# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:42:01 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2S)-2-amino-4-methylpentanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C=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
 LCZ  LCZ  (2S)-2-amino-4-methylpentanal  peptide  21  8  .  2019-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LCZ
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
 LCZ  N     N  NH2   0  -0.801  45.5036  -139.8852  59.5598
 LCZ  CA    C  CH1   0  -0.203  45.6436  -139.8573  60.9972
 LCZ  C     C  C1    0   0.183  45.0125  -141.0625  61.6321
 LCZ  CB    C  CH2   0  -0.406  44.9887  -138.6117  61.6065
 LCZ  CG    C  CH1   0  -0.247  45.5654  -137.2738  61.1368
 LCZ  CD1   C  CH3   0  -0.646  44.8151  -136.1328  61.8172
 LCZ  CD2   C  CH3   0  -0.660  47.0635  -137.1650  61.3999
 LCZ  O     O  O     0  -0.372  44.5019  -141.9790  61.0395
 LCZ  HN1   H  HNH2  0   0.355  46.0439  -139.1339  59.1514
 LCZ  HN2   H  HNH2  0   0.349  45.8953  -140.7406  59.1865
 LCZ  HA    H  HCH1  0   0.241  46.6910  -139.8894  61.3507
 LCZ  HC2   H  H     0   0.187  45.0651  -141.0561  62.7371
 LCZ  HB1   H  HCH2  0   0.234  43.9174  -138.6360  61.3822
 LCZ  HB2   H  HCH2  0   0.223  45.0840  -138.6676  62.6965
 LCZ  HG    H  HCH1  0   0.220  45.3962  -137.1809  60.0583
 LCZ  HD11  H  HCH3  0   0.225  43.7424  -136.1904  61.6248
 LCZ  HD12  H  HCH3  0   0.214  44.9599  -136.1625  62.8997
 LCZ  HD13  H  HCH3  0   0.227  45.1655  -135.1626  61.4617
 LCZ  HD21  H  HCH3  0   0.230  47.4373  -136.1821  61.1086
 LCZ  HD22  H  HCH3  0   0.216  47.2846  -137.3020  62.4611
 LCZ  HD23  H  HCH3  0   0.230  47.6384  -137.9058  60.8417

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
 LCZ  N    CA    single  1.458  0.019  1.458
 LCZ  CA   C     single  1.525  0.021  1.525
 LCZ  CA   CB    single  1.521  0.033  1.521
 LCZ  O    C     double  1.231  0.020  1.231
 LCZ  CG   CD2   single  1.525  0.020  1.525
 LCZ  CG   CB    single  1.531  0.020  1.531
 LCZ  CG   CD1   single  1.526  0.020  1.526
 LCZ  N    HN1   single  0.890  0.020  1.040
 LCZ  CA   HA    single  0.970  0.020  0.970
 LCZ  C    HC2   single  0.930  0.020  1.080
 LCZ  CB   HB1   single  0.970  0.020  1.090
 LCZ  CB   HB2   single  0.970  0.020  1.090
 LCZ  CG   HG    single  0.970  0.020  1.090
 LCZ  CD1  HD11  single  0.970  0.020  1.090
 LCZ  CD1  HD12  single  0.970  0.020  1.090
 LCZ  CD1  HD13  single  0.970  0.020  1.090
 LCZ  CD2  HD21  single  0.970  0.020  1.090
 LCZ  CD2  HD22  single  0.970  0.020  1.090
 LCZ  CD2  HD23  single  0.970  0.020  1.090
 LCZ  N    HN2   single  0.890  0.020  1.040

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
 LCZ  HN2   N    HN1   105.79  3.000
 LCZ  HN2   N    CA    110.23  3.000
 LCZ  HN1   N    CA    109.61  3.000
 LCZ  HA    CA   CB    109.00  3.000
 LCZ  HA    CA   C     110.00  3.000
 LCZ  CB    CA   C     110.50  1.500
 LCZ  HA    CA   N     110.00  3.000
 LCZ  CB    CA   N     110.40  1.500
 LCZ  C     CA   N     111.00  2.800
 LCZ  HC2   C    O     121.06  3.000
 LCZ  HC2   C    CA    113.44  3.000
 LCZ  O     C    CA    120.80  1.700
 LCZ  HB2   CB   HB1   106.73  3.000
 LCZ  HB2   CB   CG    108.49  3.000
 LCZ  HB1   CB   CG    108.97  3.000
 LCZ  HB2   CB   CA    108.47  3.000
 LCZ  HB1   CB   CA    108.57  3.000
 LCZ  CG    CB   CA    115.29  3.000
 LCZ  HG    CG   CD2   108.39  3.000
 LCZ  HG    CG   CD1   107.43  3.000
 LCZ  CD2   CG   CD1   110.66  3.000
 LCZ  HG    CG   CB    108.55  3.000
 LCZ  CD1   CG   CB    109.36  3.000
 LCZ  CD2   CG   CB    112.31  3.000
 LCZ  HD13  CD1  HD12  107.72  3.000
 LCZ  HD13  CD1  HD11  107.77  3.000
 LCZ  HD12  CD1  HD11  107.67  3.000
 LCZ  HD13  CD1  CG    111.21  3.000
 LCZ  HD12  CD1  CG    110.87  3.000
 LCZ  HD11  CD1  CG    111.42  3.000
 LCZ  HD23  CD2  HD22  107.76  3.000
 LCZ  HD23  CD2  HD21  107.13  3.000
 LCZ  HD22  CD2  HD21  107.63  3.000
 LCZ  HD23  CD2  CG    112.39  3.000
 LCZ  HD22  CD2  CG    110.94  3.000
 LCZ  HD21  CD2  CG    110.78  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
 LCZ  Var_01  CD2   CG   CB  CA   -57.04  30.0  2
 LCZ  Var_02  HD21  CD2  CG  CB  -176.76  30.0  3
 LCZ  Var_03  HD11  CD1  CG  CB   -56.60  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
 LCZ  chir_01  CA  N  C  CB  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
 LCZ  plan-1  CA   0.020
 LCZ  plan-1  C    0.020
 LCZ  plan-1  O    0.020
 LCZ  plan-1  HC2  0.020

