# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:27:37 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: 2-methyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@](C)(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
 2ML  2ML  '2-methyl-L-leucine       '  L-peptide  24  10  .  2016-04-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2ML
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
 2ML  N     N  NH2    0  -0.783  62.6611  3.8886  14.0021
 2ML  CA    C  CT     0  -0.045  64.0786  3.7952  14.3467
 2ML  CB1   C  CH2    0  -0.344  64.8957  4.6663  13.3765
 2ML  CB2   C  CH3    0  -0.657  64.5719  2.3425  14.2107
 2ML  CG    C  CH1    0  -0.238  64.9039  6.1870  13.5610
 2ML  CD1   C  CH3    0  -0.649  65.8164  6.8117  12.5061
 2ML  CD2   C  CH3    0  -0.632  63.5283  6.8435  13.5096
 2ML  C     C  C      0   0.424  64.3077  4.2211  15.8238
 2ML  O     O  O      0  -0.611  65.4995  4.3125  16.1859
 2ML  OXT   O  OC    -1  -0.598  63.3021  4.3984  16.5398
 2ML  H2    H  HNH2   0   0.324  62.1178  3.4470  14.7326
 2ML  H     H  HNH2   0   0.319  62.4932  3.3550  13.1563
 2ML  HB11  H  HCH2   0   0.201  65.9370  4.3337  13.4157
 2ML  HB12  H  HCH2   0   0.189  64.5523  4.4397  12.3579
 2ML  HB21  H  HCH3   0   0.211  65.6247  2.2338  14.4722
 2ML  HB22  H  HCH3   0   0.215  63.9952  1.6740  14.8551
 2ML  HB23  H  HCH3   0   0.208  64.4489  1.9929  13.1814
 2ML  HG    H  HCH1   0   0.205  65.3413  6.3999  14.5412
 2ML  HD11  H  HCH3   0   0.218  65.9019  7.8916  12.6427
 2ML  HD12  H  HCH3   0   0.216  66.8237  6.3923  12.5441
 2ML  HD13  H  HCH3   0   0.206  65.4248  6.6380  11.5002
 2ML  HD21  H  HCH3   0   0.201  63.6211  7.9282  13.6015
 2ML  HD22  H  HCH3   0   0.196  63.0283  6.6319  12.5614
 2ML  HD23  H  HCH3   0   0.225  62.8804  6.4870  14.3062

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
 2ML  N    CA    single  1.458  0.019  1.458
 2ML  N    H2    single  0.890  0.020  1.040
 2ML  N    H     single  0.860  0.020  0.860
 2ML  CA   CB1   single  1.539  0.020  1.539
 2ML  CA   CB2   single  1.540  0.020  1.540
 2ML  CA   C     single  1.525  0.021  1.525
 2ML  CB1  CG    single  1.532  0.020  1.532
 2ML  CB1  HB11  single  0.970  0.020  1.090
 2ML  CB1  HB12  single  0.970  0.020  1.090
 2ML  CB2  HB21  single  0.970  0.020  1.090
 2ML  CB2  HB22  single  0.970  0.020  1.090
 2ML  CB2  HB23  single  0.970  0.020  1.090
 2ML  CG   CD1   single  1.528  0.020  1.528
 2ML  CG   CD2   single  1.525  0.020  1.525
 2ML  CG   HG    single  0.970  0.020  1.090
 2ML  CD1  HD11  single  0.970  0.020  1.090
 2ML  CD1  HD12  single  0.970  0.020  1.090
 2ML  CD1  HD13  single  0.970  0.020  1.090
 2ML  CD2  HD21  single  0.970  0.020  1.090
 2ML  CD2  HD22  single  0.970  0.020  1.090
 2ML  CD2  HD23  single  0.970  0.020  1.090
 2ML  C    O     deloc   1.231  0.020  1.231
 2ML  C    OXT   deloc   1.247  0.020  1.247

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
 2ML  H     N    H2    106.48  3.000
 2ML  H     N    CA    114.00  3.000
 2ML  H2    N    CA    108.82  3.000
 2ML  C     CA   CB2   107.17  3.000
 2ML  C     CA   CB1   111.46  3.000
 2ML  CB2   CA   CB1   107.95  3.000
 2ML  C     CA   N     111.00  2.800
 2ML  CB2   CA   N     110.49  3.000
 2ML  CB1   CA   N     109.28  3.000
 2ML  HB12  CB1  HB11  105.55  3.000
 2ML  HB12  CB1  CG    108.54  3.000
 2ML  HB11  CB1  CG    107.01  3.000
 2ML  HB12  CB1  CA    107.57  3.000
 2ML  HB11  CB1  CA    108.11  3.000
 2ML  CG    CB1  CA    119.27  3.000
 2ML  HB23  CB2  HB22  107.46  3.000
 2ML  HB23  CB2  HB21  107.60  3.000
 2ML  HB22  CB2  HB21  107.89  3.000
 2ML  HB23  CB2  CA    110.39  3.000
 2ML  HB22  CB2  CA    110.84  3.000
 2ML  HB21  CB2  CA    112.46  3.000
 2ML  HG    CG   CD2   107.88  3.000
 2ML  HG    CG   CD1   107.46  3.000
 2ML  CD2   CG   CD1   109.84  3.000
 2ML  HG    CG   CB1   107.64  3.000
 2ML  CD2   CG   CB1   114.74  3.000
 2ML  CD1   CG   CB1   109.02  3.000
 2ML  HD13  CD1  HD12  107.55  3.000
 2ML  HD13  CD1  HD11  107.47  3.000
 2ML  HD12  CD1  HD11  107.66  3.000
 2ML  HD13  CD1  CG    110.87  3.000
 2ML  HD12  CD1  CG    111.70  3.000
 2ML  HD11  CD1  CG    111.39  3.000
 2ML  HD23  CD2  HD22  107.44  3.000
 2ML  HD23  CD2  HD21  108.34  3.000
 2ML  HD22  CD2  HD21  107.71  3.000
 2ML  HD23  CD2  CG    111.83  3.000
 2ML  HD22  CD2  CG    111.02  3.000
 2ML  HD21  CD2  CG    110.36  3.000
 2ML  OXT   C    O     126.34  3.000
 2ML  OXT   C    CA    117.76  3.000
 2ML  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
 2ML  Var_01  CD1   CG   CB1  CA    178.26  30.0  3
 2ML  Var_02  HD11  CD1  CG   CB1  -176.31  30.0  3
 2ML  Var_03  HD21  CD2  CG   CB1  -177.35  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
 2ML  chir_01  CA  CB1  CB2  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
 2ML  plan-1  CA   0.020
 2ML  plan-1  C    0.020
 2ML  plan-1  O    0.020
 2ML  plan-1  OXT  0.020

