# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 10:45:11 2022
#   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  "4-methylisoleucine"  L-peptide  24  10  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.804  7.7373  -29.6932  -40.0387
 SKG  CA   C  CH1    0  -0.159  8.0013  -31.0904  -40.3714
 SKG  C    C  C      0   0.394  8.5673  -31.2230  -41.8047
 SKG  O    O  O      0  -0.602  8.2881  -30.3265  -42.6244
 SKG  CB   C  CH1    0  -0.207  6.6982  -31.8911  -40.1395
 SKG  CG   C  CH1    0  -0.211  6.8951  -33.4200  -40.0051
 SKG  CD1  C  CH3    0  -0.657  5.9265  -33.9880  -38.9681
 SKG  CD2  C  CH3    0  -0.670  6.7574  -34.2051  -41.3073
 SKG  OXT  O  OC    -1  -0.611  9.2694  -32.2338  -42.0241
 SKG  CAE  C  CH3    0  -0.661  5.5931  -31.5175  -41.1219
 SKG  H1   H  HNH2   0   0.326  7.6330  -29.6111  -39.0344
 SKG  H2   H  HNH2   0   0.330  8.5376  -29.1247  -40.2827
 SKG  H4   H  HCH1   0   0.178  8.7530  -31.5292  -39.6957
 SKG  H5   H  HCH1   0   0.202  6.3566  -31.5564  -39.1496
 SKG  H6   H  HCH1   0   0.204  7.9099  -33.5860  -39.6265
 SKG  H7   H  HCH3   0   0.218  6.0743  -33.5299  -37.9884
 SKG  H8   H  HCH3   0   0.211  4.8880  -33.8147  -39.2614
 SKG  H9   H  HCH3   0   0.218  6.0553  -35.0662  -38.8528
 SKG  H10  H  HCH3   0   0.214  7.0228  -35.2521  -41.1451
 SKG  H11  H  HCH3   0   0.205  5.7301  -34.1890  -41.6767
 SKG  H12  H  HCH3   0   0.236  7.4071  -33.8143  -42.0859
 SKG  H14  H  HCH3   0   0.212  4.6535  -32.0093  -40.8616
 SKG  H15  H  HCH3   0   0.220  5.4187  -30.4427  -41.1075
 SKG  H16  H  HCH3   0   0.214  5.8375  -31.7983  -42.1466

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    deloc   1.231  0.020  1.231
 SKG  OXT  C    deloc   1.250  0.020  1.250
 SKG  C    CA   single  1.525  0.021  1.525
 SKG  CD2  CG   single  1.527  0.020  1.527
 SKG  CAE  CB   single  1.525  0.020  1.525
 SKG  CA   N    single  1.458  0.019  1.458
 SKG  CA   CB   single  1.521  0.033  1.521
 SKG  CB   CG   single  1.547  0.020  1.547
 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  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   105.96  3.000
 SKG  H2   N    CA   109.86  3.000
 SKG  H1   N    CA   108.78  3.000
 SKG  H4   CA   CB   106.06  3.000
 SKG  H4   CA   C    106.53  3.000
 SKG  CB   CA   C    110.50  1.500
 SKG  H4   CA   N    111.38  3.000
 SKG  CB   CA   N    110.40  1.500
 SKG  C    CA   N    111.00  2.800
 SKG  OXT  C    O    126.29  3.000
 SKG  OXT  C    CA   120.80  1.700
 SKG  O    C    CA   120.80  1.700
 SKG  H5   CB   CAE  106.28  3.000
 SKG  H5   CB   CG   105.20  3.000
 SKG  CAE  CB   CG   112.96  3.000
 SKG  H5   CB   CA   103.84  3.000
 SKG  CG   CB   CA   114.66  3.000
 SKG  CAE  CB   CA   112.77  3.000
 SKG  H6   CG   CD2  107.47  3.000
 SKG  H6   CG   CD1  107.23  3.000
 SKG  CD2  CG   CD1  109.30  3.000
 SKG  H6   CG   CB   107.31  3.000
 SKG  CD1  CG   CB   110.21  3.000
 SKG  CD2  CG   CB   114.99  3.000
 SKG  H9   CD1  H8   107.27  3.000
 SKG  H9   CD1  H7   107.68  3.000
 SKG  H8   CD1  H7   107.64  3.000
 SKG  H9   CD1  CG   111.34  3.000
 SKG  H8   CD1  CG   111.17  3.000
 SKG  H7   CD1  CG   111.54  3.000
 SKG  H12  CD2  H11  108.35  3.000
 SKG  H12  CD2  H10  107.81  3.000
 SKG  H11  CD2  H10  107.04  3.000
 SKG  H12  CD2  CG   111.86  3.000
 SKG  H11  CD2  CG   111.46  3.000
 SKG  H10  CD2  CG   110.14  3.000
 SKG  H16  CAE  H15  107.61  3.000
 SKG  H16  CAE  H14  107.51  3.000
 SKG  H15  CAE  H14  107.67  3.000
 SKG  H16  CAE  CB   112.33  3.000
 SKG  H15  CAE  CB   110.44  3.000
 SKG  H14  CAE  CB   111.08  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  Var_01  H10  CD2  CG  CB    173.51  30.0  3
 SKG  Var_02  H11  CD2  CG  CB    -67.84  30.0  3
 SKG  Var_03  H12  CD2  CG  CB     53.64  30.0  3
 SKG  Var_04  H7   CD1  CG  CB    -59.25  30.0  3
 SKG  Var_05  H8   CD1  CG  CB     60.90  30.0  3
 SKG  Var_06  H9   CD1  CG  CB   -179.56  30.0  3
 SKG  Var_07  H10  CD2  CG  CD1   -61.94  30.0  3
 SKG  Var_08  H11  CD2  CG  CD1    56.71  30.0  3
 SKG  Var_09  H12  CD2  CG  CD1   178.18  30.0  3
 SKG  Var_10  H7   CD1  CG  CD2   173.46  30.0  3
 SKG  Var_11  H8   CD1  CG  CD2   -66.40  30.0  3
 SKG  Var_12  H9   CD1  CG  CD2    53.15  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

