# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:09:28 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (2~{R})-2-azanyl-2-methyl-heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[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
 J7H  J7H  '(2~{R})-2-azanyl-2-methyl-heptanoic acid'  D-peptide  28  11  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J7H
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
 J7H  N    N  NH2   0  -0.791  -1.4243   1.5615  -0.7554
 J7H  CA   C  CT    0  -0.053  -1.3046   0.4704   0.2004
 J7H  C    C  C     0   0.574  -2.4638  -0.5058   0.0292
 J7H  O    O  O     0  -0.451  -2.7908  -1.3065   0.8715
 J7H  CB1  C  CH2   0  -0.418  -0.0210  -0.3809   0.0219
 J7H  CB2  C  CH3   0  -0.654  -1.3827   1.0591   1.6093
 J7H  CG   C  CH2   0  -0.428   1.2799   0.4050   0.1277
 J7H  CD   C  CH2   0  -0.405   2.5031  -0.4766  -0.0953
 J7H  CE   C  CH2   0  -0.419   3.8146   0.2977  -0.0440
 J7H  CZ   C  CH3   0  -0.663   5.0331  -0.5940  -0.2368
 J7H  OXT  O  OH1   0  -0.585  -3.0475  -0.4342  -1.1582
 J7H  H1   H  HNH2  0   0.352  -0.7199   2.2583  -0.5484
 J7H  H2   H  HNH2  0   0.348  -1.2269   1.2413  -1.6962
 J7H  H4   H  HCH2  0   0.229  -0.0178  -1.1862   0.7627
 J7H  H5   H  HCH2  0   0.233  -0.0559  -0.8669  -0.9607
 J7H  H6   H  HCH3  0   0.243  -2.3404   1.5540   1.7725
 J7H  H7   H  HCH3  0   0.237  -1.2571   0.2917   2.3707
 J7H  H8   H  HCH3  0   0.238  -0.6006   1.8046   1.7536
 J7H  H9   H  HCH2  0   0.209   1.2877   1.2161  -0.6072
 J7H  H10  H  HCH2  0   0.223   1.3567   0.8783   1.1111
 J7H  H11  H  HCH2  0   0.210   2.5217  -1.2724   0.6576
 J7H  H12  H  HCH2  0   0.209   2.4196  -0.9794  -1.0654
 J7H  H13  H  HCH2  0   0.211   3.8043   1.0762  -0.8131
 J7H  H14  H  HCH2  0   0.211   3.8889   0.8212   0.9144
 J7H  H15  H  HCH3  0   0.216   5.1010  -1.3465   0.5511
 J7H  H16  H  HCH3  0   0.216   4.9875  -1.1223  -1.1913
 J7H  H17  H  HCH3  0   0.226   5.9592  -0.0179  -0.2243
 J7H  H18  H  HOH1  0   0.480  -3.7359  -1.1132  -1.2243

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
 J7H  N    CA   single  1.458  0.019  1.458
 J7H  C    O    double  1.231  0.020  1.231
 J7H  C    CA   single  1.525  0.021  1.525
 J7H  CA   CB1  single  1.551  0.020  1.551
 J7H  CA   CB2  single  1.529  0.020  1.529
 J7H  CB1  CG   single  1.524  0.020  1.524
 J7H  CG   CD   single  1.524  0.020  1.524
 J7H  CD   CE   single  1.524  0.020  1.524
 J7H  CE   CZ   single  1.522  0.020  1.522
 J7H  C    OXT  single  1.325  0.020  1.325
 J7H  N    H1   single  0.890  0.020  1.040
 J7H  N    H2   single  0.890  0.020  1.040
 J7H  CB1  H4   single  0.970  0.020  1.090
 J7H  CB1  H5   single  0.970  0.020  1.090
 J7H  CB2  H6   single  0.970  0.020  1.090
 J7H  CB2  H7   single  0.970  0.020  1.090
