# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:23:29 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2R)-2-amino-2-methylnonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC[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
 0EH  0EH  '(2R)-2-amino-2-methylnonanoic acid'  D-peptide  34  13  .  2022-03-08  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0EH
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
 0EH  OAD  O  O     0  -0.448  -3.4942  -1.6962   0.4698
 0EH  CAE  C  C     0   0.559  -3.5122  -0.5847  -0.0017
 0EH  CAF  C  CT    0  -0.051  -2.3432   0.4104   0.0676
 0EH  CAA  C  CH3   0  -0.662  -2.4703   1.0936   1.4362
 0EH  CAB  C  CH2   0  -0.404  -1.0318  -0.3826  -0.0489
 0EH  NAC  N  NH2   0  -0.782  -2.3715   1.4328  -0.9604
 0EH  CAO  C  CH2   0  -0.415   0.2365   0.4468   0.1002
 0EH  CAP  C  CH2   0  -0.411   1.4931  -0.3958  -0.0841
 0EH  CAQ  C  CH2   0  -0.411   2.7781   0.4090   0.0616
 0EH  CAR  C  CH2   0  -0.406   4.0369  -0.4300  -0.1160
 0EH  CAS  C  CH2   0  -0.418   5.3238   0.3739   0.0219
 0EH  CAT  C  CH3   0  -0.662   6.5739  -0.4763  -0.1564
 0EH  H2   H  HCH3  0   0.239  -2.3619   0.3776   2.2505
 0EH  H3   H  HCH3  0   0.250  -1.7016   1.8573   1.5432
 0EH  H4   H  HCH3  0   0.242  -3.4385   1.5872   1.5427
 0EH  H5   H  HCH2  0   0.229  -1.0266  -1.1793   0.6982
 0EH  H6   H  HCH2  0   0.227  -1.0160  -0.8823  -1.0252
 0EH  H7   H  HNH2  0   0.346  -2.3672   1.0155  -1.8832
 0EH  H8   H  HNH2  0   0.350  -3.2124   1.9923  -0.8989
 0EH  H10  H  HCH2  0   0.216   0.2336   1.2643  -0.6248
 0EH  H11  H  HCH2  0   0.214   0.2659   0.9133   1.0896
 0EH  H12  H  HCH2  0   0.207   1.4938  -1.2144   0.6447
 0EH  H13  H  HCH2  0   0.207   1.4734  -0.8710  -1.0713
 0EH  H14  H  HCH2  0   0.206   2.7791   1.2247  -0.6701
 0EH  H15  H  HCH2  0   0.206   2.7965   0.8874   1.0473
 0EH  H16  H  HCH2  0   0.205   4.0384  -1.2436   0.6183
 0EH  H17  H  HCH2  0   0.205   4.0165  -0.9126  -1.0999
 0EH  H18  H  HCH2  0   0.210   5.3244   1.1839  -0.7143
 0EH  H19  H  HCH2  0   0.210   5.3448   0.8579   1.0034
 0EH  H20  H  HCH3  0   0.215   6.6221  -1.2706   0.5910
 0EH  H21  H  HCH3  0   0.215   6.5896  -0.9507  -1.1396
 0EH  H22  H  HCH3  0   0.225   7.4829   0.1195  -0.0638
 0EH  O1   O  OH1   0  -0.589  -4.5864  -0.0793  -0.5955
 0EH  H1   H  HOH1  0   0.479  -5.3116  -0.7212  -0.5618

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
 0EH  CAT  CAS  single  1.522  0.020  1.522
 0EH  OAD  CAE  double  1.207  0.020  1.207
 0EH  CAR  CAS  single  1.524  0.020  1.524
 0EH  CAR  CAQ  single  1.523  0.020  1.523
 0EH  CAE  CAF  single  1.537  0.020  1.537
 0EH  CAA  CAF  single  1.535  0.020  1.535
 0EH  CAO  CAP  single  1.524  0.020  1.524
 0EH  CAO  CAB  single  1.523  0.020  1.523
 0EH  CAQ  CAP  single  1.523  0.020  1.523
 0EH  CAF  CAB  single  1.537  0.020  1.537
 0EH  CAF  NAC  single  1.450  0.020  1.450
 0EH  CAA  H2   single  0.970  0.020  1.090
 0EH  CAA  H3   single  0.970  0.020  1.090
 0EH  CAA  H4   single  0.970  0.020  1.090
 0EH  CAB  H5   single  0.970  0.020  1.090
 0EH  CAB  H6   single  0.970  0.020  1.090
 0EH  NAC  H7   single  0.890  0.020  1.040
 0EH  NAC  H8   single  0.890  0.020  1.040
 0EH  CAO  H10  single  0.970  0.020  1.090
 0EH  CAO  H11  single  0.970  0.020  1.090
 0EH  CAP  H12  single  0.970  0.020  1.090
