# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 13:53:28 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(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
 DVA  DVA  'D-valine                 '  D-peptide  19  8  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DVA
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
 DVA  N     N  NH2   0  -0.778  -1.8980  -0.2959   0.1972
 DVA  CA    C  CH1   0  -0.164  -0.4572  -0.4137   0.0934
 DVA  CB    C  CH1   0  -0.247   0.2383   0.3863   1.2113
 DVA  CG1   C  CH3   0  -0.646  -0.2170  -0.1068   2.5800
 DVA  CG2   C  CH3   0  -0.665   1.7604   0.3179   1.1090
 DVA  C     C  C     0   0.518   0.0540   0.0568  -1.2612
 DVA  O     O  O     0  -0.447  -0.2855   1.0926  -1.7805
 DVA  OXT   O  OH1   0  -0.589   0.9115  -0.7887  -1.8189
 DVA  H     H  HNH2  0   0.355  -2.3497  -0.8815  -0.4938
 DVA  H2    H  HNH2  0   0.344  -2.1861   0.6553   0.0004
 DVA  HA    H  HCH1  0   0.251  -0.1940  -1.4684   0.2180
 DVA  HB    H  HCH1  0   0.227  -0.0658   1.4340   1.0996
 DVA  HG11  H  HCH3  0   0.226   0.2376   0.4921   3.3703
 DVA  HG12  H  HCH3  0   0.235  -1.2980  -0.0506   2.6898
 DVA  HG13  H  HCH3  0   0.213   0.0849  -1.1451   2.7369
 DVA  HG21  H  HCH3  0   0.222   2.1108  -0.7161   1.1469
 DVA  HG22  H  HCH3  0   0.232   2.1491   0.7709   0.1958
 DVA  HG23  H  HCH3  0   0.236   2.2159   0.8495   1.9452
 DVA  HXT   H  HOH1  0   0.478   1.2231  -0.4383  -2.6679

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
 DVA  N    CA    single  1.458  0.019  1.458
 DVA  N    H     single  0.860  0.020  0.860
 DVA  N    H2    single  0.890  0.020  1.040
 DVA  CA   CB    single  1.521  0.033  1.521
 DVA  CA   C     single  1.525  0.021  1.525
 DVA  CA   HA    single  0.970  0.020  0.970
 DVA  CB   CG1   single  1.524  0.020  1.524
 DVA  CB   CG2   single  1.527  0.020  1.527
 DVA  CB   HB    single  0.970  0.020  1.090
 DVA  CG1  HG11  single  0.970  0.020  1.090
 DVA  CG1  HG12  single  0.970  0.020  1.090
 DVA  CG1  HG13  single  0.970  0.020  1.090
 DVA  CG2  HG21  single  0.970  0.020  1.090
 DVA  CG2  HG22  single  0.970  0.020  1.090
 DVA  CG2  HG23  single  0.970  0.020  1.090
 DVA  C    O     double  1.231  0.020  1.231
 DVA  C    OXT   single  1.327  0.020  1.327
 DVA  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
 DVA  H2    N    H     106.48  3.000
 DVA  H2    N    CA    110.19  3.000
 DVA  H     N    CA    114.00  3.000
 DVA  HA    CA   C     110.00  3.000
 DVA  HA    CA   CB    109.00  3.000
 DVA  C     CA   CB    110.50  1.500
 DVA  HA    CA   N     110.00  3.000
 DVA  C     CA   N     111.00  2.800
 DVA  CB    CA   N     110.40  1.500
 DVA  HB    CB   CG2   108.20  3.000
 DVA  HB    CB   CG1   108.52  3.000
 DVA  CG2   CB   CG1   110.08  3.000
 DVA  HB    CB   CA    107.29  3.000
 DVA  CG2   CB   CA    112.21  3.000
 DVA  CG1   CB   CA    110.41  3.000
 DVA  HG13  CG1  HG12  108.01  3.000
 DVA  HG13  CG1  HG11  107.61  3.000
 DVA  HG12  CG1  HG11  108.21  3.000
 DVA  HG13  CG1  CB    110.72  3.000
 DVA  HG12  CG1  CB    111.76  3.000
 DVA  HG11  CG1  CB    110.39  3.000
 DVA  HG23  CG2  HG22  106.89  3.000
 DVA  HG23  CG2  HG21  107.50  3.000
 DVA  HG22  CG2  HG21  107.93  3.000
 DVA  HG23  CG2  CB    110.07  3.000
 DVA  HG22  CG2  CB    113.12  3.000
 DVA  HG21  CG2  CB    111.09  3.000
 DVA  OXT   C    O     123.20  3.000
 DVA  OXT   C    CA    120.80  1.700
 DVA  O     C    CA    120.80  1.700
 DVA  HXT   OXT  C     110.20  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
 DVA  CONST_01  HXT   OXT  C   CA   180.00   0.0  0
 DVA  Var_01    HG11  CG1  CB  CA  -177.21  30.0  3
 DVA  Var_02    HG21  CG2  CB  CA   -58.01  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
 DVA  chir_01  CA  N  CB  C  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
 DVA  plan-1  CA   0.020
 DVA  plan-1  C    0.020
 DVA  plan-1  O    0.020
 DVA  plan-1  OXT  0.020
 DVA  plan-1  HXT  0.020

