# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:51:48 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: methyl L-leucinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)CC(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
 MLL  MLL  'methyl L-leucinate       '  L-peptide  25  10  .  2019-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MLL
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
 MLL  N     N  NH2   0  -0.808  144.0022  236.9873  103.3489
 MLL  CA    C  CH1   0  -0.212  144.7675  236.2456  104.3537
 MLL  CB    C  CH2   0  -0.425  143.9726  236.0682  105.6467
 MLL  CG    C  CH1   0  -0.233  144.2308  237.1464  106.7034
 MLL  CD2   C  CH3   0  -0.650  143.4191  236.8413  107.9584
 MLL  CD1   C  CH3   0  -0.679  143.9439  238.5649  106.2200
 MLL  C     C  C     0   0.618  145.0755  234.9091  103.6955
 MLL  O     O  O     0  -0.443  144.4817  233.8784  103.8850
 MLL  O9    O  O2    0  -0.455  146.0678  235.0316  102.8225
 MLL  C10   C  CH3   0  -0.422  146.4144  233.8840  102.0478
 MLL  H     H  HNH2  0   0.367  143.5184  237.7578  103.7897
 MLL  H2    H  HNH2  0   0.353  144.6269  237.4008  102.6683
 MLL  HA    H  HCH1  0   0.240  145.7253  236.7275  104.5989
 MLL  HB2   H  HCH2  0   0.224  142.9038  236.0253  105.4099
 MLL  HB3   H  HCH2  0   0.240  144.2203  235.1039  106.0952
 MLL  HG    H  HCH1  0   0.218  145.2931  237.0942  106.9697
 MLL  HD21  H  HCH3  0   0.224  143.6338  235.8422  108.3418
 MLL  HD22  H  HCH3  0   0.226  143.6374  237.5563  108.7532
 MLL  HD23  H  HCH3  0   0.214  142.3472  236.8935  107.7530
 MLL  HD11  H  HCH3  0   0.234  144.1105  239.2851  107.0228
 MLL  HD12  H  HCH3  0   0.229  144.5880  238.8608  105.3902
 MLL  HD13  H  HCH3  0   0.216  142.9044  238.6706  105.8981
 MLL  H101  H  HCH3  0   0.237  145.5768  233.5464  101.4377
 MLL  H102  H  HCH3  0   0.249  147.2287  234.1945  101.3996
 MLL  H103  H  HCH3  0   0.237  146.7509  233.0626  102.6802

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
 MLL  N    CA    single  1.458  0.019  1.458
 MLL  N    H     single  0.860  0.020  0.860
 MLL  N    H2    single  0.890  0.020  1.040
 MLL  CA   CB    single  1.530  0.020  1.530
 MLL  CA   C     single  1.525  0.021  1.525
 MLL  CA   HA    single  0.970  0.020  0.970
 MLL  CB   CG    single  1.532  0.020  1.532
 MLL  CB   HB2   single  0.970  0.020  1.090
 MLL  CB   HB3   single  0.970  0.020  1.090
 MLL  CG   CD2   single  1.525  0.020  1.525
 MLL  CG   CD1   single  1.526  0.020  1.526
 MLL  CG   HG    single  0.970  0.020  1.090
 MLL  CD2  HD21  single  0.970  0.020  1.090
 MLL  CD2  HD22  single  0.970  0.020  1.090
 MLL  CD2  HD23  single  0.970  0.020  1.090
 MLL  CD1  HD11  single  0.970  0.020  1.090
 MLL  CD1  HD12  single  0.970  0.020  1.090
 MLL  CD1  HD13  single  0.970  0.020  1.090
 MLL  C    O     double  1.231  0.020  1.231
 MLL  C    O9    single  1.327  0.020  1.327
 MLL  O9   C10   single  1.427  0.020  1.427
 MLL  C10  H101  single  0.970  0.020  1.090
 MLL  C10  H102  single  0.970  0.020  1.090
 MLL  C10  H103  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
 MLL  H2    N    H     106.10  3.000
 MLL  H2    N    CA    110.22  3.000
 MLL  H     N    CA    114.00  3.000
 MLL  HA    CA   C     109.00  3.000
 MLL  HA    CA   CB    109.00  3.000
 MLL  C     CA   CB    110.10  1.900
 MLL  HA    CA   N     110.00  3.000
 MLL  C     CA   N     111.00  2.800
 MLL  CB    CA   N     110.50  1.700
 MLL  HB3   CB   HB2   105.99  3.000
 MLL  HB3   CB   CG    107.46  3.000
 MLL  HB2   CB   CG    109.94  3.000
 MLL  HB3   CB   CA    109.40  3.000
 MLL  HB2   CB   CA    109.21  3.000
 MLL  CG    CB   CA    114.48  3.000
 MLL  HG    CG   CD1   107.66  3.000
 MLL  HG    CG   CD2   107.83  3.000
 MLL  CD1   CG   CD2   110.28  3.000
 MLL  HG    CG   CB    107.30  3.000
 MLL  CD1   CG   CB    113.84  3.000
 MLL  CD2   CG   CB    109.70  3.000
 MLL  HD23  CD2  HD22  107.57  3.000
 MLL  HD23  CD2  HD21  107.62  3.000
 MLL  HD22  CD2  HD21  107.74  3.000
 MLL  HD23  CD2  CG    110.96  3.000
 MLL  HD22  CD2  CG    111.21  3.000
 MLL  HD21  CD2  CG    111.55  3.000
 MLL  HD13  CD1  HD12  108.11  3.000
 MLL  HD13  CD1  HD11  107.33  3.000
 MLL  HD12  CD1  HD11  106.88  3.000
 MLL  HD13  CD1  CG    111.22  3.000
 MLL  HD12  CD1  CG    112.46  3.000
 MLL  HD11  CD1  CG    110.59  3.000
 MLL  O9    C    O     123.43  3.000
 MLL  O9    C    CA    110.79  3.000
 MLL  O     C    CA    120.80  1.700
 MLL  C10   O9   C     117.67  3.000
 MLL  H103  C10  H102  109.29  3.000
 MLL  H103  C10  H101  109.19  3.000
 MLL  H102  C10  H101  109.31  3.000
 MLL  H103  C10  O9    111.47  3.000
 MLL  H102  C10  O9    106.03  3.000
 MLL  H101  C10  O9    111.48  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
 MLL  Var_01  CD2   CG   CB  CA  -178.27  30.0  3
 MLL  Var_02  HD21  CD2  CG  CB    55.75  30.0  3
 MLL  Var_03  HD11  CD1  CG  CB   177.97  30.0  3
 MLL  Var_04  H101  C10  O9  C     60.56  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
 MLL  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
 MLL  plan-1  CA  0.020
 MLL  plan-1  C   0.020
 MLL  plan-1  O   0.020
 MLL  plan-1  O9  0.020

