# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:44:10 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: D-isoleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](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
 DIL  DIL  'D-isoleucine             '  D-peptide  21  9  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DIL
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
 DIL  N     N  NH2    0  -0.800   1.6689  -1.4250  2.1926
 DIL  CA    C  CH1    0  -0.195   2.2315  -1.1453  3.5131
 DIL  C     C  C      0   0.388   2.9703   0.2140  3.6030
 DIL  O     O  O      0  -0.607   3.8691   0.3119  4.4635
 DIL  CB    C  CH1    0  -0.201   1.1186  -1.2655  4.5766
 DIL  CG1   C  CH2    0  -0.406   1.6614  -1.3189  6.0067
 DIL  CG2   C  CH3    0  -0.671   0.0459  -0.1901  4.4210
 DIL  CD1   C  CH3    0  -0.667   0.6283  -1.7626  7.0357
 DIL  OXT   O  OC    -1  -0.606   2.5949   1.1087  2.8155
 DIL  H     H  HNH2   0   0.324   1.3156  -0.5470  1.8278
 DIL  H2    H  HNH2   0   0.330   2.4283  -1.6640  1.5655
 DIL  HA    H  HCH1   0   0.202   2.9539  -1.9394  3.7316
 DIL  HB    H  HCH1   0   0.196   0.6438  -2.2347  4.3760
 DIL  HG12  H  HCH2   0   0.207   2.0632  -0.3433  6.2890
 DIL  HG13  H  HCH2   0   0.205   2.5084  -2.0110  6.0365
 DIL  HG21  H  HCH3   0   0.220  -0.3340  -0.1413  3.3997
 DIL  HG22  H  HCH3   0   0.210   0.4283   0.7985  4.6819
 DIL  HG23  H  HCH3   0   0.221  -0.8102  -0.3901  5.0664
 DIL  HD11  H  HCH3   0   0.217  -0.1931  -1.0510  7.1275
 DIL  HD12  H  HCH3   0   0.223   1.0784  -1.8635  8.0243
 DIL  HD13  H  HCH3   0   0.211   0.1962  -2.7299  6.7709

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
 DIL  N    CA    single  1.458  0.019  1.458
 DIL  N    H     single  0.860  0.020  0.860
 DIL  N    H2    single  0.890  0.020  1.040
 DIL  CA   C     single  1.525  0.021  1.525
 DIL  CA   CB    single  1.521  0.033  1.521
 DIL  CA   HA    single  0.970  0.020  0.970
 DIL  C    O     deloc   1.231  0.020  1.231
 DIL  C    OXT   deloc   1.250  0.020  1.250
 DIL  CB   CG1   single  1.531  0.020  1.531
 DIL  CB   CG2   single  1.527  0.020  1.527
 DIL  CB   HB    single  0.970  0.020  1.090
 DIL  CG1  CD1   single  1.524  0.020  1.524
 DIL  CG1  HG12  single  0.970  0.020  1.090
 DIL  CG1  HG13  single  0.970  0.020  1.090
 DIL  CG2  HG21  single  0.970  0.020  1.090
 DIL  CG2  HG22  single  0.970  0.020  1.090
 DIL  CG2  HG23  single  0.970  0.020  1.090
 DIL  CD1  HD11  single  0.970  0.020  1.090
 DIL  CD1  HD12  single  0.970  0.020  1.090
 DIL  CD1  HD13  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
 DIL  H2    N    H     104.04  3.000
 DIL  H2    N    CA    108.39  3.000
 DIL  H     N    CA    114.00  3.000
 DIL  HA    CA   CB    109.00  3.000
 DIL  HA    CA   C     110.00  3.000
 DIL  CB    CA   C     110.50  1.500
 DIL  HA    CA   N     110.00  3.000
 DIL  CB    CA   N     110.40  1.500
 DIL  C     CA   N     111.00  2.800
 DIL  OXT   C    O     126.49  3.000
 DIL  OXT   C    CA    120.80  1.700
 DIL  O     C    CA    120.80  1.700
 DIL  HB    CB   CG2   107.42  3.000
 DIL  HB    CB   CG1   107.06  3.000
 DIL  CG2   CB   CG1   111.65  3.000
 DIL  HB    CB   CA    104.75  3.000
 DIL  CG2   CB   CA    112.41  3.000
 DIL  CG1   CB   CA    112.99  3.000
 DIL  HG13  CG1  HG12  105.86  3.000
 DIL  HG13  CG1  CD1   108.79  3.000
 DIL  HG12  CG1  CD1   109.56  3.000
 DIL  HG13  CG1  CB    108.79  3.000
 DIL  HG12  CG1  CB    109.93  3.000
 DIL  CD1   CG1  CB    113.61  3.000
 DIL  HG23  CG2  HG22  107.44  3.000
 DIL  HG23  CG2  HG21  106.79  3.000
 DIL  HG22  CG2  HG21  107.77  3.000
 DIL  HG23  CG2  CB    111.22  3.000
 DIL  HG22  CG2  CB    111.55  3.000
 DIL  HG21  CG2  CB    111.81  3.000
 DIL  HD13  CD1  HD12  107.52  3.000
 DIL  HD13  CD1  HD11  107.47  3.000
 DIL  HD12  CD1  HD11  107.14  3.000
 DIL  HD13  CD1  CG1   111.25  3.000
 DIL  HD12  CD1  CG1   111.05  3.000
 DIL  HD11  CD1  CG1   112.18  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
 DIL  Var_01  HD11  CD1  CG1  CB  -64.72  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
 DIL  chir_01  CA  N   C    CB   negativ
 DIL  chir_02  CB  CA  CG1  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
 DIL  plan-1  CA   0.020
 DIL  plan-1  C    0.020
 DIL  plan-1  O    0.020
 DIL  plan-1  OXT  0.020

