# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 22:56:58 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: (3R)-3-hydroxy-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](O)[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
 VAH  VAH  (3R)-3-hydroxy-L-norvaline  L-peptide  19  9  .  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_VAH
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
 VAH  C     C  C      0   0.439  24.8733  -1.2078  -10.7332
 VAH  N     N  NH2    0  -0.806  26.9382  -2.1141  -11.7641
 VAH  O     O  O      0  -0.614  23.6234  -1.0648  -10.8246
 VAH  CA    C  CH1    0  -0.258  25.5898  -1.6487  -12.0300
 VAH  CB    C  CH1    0   0.052  24.7848  -2.7216  -12.7897
 VAH  CG2   C  CH2    0  -0.430  24.6432  -4.0281  -12.0105
 VAH  OG1   O  OH1    0  -0.707  23.5319  -2.2013  -13.1752
 VAH  OXT   O  OC    -1  -0.571  25.5564  -0.9874   -9.7239
 VAH  H     H  HNH2   0   0.334  27.5008  -2.0293  -12.6006
 VAH  H2    H  HNH2   0   0.336  27.3579  -1.5164  -11.0650
 VAH  HA    H  HCH1   0   0.214  25.5822  -0.7537  -12.6783
 VAH  HB    H  HCH1   0   0.189  25.3350  -2.9503  -13.7138
 VAH  HD11  H  HCH3   0   0.220  23.8858  -6.0496  -12.2410
 VAH  HD12  H  HCH3   0   0.214  22.9508  -4.8382  -13.1090
 VAH  HD13  H  HCH3   0   0.209  24.5166  -5.3520  -13.7280
 VAH  HG21  H  HCH2   0   0.208  25.6366  -4.3620  -11.7042
 VAH  HG22  H  HCH2   0   0.204  24.0799  -3.8467  -11.0892
 VAH  HOG1  H  HOH1   0   0.426  23.2486  -1.7157  -12.3667
 VAH  CD1   C  CH3    0  -0.661  23.9605  -5.1254  -12.8155

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
 VAH  CA   C     single  1.525  0.021  1.525
 VAH  O    C     deloc   1.231  0.020  1.231
 VAH  C    OXT   deloc   1.239  0.020  1.239
 VAH  CA   N     single  1.458  0.019  1.458
 VAH  N    H     single  0.860  0.020  0.860
 VAH  N    H2    single  0.890  0.020  1.040
 VAH  CB   CA    single  1.540  0.027  1.540
 VAH  CA   HA    single  0.970  0.020  0.970
 VAH  OG1  CB    single  1.410  0.020  1.410
 VAH  CB   CG2   single  1.528  0.020  1.528
 VAH  CB   HB    single  0.970  0.020  1.090
 VAH  CD1  CG2   single  1.523  0.020  1.523
 VAH  CD1  HD11  single  0.970  0.020  1.090
 VAH  CD1  HD12  single  0.970  0.020  1.090
 VAH  CD1  HD13  single  0.970  0.020  1.090
 VAH  CG2  HG21  single  0.970  0.020  1.090
 VAH  CG2  HG22  single  0.970  0.020  1.090
 VAH  OG1  HOG1  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
 VAH  OXT   C    CA    118.60  3.000
 VAH  OXT   C    O     125.84  3.000
 VAH  CA    C    O     120.80  1.700
 VAH  H2    N    H     106.94  3.000
 VAH  H2    N    CA    108.83  3.000
 VAH  H     N    CA    114.00  3.000
 VAH  HA    CA   CB    109.00  3.000
 VAH  HA    CA   N     110.00  3.000
 VAH  CB    CA   N     111.50  1.700
 VAH  HA    CA   C     109.00  3.000
 VAH  CB    CA   C     111.40  1.900
 VAH  N     CA   C     111.00  2.800
 VAH  HB    CB   OG1   106.95  3.000
 VAH  HB    CB   CG2   107.29  3.000
 VAH  OG1   CB   CG2   111.87  3.000
 VAH  HB    CB   CA    107.32  3.000
 VAH  CG2   CB   CA    113.09  3.000
 VAH  OG1   CB   CA    109.99  3.000
 VAH  HG22  CG2  HG21  106.42  3.000
 VAH  HG22  CG2  CD1   109.49  3.000
 VAH  HG21  CG2  CD1   109.63  3.000
 VAH  HG22  CG2  CB    109.58  3.000
 VAH  HG21  CG2  CB    108.68  3.000
 VAH  CD1   CG2  CB    112.84  3.000
 VAH  HOG1  OG1  CB    102.30  3.000
 VAH  HD13  CD1  HD12  107.54  3.000
 VAH  HD13  CD1  HD11  107.40  3.000
 VAH  HD12  CD1  HD11  107.55  3.000
 VAH  HD13  CD1  CG2   111.28  3.000
 VAH  HD12  CD1  CG2   111.58  3.000
 VAH  HD11  CD1  CG2   111.28  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
 VAH  Var_01  HD11  CD1  CG2  CB  179.17  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
 VAH  chir_01  CA  C    N   CB   negativ
 VAH  chir_02  CB  OG1  CA  CG2  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
 VAH  plan-1  C    0.020
 VAH  plan-1  O    0.020
 VAH  plan-1  CA   0.020
 VAH  plan-1  OXT  0.020

