# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 21:29:19 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (2R)-2-(aminomethyl)-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](CN)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
 4L8  4L8  '(2R)-2-(aminomethyl)-4-methylpentanoic acid'  L-peptide  24  10  .  2022-03-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4L8
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
 4L8  CB   C  CH2    0  -0.400   0.8852  -0.6030   0.2159
 4L8  C1   C  CH2    0  -0.263  -0.6053   1.3890   0.6948
 4L8  C    C  C      0   0.420  -1.5781  -0.8513  -0.0825
 4L8  O    O  O      0  -0.607  -2.3853  -0.7384   0.8654
 4L8  CA   C  CH1    0  -0.364  -0.4007   0.1473  -0.1587
 4L8  CG   C  CH1    0  -0.239   2.2018   0.1655   0.0700
 4L8  CD1  C  CH3    0  -0.647   3.3646  -0.7193   0.5119
 4L8  CD2  C  CH3    0  -0.656   2.4219   0.6567  -1.3570
 4L8  OXT  O  OC    -1  -0.621  -1.6148  -1.7262  -0.9722
 4L8  H1   H  HCH2   0   0.207   0.7986  -0.9547   1.2513
 4L8  H2   H  HCH2   0   0.210   0.9474  -1.5011  -0.4071
 4L8  H3   H  HCH2   0   0.173  -0.6331   1.0937   1.7542
 4L8  H4   H  HCH2   0   0.206   0.2616   2.0461   0.5856
 4L8  H6   H  HCH1   0   0.203  -0.3194   0.4683  -1.2042
 4L8  H7   H  HCH1   0   0.212   2.1839   1.0379   0.7323
 4L8  H8   H  HCH3   0   0.210   3.4567  -1.5943  -0.1364
 4L8  H9   H  HCH3   0   0.222   4.3126  -0.1791   0.4749
 4L8  H10  H  HCH3   0   0.221   3.2290  -1.0779   1.5342
 4L8  H11  H  HCH3   0   0.226   1.6742   1.3906  -1.6601
 4L8  H12  H  HCH3   0   0.222   3.4012   1.1266  -1.4652
 4L8  H13  H  HCH3   0   0.211   2.3730  -0.1762  -2.0633
 4L8  N    N  NH2    0  -0.812  -1.7794   2.1418   0.2707
 4L8  H5   H  HNH2   0   0.334  -2.5980   1.5919   0.4997
 4L8  H15  H  HNH2   0   0.335  -1.8508   2.9866   0.8237

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
 4L8  CD2  CG   single  1.525  0.020  1.525
 4L8  CD1  CG   single  1.526  0.020  1.526
 4L8  CG   CB   single  1.531  0.020  1.531
 4L8  O    C    deloc   1.231  0.020  1.231
 4L8  CB   CA   single  1.521  0.033  1.521
 4L8  CA   C    single  1.525  0.021  1.525
 4L8  CA   C1   single  1.521  0.020  1.521
 4L8  C    OXT  deloc   1.248  0.020  1.248
 4L8  CB   H1   single  0.970  0.020  1.090
 4L8  CB   H2   single  0.970  0.020  1.090
 4L8  C1   H3   single  0.970  0.020  1.090
 4L8  C1   H4   single  0.970  0.020  1.090
 4L8  CA   H6   single  0.970  0.020  1.090
 4L8  CG   H7   single  0.970  0.020  1.090
 4L8  CD1  H8   single  0.970  0.020  1.090
 4L8  CD1  H9   single  0.970  0.020  1.090
 4L8  CD1  H10  single  0.970  0.020  1.090
 4L8  CD2  H11  single  0.970  0.020  1.090
 4L8  CD2  H12  single  0.970  0.020  1.090
 4L8  CD2  H13  single  0.970  0.020  1.090
 4L8  C1   N    single  1.458  0.020  1.458
 4L8  N    H5   single  0.890  0.020  1.040
 4L8  N    H15  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
 4L8  H2   CB   H1   106.18  3.000
 4L8  H2   CB   CG   107.98  3.000
 4L8  H1   CB   CG   108.58  3.000
 4L8  H2   CB   CA   108.03  3.000
 4L8  H1   CB   CA   108.72  3.000
 4L8  CG   CB   CA   116.85  3.000
 4L8  N    C1   H4   107.42  3.000
 4L8  N    C1   H3   113.48  3.000
 4L8  H4   C1   H3   106.11  3.000
 4L8  N    C1   CA   111.51  3.000
 4L8  H4   C1   CA   109.15  3.000
 4L8  H3   C1   CA   108.95  3.000
 4L8  OXT  C    CA   120.80  1.700
 4L8  OXT  C    O    125.78  3.000
 4L8  CA   C    O    120.80  1.700
 4L8  H6   CA   C    107.01  3.000
 4L8  H6   CA   C1   107.83  3.000
 4L8  C    CA   C1   113.42  3.000
 4L8  H6   CA   CB   108.27  3.000
 4L8  C1   CA   CB   112.01  3.000
 4L8  C    CA   CB   110.50  1.500
 4L8  H7   CG   CD2  108.15  3.000
 4L8  H7   CG   CD1  107.40  3.000
 4L8  CD2  CG   CD1  110.34  3.000
 4L8  H7   CG   CB   109.14  3.000
 4L8  CD1  CG   CB   109.66  3.000
 4L8  CD2  CG   CB   112.01  3.000
 4L8  H10  CD1  H9   107.58  3.000
 4L8  H10  CD1  H8   107.63  3.000
 4L8  H9   CD1  H8   107.64  3.000
 4L8  H10  CD1  CG   111.51  3.000
 4L8  H9   CD1  CG   111.40  3.000
 4L8  H8   CD1  CG   110.89  3.000
 4L8  H13  CD2  H12  107.70  3.000
 4L8  H13  CD2  H11  107.61  3.000
 4L8  H12  CD2  H11  107.32  3.000
 4L8  H13  CD2  CG   110.65  3.000
 4L8  H12  CD2  CG   111.15  3.000
 4L8  H11  CD2  CG   112.20  3.000
 4L8  H15  N    H5   105.83  3.000
 4L8  H15  N    C1   109.20  3.000
 4L8  H5   N    C1   107.76  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
 4L8  Var_01  CD2  CG   CB  CA  -58.34  30.0  2
 4L8  Var_02  H11  CD2  CG  CB   64.70  30.0  3
 4L8  Var_03  H8   CD1  CG  CB   63.48  30.0  3
 4L8  Var_04  H5   N    C1  CA   68.85  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
 4L8  chir_01  CA  CB  C  C1  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
 4L8  plan-1  C    0.020
 4L8  plan-1  O    0.020
 4L8  plan-1  CA   0.020
 4L8  plan-1  OXT  0.020

