# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:38:44 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: methyl L-valinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)C(C)C
#
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
 VME  VME  'methyl L-valinate        '  peptide  22  9  .  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_VME
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
 VME  N     N  NH2   0  -0.778   1.0480   1.8503  -0.2746
 VME  CA    C  CH1   0  -0.172   0.5742   0.4833  -0.3602
 VME  C     C  C     0   0.567  -0.8513   0.3394   0.1533
 VME  O     O  O     0  -0.454  -1.2421   0.8223   1.1890
 VME  CB    C  CH1   0  -0.238   1.5036  -0.4594   0.4279
 VME  CG1   C  CH3   0  -0.667   0.9812  -1.8936   0.4573
 VME  CG2   C  CH3   0  -0.650   2.9110  -0.4197  -0.1567
 VME  CM    C  CH3   0  -0.427  -2.9684  -0.6125  -0.2491
 VME  O2    O  O2    0  -0.448  -1.6193  -0.3761  -0.6547
 VME  HN1   H  HNH2  0   0.355   0.4987   2.4537  -0.8735
 VME  HN2   H  HNH2  0   0.344   0.9319   2.1981   0.6696
 VME  HA    H  HCH1  0   0.250   0.5985   0.1786  -1.4107
 VME  HB    H  HCH1  0   0.226   1.5463  -0.0908   1.4597
 VME  HG11  H  HCH3  0   0.236   1.6986  -2.5455   0.9565
 VME  HG12  H  HCH3  0   0.230   0.0382  -1.9904   0.9980
 VME  HG13  H  HCH3  0   0.222   0.8309  -2.2808  -0.5529
 VME  HG21  H  HCH3  0   0.234   3.3052   0.5942  -0.1795
 VME  HG22  H  HCH3  0   0.227   3.5902  -1.0359   0.4340
 VME  HG23  H  HCH3  0   0.213   2.9172  -0.8055  -1.1793
 VME  HMC1  H  HCH3  0   0.238  -3.0124  -1.1367   0.7055
 VME  HMC2  H  HCH3  0   0.240  -3.5294   0.3186  -0.1732
 VME  HMC3  H  HCH3  0   0.251  -3.4080  -1.2355  -1.0223

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
 VME  N    CA    single  1.458  0.019  1.458
 VME  N    HN1   single  0.890  0.020  1.040
 VME  N    HN2   single  0.890  0.020  1.040
 VME  CA   C     single  1.525  0.021  1.525
 VME  CA   CB    single  1.521  0.033  1.521
 VME  CA   HA    single  0.970  0.020  0.970
 VME  C    O     double  1.231  0.020  1.231
 VME  C    O2    single  1.325  0.020  1.325
 VME  CB   CG1   single  1.527  0.020  1.527
 VME  CB   CG2   single  1.524  0.020  1.524
 VME  CB   HB    single  0.970  0.020  1.090
 VME  CG1  HG11  single  0.970  0.020  1.090
 VME  CG1  HG12  single  0.970  0.020  1.090
 VME  CG1  HG13  single  0.970  0.020  1.090
 VME  CG2  HG21  single  0.970  0.020  1.090
 VME  CG2  HG22  single  0.970  0.020  1.090
 VME  CG2  HG23  single  0.970  0.020  1.090
 VME  CM   O2    single  1.429  0.020  1.429
 VME  CM   HMC1  single  0.970  0.020  1.090
 VME  CM   HMC2  single  0.970  0.020  1.090
 VME  CM   HMC3  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
 VME  HN2   N    HN1   106.54  3.000
 VME  HN2   N    CA    109.96  3.000
 VME  HN1   N    CA    110.48  3.000
 VME  HA    CA   CB    109.00  3.000
 VME  HA    CA   C     110.00  3.000
 VME  CB    CA   C     110.50  1.500
 VME  HA    CA   N     110.00  3.000
 VME  CB    CA   N     110.40  1.500
 VME  C     CA   N     111.00  2.800
 VME  O2    C    O     123.47  3.000
 VME  O2    C    CA    112.85  3.000
 VME  O     C    CA    120.80  1.700
 VME  HB    CB   CG2   108.43  3.000
 VME  HB    CB   CG1   108.12  3.000
 VME  CG2   CB   CG1   110.35  3.000
 VME  HB    CB   CA    107.40  3.000
 VME  CG2   CB   CA    110.17  3.000
 VME  CG1   CB   CA    112.23  3.000
 VME  HG13  CG1  HG12  107.93  3.000
 VME  HG13  CG1  HG11  107.58  3.000
 VME  HG12  CG1  HG11  106.78  3.000
 VME  HG13  CG1  CB    111.24  3.000
 VME  HG12  CG1  CB    112.87  3.000
 VME  HG11  CG1  CB    110.20  3.000
 VME  HG23  CG2  HG22  107.69  3.000
 VME  HG23  CG2  HG21  107.89  3.000
 VME  HG22  CG2  HG21  108.18  3.000
 VME  HG23  CG2  CB    110.78  3.000
 VME  HG22  CG2  CB    110.64  3.000
 VME  HG21  CG2  CB    111.51  3.000
 VME  HMC3  CM   HMC2  109.36  3.000
 VME  HMC3  CM   HMC1  109.36  3.000
 VME  HMC2  CM   HMC1  109.22  3.000
 VME  HMC3  CM   O2    105.97  3.000
 VME  HMC2  CM   O2    111.38  3.000
 VME  HMC1  CM   O2    111.49  3.000
 VME  CM    O2   C     117.63  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
 VME  Var_01  HG11  CG1  CB  CA  175.73  30.0  3
 VME  Var_02  HG21  CG2  CB  CA   55.96  30.0  3
 VME  Var_03  HMC1  CM   O2  C   -59.28  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
 VME  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
 VME  plan-1  CA  0.020
 VME  plan-1  C   0.020
 VME  plan-1  O   0.020
 VME  plan-1  O2  0.020

