# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 17:47:08 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  22  9  .  2022-03-22  2022-11-17
;
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  -0.598   1.5831   0.6124  -0.1318
 MV9  CA    C  CH1   0  -0.146   0.3218   0.1343   0.3967
 MV9  C     C  C     0   0.519  -0.7795   1.0894  -0.0124
 MV9  O     O  O     0  -0.440  -0.6886   1.9159  -0.8859
 MV9  CB    C  CH1   0  -0.247   0.0320  -1.3020  -0.1085
 MV9  CG1   C  CH3   0  -0.652  -1.0630  -2.0201   0.6724
 MV9  CG2   C  CH3   0  -0.661  -0.2311  -1.3456  -1.6091
 MV9  CN    C  CH3   0  -0.530   2.7388   0.0694   0.5543
 MV9  OXT   O  OH1   0  -0.586  -1.8814   0.9172   0.7066
 MV9  H     H  HNH1  0   0.353   1.6196   1.6209  -0.0704
 MV9  HA    H  HCH1  0   0.244   0.3271   0.0989   1.5002
 MV9  HB    H  HCH1  0   0.244   0.9568  -1.8547   0.0797
 MV9  HG12  H  HCH3  0   0.222  -2.0585  -1.6490   0.4311
 MV9  HG11  H  HCH3  0   0.228  -1.0473  -3.0843   0.4331
 MV9  HG13  H  HCH3  0   0.226  -0.9199  -1.9237   1.7498
 MV9  HG21  H  HCH3  0   0.233   0.5340  -0.8001  -2.1607
 MV9  HG22  H  HCH3  0   0.232  -0.2294  -2.3772  -1.9642
 MV9  HG23  H  HCH3  0   0.216  -1.2052  -0.9207  -1.8631
 MV9  HN2   H  HCH3  0   0.198   2.7011   0.1834   1.6467
 MV9  HN1   H  HCH3  0   0.227   2.8603  -0.9930   0.3411
 MV9  HN3   H  HCH3  0   0.239   3.6357   0.5723   0.1947
 MV9  HXT   H  HOH1  0   0.480  -2.5769   1.5149   0.3928

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  1.450  0.020  1.450
 MV9  N    CA    single  1.458  0.019  1.458
 MV9  O    C     double  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  1.525  0.020  1.525
 MV9  C    OXT   single  1.327  0.020  1.327
 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
 MV9  OXT  HXT   single  0.850  0.020  0.980

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    108.43  3.000
 MV9  H     N    CA    114.00  3.000
 MV9  CN    N    CA    113.45  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     122.96  3.000
 MV9  OXT   C    CA    120.80  1.700
 MV9  O     C    CA    120.80  1.700
 MV9  HB    CB   CG2   107.51  3.000
 MV9  HB    CB   CG1   106.33  3.000
 MV9  CG2   CB   CG1   111.52  3.000
 MV9  HB    CB   CA    104.73  3.000
 MV9  CG1   CB   CA    113.82  3.000
 MV9  CG2   CB   CA    112.31  3.000
 MV9  HG13  CG1  HG11  107.51  3.000
 MV9  HG13  CG1  HG12  107.97  3.000
 MV9  HG11  CG1  HG12  107.27  3.000
 MV9  HG13  CG1  CB    111.71  3.000
 MV9  HG11  CG1  CB    109.68  3.000
 MV9  HG12  CG1  CB    112.48  3.000
 MV9  HG23  CG2  HG22  107.06  3.000
 MV9  HG23  CG2  HG21  108.28  3.000
 MV9  HG22  CG2  HG21  107.91  3.000
 MV9  HG23  CG2  CB    111.82  3.000
 MV9  HG22  CG2  CB    110.31  3.000
 MV9  HG21  CG2  CB    111.28  3.000
 MV9  HN3   CN   HN1   107.07  3.000
 MV9  HN3   CN   HN2   107.97  3.000
 MV9  HN1   CN   HN2   107.41  3.000
 MV9  HN3   CN   N     109.11  3.000
 MV9  HN1   CN   N     111.18  3.000
 MV9  HN2   CN   N     113.84  3.000
 MV9  HXT   OXT  C     109.90  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  CONST_01  HXT   OXT  C   CA  180.00   0.0  0
 MV9  Var_01    HN2   CN   N   CA  -51.79  30.0  3
 MV9  Var_02    HG21  CG2  CB  CA   48.79  30.0  3
 MV9  Var_03    HG12  CG1  CB  CA   74.42  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
 MV9  plan-1  HXT  0.020

