# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:15:45 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  39  15  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (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  -0.786   3.5305   1.8246   0.2995
 5T3  CA   C  CH1   0  -0.216   3.3718   0.3885   0.3874
 5T3  C    C  C     0   0.546   4.5733  -0.2827  -0.2451
 5T3  O    O  O     0  -0.440   5.3428   0.2529  -1.0018
 5T3  CB   C  CH2   0  -0.436   2.0861  -0.1819  -0.2433
 5T3  CG   C  CH2   0  -0.429   0.8190   0.3775   0.3896
 5T3  CD   C  CH2   0  -0.421  -0.4457  -0.2382  -0.1952
 5T3  CE   C  CH2   0  -0.269  -1.7057   0.2980   0.4734
 5T3  NZ   N  NT    0  -0.413  -2.9179  -0.2910  -0.0661
 5T3  CH1  C  CH1   0  -0.103  -4.0941   0.5768  -0.0107
 5T3  CH2  C  CH2   0  -0.290  -3.1792  -1.6277   0.4442
 5T3  CT1  C  CH3   0  -0.669  -4.3542   1.2114   1.3594
 5T3  CT2  C  CH3   0  -0.659  -3.8843  -2.5118  -0.5729
 5T3  CT3  C  CH3   0  -0.645  -4.0420   1.6362  -1.1055
 5T3  H    H  HNH2  0   0.344   3.4041   2.1347  -0.6569
 5T3  H2   H  HNH2  0   0.358   2.8021   2.2735   0.8385
 5T3  HA   H  HCH1  0   0.267   3.3689   0.1204   1.4494
 5T3  HB2  H  HCH2  0   0.228   2.0871   0.0315  -1.3180
 5T3  HB3  H  HCH2  0   0.233   2.0790  -1.2704  -0.1426
 5T3  HG2  H  HCH2  0   0.218   0.8461   0.1974   1.4702
 5T3  HG3  H  HCH2  0   0.214   0.7800   1.4634   0.2597
 5T3  HD2  H  HCH2  0   0.215  -0.5012  -0.0348  -1.2687
 5T3  HD3  H  HCH2  0   0.216  -0.3941  -1.3266  -0.0912
 5T3  HE2  H  HCH2  0   0.192  -1.6230   0.1599   1.5644
 5T3  HE3  H  HCH2  0   0.224  -1.7334   1.3785   0.3142
 5T3  H15  H  HCH1  0   0.224  -4.9523  -0.0644  -0.2327
 5T3  H16  H  HCH2  0   0.227  -2.2267  -2.0950   0.7010
 5T3  H17  H  HCH2  0   0.197  -3.7583  -1.6043   1.3807
 5T3  H18  H  HCH3  0   0.215  -3.6083   1.9708   1.6021
 5T3  H19  H  HCH3  0   0.228  -5.3305   1.6986   1.3722
 5T3  H20  H  HCH3  0   0.227  -4.3480   0.4682   2.1592
 5T3  H21  H  HCH3  0   0.221  -4.8494  -2.1019  -0.8733
 5T3  H22  H  HCH3  0   0.218  -3.2761  -2.6228  -1.4711
 5T3  H23  H  HCH3  0   0.220  -4.0671  -3.5043  -0.1592
 5T3  H24  H  HCH3  0   0.225  -3.9507   1.1719  -2.0877
 5T3  H25  H  HCH3  0   0.219  -4.9497   2.2416  -1.0985
 5T3  H26  H  HCH3  0   0.215  -3.1979   2.3162  -0.9764
 5T3  OXT  O  OH1   0  -0.596   4.6683  -1.5610   0.1059
 5T3  HXT  H  HOH1  0   0.480   5.4148  -1.9762  -0.3511

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  1.523  0.020  1.523
 5T3  CG   CD   single  1.523  0.020  1.523
 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    double  1.231  0.020  1.231
 5T3  CE   NZ   single  1.452  0.020  1.452
 5T3  NZ   CH1  single  1.463  0.020  1.463
 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  single  1.329  0.020  1.329
 5T3  OXT  HXT  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
