# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:39:05 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: L-valinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)C(N)=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
 VLM  VLM  'L-valinamide             '  L-peptide  20  8  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VLM
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
 VLM  N     N  NH2   0  -0.793  -0.0577   1.8261   0.4409
 VLM  CA    C  CH1   0  -0.182  -0.0994   0.3719   0.4149
 VLM  C     C  C     0   0.526   1.2595  -0.0905  -0.0973
 VLM  O     O  O     0  -0.498   1.6707   0.2689  -1.1929
 VLM  CB    C  CH1   0  -0.249  -1.2216  -0.2517  -0.4370
 VLM  CG1   C  CH3   0  -0.665  -1.1804  -1.7772  -0.3887
 VLM  CG2   C  CH3   0  -0.664  -2.5908   0.2459   0.0155
 VLM  NT    N  NH2   0  -0.798   1.9516  -0.8968   0.7164
 VLM  H     H  HNH2  0   0.342  -0.0382   2.1800  -0.5082
 VLM  H2    H  HNH2  0   0.356  -0.9056   2.1850   0.8602
 VLM  HA    H  HCH1  0   0.238  -0.2341   0.0313   1.4482
 VLM  HB    H  HCH1  0   0.222  -1.0623   0.0664  -1.4740
 VLM  HG11  H  HCH3  0   0.233  -1.9753  -2.2003  -1.0043
 VLM  HG12  H  HCH3  0   0.232  -0.2372  -2.1865  -0.7529
 VLM  HG13  H  HCH3  0   0.218  -1.3280  -2.1402   0.6317
 VLM  HG21  H  HCH3  0   0.226  -2.7030   1.3247  -0.0957
 VLM  HG22  H  HCH3  0   0.234  -3.3804  -0.2202  -0.5753
 VLM  HG23  H  HCH3  0   0.218  -2.7712  -0.0065   1.0632
 VLM  HNT1  H  HNH2  0   0.406   1.6019  -1.1671   1.6186
 VLM  HNT2  H  HNH2  0   0.399   2.8590  -1.2434   0.4480

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
 VLM  N    CA    single  1.458  0.019  1.458
 VLM  N    H     single  0.860  0.020  0.860
 VLM  N    H2    single  0.890  0.020  1.040
 VLM  CA   C     single  1.525  0.021  1.525
 VLM  CA   CB    single  1.521  0.033  1.521
 VLM  CA   HA    single  0.970  0.020  0.970
 VLM  C    O     double  1.231  0.020  1.231
 VLM  C    NT    single  1.338  0.020  1.338
 VLM  CB   CG1   single  1.527  0.020  1.527
 VLM  CB   CG2   single  1.525  0.020  1.525
 VLM  CB   HB    single  0.970  0.020  1.090
 VLM  CG1  HG11  single  0.970  0.020  1.090
 VLM  CG1  HG12  single  0.970  0.020  1.090
 VLM  CG1  HG13  single  0.970  0.020  1.090
 VLM  CG2  HG21  single  0.970  0.020  1.090
 VLM  CG2  HG22  single  0.970  0.020  1.090
 VLM  CG2  HG23  single  0.970  0.020  1.090
 VLM  NT   HNT1  single  0.860  0.020  1.020
 VLM  NT   HNT2  single  0.860  0.020  1.020

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
 VLM  H2    N    H     106.29  3.000
 VLM  H2    N    CA    109.75  3.000
 VLM  H     N    CA    114.00  3.000
 VLM  HA    CA   CB    109.00  3.000
 VLM  HA    CA   C     110.00  3.000
 VLM  CB    CA   C     110.50  1.500
 VLM  HA    CA   N     110.00  3.000
 VLM  CB    CA   N     110.40  1.500
 VLM  C     CA   N     111.00  2.800
 VLM  NT    C    O     123.18  3.000
 VLM  NT    C    CA    116.08  3.000
 VLM  O     C    CA    120.80  1.700
 VLM  HB    CB   CG2   108.44  3.000
 VLM  HB    CB   CG1   108.41  3.000
 VLM  CG2   CB   CG1   109.92  3.000
 VLM  HB    CB   CA    107.44  3.000
 VLM  CG2   CB   CA    110.96  3.000
 VLM  CG1   CB   CA    111.54  3.000
 VLM  HG13  CG1  HG12  107.69  3.000
 VLM  HG13  CG1  HG11  107.44  3.000
 VLM  HG12  CG1  HG11  107.23  3.000
 VLM  HG13  CG1  CB    110.96  3.000
 VLM  HG12  CG1  CB    112.81  3.000
 VLM  HG11  CG1  CB    110.49  3.000
 VLM  HG23  CG2  HG22  107.52  3.000
 VLM  HG23  CG2  HG21  108.02  3.000
 VLM  HG22  CG2  HG21  107.04  3.000
 VLM  HG23  CG2  CB    110.93  3.000
 VLM  HG22  CG2  CB    110.47  3.000
 VLM  HG21  CG2  CB    112.64  3.000
 VLM  HNT2  NT   HNT1  117.39  3.000
 VLM  HNT2  NT   C     120.73  3.000
 VLM  HNT1  NT   C     121.87  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
 VLM  CONST_01  HNT1  NT   C   CA     0.00   0.0  0
 VLM  CONST_02  HNT2  NT   C   CA   180.00   0.0  0
 VLM  Var_01    HG11  CG1  CB  CA  -179.47  30.0  3
 VLM  Var_02    HG21  CG2  CB  CA    61.84  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
 VLM  chir_01  CA  N  C  CB  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
 VLM  plan-1  CA    0.020
 VLM  plan-1  C     0.020
 VLM  plan-1  O     0.020
 VLM  plan-1  NT    0.020
 VLM  plan-1  HNT1  0.020
 VLM  plan-1  HNT2  0.020

