# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:33:46 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2R)-2,8-diamino-2-methyloctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](N)(CCCCCCN)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
 0XQ  0XQ  '(2R)-2,8-diamino-2-methyloctanoic acid'  D-peptide  33  13  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0XQ
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
 0XQ  CAD  C  CT    0  -0.051  -2.3653   0.4186   0.0525
 0XQ  CAE  C  C     0   0.559  -3.5411  -0.5696  -0.0024
 0XQ  CAZ  C  CH2   0  -0.404  -1.0592  -0.3851  -0.0477
 0XQ  NAC  N  NH2   0  -0.782  -2.3853   1.4233  -0.9927
 0XQ  OAG  O  O     0  -0.448  -3.5291  -1.6771   0.4784
 0XQ  CBA  C  CH3   0  -0.663  -2.4905   1.1261   1.4088
 0XQ  C01  C  CH2   0  -0.426   4.0073  -0.4679  -0.1026
 0XQ  C02  C  CH2   0  -0.271   5.2899   0.3401   0.0172
 0XQ  N02  N  NH2   0  -0.801   6.4623  -0.5134  -0.1198
 0XQ  C3   C  CH2   0  -0.417   2.7547   0.3835   0.0557
 0XQ  C05  C  CH2   0  -0.415   0.2143   0.4380   0.0915
 0XQ  C06  C  CH2   0  -0.411   1.4651  -0.4158  -0.0798
 0XQ  H7   H  HCH2  0   0.229  -1.0611  -1.1699   0.7117
 0XQ  H8   H  HNH2  0   0.346  -2.3831   0.9910  -1.9085
 0XQ  H13  H  HCH3  0   0.250  -1.7162   1.8857   1.5051
 0XQ  H14  H  HCH3  0   0.243  -3.4553   1.6287   1.5040
 0XQ  H15  H  HCH3  0   0.239  -2.3903   0.4236   2.2359
 0XQ  H41  H  HCH2  0   0.209   3.9856  -0.9678  -1.0782
 0XQ  H42  H  HCH2  0   0.211   4.0139  -1.2626   0.6504
 0XQ  H43  H  HCH2  0   0.185   5.2603   1.1626  -0.7131
 0XQ  H44  H  HCH2  0   0.209   5.3226   0.8113   1.0039
 0XQ  H45  H  HNH2  0   0.336   6.4875  -0.8925  -1.0590
 0XQ  H46  H  HCH2  0   0.208   2.7727   0.8786   1.0332
 0XQ  H47  H  HCH2  0   0.208   2.7612   1.1864  -0.6899
 0XQ  H48  H  HCH2  0   0.216   0.2178   1.2453  -0.6448
 0XQ  H49  H  HCH2  0   0.208   1.4435  -0.9034  -1.0610
 0XQ  H50  H  HCH2  0   0.208   1.4603  -1.2246   0.6594
 0XQ  H51  H  HCH2  0   0.227  -1.0442  -0.9006  -1.0158
 0XQ  H34  H  HCH2  0   0.214   0.2456   0.9178   1.0744
 0XQ  OXT  O  OH1   0  -0.590  -4.6147  -0.0615  -0.5955
 0XQ  HXT  H  HOH1  0   0.479  -5.3442  -0.6979  -0.5530
 0XQ  H2   H  HNH2  0   0.350  -3.2214   1.9908  -0.9409
 0XQ  H1   H  HNH2  0   0.344   7.2998   0.0486  -0.0345

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
 0XQ  CAE  OAG  double  1.207  0.020  1.207
 0XQ  CAE  CAD  single  1.537  0.020  1.537
 0XQ  NAC  CAD  single  1.450  0.020  1.450
 0XQ  CAD  CBA  single  1.535  0.020  1.535
 0XQ  CAD  CAZ  single  1.537  0.020  1.537
 0XQ  CAZ  C05  single  1.523  0.020  1.523
 0XQ  N02  C02  single  1.457  0.020  1.457
 0XQ  C05  C06  single  1.524  0.020  1.524
 0XQ  C02  C01  single  1.521  0.020  1.521
 0XQ  C06  C3   single  1.523  0.020  1.523
 0XQ  C01  C3   single  1.523  0.020  1.523
 0XQ  CAZ  H7   single  0.970  0.020  1.090
 0XQ  NAC  H8   single  0.890  0.020  1.040
 0XQ  CBA  H13  single  0.970  0.020  1.090
 0XQ  CBA  H14  single  0.970  0.020  1.090
 0XQ  CBA  H15  single  0.970  0.020  1.090
 0XQ  C01  H41  single  0.970  0.020  1.090
 0XQ  C01  H42  single  0.970  0.020  1.090
 0XQ  C02  H43  single  0.970  0.020  1.090