 0EH  CAP  H13  single  0.970  0.020  1.090
 0EH  CAQ  H14  single  0.970  0.020  1.090
 0EH  CAQ  H15  single  0.970  0.020  1.090
 0EH  CAR  H16  single  0.970  0.020  1.090
 0EH  CAR  H17  single  0.970  0.020  1.090
 0EH  CAS  H18  single  0.970  0.020  1.090
 0EH  CAS  H19  single  0.970  0.020  1.090
 0EH  CAT  H20  single  0.970  0.020  1.090
 0EH  CAT  H21  single  0.970  0.020  1.090
 0EH  CAT  H22  single  0.970  0.020  1.090
 0EH  CAE  O1   single  1.327  0.020  1.327
 0EH  O1   H1   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
 0EH  O1   CAE  CAF  112.91  3.000
 0EH  O1   CAE  OAD  122.49  3.000
 0EH  CAF  CAE  OAD  124.55  3.000
 0EH  NAC  CAF  CAB  109.07  3.000
 0EH  NAC  CAF  CAA  108.46  3.000
 0EH  CAB  CAF  CAA  111.58  3.000
 0EH  NAC  CAF  CAE  114.19  3.000
 0EH  CAB  CAF  CAE  108.15  3.000
 0EH  CAA  CAF  CAE  105.39  3.000
 0EH  H4   CAA  H3   107.41  3.000
 0EH  H4   CAA  H2   108.20  3.000
 0EH  H3   CAA  H2   108.49  3.000
 0EH  H4   CAA  CAF  111.20  3.000
 0EH  H3   CAA  CAF  109.96  3.000
 0EH  H2   CAA  CAF  111.44  3.000
 0EH  H6   CAB  H5   106.05  3.000
 0EH  H6   CAB  CAO  108.86  3.000
 0EH  H5   CAB  CAO  109.05  3.000
 0EH  H6   CAB  CAF  108.35  3.000
 0EH  H5   CAB  CAF  109.18  3.000
 0EH  CAO  CAB  CAF  114.97  3.000
 0EH  H8   NAC  H7   106.66  3.000
 0EH  H8   NAC  CAF  111.28  3.000
 0EH  H7   NAC  CAF  110.81  3.000
 0EH  H11  CAO  H10  106.33  3.000
 0EH  H11  CAO  CAP  108.84  3.000
 0EH  H10  CAO  CAP  109.61  3.000
 0EH  H11  CAO  CAB  110.06  3.000
 0EH  H10  CAO  CAB  109.89  3.000
 0EH  CAP  CAO  CAB  111.94  3.000
 0EH  H13  CAP  H12  105.97  3.000
 0EH  H13  CAP  CAQ  109.30  3.000
 0EH  H12  CAP  CAQ  109.30  3.000
 0EH  H13  CAP  CAO  109.50  3.000
 0EH  H12  CAP  CAO  109.46  3.000
 0EH  CAQ  CAP  CAO  113.07  3.000
 0EH  H15  CAQ  H14  106.00  3.000
 0EH  H15  CAQ  CAR  109.36  3.000
 0EH  H14  CAQ  CAR  109.35  3.000
 0EH  H15  CAQ  CAP  109.33  3.000
 0EH  H14  CAQ  CAP  109.28  3.000
 0EH  CAR  CAQ  CAP  113.27  3.000
 0EH  H17  CAR  H16  105.94  3.000
 0EH  H17  CAR  CAS  109.23  3.000
 0EH  H16  CAR  CAS  109.26  3.000
 0EH  H17  CAR  CAQ  109.38  3.000
 0EH  H16  CAR  CAQ  109.38  3.000
 0EH  CAS  CAR  CAQ  113.39  3.000
 0EH  H19  CAS  H18  106.01  3.000
 0EH  H19  CAS  CAT  109.65  3.000
 0EH  H18  CAS  CAT  109.52  3.000
 0EH  H19  CAS  CAR  109.31  3.000
 0EH  H18  CAS  CAR  109.27  3.000
 0EH  CAT  CAS  CAR  112.86  3.000
 0EH  H22  CAT  H21  107.57  3.000
 0EH  H22  CAT  H20  107.61  3.000
 0EH  H21  CAT  H20  107.44  3.000
 0EH  H22  CAT  CAS  111.68  3.000
 0EH  H21  CAT  CAS  111.10  3.000
 0EH  H20  CAT  CAS  111.25  3.000
 0EH  H1   O1   CAE  109.75  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
 0EH  CONST_01  H1   O1   CAE  OAD     0.00   0.0  0
 0EH  Var_01    CAP  CAO  CAB  CAF  -177.64  30.0  1
 0EH  Var_02    CAQ  CAP  CAO  CAB  -179.93  30.0  3
 0EH  Var_03    CAR  CAQ  CAP  CAO   179.76  30.0  1
 0EH  Var_04    CAS  CAR  CAQ  CAP   179.70  30.0  1
 0EH  Var_05    CAT  CAS  CAR  CAQ   179.94  30.0  3
 0EH  Var_06    H20  CAT  CAS  CAR   -60.31  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
 0EH  chir_01  CAF  CAA  CAB  NAC  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
 0EH  plan-1  OAD  0.020
 0EH  plan-1  CAE  0.020
 0EH  plan-1  CAF  0.020
 0EH  plan-1  O1   0.020
 0EH  plan-1  H1   0.020

