# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:30:47 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 2-methyl-D-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](N)(CCCCN)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
 0XO  0XO  '2-methyl-D-lysine        '  D-peptide  27  11  .  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_0XO
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
 0XO  CAD  C  CT    0  -0.058  -1.2831   0.3967   0.0918
 0XO  CAE  C  C     0   0.573  -2.4782  -0.5494  -0.0084
 0XO  CAZ  C  CH2   0  -0.405   0.0045  -0.4466  -0.0217
 0XO  NAC  N  NH2   0  -0.785  -1.3900   1.4416  -0.9126
 0XO  OAG  O  O     0  -0.451  -2.5077  -1.6399   0.5099
 0XO  CBA  C  CH3   0  -0.660  -1.3957   1.0551   1.4750
 0XO  C02  C  CH2   0  -0.270   3.8248   0.2737   0.0127
 0XO  N02  N  NH2   0  -0.801   4.9829  -0.5935  -0.1529
 0XO  C3   C  CH2   0  -0.423   2.5304  -0.5188  -0.0823
 0XO  C4   C  CH2   0  -0.435   1.2950   0.3538   0.1010
 0XO  H7   H  HCH2  0   0.226   0.0002  -1.2314   0.7381
 0XO  H8   H  HCH2  0   0.228  -0.0014  -0.9584  -0.9914
 0XO  H9   H  HNH2  0   0.350  -0.6653   2.1294  -0.7511
 0XO  H14  H  HCH3  0   0.244  -0.6183   1.8096   1.6000
 0XO  H15  H  HCH3  0   0.247  -2.3575   1.5555   1.5929
 0XO  H16  H  HCH3  0   0.240  -1.2839   0.3221   2.2731
 0XO  H41  H  HCH2  0   0.211   3.8849   0.7410   0.9999
 0XO  H42  H  HCH2  0   0.186   3.7889   1.0990  -0.7142
 0XO  H43  H  HNH2  0   0.336   4.9857  -0.9661  -1.0950
 0XO  H44  H  HCH2  0   0.212   2.4831  -1.0158  -1.0582
 0XO  H45  H  HCH2  0   0.214   2.5408  -1.3147   0.6691
 0XO  H46  H  HCH2  0   0.207   1.3143   1.1563  -0.6433
 0XO  H47  H  HCH2  0   0.223   1.3448   0.8406   1.0799
 0XO  OXT  O  OH1   0  -0.577  -3.5062  -0.0498  -0.6772
 0XO  HXT  H  HOH1  0   0.476  -4.2359  -0.6874  -0.6590
 0XO  H2   H  HNH2  0   0.346  -1.2127   1.0649  -1.8369
 0XO  H1   H  HNH2  0   0.345   5.8290  -0.0430  -0.0790

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
 0XO  CAE  OAG  double  1.208  0.020  1.208
 0XO  CAE  CAD  single  1.528  0.020  1.528
 0XO  NAC  CAD  single  1.453  0.020  1.453
 0XO  CAD  CBA  single  1.536  0.020  1.536
 0XO  CAD  CAZ  single  1.543  0.020  1.543
 0XO  CAZ  C4   single  1.524  0.020  1.524
 0XO  C4   C3   single  1.524  0.020  1.524
 0XO  N02  C02  single  1.456  0.020  1.456
 0XO  C02  C3   single  1.521  0.020  1.521
 0XO  CAZ  H7   single  0.970  0.020  1.090
 0XO  CAZ  H8   single  0.970  0.020  1.090
 0XO  NAC  H9   single  0.890  0.020  1.040
 0XO  CBA  H14  single  0.970  0.020  1.090
 0XO  CBA  H15  single  0.970  0.020  1.090
 0XO  CBA  H16  single  0.970  0.020  1.090