 0XQ  C02  H44  single  0.970  0.020  1.090
 0XQ  N02  H45  single  0.890  0.020  1.040
 0XQ  C3   H46  single  0.970  0.020  1.090
 0XQ  C3   H47  single  0.970  0.020  1.090
 0XQ  C05  H48  single  0.970  0.020  1.090
 0XQ  C06  H49  single  0.970  0.020  1.090
 0XQ  C06  H50  single  0.970  0.020  1.090
 0XQ  CAZ  H51  single  0.970  0.020  1.090
 0XQ  C05  H34  single  0.970  0.020  1.090
 0XQ  CAE  OXT  single  1.328  0.020  1.328
 0XQ  OXT  HXT  single  0.850  0.020  0.980
 0XQ  NAC  H2   single  0.890  0.020  1.040
 0XQ  N02  H1   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
 0XQ  CBA  CAD  NAC  108.45  3.000
 0XQ  CBA  CAD  CAZ  111.60  3.000
 0XQ  NAC  CAD  CAZ  109.09  3.000
 0XQ  CAZ  CAD  CAE  108.16  3.000
 0XQ  CBA  CAD  CAE  105.40  3.000
 0XQ  NAC  CAD  CAE  114.15  3.000
 0XQ  OXT  CAE  OAG  122.48  3.000
 0XQ  OXT  CAE  CAD  112.87  3.000
 0XQ  OAG  CAE  CAD  124.61  3.000
 0XQ  H51  CAZ  H7   106.03  3.000
 0XQ  H51  CAZ  C05  108.86  3.000
 0XQ  H7   CAZ  C05  109.04  3.000
 0XQ  H51  CAZ  CAD  108.36  3.000
 0XQ  H7   CAZ  CAD  109.21  3.000
 0XQ  C05  CAZ  CAD  114.97  3.000
 0XQ  H2   NAC  H8   106.71  3.000
 0XQ  H2   NAC  CAD  111.29  3.000
 0XQ  H8   NAC  CAD  110.86  3.000
 0XQ  H15  CBA  H14  108.17  3.000
 0XQ  H15  CBA  H13  108.48  3.000
 0XQ  H14  CBA  H13  107.43  3.000
 0XQ  H15  CBA  CAD  111.47  3.000
 0XQ  H14  CBA  CAD  111.18  3.000
 0XQ  H13  CBA  CAD  109.98  3.000
 0XQ  H42  C01  H41  106.33  3.000
 0XQ  H42  C01  C3   109.83  3.000
 0XQ  H41  C01  C3   109.34  3.000
 0XQ  H42  C01  C02  109.06  3.000
 0XQ  H41  C01  C02  109.21  3.000
 0XQ  C3   C01  C02  112.86  3.000
 0XQ  H44  C02  H43  106.11  3.000
 0XQ  H44  C02  N02  108.24  3.000
 0XQ  H43  C02  N02  113.40  3.000
 0XQ  H44  C02  C01  108.98  3.000
 0XQ  H43  C02  C01  108.80  3.000
 0XQ  N02  C02  C01  111.11  3.000
 0XQ  H1   N02  H45  105.39  3.000
 0XQ  H1   N02  C02  109.44  3.000
 0XQ  H45  N02  C02  109.05  3.000
 0XQ  H47  C3   H46  106.01  3.000
 0XQ  H47  C3   C06  109.21  3.000
 0XQ  H46  C3   C06  109.29  3.000
 0XQ  H47  C3   C01  109.51  3.000
 0XQ  H46  C3   C01  109.38  3.000
 0XQ  C06  C3   C01  113.19  3.000
 0XQ  H34  C05  H48  106.33  3.000
 0XQ  H34  C05  C06  108.85  3.000
 0XQ  H48  C05  C06  109.60  3.000
 0XQ  H34  C05  CAZ  110.07  3.000
 0XQ  H48  C05  CAZ  109.91  3.000
 0XQ  C06  C05  CAZ  111.92  3.000
 0XQ  H50  C06  H49  105.99  3.000
 0XQ  H50  C06  C05  109.52  3.000
 0XQ  H49  C06  C05  109.49  3.000
 0XQ  H50  C06  C3   109.33  3.000
 0XQ  H49  C06  C3   109.26  3.000
 0XQ  C05  C06  C3   113.01  3.000
 0XQ  HXT  OXT  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
 0XQ  CONST_01  HXT  OXT  CAE  CAD   180.00   0.0  0
 0XQ  Var_01    C06  C05  CAZ  CAD  -177.48  30.0  3
 0XQ  Var_02    C3   C06  C05  CAZ  -179.96  30.0  3
 0XQ  Var_03    C05  C06  C3   C01   179.49  30.0  1
 0XQ  Var_04    C3   C01  C02  N02   179.14  30.0  3
 0XQ  Var_05    H45  N02  C02  C01    65.30  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
 0XQ  chir_01  CAD  NAC  CBA  CAZ  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
 0XQ  plan-1  CAD  0.020
 0XQ  plan-1  CAE  0.020
 0XQ  plan-1  OAG  0.020
 0XQ  plan-1  OXT  0.020
 0XQ  plan-1  HXT  0.020

