# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:31:05 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@H](O)CNCCCC[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
 5CT  5CT  N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine  peptide  39  16  .  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_5CT
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
 5CT  CG   C  CH2   0  -0.427   2.0465   0.5057   0.3306
 5CT  CD   C  CH2   0  -0.440   0.7855  -0.1005  -0.2712
 5CT  CE   C  CH2   0  -0.248  -0.4855   0.5002   0.3071
 5CT  NZ   N  NH1   0  -0.597  -1.6689  -0.1057  -0.2710
 5CT  C1   C  CH2   0  -0.265  -2.8973   0.4206   0.2830
 5CT  C2   C  CH1   0   0.006  -4.1341  -0.2374  -0.3187
 5CT  C3   C  CH2   0  -0.458  -5.4040   0.3960   0.2400
 5CT  C4   C  CH2   0  -0.270  -6.6802  -0.1502  -0.3806
 5CT  N1   N  NH2   0  -0.800  -7.8478   0.4978   0.1991
 5CT  O1   O  OH1   0  -0.664  -4.1259  -1.6411  -0.1587
 5CT  CB   C  CH2   0  -0.436   3.3140  -0.1392  -0.2141
 5CT  CA   C  CH1   0  -0.216   4.5974   0.4399   0.4131
 5CT  C    C  C     0   0.546   5.7856  -0.3561  -0.0847
 5CT  O    O  O     0  -0.441   6.5818   0.0347  -0.9006
 5CT  N    N  NH2   0  -0.785   4.8354   1.8468   0.1675
 5CT  OXT  O  OH1   0  -0.595   5.8332  -1.5686   0.4566
 5CT  H1   H  HCH2  0   0.214   2.0565   1.5822   0.1363
 5CT  H2   H  HCH2  0   0.220   2.0232   0.3883   1.4197
 5CT  H3   H  HCH2  0   0.217   0.7961   0.0434  -1.3574
 5CT  H4   H  HCH2  0   0.218   0.7779  -1.1817  -0.1033
 5CT  H5   H  HCH2  0   0.213  -0.5077   0.3255   1.3881
 5CT  H6   H  HCH2  0   0.183  -0.4630   1.5958   0.1796
 5CT  H7   H  HNH1  0   0.334  -1.6628   0.0581  -1.2719
 5CT  H9   H  HCH2  0   0.214  -2.8897   0.2477   1.3663
 5CT  H10  H  HCH2  0   0.192  -2.9918   1.5116   0.1549
 5CT  H11  H  HCH1  0   0.214  -4.1155  -0.0745  -1.4037
 5CT  H12  H  HCH2  0   0.218  -5.4398   0.2564   1.3267
 5CT  H13  H  HCH2  0   0.220  -5.3558   1.4771   0.0717
 5CT  H14  H  HCH2  0   0.187  -6.6160  -0.0439  -1.4740
 5CT  H15  H  HCH2  0   0.215  -6.7521  -1.2212  -0.1810
 5CT  H16  H  HNH2  0   0.336  -7.8565   1.4748  -0.0679
 5CT  H17  H  HNH2  0   0.345  -8.6877   0.0993  -0.2004
 5CT  H19  H  HOH1  0   0.438  -4.1137  -1.8344   0.7850
 5CT  H20  H  HCH2  0   0.234   3.2662  -1.2159  -0.0305
 5CT  H21  H  HCH2  0   0.229   3.3580  -0.0100  -1.3013
 5CT  H22  H  HCH1  0   0.267   4.5333   0.2958   1.4967
 5CT  H23  H  HNH2  0   0.344   4.7805   2.0426  -0.8250
 5CT  H24  H  HNH2  0   0.357   4.1048   2.3931   0.6038
 5CT  H26  H  HOH1  0   0.481   6.5668  -2.0730   0.0748

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
 5CT  N    CA   single  1.458  0.019  1.458
 5CT  CA   C    single  1.525  0.021  1.525
 5CT  CA   CB   single  1.530  0.020  1.530
 5CT  C    O    double  1.231  0.020  1.231
 5CT  CB   CG   single  1.523  0.020  1.523
 5CT  N1   C4   single  1.456  0.020  1.456
 5CT  CG   CD   single  1.523  0.020  1.523
 5CT  CD   CE   single  1.520  0.020  1.520
 5CT  C4   C3   single  1.521  0.020  1.521
 5CT  C3   C2   single  1.525  0.020  1.525
 5CT  CE   NZ   single  1.450  0.020  1.450
 5CT  C1   NZ   single  1.447  0.020  1.447
 5CT  C1   C2   single  1.525  0.020  1.525
 5CT  C2   O1   single  1.413  0.020  1.413
 5CT  C    OXT  single  1.329  0.020  1.329
 5CT  CG   H1   single  0.970  0.020  1.090
 5CT  CG   H2   single  0.970  0.020  1.090
 5CT  CD   H3   single  0.970  0.020  1.090
 5CT  CD   H4   single  0.970  0.020  1.090
 5CT  CE   H5   single  0.970  0.020  1.090
 5CT  CE   H6   single  0.970  0.020  1.090
 5CT  NZ   H7   single  0.890  0.020  1.040
 5CT  C1   H9   single  0.970  0.020  1.090
 5CT  C1   H10  single  0.970  0.020  1.090
