# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 22:17:34 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N~6~-ethyl-N~6~-propan-2-yl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CCCC[C@H](N)C(O)=O)C(C)C
#
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
 5T3  5T3  N~6~-ethyl-N~6~-propan-2-yl-L-lysine  L-peptide  38  15  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_5T3
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
 5T3  N    N  NH2    0  -0.803   3.5171   1.8890   0.2268
 5T3  CA   C  CH1    0  -0.199   3.3739   0.4464   0.3507
 5T3  C    C  C      0   0.403   4.5667  -0.2730  -0.3140
 5T3  O    O  O      0  -0.610   5.1317   0.3162  -1.2578
 5T3  CB   C  CH2    0  -0.425   2.0765  -0.1272  -0.2440
 5T3  CG   C  CH2    0  -0.427   0.8020   0.4028   0.4016
 5T3  CD   C  CH2    0  -0.418  -0.4609  -0.2186  -0.1822
 5T3  CE   C  CH2    0  -0.268  -1.7250   0.2983   0.4933
 5T3  NZ   N  NT     0  -0.414  -2.9352  -0.2730  -0.0698
 5T3  CH1  C  CH1    0  -0.102  -4.1125   0.5904   0.0090
 5T3  CH2  C  CH2    0  -0.290  -3.1994  -1.6276   0.3889
 5T3  CT1  C  CH3    0  -0.669  -4.3840   1.1738   1.3992
 5T3  CT2  C  CH3    0  -0.659  -3.8805  -2.4767  -0.6739
 5T3  CT3  C  CH3    0  -0.646  -4.0580   1.6878  -1.0476
 5T3  H    H  HNH2   0   0.325   3.6974   2.1070  -0.7452
 5T3  H2   H  HNH2   0   0.332   2.6517   2.3521   0.4742
 5T3  HA   H  HCH1   0   0.195   3.3801   0.1970   1.4189
 5T3  HB2  H  HCH2   0   0.205   2.0539   0.0801  -1.3207
 5T3  HB3  H  HCH2   0   0.209   2.0949  -1.2166  -0.1396
 5T3  HG2  H  HCH2   0   0.210   0.8386   0.2132   1.4805
 5T3  HG3  H  HCH2   0   0.202   0.7414   1.4909   0.2867
 5T3  HD2  H  HCH2   0   0.210  -0.5217  -0.0046  -1.2536
 5T3  HD3  H  HCH2   0   0.212  -0.3979  -1.3078  -0.0907
 5T3  HE2  H  HCH2   0   0.190  -1.6485   0.1315   1.5808
 5T3  HE3  H  HCH2   0   0.222  -1.7514   1.3829   0.3629
 5T3  H15  H  HCH1   0   0.224  -4.9677  -0.0435  -0.2436
 5T3  H16  H  HCH2   0   0.227  -2.2503  -2.1002   0.6485
 5T3  H17  H  HCH2   0   0.197  -3.7982  -1.6389   1.3131
 5T3  H18  H  HCH3   0   0.216  -3.6431   1.9268   1.6748
 5T3  H19  H  HCH3   0   0.228  -5.3625   1.6561   1.4237
 5T3  H20  H  HCH3   0   0.227  -4.3789   0.4020   2.1713
 5T3  H21  H  HCH3   0   0.221  -4.8390  -2.0559  -0.9808
 5T3  H22  H  HCH3   0   0.218  -3.2521  -2.5555  -1.5615
 5T3  H23  H  HCH3   0   0.219  -4.0717  -3.4835  -0.3002
 5T3  H24  H  HCH3   0   0.224  -3.9650   1.2575  -2.0451
 5T3  H25  H  HCH3   0   0.219  -4.9662   2.2918  -1.0219
 5T3  H26  H  HCH3   0   0.215  -3.2150   2.3648  -0.8956
 5T3  OXT  O  OC    -1  -0.621   4.8371  -1.4126   0.1159

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
 5T3  N    CA   single  1.458  0.019  1.458
 5T3  CA   CB   single  1.530  0.020  1.530
 5T3  CA   C    single  1.525  0.021  1.525
 5T3  CG   CB   single  1.524  0.020  1.524
 5T3  CG   CD   single  1.524  0.020  1.524
 5T3  CH2  NZ   single  1.454  0.020  1.454
 5T3  CH2  CT2  single  1.521  0.020  1.521
 5T3  CD   CE   single  1.524  0.020  1.524
 5T3  C    O    deloc   1.231  0.020  1.231
 5T3  CE   NZ   single  1.452  0.020  1.452
 5T3  NZ   CH1  single  1.462  0.020  1.462
 5T3  CH1  CT3  single  1.524  0.020  1.524
 5T3  CH1  CT1  single  1.532  0.020  1.532
 5T3  N    H    single  0.860  0.020  0.860
 5T3  N    H2   single  0.890  0.020  1.040
 5T3  CA   HA   single  0.970  0.020  0.970
 5T3  CB   HB2  single  0.970  0.020  1.090
 5T3  CB   HB3  single  0.970  0.020  1.090
 5T3  CG   HG2  single  0.970  0.020  1.090
 5T3  CG   HG3  single  0.970  0.020  1.090
 5T3  CD   HD2  single  0.970  0.020  1.090
 5T3  CD   HD3  single  0.970  0.020  1.090
 5T3  CE   HE2  single  0.970  0.020  1.090
 5T3  CE   HE3  single  0.970  0.020  1.090
 5T3  CH1  H15  single  0.970  0.020  1.090
 5T3  CH2  H16  single  0.970  0.020  1.090
 5T3  CH2  H17  single  0.970  0.020  1.090
 5T3  CT1  H18  single  0.970  0.020  1.090
 5T3  CT1  H19  single  0.970  0.020  1.090
 5T3  CT1  H20  single  0.970  0.020  1.090
 5T3  CT2  H21  single  0.970  0.020  1.090
 5T3  CT2  H22  single  0.970  0.020  1.090
 5T3  CT2  H23  single  0.970  0.020  1.090
 5T3  CT3  H24  single  0.970  0.020  1.090
 5T3  CT3  H25  single  0.970  0.020  1.090
 5T3  CT3  H26  single  0.970  0.020  1.090
 5T3  C    OXT  deloc   1.248  0.020  1.248

