# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 16:24:13 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: (2S,3R)-2-amino-3,5-dimethylhex-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C=C(C)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
 WVL  WVL  '(2S,3R)-2-amino-3,5-dimethylhex-4-enoic acid'  L-peptide  25  11  .  2016-04-26  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WVL
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
 WVL  C    C  C      0   0.393  -24.1302  12.8577  -3.7557
 WVL  CA   C  CH1    0  -0.139  -23.9318  13.4400  -2.3331
 WVL  O    O  O      0  -0.608  -23.5712  13.4660  -4.6913
 WVL  CB   C  CH1    0  -0.293  -24.5475  14.8470  -2.2541
 WVL  CG2  C  CH3    0  -0.661  -24.3571  15.4826  -0.8743
 WVL  CG1  C  C1     0  -0.229  -26.0116  14.7754  -2.5718
 WVL  CD   C  C      0   0.072  -26.6954  15.4385  -3.5073
 WVL  CE1  C  CH3    0  -0.704  -28.1764  15.2428  -3.6648
 WVL  CE2  C  CH3    0  -0.719  -26.1002  16.4166  -4.4773
 WVL  N    N  NH2    0  -0.817  -22.5050  13.4957  -2.0152
 WVL  OXT  O  OC    -1  -0.608  -24.8327  11.8311  -3.8499
 WVL  H1   H  HCH1   0   0.163  -24.4842  12.7994  -1.6270
 WVL  H2   H  HCH1   0   0.217  -24.0260  15.4638  -2.9897
 WVL  H3   H  HCH3   0   0.222  -23.3026  15.5990  -0.6204
 WVL  H4   H  HCH3   0   0.229  -24.8078  16.4754  -0.8414
 WVL  H5   H  HCH3   0   0.211  -24.8276  14.8806  -0.0926
 WVL  H6   H  H      0   0.211  -26.5749  14.0992  -1.9290
 WVL  H7   H  HCH3   0   0.233  -28.5736  14.5201  -2.9522
 WVL  H8   H  HCH3   0   0.226  -28.7151  16.1842  -3.5264
 WVL  H9   H  HCH3   0   0.227  -28.4209  14.8934  -4.6715
 WVL  H10  H  HCH3   0   0.239  -25.0305  16.5633  -4.3481
 WVL  H11  H  HCH3   0   0.230  -26.2713  16.0889  -5.5061
 WVL  H12  H  HCH3   0   0.229  -26.5843  17.3919  -4.3817
 WVL  H13  H  HNH2   0   0.337  -22.3907  13.6647  -1.0233
 WVL  H14  H  HNH2   0   0.337  -22.0927  12.5836  -2.1709

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
 WVL  O    C    deloc   1.231  0.020  1.231
 WVL  CE2  CD   single  1.501  0.020  1.501
 WVL  OXT  C    deloc   1.248  0.020  1.248
 WVL  C    CA   single  1.525  0.021  1.525
 WVL  CE1  CD   single  1.502  0.020  1.502
 WVL  CD   CG1  double  1.335  0.020  1.335
 WVL  CG1  CB   single  1.500  0.020  1.500
 WVL  CA   CB   single  1.540  0.027  1.540
 WVL  CA   N    single  1.458  0.019  1.458
 WVL  CB   CG2  single  1.531  0.020  1.531
 WVL  CA   H1   single  0.970  0.020  1.090
 WVL  CB   H2   single  0.970  0.020  1.090
 WVL  CG2  H3   single  0.970  0.020  1.090
 WVL  CG2  H4   single  0.970  0.020  1.090
 WVL  CG2  H5   single  0.970  0.020  1.090
 WVL  CG1  H6   single  0.930  0.020  1.080
 WVL  CE1  H7   single  0.970  0.020  1.090
 WVL  CE1  H8   single  0.970  0.020  1.090
 WVL  CE1  H9   single  0.970  0.020  1.090
 WVL  CE2  H10  single  0.970  0.020  1.090
 WVL  CE2  H11  single  0.970  0.020  1.090
 WVL  CE2  H12  single  0.970  0.020  1.090
 WVL  N    H13  single  0.890  0.020  1.040
 WVL  N    H14  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
 WVL  OXT  C    O    126.63  3.000
 WVL  OXT  C    CA   116.78  3.000
 WVL  O    C    CA   120.80  1.700
 WVL  H1   CA   N    111.83  3.000
 WVL  H1   CA   CB   107.36  3.000
 WVL  N    CA   CB   111.50  1.700
 WVL  H1   CA   C    107.80  3.000
 WVL  N    CA   C    111.00  2.800
 WVL  CB   CA   C    111.40  1.900
 WVL  H2   CB   CG1  110.50  3.000
 WVL  H2   CB   CG2  108.24  3.000
 WVL  CG1  CB   CG2  109.40  3.000
 WVL  H2   CB   CA   106.91  3.000
 WVL  CG2  CB   CA   112.11  3.000
 WVL  CG1  CB   CA   109.65  3.000
 WVL  H5   CG2  H4   107.57  3.000
 WVL  H5   CG2  H3   107.96  3.000
 WVL  H4   CG2  H3   107.18  3.000
 WVL  H5   CG2  CB   111.24  3.000
 WVL  H4   CG2  CB   110.71  3.000
 WVL  H3   CG2  CB   111.98  3.000
 WVL  H6   CG1  CD   117.17  3.000
 WVL  H6   CG1  CB   114.15  3.000
 WVL  CD   CG1  CB   128.66  3.000
 WVL  CE2  CD   CE1  114.09  3.000
 WVL  CE1  CD   CG1  120.92  3.000
 WVL  CE2  CD   CG1  125.00  3.000
 WVL  H9   CE1  H8   106.36  3.000
 WVL  H9   CE1  H7   107.97  3.000
 WVL  H8   CE1  H7   107.97  3.000
 WVL  H9   CE1  CD   111.02  3.000
 WVL  H8   CE1  CD   111.12  3.000
 WVL  H7   CE1  CD   112.15  3.000
 WVL  H12  CE2  H11  106.29  3.000
 WVL  H12  CE2  H10  107.75  3.000
 WVL  H11  CE2  H10  107.83  3.000
 WVL  H12  CE2  CD   110.45  3.000
 WVL  H11  CE2  CD   110.54  3.000
 WVL  H10  CE2  CD   113.66  3.000
 WVL  H14  N    H13  104.77  3.000
 WVL  H14  N    CA   109.22  3.000
 WVL  H13  N    CA   109.22  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
 WVL  Var_01  CE2  CD   CG1  CB    0.81   0.0  2
 WVL  Var_02  H10  CE2  CD   CG1  -0.90  30.0  3
 WVL  Var_03  H7   CE1  CD   CG1  -0.47  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
 WVL  chir_01  CA  C    CB  N    positiv
 WVL  chir_02  CB  CG1  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
 WVL  plan-1  C    0.020
 WVL  plan-1  CA   0.020
 WVL  plan-1  O    0.020
 WVL  plan-1  OXT  0.020
 WVL  plan-2  CB   0.020
 WVL  plan-2  CG1  0.020
 WVL  plan-2  CD   0.020
 WVL  plan-2  CE1  0.020
 WVL  plan-2  CE2  0.020
 WVL  plan-2  H6   0.020

