# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:08:58 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: D-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)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
 DLE  DLE  'D-leucine                '  D-peptide  21  9  .  2022-07-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_DLE
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
 DLE  N     N  NH2    0  -0.786   1.5345   0.9496  -0.4785
 DLE  CA    C  CH1    0  -0.219   0.1771   0.4287  -0.5396
 DLE  CB    C  CH2    0  -0.401  -0.0545  -0.5571   0.6101
 DLE  CG    C  CH1    0  -0.217   0.1805  -0.0033   2.0160
 DLE  CD1   C  CH3    0  -0.660  -0.7660   1.1474   2.3414
 DLE  CD2   C  CH3    0  -0.650   0.0399  -1.1197   3.0470
 DLE  C     C  C      0   0.388  -0.2092  -0.2609  -1.8710
 DLE  O     O  O      0  -0.610   0.7136  -0.5848  -2.6453
 DLE  OXT   O  OC    -1  -0.626  -1.4299  -0.4605  -2.0495
 DLE  H     H  HNH2   0   0.332   1.6421   1.6680  -1.1848
 DLE  H2    H  HNH2   0   0.321   2.1617   0.2106  -0.7773
 DLE  HA    H  HCH1   0   0.210  -0.5072   1.2739  -0.4085
 DLE  HB2   H  HCH2   0   0.205   0.6039  -1.4229   0.4600
 DLE  HB3   H  HCH2   0   0.208  -1.0785  -0.9379   0.5458
 DLE  HG    H  HCH1   0   0.208   1.2055   0.3762   2.0629
 DLE  HD11  H  HCH3   0   0.220  -0.6043   1.5175   3.3559
 DLE  HD12  H  HCH3   0   0.225  -0.6322   1.9910   1.6631
 DLE  HD13  H  HCH3   0   0.207  -1.8088   0.8256   2.2692
 DLE  HD21  H  HCH3   0   0.208  -0.9707  -1.5369   3.0396
 DLE  HD22  H  HCH3   0   0.219   0.7342  -1.9376   2.8437
 DLE  HD23  H  HCH3   0   0.220   0.2393  -0.7586   4.0577

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
 DLE  N    CA    single  1.458  0.019  1.458
 DLE  N    H     single  0.860  0.020  0.860
 DLE  N    H2    single  0.890  0.020  1.040
 DLE  CA   CB    single  1.521  0.033  1.521
 DLE  CA   C     single  1.525  0.021  1.525
 DLE  CA   HA    single  0.970  0.020  0.970
 DLE  CB   CG    single  1.529  0.020  1.529
 DLE  CB   HB2   single  0.970  0.020  1.090
 DLE  CB   HB3   single  0.970  0.020  1.090
 DLE  CG   CD1   single  1.525  0.020  1.525
 DLE  CG   CD2   single  1.526  0.020  1.526
 DLE  CG   HG    single  0.970  0.020  1.090
 DLE  CD1  HD11  single  0.970  0.020  1.090
 DLE  CD1  HD12  single  0.970  0.020  1.090
 DLE  CD1  HD13  single  0.970  0.020  1.090
 DLE  CD2  HD21  single  0.970  0.020  1.090
 DLE  CD2  HD22  single  0.970  0.020  1.090
 DLE  CD2  HD23  single  0.970  0.020  1.090
 DLE  C    O     deloc   1.231  0.020  1.231
 DLE  C    OXT   deloc   1.250  0.020  1.250

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
 DLE  H2    N    H     104.22  3.000
 DLE  H2    N    CA    107.67  3.000
 DLE  H     N    CA    114.00  3.000
 DLE  HA    CA   C     110.00  3.000
 DLE  HA    CA   CB    109.00  3.000
 DLE  C     CA   CB    110.50  1.500
 DLE  HA    CA   N     110.00  3.000
 DLE  C     CA   N     111.00  2.800
 DLE  CB    CA   N     110.40  1.500
 DLE  HB3   CB   HB2   106.18  3.000
 DLE  HB3   CB   CG    108.90  3.000
 DLE  HB2   CB   CG    108.61  3.000
 DLE  HB3   CB   CA    108.74  3.000
 DLE  HB2   CB   CA    108.31  3.000
 DLE  CG    CB   CA    115.70  3.000
 DLE  HG    CG   CD2   108.12  3.000
 DLE  HG    CG   CD1   108.10  3.000
 DLE  CD2   CG   CD1   110.53  3.000
 DLE  HG    CG   CB    108.00  3.000
 DLE  CD2   CG   CB    110.00  3.000
 DLE  CD1   CG   CB    111.96  3.000
 DLE  HD13  CD1  HD12  107.66  3.000
 DLE  HD13  CD1  HD11  107.59  3.000
 DLE  HD12  CD1  HD11  107.31  3.000
 DLE  HD13  CD1  CG    110.83  3.000
 DLE  HD12  CD1  CG    112.01  3.000
 DLE  HD11  CD1  CG    111.23  3.000
 DLE  HD23  CD2  HD22  107.70  3.000
 DLE  HD23  CD2  HD21  107.54  3.000
 DLE  HD22  CD2  HD21  107.50  3.000
 DLE  HD23  CD2  CG    111.51  3.000
 DLE  HD22  CD2  CG    111.32  3.000
 DLE  HD21  CD2  CG    111.08  3.000
 DLE  OXT   C    O     126.33  3.000
 DLE  OXT   C    CA    120.80  1.700
 DLE  O     C    CA    120.80  1.700

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
 DLE  Var_01  CD1   CG   CB  CA   61.89  30.0  3
 DLE  Var_02  HD11  CD1  CG  CB  178.62  30.0  3
 DLE  Var_03  HD21  CD2  CG  CB  -62.16  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
 DLE  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
 DLE  plan-1  CA   0.020
 DLE  plan-1  C    0.020
 DLE  plan-1  O    0.020
 DLE  plan-1  OXT  0.020

