  CD2  H10  single  0.970  0.020  1.090
 SKG  CD2  H11  single  0.970  0.020  1.090
 SKG  CD2  H12  single  0.970  0.020  1.090
 SKG  OXT  HXT  single  0.850  0.020  0.980
 SKG  CAE  H14  single  0.970  0.020  1.090
 SKG  CAE  H15  single  0.970  0.020  1.090
 SKG  CAE  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
 SKG  H2   N    H1   105.49  3.000
 SKG  H2   N    CA   109.99  3.000
 SKG  H1   N    CA   108.47  3.000
 SKG  H4   CA   CB   106.16  3.000
 SKG  H4   CA   C    107.26  3.000
 SKG  CB   CA   C    110.50  1.500
 SKG  H4   CA   N    112.82  3.000
 SKG  CB   CA   N    110.40  1.500
 SKG  C    CA   N    111.00  2.800
 SKG  OXT  C    O    122.89  3.000
 SKG  OXT  C    CA   120.80  1.700
 SKG  O    C    CA   120.80  1.700
 SKG  H5   CB   CAE  106.82  3.000
 SKG  H5   CB   CG   105.93  3.000
 SKG  CAE  CB   CG   113.22  3.000
 SKG  H5   CB   CA   102.81  3.000
 SKG  CG   CB   CA   113.58  3.000
 SKG  CAE  CB   CA   113.38  3.000
 SKG  H6   CG   CD2  107.74  3.000
 SKG  H6   CG   CD1  107.06  3.000
 SKG  CD2  CG   CD1  109.30  3.000
 SKG  H6   CG   CB   107.60  3.000
 SKG  CD1  CG   CB   110.08  3.000
 SKG  CD2  CG   CB   114.75  3.000
 SKG  H9   CD1  H8   107.41  3.000
 SKG  H9   CD1  H7   107.67  3.000
 SKG  H8   CD1  H7   107.72  3.000
 SKG  H9   CD1  CG   111.14  3.000
 SKG  H8   CD1  CG   111.34  3.000
 SKG  H7   CD1  CG   111.36  3.000
 SKG  H12  CD2  H11  107.41  3.000
 SKG  H12  CD2  H10  107.06  3.000
 SKG  H11  CD2  H10  107.22  3.000
 SKG  H12  CD2  CG   113.69  3.000
 SKG  H11  CD2  CG   111.37  3.000
 SKG  H10  CD2  CG   109.81  3.000
 SKG  HXT  OXT  C    109.93  3.000
 SKG  H16  CAE  H15  107.66  3.000
 SKG  H16  CAE  H14  107.38  3.000
 SKG  H15  CAE  H14  107.52  3.000
 SKG  H16  CAE  CB   112.73  3.000
 SKG  H15  CAE  CB   111.01  3.000
 SKG  H14  CAE  CB   110.32  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
 SKG  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 SKG  Var_01    H10  CD2  CG  CB  172.36  30.0  3
 SKG  Var_02    H7   CD1  CG  CB  -61.04  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
 SKG  chir_01  CA  C    N   CB  negativ
 SKG  chir_02  CB  CAE  CA  CG  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
 SKG  plan-1  CA   0.020
 SKG  plan-1  C    0.020
 SKG  plan-1  O    0.020
 SKG  plan-1  OXT  0.020
 SKG  plan-1  HXT  0.020

