# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 21:56:53 2022
#   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  "Hypusine"  peptide  38  16  .  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_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  -0.425   2.0294   0.4706   0.3927
 5CT  CD   C  CH2    0  -0.438   0.7706  -0.1362  -0.2136
 5CT  CE   C  CH2    0  -0.248  -0.5053   0.4654   0.3533
 5CT  NZ   N  NH1    0  -0.596  -1.6855  -0.1354  -0.2364
 5CT  C1   C  CH2    0  -0.265  -2.9167   0.3996   0.3017
 5CT  C2   C  CH1    0   0.006  -4.1510  -0.2492  -0.3148
 5CT  C3   C  CH2    0  -0.457  -5.4233   0.3898   0.2324
 5CT  C4   C  CH2    0  -0.270  -6.6954  -0.1486  -0.4030
 5CT  N1   N  NH2    0  -0.800  -7.8659   0.5013   0.1682
 5CT  O1   O  OH1    0  -0.664  -4.1531  -1.6535  -0.1589
 5CT  CB   C  CH2    0  -0.425   3.3070  -0.1639  -0.1431
 5CT  CA   C  CH1    0  -0.203   4.5973   0.4079   0.4678
 5CT  C    C  C      0   0.404   5.7877  -0.4439  -0.0213
 5CT  O    O  O      0  -0.610   6.4765   0.0175  -0.9532
 5CT  N    N  NH2    0  -0.800   4.8283   1.8173   0.1927
 5CT  OXT  O  OC    -1  -0.623   5.9359  -1.5527   0.5320
 5CT  H1   H  HCH2   0   0.204   2.0301   1.5495   0.2023
 5CT  H2   H  HCH2   0   0.210   2.0017   0.3549   1.4822
 5CT  H3   H  HCH2   0   0.212   0.7879   0.0054  -1.3004
 5CT  H4   H  HCH2   0   0.214   0.7621  -1.2173  -0.0444
 5CT  H5   H  HCH2   0   0.211  -0.5386   0.2894   1.4338
 5CT  H6   H  HCH2   0   0.181  -0.4780   1.5613   0.2278
 5CT  H7   H  HNH1   0   0.333  -1.6667   0.0241  -1.2377
 5CT  H9   H  HCH2   0   0.214  -2.9238   0.2273   1.3852
 5CT  H10  H  HCH2   0   0.191  -3.0031   1.4913   0.1726
 5CT  H11  H  HCH1   0   0.214  -4.1201  -0.0834  -1.3991
 5CT  H12  H  HCH2   0   0.217  -5.4708   0.2474   1.3183
 5CT  H13  H  HCH2   0   0.220  -5.3682   1.4711   0.0672
 5CT  H14  H  HCH2   0   0.186  -6.6199  -0.0382  -1.4953
 5CT  H15  H  HCH2   0   0.215  -6.7735  -1.2201  -0.2085
 5CT  H16  H  HNH2   0   0.336  -7.8721   1.4783  -0.0993
 5CT  H17  H  HNH2   0   0.345  -8.7037   0.1032  -0.2361
 5CT  H19  H  HOH1   0   0.438  -4.1375  -1.8499   0.7841
 5CT  H20  H  HCH2   0   0.210   3.2708  -1.2400   0.0519
 5CT  H21  H  HCH2   0   0.205   3.3458  -0.0475  -1.2331
 5CT  H22  H  HCH1   0   0.197   4.5219   0.2854   1.5553
 5CT  H23  H  HNH2   0   0.325   5.0505   1.9196  -0.7897
 5CT  H24  H  HNH2   0   0.332   3.9845   2.3515   0.3582

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    deloc   1.231  0.020  1.231
 5CT  CB  CG   single  1.524  0.020  1.524
 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  1.446  0.020  1.446
 5CT  C1  C2   single  1.525  0.020  1.525
 5CT  C2  O1   single  1.413  0.020  1.413
 5CT  C   OXT  deloc   1.248  0.020  1.248
 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

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   106.07  3.000
 5CT  H2   CG  CB   109.07  3.000
 5CT  H1   CG  CB   110.39  3.000
 5CT  H2   CG  CD   109.43  3.000
 5CT  H1   CG  CD   108.88  3.000
 5CT  CB   CG  CD   112.77  3.000
 5CT  H4   CD  H3   106.32  3.000
 5CT  H4   CD  CE   109.07  3.000
 5CT  H3   CD  CE   109.38  3.000
 5CT  H4   CD  CG   109.78  3.000
 5CT  H3   CD  CG   109.28  3.000
 5CT  CE   CD  CG   112.80  3.000
 5CT  H6   CE  H5   105.82  3.000