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
 5T3  H2   N    H    106.77  3.000
 5T3  H2   N    CA   110.40  3.000
 5T3  H    N    CA   114.00  3.000
 5T3  HA   CA   CB   109.00  3.000
 5T3  HA   CA   C    109.00  3.000
 5T3  CB   CA   C    110.10  1.900
 5T3  HA   CA   N    110.00  3.000
 5T3  C    CA   N    111.00  2.800
 5T3  CB   CA   N    110.50  1.700
 5T3  OXT  C    O    126.42  3.000
 5T3  OXT  C    CA   116.41  3.000
 5T3  O    C    CA   120.80  1.700
 5T3  HB3  CB   HB2  106.39  3.000
 5T3  HB3  CB   CG   108.66  3.000
 5T3  HB2  CB   CG   109.45  3.000
 5T3  HB3  CB   CA   108.67  3.000
 5T3  HB2  CB   CA   109.05  3.000
 5T3  CG   CB   CA   114.33  3.000
 5T3  HG3  CG   HG2  106.07  3.000
 5T3  HG3  CG   CD   108.60  3.000
 5T3  HG2  CG   CD   109.53  3.000
 5T3  HG3  CG   CB   110.32  3.000
 5T3  HG2  CG   CB   109.20  3.000
 5T3  CD   CG   CB   112.89  3.000
 5T3  HD3  CD   HD2  106.23  3.000
 5T3  HD3  CD   CE   110.38  3.000
 5T3  HD2  CD   CE   108.76  3.000
 5T3  HD3  CD   CG   109.03  3.000
 5T3  HD2  CD   CG   109.96  3.000
 5T3  CE   CD   CG   112.30  3.000
 5T3  HE3  CE   HE2  105.63  3.000
 5T3  HE3  CE   NZ   108.92  3.000
 5T3  HE2  CE   NZ   112.38  3.000
 5T3  HE3  CE   CD   107.69  3.000
 5T3  HE2  CE   CD   109.16  3.000
 5T3  NZ   CE   CD   112.72  3.000
 5T3  CH2  NZ   CH1  112.75  3.000
 5T3  CH1  NZ   CE   114.71  3.000
 5T3  CH2  NZ   CE   113.30  3.000
 5T3  H15  CH1  CT3  106.56  3.000
 5T3  H15  CH1  CT1  106.96  3.000
 5T3  CT3  CH1  CT1  111.18  3.000
 5T3  H15  CH1  NZ   105.95  3.000
 5T3  CT1  CH1  NZ   114.61  3.000
 5T3  CT3  CH1  NZ   111.04  3.000
 5T3  H17  CH2  H16  105.59  3.000
 5T3  H17  CH2  CT2  109.70  3.000
 5T3  H16  CH2  CT2  108.28  3.000
 5T3  H17  CH2  NZ   111.90  3.000
 5T3  H16  CH2  NZ   108.68  3.000
 5T3  CT2  CH2  NZ   112.39  3.000
 5T3  H20  CT1  H19  107.50  3.000
 5T3  H20  CT1  H18  107.81  3.000
 5T3  H19  CT1  H18  107.34  3.000
 5T3  H20  CT1  CH1  111.83  3.000
 5T3  H19  CT1  CH1  110.34  3.000
 5T3  H18  CT1  CH1  111.81  3.000
 5T3  H23  CT2  H22  108.25  3.000
 5T3  H23  CT2  H21  107.36  3.000
 5T3  H22  CT2  H21  107.77  3.000
 5T3  H23  CT2  CH2  110.75  3.000
 5T3  H22  CT2  CH2  110.55  3.000
 5T3  H21  CT2  CH2  112.00  3.000
 5T3  H26  CT3  H25  107.23  3.000
 5T3  H26  CT3  H24  107.83  3.000
 5T3  H25  CT3  H24  108.12  3.000
 5T3  H26  CT3  CH1  112.18  3.000
 5T3  H25  CT3  CH1  110.64  3.000
 5T3  H24  CT3  CH1  110.68  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
 5T3  Var_01  CD   CG   CB   CA  -178.21  30.0  1
 5T3  Var_02  CE   CD   CG   CB   178.76  30.0  3
 5T3  Var_03  NZ   CE   CD   CG   179.13  30.0  3
 5T3  Var_04  CH2  NZ   CE   CD    77.86  30.0  3
 5T3  Var_05  CT2  CH2  NZ   CE  -147.10  30.0  2
 5T3  Var_06  CT3  CH1  NZ   CE    76.75  30.0  3
 5T3  Var_07  H21  CT2  CH2  NZ   -59.81  30.0  3
 5T3  Var_08  H24  CT3  CH1  NZ    56.83  30.0  3
 5T3  Var_09  H18  CT1  CH1  NZ    70.61  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
 5T3  chir_01  CA  N  CB  C  negativ

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
 5T3  plan-1  CA   0.020
 5T3  plan-1  C    0.020
 5T3  plan-1  O    0.020
 5T3  plan-1  OXT  0.020