 5T3  H2   N    H    106.11  3.000
 5T3  H2   N    CA   109.21  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    123.21  3.000
 5T3  OXT  C    CA   111.88  3.000
 5T3  O    C    CA   120.80  1.700
 5T3  HB3  CB   HB2  106.52  3.000
 5T3  HB3  CB   CG   108.79  3.000
 5T3  HB2  CB   CG   109.69  3.000
 5T3  HB3  CB   CA   109.64  3.000
 5T3  HB2  CB   CA   109.18  3.000
 5T3  CG   CB   CA   112.83  3.000
 5T3  HG3  CG   HG2  106.32  3.000
 5T3  HG3  CG   CD   109.02  3.000
 5T3  HG2  CG   CD   109.43  3.000
 5T3  HG3  CG   CB   110.17  3.000
 5T3  HG2  CG   CB   109.21  3.000
 5T3  CD   CG   CB   112.51  3.000
 5T3  HD3  CD   HD2  106.29  3.000
 5T3  HD3  CD   CE   110.32  3.000
 5T3  HD2  CD   CE   108.86  3.000
 5T3  HD3  CD   CG   109.04  3.000
 5T3  HD2  CD   CG   110.10  3.000
 5T3  CE   CD   CG   112.08  3.000
 5T3  HE3  CE   HE2  105.66  3.000
 5T3  HE3  CE   NZ   109.02  3.000
 5T3  HE2  CE   NZ   112.30  3.000
 5T3  HE3  CE   CD   107.76  3.000
 5T3  HE2  CE   CD   109.15  3.000
 5T3  NZ   CE   CD   112.62  3.000
 5T3  CH2  NZ   CH1  112.80  3.000
 5T3  CH1  NZ   CE   114.62  3.000
 5T3  CH2  NZ   CE   113.11  3.000
 5T3  H15  CH1  CT3  106.76  3.000
 5T3  H15  CH1  CT1  106.92  3.000
 5T3  CT3  CH1  CT1  111.11  3.000
 5T3  H15  CH1  NZ   105.98  3.000
 5T3  CT1  CH1  NZ   114.59  3.000
 5T3  CT3  CH1  NZ   110.96  3.000
 5T3  H17  CH2  H16  105.54  3.000
 5T3  H17  CH2  CT2  109.71  3.000
 5T3  H16  CH2  CT2  108.24  3.000
 5T3  H17  CH2  NZ   111.92  3.000
 5T3  H16  CH2  NZ   108.62  3.000
 5T3  CT2  CH2  NZ   112.51  3.000
 5T3  H20  CT1  H19  107.48  3.000
 5T3  H20  CT1  H18  107.86  3.000
 5T3  H19  CT1  H18  107.34  3.000
 5T3  H20  CT1  CH1  111.85  3.000
 5T3  H19  CT1  CH1  110.33  3.000
 5T3  H18  CT1  CH1  111.77  3.000
 5T3  H23  CT2  H22  108.25  3.000
 5T3  H23  CT2  H21  107.34  3.000
 5T3  H22  CT2  H21  107.75  3.000
 5T3  H23  CT2  CH2  110.67  3.000
 5T3  H22  CT2  CH2  110.58  3.000
 5T3  H21  CT2  CH2  112.08  3.000
 5T3  H26  CT3  H25  107.27  3.000
 5T3  H26  CT3  H24  107.88  3.000
 5T3  H25  CT3  H24  108.17  3.000
 5T3  H26  CT3  CH1  111.99  3.000
 5T3  H25  CT3  CH1  110.65  3.000
 5T3  H24  CT3  CH1  110.73  3.000
 5T3  HXT  OXT  C    110.04  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  CONST_01  HXT  OXT  C    CA   180.00   0.0  0
 5T3  Var_01    CD   CG   CB   CA  -177.38  30.0  1
 5T3  Var_02    CE   CD   CG   CB   178.31  30.0  3
 5T3  Var_03    NZ   CE   CD   CG  -179.42  30.0  3
 5T3  Var_04    CH2  NZ   CE   CD    78.32  30.0  3
 5T3  Var_05    CT2  CH2  NZ   CE  -148.08  30.0  1
 5T3  Var_06    CT3  CH1  NZ   CE    76.89  30.0  3
 5T3  Var_07    H21  CT2  CH2  NZ   -60.08  30.0  3
 5T3  Var_08    H24  CT3  CH1  NZ    56.60  30.0  3
 5T3  Var_09    H18  CT1  CH1  NZ    70.45  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
 5T3  plan-1  HXT  0.020

