# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 06:16:22 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](O)[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
 HL2  HL2  '(2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid (non-preferred name)'  L-peptide  22  10  .  2016-04-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HL2
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
 HL2  C     C  C      0   0.408   9.6790  -22.9965  -43.3084
 HL2  N     N  NH2    0  -0.813   9.5254  -24.7591  -44.9308
 HL2  O     O  O      0  -0.598  10.8594  -22.9841  -42.9101
 HL2  CA    C  CH1    0  -0.199   9.0383  -24.3814  -43.6022
 HL2  CB    C  CH1    0   0.092   9.4150  -25.4642  -42.5874
 HL2  CG    C  CH1    0  -0.249   8.6337  -25.3645  -41.2662
 HL2  OH    O  OH1    0  -0.686   9.1529  -26.7263  -43.1919
 HL2  CD1   C  CH3    0  -0.667   8.7545  -24.0120  -40.5705
 HL2  CD2   C  CH3    0  -0.671   9.0618  -26.4678  -40.2990
 HL2  OXT   O  OC    -1  -0.613   8.9687  -22.0023  -43.5657
 HL2  HN    H  HNH2   0   0.335   9.0851  -25.6223  -45.2188
 HL2  HNA   H  HNH2   0   0.332   9.2253  -24.0587  -45.5979
 HL2  HA    H  HCH1   0   0.170   7.9419  -24.2633  -43.5836
 HL2  HB    H  HCH1   0   0.183  10.4881  -25.3681  -42.3750
 HL2  HG    H  HCH1   0   0.205   7.5752  -25.5193  -41.5111
 HL2  HOH   H  HOH1   0   0.447   9.6961  -27.3901  -42.7600
 HL2  HD1   H  HCH3   0   0.222   8.2093  -24.0328  -39.6250
 HL2  HD1A  H  HCH3   0   0.212   9.7942  -23.7695  -40.3457
 HL2  HD1B  H  HCH3   0   0.227   8.3390  -23.1980  -41.1629
 HL2  HD2   H  HCH3   0   0.227   8.5155  -26.3902  -39.3577
 HL2  HD2A  H  HCH3   0   0.221   8.8761  -27.4687  -40.6900
 HL2  HD2B  H  HCH3   0   0.213  10.1272  -26.3897  -40.0663

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
 HL2  C    O     deloc   1.231  0.020  1.231
 HL2  C    CA    single  1.525  0.021  1.525
 HL2  C    OXT   deloc   1.249  0.020  1.249
 HL2  N    CA    single  1.458  0.019  1.458
 HL2  N    HN    single  0.890  0.020  1.040
 HL2  N    HNA   single  0.890  0.020  1.040
 HL2  CA   CB    single  1.530  0.020  1.530
 HL2  CA   HA    single  0.970  0.020  0.970
 HL2  CB   CG    single  1.538  0.020  1.538
 HL2  CB   OH    single  1.424  0.020  1.424
 HL2  CB   HB    single  0.970  0.020  1.090
 HL2  CG   CD1   single  1.526  0.020  1.526
 HL2  CG   CD2   single  1.528  0.020  1.528
 HL2  CG   HG    single  0.970  0.020  1.090
 HL2  OH   HOH   single  0.850  0.020  0.980
 HL2  CD1  HD1   single  0.970  0.020  1.090
 HL2  CD1  HD1A  single  0.970  0.020  1.090
 HL2  CD1  HD1B  single  0.970  0.020  1.090
 HL2  CD2  HD2   single  0.970  0.020  1.090
 HL2  CD2  HD2A  single  0.970  0.020  1.090
 HL2  CD2  HD2B  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
 HL2  OXT   C    CA    115.86  3.000
 HL2  OXT   C    O     126.65  3.000
 HL2  CA    C    O     120.80  1.700
 HL2  HNA   N    HN    105.88  3.000
 HL2  HNA   N    CA    108.71  3.000
 HL2  HN    N    CA    109.50  3.000
 HL2  HA    CA   CB    109.00  3.000
 HL2  HA    CA   N     110.00  3.000
 HL2  CB    CA   N     110.50  1.700
 HL2  HA    CA   C     109.00  3.000
 HL2  CB    CA   C     110.10  1.900
 HL2  N     CA   C     111.00  2.800
 HL2  HB    CB   OH    109.86  3.000
 HL2  HB    CB   CG    108.94  3.000
 HL2  OH    CB   CG    109.19  3.000
 HL2  HB    CB   CA    107.86  3.000
 HL2  OH    CB   CA    107.47  3.000
 HL2  CG    CB   CA    113.48  3.000
 HL2  HG    CG   CD2   108.03  3.000
 HL2  HG    CG   CD1   107.65  3.000
 HL2  CD2   CG   CD1   109.22  3.000
 HL2  HG    CG   CB    106.80  3.000
 HL2  CD2   CG   CB    110.76  3.000
 HL2  CD1   CG   CB    114.14  3.000
 HL2  HOH   OH   CB    108.53  3.000
 HL2  HD1B  CD1  HD1A  108.03  3.000
 HL2  HD1B  CD1  HD1   107.14  3.000
 HL2  HD1A  CD1  HD1   107.57  3.000
 HL2  HD1B  CD1  CG    112.60  3.000
 HL2  HD1A  CD1  CG    111.50  3.000
 HL2  HD1   CD1  CG    109.79  3.000
 HL2  HD2B  CD2  HD2A  107.93  3.000
 HL2  HD2B  CD2  HD2   107.40  3.000
 HL2  HD2A  CD2  HD2   106.82  3.000
 HL2  HD2B  CD2  CG    110.86  3.000
 HL2  HD2A  CD2  CG    112.83  3.000
 HL2  HD2   CD2  CG    110.75  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
 HL2  Var_01  HD1  CD1  CG  CB  -177.69  30.0  3
 HL2  Var_02  HD2  CD2  CG  CB   179.36  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
 HL2  chir_01  CA  C   N   CB  negativ
 HL2  chir_02  CB  OH  CA  CG  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
 HL2  plan-1  C    0.020
 HL2  plan-1  O    0.020
 HL2  plan-1  CA   0.020
 HL2  plan-1  OXT  0.020

