# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 14:17:31 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(N)=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
 CLE  CLE  'L-leucinamide            '  L-peptide  23  9  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CLE
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
 CLE  N     N  NH2   0  -0.788  -1.6220   0.8070  -0.5720
 CLE  CA    C  CH1   0  -0.231  -0.2163   0.4527  -0.5606
 CLE  CB    C  CH2   0  -0.411   0.2135  -0.5285   0.5461
 CLE  CG    C  CH1   0  -0.243  -0.1168  -0.0794   1.9696
 CLE  CD1   C  CH3   0  -0.647   0.2759  -1.1717   2.9596
 CLE  CD2   C  CH3   0  -0.660   0.5610   1.2393   2.3299
 CLE  C     C  C     0   0.525   0.1383  -0.1787  -1.9009
 CLE  O     O  O     0  -0.494  -0.6485  -0.9005  -2.4974
 CLE  N2    N  NH2   0  -0.799   1.3786   0.0738  -2.3410
 CLE  H2    H  HNH2  0   0.352  -1.8654   1.2599   0.2996
 CLE  H     H  HNH2  0   0.341  -2.1864  -0.0330  -0.6229
 CLE  HA    H  HCH1  0   0.252   0.3561   1.3789  -0.4491
 CLE  HB2   H  HCH2  0   0.220   1.2937  -0.7001   0.4724
 CLE  HB3   H  HCH2  0   0.229  -0.2659  -1.4956   0.3566
 CLE  HG    H  HCH1  0   0.211  -1.2014   0.0587   2.0468
 CLE  HD11  H  HCH3  0   0.226  -0.0006  -0.8986   3.9793
 CLE  HD12  H  HCH3  0   0.225  -0.2150  -2.1177   2.7235
 CLE  HD13  H  HCH3  0   0.214   1.3546  -1.3448   2.9431
 CLE  HD21  H  HCH3  0   0.216   1.6465   1.1586   2.2296
 CLE  HD22  H  HCH3  0   0.228   0.2325   2.0648   1.6961
 CLE  HD23  H  HCH3  0   0.230   0.3446   1.5199   3.3621
 CLE  HN21  H  HNH2  0   0.399   1.7283  -0.3706  -3.1743
 CLE  HN22  H  HNH2  0   0.406   2.0047   0.6839  -1.8450

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
 CLE  N    CA    single  1.458  0.019  1.458
 CLE  N    H2    single  0.890  0.020  1.040
 CLE  N    H     single  0.860  0.020  0.860
 CLE  CA   CB    single  1.530  0.020  1.530
 CLE  CA   C     single  1.525  0.021  1.525
 CLE  CA   HA    single  0.970  0.020  0.970
 CLE  CB   CG    single  1.529  0.020  1.529
 CLE  CB   HB2   single  0.970  0.020  1.090
 CLE  CB   HB3   single  0.970  0.020  1.090
 CLE  CG   CD1   single  1.526  0.020  1.526
 CLE  CG   CD2   single  1.526  0.020  1.526
 CLE  CG   HG    single  0.970  0.020  1.090
 CLE  CD1  HD11  single  0.970  0.020  1.090
 CLE  CD1  HD12  single  0.970  0.020  1.090
 CLE  CD1  HD13  single  0.970  0.020  1.090
 CLE  CD2  HD21  single  0.970  0.020  1.090
 CLE  CD2  HD22  single  0.970  0.020  1.090
 CLE  CD2  HD23  single  0.970  0.020  1.090
 CLE  C    O     double  1.231  0.020  1.231
 CLE  C    N2    single  1.340  0.020  1.340
 CLE  N2   HN21  single  0.860  0.020  1.020
 CLE  N2   HN22  single  0.860  0.020  1.020

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
 CLE  H     N    H2    106.28  3.000
 CLE  H     N    CA    114.00  3.000
 CLE  H2    N    CA    109.62  3.000
 CLE  HA    CA   C     109.00  3.000
 CLE  HA    CA   CB    109.00  3.000
 CLE  C     CA   CB    110.10  1.900
 CLE  HA    CA   N     110.00  3.000
 CLE  C     CA   N     111.00  2.800
 CLE  CB    CA   N     110.50  1.700
 CLE  HB3   CB   HB2   106.34  3.000
 CLE  HB3   CB   CG    109.01  3.000
 CLE  HB2   CB   CG    108.75  3.000
 CLE  HB3   CB   CA    108.42  3.000
 CLE  HB2   CB   CA    109.05  3.000
 CLE  CG    CB   CA    114.93  3.000
 CLE  HG    CG   CD2   108.31  3.000
 CLE  HG    CG   CD1   107.41  3.000
 CLE  CD2   CG   CD1   110.56  3.000
 CLE  HG    CG   CB    108.44  3.000
 CLE  CD2   CG   CB    112.20  3.000
 CLE  CD1   CG   CB    109.77  3.000
 CLE  HD13  CD1  HD12  107.67  3.000
 CLE  HD13  CD1  HD11  107.69  3.000
 CLE  HD12  CD1  HD11  107.76  3.000
 CLE  HD13  CD1  CG    110.96  3.000
 CLE  HD12  CD1  CG    111.37  3.000
 CLE  HD11  CD1  CG    111.22  3.000
 CLE  HD23  CD2  HD22  107.16  3.000
 CLE  HD23  CD2  HD21  107.62  3.000
 CLE  HD22  CD2  HD21  107.55  3.000
 CLE  HD23  CD2  CG    110.94  3.000
 CLE  HD22  CD2  CG    112.52  3.000
 CLE  HD21  CD2  CG    110.83  3.000
 CLE  N2    C    O     123.13  3.000
 CLE  N2    C    CA    115.23  3.000
 CLE  O     C    CA    120.80  1.700
 CLE  HN22  N2   HN21  117.38  3.000
 CLE  HN22  N2   C     121.93  3.000
 CLE  HN21  N2   C     120.66  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
 CLE  CONST_01  HN21  N2   C   CA   180.00   0.0  0
 CLE  CONST_02  HN22  N2   C   CA     0.00   0.0  0
 CLE  Var_01    CD1   CG   CB  CA   176.37  30.0  3
 CLE  Var_02    HD11  CD1  CG  CB  -176.84  30.0  3
 CLE  Var_03    HD21  CD2  CG  CB   -58.20  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
 CLE  chir_01  CA  N  CB  C  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
 CLE  plan-1  CA    0.020
 CLE  plan-1  C     0.020
 CLE  plan-1  O     0.020
 CLE  plan-1  N2    0.020
 CLE  plan-1  HN21  0.020
 CLE  plan-1  HN22  0.020

