# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 05:59:13 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N~6~-propan-2-yl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NCCCC[C@H](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
 ILY  ILY  N~6~-propan-2-yl-L-lysine  ligand  33  13  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ILY
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
 ILY  CH1  C  CH3   0  -0.667  -5.0046   1.3084  -0.0409
 ILY  C1   C  CH1   0  -0.085  -4.6149  -0.1395   0.2605
 ILY  CH2  C  CH3   0  -0.656  -5.6703  -1.0996  -0.2720
 ILY  NZ   N  NH1   0  -0.592  -3.3123  -0.5326  -0.2618
 ILY  CE   C  CH2   0  -0.251  -2.1784   0.1578   0.3225
 ILY  CD   C  CH2   0  -0.440  -0.8663  -0.3785  -0.2280
 ILY  CG   C  CH2   0  -0.412   0.3491   0.3104   0.3788
 ILY  CB   C  CH2   0  -0.431   1.6559  -0.2373  -0.1778
 ILY  CA   C  CH1   0  -0.206   2.8976   0.4147   0.4469
 ILY  N    N  NH2   0  -0.776   2.9200   1.8333   0.1822
 ILY  C    C  C     0   0.520   4.1381  -0.3162  -0.0493
 ILY  O    O  O     0  -0.442   4.9069   0.1167  -0.8716
 ILY  OXT  O  OH1   0  -0.594   4.2735  -1.5123   0.5136
 ILY  H1   H  HCH3  0   0.223  -5.9595   1.5633   0.4215
 ILY  H2   H  HCH3  0   0.229  -4.2628   2.0167   0.3298
 ILY  H3   H  HCH3  0   0.211  -5.1059   1.4614  -1.1186
 ILY  H4   H  HCH1  0   0.213  -4.5614  -0.2590   1.3489
 ILY  H5   H  HCH3  0   0.227  -5.4363  -2.1306  -0.0052
 ILY  H6   H  HCH3  0   0.222  -6.6571  -0.8612   0.1266
 ILY  H7   H  HCH3  0   0.214  -5.7328  -1.0390  -1.3619
 ILY  H8   H  HCH2  0   0.186  -2.2032   1.2487   0.1756
 ILY  H9   H  HCH2  0   0.214  -0.8133  -1.4565  -0.0477
 ILY  H10  H  HCH2  0   0.213  -0.8510  -0.2468  -1.3161
 ILY  H11  H  HCH2  0   0.223   0.2942   1.3867   0.2008
 ILY  H12  H  HCH2  0   0.213   0.3387   0.1780   1.4663
 ILY  H13  H  HCH2  0   0.239   1.6903  -1.3167  -0.0112
 ILY  H14  H  HCH2  0   0.228   1.6851  -0.0934  -1.2639
 ILY  H15  H  HCH1  0   0.264   2.8426   0.2687   1.5307
 ILY  H16  H  HNH2  0   0.353   3.7068   2.2674   0.6475
 ILY  H17  H  HNH2  0   0.342   3.0493   2.0001  -0.8085
 ILY  HXT  H  HOH1  0   0.480   5.0448  -1.9683   0.1448
 ILY  H18  H  HNH1  0   0.328  -3.3049  -0.3933  -1.2674
 ILY  H19  H  HCH2  0   0.210  -2.2103   0.0003   1.4061

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
 ILY  N    CA   single  1.443  0.020  1.443
 ILY  CA   C    single  1.523  0.020  1.523
 ILY  CA   CB   single  1.535  0.020  1.535
 ILY  C    O    double  1.206  0.020  1.206
 ILY  CB   CG   single  1.522  0.020  1.522
 ILY  CG   CD   single  1.523  0.020  1.523
 ILY  CD   CE   single  1.521  0.020  1.521
 ILY  CH2  C1   single  1.523  0.020  1.523
 ILY  CE   NZ   single  1.450  0.020  1.450
 ILY  C1   NZ   single  1.457  0.020  1.457
 ILY  C1   CH1  single  1.529  0.020  1.529
 ILY  C    OXT  single  1.329  0.020  1.329
 ILY  CH1  H1   single  0.970  0.020  1.090
 ILY  CH1  H2   single  0.970  0.020  1.090
 ILY  CH1  H3   single  0.970  0.020  1.090
 ILY  C1   H4   single  0.970  0.020  1.090
 ILY  CH2  H5   single  0.970  0.020  1.090
 ILY  CH2  H6   single  0.970  0.020  1.090
 ILY  CH2  H7   single  0.970  0.020  1.090
 ILY  CE   H8   single  0.970  0.020  1.090
 ILY  CD   H9   single  0.970  0.020  1.090