 0XO  C02  H41  single  0.970  0.020  1.090
 0XO  C02  H42  single  0.970  0.020  1.090
 0XO  N02  H43  single  0.890  0.020  1.040
 0XO  C3   H44  single  0.970  0.020  1.090
 0XO  C3   H45  single  0.970  0.020  1.090
 0XO  C4   H46  single  0.970  0.020  1.090
 0XO  C4   H47  single  0.970  0.020  1.090
 0XO  CAE  OXT  single  1.324  0.020  1.324
 0XO  OXT  HXT  single  0.850  0.020  0.980
 0XO  NAC  H2   single  0.890  0.020  1.040
 0XO  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
 0XO  CBA  CAD  NAC  107.98  3.000
 0XO  CBA  CAD  CAZ  111.20  3.000
 0XO  NAC  CAD  CAZ  113.79  3.000
 0XO  CAZ  CAD  CAE  108.03  3.000
 0XO  CBA  CAD  CAE  105.50  3.000
 0XO  NAC  CAD  CAE  110.02  3.000
 0XO  OXT  CAE  OAG  122.58  3.000
 0XO  OXT  CAE  CAD  114.00  3.000
 0XO  OAG  CAE  CAD  123.38  3.000
 0XO  H8   CAZ  H7   106.24  3.000
 0XO  H8   CAZ  C4   108.72  3.000
 0XO  H7   CAZ  C4   108.95  3.000
 0XO  H8   CAZ  CAD  108.40  3.000
 0XO  H7   CAZ  CAD  109.76  3.000
 0XO  C4   CAZ  CAD  114.44  3.000
 0XO  H2   NAC  H9   105.83  3.000
 0XO  H2   NAC  CAD  110.49  3.000
 0XO  H9   NAC  CAD  109.00  3.000
 0XO  H16  CBA  H15  108.67  3.000
 0XO  H16  CBA  H14  107.96  3.000
 0XO  H15  CBA  H14  107.38  3.000
 0XO  H16  CBA  CAD  111.34  3.000
 0XO  H15  CBA  CAD  111.02  3.000
 0XO  H14  CBA  CAD  110.34  3.000
 0XO  H42  C02  H41  106.12  3.000
 0XO  H42  C02  C3   108.78  3.000
 0XO  H41  C02  C3   109.01  3.000
 0XO  H42  C02  N02  113.42  3.000
 0XO  H41  C02  N02  108.26  3.000
 0XO  C3   C02  N02  111.06  3.000
 0XO  H1   N02  H43  105.40  3.000
 0XO  H1   N02  C02  109.42  3.000
 0XO  H43  N02  C02  109.08  3.000
 0XO  H45  C3   H44  106.38  3.000
 0XO  H45  C3   C4   109.97  3.000
 0XO  H44  C3   C4   109.38  3.000
 0XO  H45  C3   C02  109.15  3.000
 0XO  H44  C3   C02  109.19  3.000
 0XO  C4   C3   C02  112.59  3.000
 0XO  H47  C4   H46  106.34  3.000
 0XO  H47  C4   C3   109.00  3.000
 0XO  H46  C4   C3   108.89  3.000
 0XO  H47  C4   CAZ  110.14  3.000
 0XO  H46  C4   CAZ  110.20  3.000
 0XO  C3   C4   CAZ  112.10  3.000
 0XO  HXT  OXT  CAE  109.07  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
 0XO  CONST_01  HXT  OXT  CAE  CAD   180.00   0.0  0
 0XO  Var_01    C3   C4   CAZ  CAD  -177.38  30.0  3
 0XO  Var_02    C02  C3   C4   CAZ   178.95  30.0  3
 0XO  Var_03    C4   C3   C02  N02   179.40  30.0  3
 0XO  Var_04    H43  N02  C02  C3     65.56  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
 0XO  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
 0XO  plan-1  CAD  0.020
 0XO  plan-1  CAE  0.020
 0XO  plan-1  OAG  0.020
 0XO  plan-1  OXT  0.020
 0XO  plan-1  HXT  0.020

