# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:42:08 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 5-amino-D-isoleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCN)[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
 MD0  MD0  '5-amino-D-isoleucine     '  D-peptide  23  10  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MD0
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
 MD0  C     C  C      0   0.401  49.6484  42.5268   1.8756
 MD0  N     N  NH2    0  -0.810  49.3253  41.8764  -0.4747
 MD0  OXT   O  OC     0  -0.604  50.4885  42.9340   2.7024
 MD0  CA    C  CH1    0  -0.161  50.1869  41.6959   0.6861
 MD0  CB    C  CH1    0  -0.253  50.3845  40.2086   1.0733
 MD0  NE    N  NH2    0  -0.798  53.1658  38.4125   2.9936
 MD0  CG    C  CH2    0  -0.413  51.5671  39.9953   2.0177
 MD0  CG2   C  CH3    0  -0.664  49.1058  39.5636   1.6029
 MD0  O     O  O     -1  -0.604  48.4131  42.7047   1.9248
 MD0  HN    H  HNH2   0   0.324  49.4363  41.0995  -1.1155
 MD0  HNA   H  HNH2   0   0.329  48.3641  41.8612  -0.1574
 MD0  HA    H  HCH1   0   0.192  51.1825  42.0823   0.4345
 MD0  HB    H  HCH1   0   0.202  50.6399  39.7011   0.1314
 MD0  HD    H  HCH2   0   0.211  51.1720  37.9730   2.6506
 MD0  HDA   H  HCH2   0   0.181  52.0900  38.0955   1.1624
 MD0  HNE   H  HNH2   0   0.341  53.4095  37.4350   3.0915
 MD0  HNEA  H  HNH2   0   0.333  53.9487  38.8399   2.5136
 MD0  HG    H  HCH2   0   0.205  52.4281  40.5561   1.6349
 MD0  HGA   H  HCH2   0   0.211  51.3466  40.4092   3.0044
 MD0  HG2   H  HCH3   0   0.221  49.1981  38.4779   1.6484
 MD0  HG2A  H  HCH3   0   0.212  48.8672  39.9155   2.6080
 MD0  HG2B  H  HCH3   0   0.216  48.2530  39.7850   0.9601
 MD0  CD    C  CH2    0  -0.273  51.9735  38.5353   2.1650

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
 MD0  CA   C     single  1.525  0.021  1.525
 MD0  C    O     deloc   1.231  0.020  1.231
 MD0  C    OXT   deloc   1.247  0.020  1.247
 MD0  N    CA    single  1.458  0.019  1.458
 MD0  N    HN    single  0.890  0.020  1.040
 MD0  N    HNA   single  0.890  0.020  1.040
 MD0  CA   CB    single  1.521  0.033  1.521
 MD0  CA   HA    single  0.970  0.020  0.970
 MD0  CB   CG2   single  1.527  0.020  1.527
 MD0  CB   CG    single  1.528  0.020  1.528
 MD0  CB   HB    single  0.970  0.020  1.090
 MD0  CG   CD    single  1.523  0.020  1.523
 MD0  CD   NE    single  1.457  0.020  1.457
 MD0  CD   HD    single  0.970  0.020  1.090
 MD0  CD   HDA   single  0.970  0.020  1.090
 MD0  NE   HNE   single  0.890  0.020  1.040
 MD0  NE   HNEA  single  0.890  0.020  1.040
 MD0  CG   HG    single  0.970  0.020  1.090
 MD0  CG   HGA   single  0.970  0.020  1.090
 MD0  CG2  HG2   single  0.970  0.020  1.090
 MD0  CG2  HG2A  single  0.970  0.020  1.090
 MD0  CG2  HG2B  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
 MD0  O     C    CA    120.80  1.700
 MD0  O     C    OXT   126.42  3.000
 MD0  CA    C    OXT   120.80  1.700
 MD0  HNA   N    HN    106.90  3.000
 MD0  HNA   N    CA    108.05  3.000
 MD0  HN    N    CA    110.13  3.000
 MD0  HA    CA   CB    109.00  3.000
 MD0  HA    CA   N     110.00  3.000
 MD0  CB    CA   N     110.40  1.500
 MD0  HA    CA   C     110.00  3.000
 MD0  CB    CA   C     110.50  1.500
 MD0  N     CA   C     111.00  2.800
 MD0  HB    CB   CG2   107.25  3.000
 MD0  HB    CB   CG    106.56  3.000
 MD0  CG2   CB   CG    112.01  3.000
 MD0  HB    CB   CA    104.98  3.000
 MD0  CG    CB   CA    112.77  3.000
 MD0  CG2   CB   CA    112.67  3.000
 MD0  HNEA  NE   HNE   105.50  3.000
 MD0  HNEA  NE   CD    109.11  3.000
 MD0  HNE   NE   CD    109.48  3.000
 MD0  HGA   CG   HG    106.26  3.000
 MD0  HGA   CG   CD    109.25  3.000
 MD0  HG    CG   CD    108.34  3.000
 MD0  HGA   CG   CB    110.43  3.000
 MD0  HG    CG   CB    108.70  3.000
 MD0  CD    CG   CB    113.58  3.000
 MD0  HG2B  CG2  HG2A  107.84  3.000
 MD0  HG2B  CG2  HG2   107.03  3.000
 MD0  HG2A  CG2  HG2   107.52  3.000
 MD0  HG2B  CG2  CB    111.39  3.000
 MD0  HG2A  CG2  CB    111.49  3.000
 MD0  HG2   CG2  CB    111.35  3.000
 MD0  HDA   CD   HD    106.06  3.000
 MD0  HDA   CD   CG    108.85  3.000
 MD0  HD    CD   CG    109.92  3.000
 MD0  HDA   CD   NE    113.43  3.000
 MD0  HD    CD   NE    107.70  3.000
 MD0  CG    CD   NE    110.74  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
 MD0  Var_01  NE   CD  CG  CB  175.62  30.0  3
 MD0  Var_02  HNE  NE  CD  CG  179.06  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
 MD0  chir_01  CA  C   N    CB  positiv
 MD0  chir_02  CB  CA  CG2  CG  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
 MD0  plan-1  C    0.020
 MD0  plan-1  OXT  0.020
 MD0  plan-1  CA   0.020
 MD0  plan-1  O    0.020