 ILY  CD   H10  single  0.970  0.020  1.090
 ILY  CG   H11  single  0.970  0.020  1.090
 ILY  CG   H12  single  0.970  0.020  1.090
 ILY  CB   H13  single  0.970  0.020  1.090
 ILY  CB   H14  single  0.970  0.020  1.090
 ILY  CA   H15  single  0.970  0.020  1.090
 ILY  N    H16  single  0.890  0.020  1.040
 ILY  N    H17  single  0.890  0.020  1.040
 ILY  OXT  HXT  single  0.850  0.020  0.980
 ILY  NZ   H18  single  0.890  0.020  1.040
 ILY  CE   H19  single  0.970  0.020  1.090

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
 ILY  H3   CH1  H2   107.88  3.000
 ILY  H3   CH1  H1   107.70  3.000
 ILY  H2   CH1  H1   107.43  3.000
 ILY  H3   CH1  C1   110.51  3.000
 ILY  H2   CH1  C1   112.00  3.000
 ILY  H1   CH1  C1   111.15  3.000
 ILY  H4   C1   NZ   106.43  3.000
 ILY  H4   C1   CH2  108.19  3.000
 ILY  NZ   C1   CH2  108.91  3.000
 ILY  H4   C1   CH1  108.14  3.000
 ILY  NZ   C1   CH1  114.36  3.000
 ILY  CH2  C1   CH1  110.57  3.000
 ILY  H7   CH2  H6   107.49  3.000
 ILY  H7   CH2  H5   107.98  3.000
 ILY  H6   CH2  H5   108.15  3.000
 ILY  H7   CH2  C1   110.68  3.000
 ILY  H6   CH2  C1   111.19  3.000
 ILY  H5   CH2  C1   111.21  3.000
 ILY  H18  NZ   CE   109.15  3.000
 ILY  H18  NZ   C1   108.93  3.000
 ILY  CE   NZ   C1   115.21  3.000
 ILY  H19  CE   H8   105.89  3.000
 ILY  H19  CE   CD   109.42  3.000
 ILY  H8   CE   CD   108.69  3.000
 ILY  H19  CE   NZ   107.90  3.000
 ILY  H8   CE   NZ   113.60  3.000
 ILY  CD   CE   NZ   111.15  3.000
 ILY  H10  CD   H9   106.33  3.000
 ILY  H10  CD   CG   109.27  3.000
 ILY  H9   CD   CG   109.96  3.000
 ILY  H10  CD   CE   109.21  3.000
 ILY  H9   CD   CE   109.24  3.000
 ILY  CG   CD   CE   112.63  3.000
 ILY  H12  CG   H11  106.28  3.000
 ILY  H12  CG   CB   109.13  3.000
 ILY  H11  CG   CB   109.76  3.000
 ILY  H12  CG   CD   109.47  3.000
 ILY  H11  CG   CD   109.91  3.000
 ILY  CB   CG   CD   112.12  3.000
 ILY  H14  CB   H13  106.26  3.000
 ILY  H14  CB   CA   109.02  3.000
 ILY  H13  CB   CA   109.39  3.000
 ILY  H14  CB   CG   109.76  3.000
 ILY  H13  CB   CG   109.07  3.000
 ILY  CA   CB   CG   113.12  3.000
 ILY  H15  CA   C    107.42  3.000
 ILY  H15  CA   N    108.27  3.000
 ILY  C    CA   N    113.54  3.000
 ILY  H15  CA   CB   107.79  3.000
 ILY  C    CA   CB   108.80  3.000
 ILY  N    CA   CB   110.82  3.000
 ILY  H17  N    H16  106.26  3.000
 ILY  H17  N    CA   110.07  3.000
 ILY  H16  N    CA   110.45  3.000
 ILY  OXT  C    O    123.16  3.000
 ILY  OXT  C    CA   112.15  3.000
 ILY  O    C    CA   124.68  3.000
 ILY  HXT  OXT  C    110.09  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
 ILY  CONST_01  HXT  OXT  C   CA    180.00   0.0  0
 ILY  Var_01    CE   NZ   C1  CH1    65.05  30.0  3
 ILY  Var_02    CD   CE   NZ  C1    176.68  30.0  1
 ILY  Var_03    CG   CD   CE  NZ   -179.18  30.0  1
 ILY  Var_04    CB   CG   CD  CE    179.87  30.0  1
 ILY  Var_05    CA   CB   CG  CD   -178.42  30.0  1
 ILY  Var_06    H5   CH2  C1  CH1  -176.23  30.0  3
 ILY  Var_07    H1   CH1  C1  CH2    59.91  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
 ILY  chir_01  CA  N  C  CB  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
 ILY  plan-1  CA   0.020
 ILY  plan-1  C    0.020
 ILY  plan-1  O    0.020
 ILY  plan-1  OXT  0.020
 ILY  plan-1  HXT  0.020