 J7H  CB2  H8   single  0.970  0.020  1.090
 J7H  CG   H9   single  0.970  0.020  1.090
 J7H  CG   H10  single  0.970  0.020  1.090
 J7H  CD   H11  single  0.970  0.020  1.090
 J7H  CD   H12  single  0.970  0.020  1.090
 J7H  CE   H13  single  0.970  0.020  1.090
 J7H  CE   H14  single  0.970  0.020  1.090
 J7H  CZ   H15  single  0.970  0.020  1.090
 J7H  CZ   H16  single  0.970  0.020  1.090
 J7H  CZ   H17  single  0.970  0.020  1.090
 J7H  OXT  H18  single  0.850  0.020  0.980

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
 J7H  H2   N    H1   105.78  3.000
 J7H  H2   N    CA   110.91  3.000
 J7H  H1   N    CA   108.94  3.000
 J7H  CB2  CA   CB1  111.08  3.000
 J7H  CB2  CA   C    108.12  3.000
 J7H  CB1  CA   C    105.36  3.000
 J7H  CB2  CA   N    108.20  3.000
 J7H  CB1  CA   N    113.83  3.000
 J7H  C    CA   N    111.00  2.800
 J7H  OXT  C    O    122.79  3.000
 J7H  OXT  C    CA   120.80  1.700
 J7H  O    C    CA   120.80  1.700
 J7H  H5   CB1  H4   106.30  3.000
 J7H  H5   CB1  CG   108.54  3.000
 J7H  H4   CB1  CG   109.28  3.000
 J7H  H5   CB1  CA   108.67  3.000
 J7H  H4   CB1  CA   109.18  3.000
 J7H  CG   CB1  CA   114.56  3.000
 J7H  H8   CB2  H7   107.87  3.000
 J7H  H8   CB2  H6   107.46  3.000
 J7H  H7   CB2  H6   108.46  3.000
 J7H  H8   CB2  CA   110.40  3.000
 J7H  H7   CB2  CA   111.55  3.000
 J7H  H6   CB2  CA   110.95  3.000
 J7H  H10  CG   H9   106.41  3.000
 J7H  H10  CG   CD   108.99  3.000
 J7H  H9   CG   CD   108.94  3.000
 J7H  H10  CG   CB1  110.21  3.000
 J7H  H9   CG   CB1  109.99  3.000
 J7H  CD   CG   CB1  112.13  3.000
 J7H  H12  CD   H11  106.04  3.000
 J7H  H12  CD   CE   109.18  3.000
 J7H  H11  CD   CE   109.35  3.000
 J7H  H12  CD   CG   109.50  3.000
 J7H  H11  CD   CG   109.46  3.000
 J7H  CE   CD   CG   113.07  3.000
 J7H  H14  CE   H13  106.01  3.000
 J7H  H14  CE   CZ   109.68  3.000
 J7H  H13  CE   CZ   109.58  3.000
 J7H  H14  CE   CD   109.32  3.000
 J7H  H13  CE   CD   109.25  3.000
 J7H  CZ   CE   CD   112.77  3.000
 J7H  H17  CZ   H16  107.52  3.000
 J7H  H17  CZ   H15  107.63  3.000
 J7H  H16  CZ   H15  107.46  3.000
 J7H  H17  CZ   CE   111.64  3.000
 J7H  H16  CZ   CE   111.15  3.000
 J7H  H15  CZ   CE   111.23  3.000
 J7H  H18  OXT  C    109.65  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
 J7H  CONST_01  H18  OXT  C    CA    180.00   0.0  0
 J7H  Var_01    CD   CG   CB1  CA   -178.37  30.0  3
 J7H  Var_02    CE   CD   CG   CB1   177.93  30.0  3
 J7H  Var_03    CZ   CE   CD   CG    178.73  30.0  3
 J7H  Var_04    H15  CZ   CE   CD    -61.31  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
 J7H  chir_01  CA  C  CB1  CB2  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
 J7H  plan-1  CA   0.020
 J7H  plan-1  C    0.020
 J7H  plan-1  O    0.020
 J7H  plan-1  OXT  0.020
 J7H  plan-1  H18  0.020