 5CT  C2   H11  single  0.970  0.020  1.090
 5CT  C3   H12  single  0.970  0.020  1.090
 5CT  C3   H13  single  0.970  0.020  1.090
 5CT  C4   H14  single  0.970  0.020  1.090
 5CT  C4   H15  single  0.970  0.020  1.090
 5CT  N1   H16  single  0.890  0.020  1.040
 5CT  N1   H17  single  0.890  0.020  1.040
 5CT  O1   H19  single  0.850  0.020  0.980
 5CT  CB   H20  single  0.970  0.020  1.090
 5CT  CB   H21  single  0.970  0.020  1.090
 5CT  CA   H22  single  0.970  0.020  1.090
 5CT  N    H23  single  0.890  0.020  1.040
 5CT  N    H24  single  0.890  0.020  1.040
 5CT  OXT  H26  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
 5CT  H2   CG   H1   106.39  3.000
 5CT  H2   CG   CB   109.14  3.000
 5CT  H1   CG   CB   110.22  3.000
 5CT  H2   CG   CD   109.42  3.000
 5CT  H1   CG   CD   109.21  3.000
 5CT  CB   CG   CD   112.29  3.000
 5CT  H4   CD   H3   106.38  3.000
 5CT  H4   CD   CE   109.04  3.000
 5CT  H3   CD   CE   109.47  3.000
 5CT  H4   CD   CG   109.78  3.000
 5CT  H3   CD   CG   109.35  3.000
 5CT  CE   CD   CG   112.62  3.000
 5CT  H6   CE   H5   105.84  3.000
 5CT  H6   CE   NZ   112.69  3.000
 5CT  H5   CE   NZ   108.08  3.000
 5CT  H6   CE   CD   109.35  3.000
 5CT  H5   CE   CD   109.23  3.000
 5CT  NZ   CE   CD   111.45  3.000
 5CT  H7   NZ   C1   108.92  3.000
 5CT  H7   NZ   CE   108.73  3.000
 5CT  C1   NZ   CE   112.85  3.000
 5CT  H10  C1   H9   105.74  3.000
 5CT  H10  C1   C2   108.16  3.000
 5CT  H9   C1   C2   109.10  3.000
 5CT  H10  C1   NZ   112.85  3.000
 5CT  H9   C1   NZ   108.35  3.000
 5CT  C2   C1   NZ   112.38  3.000
 5CT  H11  C2   O1   105.03  3.000
 5CT  H11  C2   C3   108.34  3.000
 5CT  O1   C2   C3   112.09  3.000
 5CT  H11  C2   C1   108.20  3.000
 5CT  O1   C2   C1   112.29  3.000
 5CT  C3   C2   C1   110.59  3.000
 5CT  H13  C3   H12  106.23  3.000
 5CT  H13  C3   C4   109.20  3.000
 5CT  H12  C3   C4   109.36  3.000
 5CT  H13  C3   C2   108.48  3.000
 5CT  H12  C3   C2   109.72  3.000
 5CT  C4   C3   C2   113.59  3.000
 5CT  H15  C4   H14  106.28  3.000
 5CT  H15  C4   N1   108.12  3.000
 5CT  H14  C4   N1   113.54  3.000
 5CT  H15  C4   C3   109.45  3.000
 5CT  H14  C4   C3   108.78  3.000
 5CT  N1   C4   C3   110.53  3.000
 5CT  H17  N1   H16  105.58  3.000
 5CT  H17  N1   C4   109.47  3.000
 5CT  H16  N1   C4   109.35  3.000
 5CT  H19  O1   C2   108.08  3.000
 5CT  H21  CB   H20  106.53  3.000
 5CT  H21  CB   CA   109.03  3.000
 5CT  H20  CB   CA   109.76  3.000
 5CT  H21  CB   CG   109.78  3.000
 5CT  H20  CB   CG   108.70  3.000
 5CT  CA   CB   CG   112.85  3.000
 5CT  H22  CA   N    107.77  3.000
 5CT  H22  CA   C    107.58  3.000
 5CT  N    CA   C    111.00  2.800
 5CT  H22  CA   CB   107.73  3.000
 5CT  C    CA   CB   110.10  1.900
 5CT  N    CA   CB   110.50  1.700
 5CT  OXT  C    O    123.24  3.000
 5CT  OXT  C    CA   111.95  3.000
 5CT  O    C    CA   120.80  1.700
 5CT  H24  N    H23  106.21  3.000
 5CT  H24  N    CA   109.45  3.000
 5CT  H23  N    CA   110.18  3.000
 5CT  H26  OXT  C    109.98  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
 5CT  CONST_01  H26  OXT  C   CA   180.00   0.0  0
 5CT  Var_01    NZ   CE   CD  CG  -179.30  30.0  3
 5CT  Var_02    CA   CB   CG  CD  -178.53  30.0  1
 5CT  Var_03    C1   NZ   CE  CD   178.54  30.0  3
 5CT  Var_04    CB   CG   CD  CE   177.76  30.0  1
 5CT  Var_05    C2   C1   NZ  CE  -179.22  30.0  1
 5CT  Var_06    N1   C4   C3  C2   179.99  30.0  1
 5CT  Var_07    H16  N1   C4  C3    66.82  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
 5CT  chir_01  C2  C3  C1  O1  negativ
 5CT  chir_02  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
 5CT  plan-1  CA   0.020
 5CT  plan-1  C    0.020
 5CT  plan-1  O    0.020
 5CT  plan-1  OXT  0.020
 5CT  plan-1  H26  0.020