 5CT  H6   CE  NZ   112.68  3.000
 5CT  H5   CE  NZ   108.06  3.000
 5CT  H6   CE  CD   109.26  3.000
 5CT  H5   CE  CD   109.26  3.000
 5CT  NZ   CE  CD   111.56  3.000
 5CT  H7   NZ  C1   108.96  3.000
 5CT  H7   NZ  CE   108.75  3.000
 5CT  C1   NZ  CE   112.85  3.000
 5CT  H10  C1  H9   105.69  3.000
 5CT  H10  C1  C2   108.09  3.000
 5CT  H9   C1  C2   109.10  3.000
 5CT  H10  C1  NZ   112.92  3.000
 5CT  H9   C1  NZ   108.35  3.000
 5CT  C2   C1  NZ   112.42  3.000
 5CT  H11  C2  O1   105.02  3.000
 5CT  H11  C2  C3   108.34  3.000
 5CT  O1   C2  C3   112.06  3.000
 5CT  H11  C2  C1   108.20  3.000
 5CT  O1   C2  C1   112.31  3.000
 5CT  C3   C2  C1   110.61  3.000
 5CT  H13  C3  H12  106.25  3.000
 5CT  H13  C3  C4   109.19  3.000
 5CT  H12  C3  C4   109.37  3.000
 5CT  H13  C3  C2   108.51  3.000
 5CT  H12  C3  C2   109.70  3.000
 5CT  C4   C3  C2   113.55  3.000
 5CT  H15  C4  H14  106.28  3.000
 5CT  H15  C4  N1   108.11  3.000
 5CT  H14  C4  N1   113.57  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  105.60  3.000
 5CT  H17  N1  C4   109.47  3.000
 5CT  H16  N1  C4   109.39  3.000
 5CT  H19  O1  C2   108.10  3.000
 5CT  H21  CB  H20  106.42  3.000
 5CT  H21  CB  CA   109.01  3.000
 5CT  H20  CB  CA   108.83  3.000
 5CT  H21  CB  CG   109.56  3.000
 5CT  H20  CB  CG   108.61  3.000
 5CT  CA   CB  CG   114.14  3.000
 5CT  H22  CA  N    107.86  3.000
 5CT  H22  CA  C    107.79  3.000
 5CT  N    CA  C    111.00  2.800
 5CT  H22  CA  CB   107.14  3.000
 5CT  C    CA  CB   110.10  1.900
 5CT  N    CA  CB   110.50  1.700
 5CT  OXT  C   O    126.46  3.000
 5CT  OXT  C   CA   116.20  3.000
 5CT  O    C   CA   120.80  1.700
 5CT  H24  N   H23  106.75  3.000
 5CT  H24  N   CA   110.37  3.000
 5CT  H23  N   CA   108.44  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  Var_01  NZ   CE  CD  CG  -179.70  30.0  3
 5CT  Var_02  CA   CB  CG  CD  -178.93  30.0  2
 5CT  Var_03  C1   NZ  CE  CD   178.92  30.0  3
 5CT  Var_04  CB   CG  CD  CE   178.15  30.0  2
 5CT  Var_05  C2   C1  NZ  CE  -179.41  30.0  1
 5CT  Var_06  N1   C4  C3  C2   179.84  30.0  1
 5CT  Var_07  H5   CE  CD  CG   -60.29  30.0  3
 5CT  Var_08  H6   CE  CD  CG    55.05  30.0  3
 5CT  Var_09  H20  CB  CG  CD   -57.33  30.0  2
 5CT  Var_10  H21  CB  CG  CD    58.52  30.0  2
 5CT  Var_11  H7   NZ  CE  CD   -60.05  30.0  3
 5CT  Var_12  H1   CG  CD  CE   -58.96  30.0  2
 5CT  Var_13  H2   CG  CD  CE    56.56  30.0  2
 5CT  Var_14  H9   C1  NZ  CE   -58.76  30.0  1
 5CT  Var_15  H10  C1  NZ  CE    57.97  30.0  1
 5CT  Var_16  H3   CD  CE  NZ    58.46  30.0  1
 5CT  Var_17  H4   CD  CE  NZ   -57.45  30.0  1
 5CT  Var_18  H5   CE  NZ  C1    58.80  30.0  1
 5CT  Var_19  H6   CE  NZ  C1   -57.75  30.0  1
 5CT  Var_20  H14  C4  C3  C2   -54.84  30.0  1
 5CT  Var_21  H15  C4  C3  C2    60.88  30.0  1
 5CT  Var_22  H7   NZ  C1  C2    59.69  30.0  3
 5CT  Var_23  H16  N1  C4  C3    67.19  30.0  3
 5CT  Var_24  H17  N1  C4  C3  -177.55  30.0  3
 5CT  Var_25  H12  C3  C4  N1    56.95  30.0  3
 5CT  Var_26  H13  C3  C4  N1   -58.93  30.0  3
 5CT  Var_27  H3   CD  CG  CB   -59.95  30.0  3
 5CT  Var_28  H4   CD  CG  CB    56.29  30.0  3
 5CT  Var_29  H1   CG  CB  CA    59.03  30.0  3
 5CT  Var_30  H2   CG  CB  CA   -57.14  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

