# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:27:30 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2~{R})-3-methyl-2-(methylamino)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](C(C)C)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
 MV9  MV9  '(2~{R})-3-methyl-2-(methylamino)butanoic acid'  D-peptide  21  9  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MV9
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
 MV9  N     N  NH1    0  -0.606   1.6301   0.5052  -0.1606
 MV9  CA    C  CH1    0  -0.177   0.3472   0.0855   0.3736
 MV9  C     C  C      0   0.402  -0.7542   1.1251   0.0508
 MV9  O     O  O      0  -0.606  -0.4050   2.1689  -0.5390
 MV9  CB    C  CH1    0  -0.201   0.0156  -1.3336  -0.1319
 MV9  CG1   C  CH3    0  -0.653  -1.0051  -2.0747   0.7237
 MV9  CG2   C  CH3    0  -0.659  -0.3785  -1.3387  -1.6042
 MV9  CN    C  CH3    0  -0.521   2.7581   0.1260   0.6573
 MV9  OXT   O  OC    -1  -0.602  -1.9089   0.8529   0.4332
 MV9  H     H  HNH1   0   0.335   1.6025   1.5081  -0.2833
 MV9  HA    H  HCH1   0   0.188   0.3909   0.0313   1.4784
 MV9  HB    H  HCH1   0   0.206   0.9520  -1.8992  -0.0508
 MV9  HG12  H  HCH3   0   0.222  -1.9906  -1.6189   0.6593
 MV9  HG11  H  HCH3   0   0.205  -1.0889  -3.1162   0.4055
 MV9  HG13  H  HCH3   0   0.208  -0.7086  -2.0776   1.7754
 MV9  HG21  H  HCH3   0   0.216   0.3476  -0.7881  -2.2041
 MV9  HG22  H  HCH3   0   0.215  -0.4262  -2.3581  -1.9932
 MV9  HG23  H  HCH3   0   0.210  -1.3602  -0.8855  -1.7559
 MV9  HN2   H  HCH3   0   0.183   2.6756   0.4385   1.7099
 MV9  HN1   H  HCH3   0   0.211   2.8924  -0.9582   0.6583
 MV9  HN3   H  HCH3   0   0.223   3.6744   0.5589   0.2531

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
 MV9  CN   N     single  1.444  0.020  1.444
 MV9  N    CA    single  1.458  0.019  1.458
 MV9  O    C     deloc   1.231  0.020  1.231
 MV9  C    CA    single  1.525  0.021  1.525
 MV9  CA   CB    single  1.521  0.033  1.521
 MV9  CB   CG2   single  1.524  0.020  1.524
 MV9  CB   CG1   single  1.524  0.020  1.524
 MV9  C    OXT   deloc   1.247  0.020  1.247
 MV9  N    H     single  0.860  0.020  0.860
 MV9  CA   HA    single  0.970  0.020  0.970
 MV9  CB   HB    single  0.970  0.020  1.090
 MV9  CG1  HG12  single  0.970  0.020  1.090
 MV9  CG1  HG11  single  0.970  0.020  1.090
 MV9  CG1  HG13  single  0.970  0.020  1.090
 MV9  CG2  HG21  single  0.970  0.020  1.090
 MV9  CG2  HG22  single  0.970  0.020  1.090
 MV9  CG2  HG23  single  0.970  0.020  1.090
 MV9  CN   HN2   single  0.970  0.020  1.090
 MV9  CN   HN1   single  0.970  0.020  1.090
 MV9  CN   HN3   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
 MV9  H     N    CN    110.52  3.000
 MV9  H     N    CA    114.00  3.000
 MV9  CN    N    CA    113.95  3.000
 MV9  HA    CA   CB    109.00  3.000
 MV9  HA    CA   C     110.00  3.000
 MV9  CB    CA   C     110.50  1.500
 MV9  HA    CA   N     110.00  3.000
 MV9  CB    CA   N     110.40  1.500
 MV9  C     CA   N     111.00  2.800
 MV9  OXT   C    O     125.91  3.000
 MV9  OXT   C    CA    116.63  3.000
 MV9  O     C    CA    120.80  1.700
 MV9  HB    CB   CG2   106.88  3.000
 MV9  HB    CB   CG1   106.23  3.000
 MV9  CG2   CB   CG1   111.56  3.000
 MV9  HB    CB   CA    105.47  3.000
 MV9  CG1   CB   CA    114.04  3.000
 MV9  CG2   CB   CA    112.04  3.000
 MV9  HG13  CG1  HG11  107.38  3.000
 MV9  HG13  CG1  HG12  107.70  3.000
 MV9  HG11  CG1  HG12  108.23  3.000
 MV9  HG13  CG1  CB    111.09  3.000
 MV9  HG11  CG1  CB    110.57  3.000
 MV9  HG12  CG1  CB    111.70  3.000
 MV9  HG23  CG2  HG22  107.38  3.000
 MV9  HG23  CG2  HG21  108.21  3.000
 MV9  HG22  CG2  HG21  107.72  3.000
 MV9  HG23  CG2  CB    111.42  3.000
 MV9  HG22  CG2  CB    111.00  3.000
 MV9  HG21  CG2  CB    110.94  3.000
 MV9  HN3   CN   HN1   106.91  3.000
 MV9  HN3   CN   HN2   107.72  3.000
 MV9  HN1   CN   HN2   106.86  3.000
 MV9  HN3   CN   N     110.01  3.000
 MV9  HN1   CN   N     110.92  3.000
 MV9  HN2   CN   N     114.11  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
 MV9  Var_01  HN2   CN   N   CA  -53.02  30.0  3
 MV9  Var_02  HG21  CG2  CB  CA   49.58  30.0  3
 MV9  Var_03  HG12  CG1  CB  CA   67.70  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
 MV9  chir_01  CA  N  C  CB  negativ

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
 MV9  plan-1  CA   0.020
 MV9  plan-1  C    0.020
 MV9  plan-1  O    0.020
 MV9  plan-1  OXT  0.020

