# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:09:00 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: N~6~-ethanethioyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=S)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
 TLY  TLY  N~6~-ethanethioyl-L-lysine  L-peptide  28  13  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_TLY
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
 TLY  C    C  C      0   0.385  13.7196  -3.1140   -6.9861
 TLY  N    N  NH2    0  -0.806  14.4081  -5.3335   -6.0926
 TLY  O    O  O      0  -0.604  13.0482  -2.8980   -5.9586
 TLY  CA   C  CH1    0  -0.158  14.0825  -4.5847   -7.3037
 TLY  CB   C  CH2    0  -0.423  12.9044  -5.2809   -7.9882
 TLY  CD   C  CH2    0  -0.472  11.4210  -5.5241  -10.0155
 TLY  CE   C  CH2    0  -0.234  10.9783  -4.9095  -11.3326
 TLY  CG   C  CH2    0  -0.423  12.5035  -4.6956   -9.3363
 TLY  CX   C  C      0   0.204   9.3015  -5.4045  -13.0604
 TLY  SX   S  S1     0  -0.404   9.5450  -3.9727  -13.8840
 TLY  CY   C  CH3    0  -0.722   8.3038  -6.4134  -13.5487
 TLY  NZ   N  NH1    0  -0.549   9.9617  -5.7259  -11.9658
 TLY  OXT  O  OC    -1  -0.615  14.1099  -2.2650   -7.8149
 TLY  H    H  HNH2   0   0.329  14.7704  -6.2411   -6.3602
 TLY  H2   H  HNH2   0   0.332  15.1652  -4.8754   -5.6002
 TLY  HA   H  HCH1   0   0.169  14.9189  -4.5687   -8.0192
 TLY  HB   H  HCH2   0   0.209  13.1631  -6.3375   -8.1298
 TLY  HBA  H  HCH2   0   0.206  12.0452  -5.2671   -7.3098
 TLY  HD   H  HCH2   0   0.231  10.5572  -5.6154   -9.3496
 TLY  HDA  H  HCH2   0   0.230  11.7922  -6.5393  -10.1902
 TLY  HE   H  HCH2   0   0.242  10.5756  -3.9064  -11.1726
 TLY  HEA  H  HCH2   0   0.241  11.8278  -4.8001  -12.0131
 TLY  HG   H  HCH2   0   0.221  12.1480  -3.6696   -9.2115
 TLY  HGA  H  HCH2   0   0.212  13.3801  -4.6379   -9.9896
 TLY  HY   H  HCH3   0   0.268   7.3258  -5.9451  -13.6451
 TLY  HYA  H  HCH3   0   0.269   8.5941  -6.7610  -14.5394
 TLY  HYB  H  HCH3   0   0.249   8.2133  -7.2782  -12.8917
 TLY  HNZ  H  HNH1   0   0.413   9.7581  -6.6176  -11.5358

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
 TLY  C   O    deloc   1.231  0.020  1.231
 TLY  C   CA   single  1.525  0.021  1.525
 TLY  C   OXT  deloc   1.249  0.020  1.249
 TLY  N   CA   single  1.458  0.019  1.458
 TLY  CA  CB   single  1.530  0.020  1.530
 TLY  CB  CG   single  1.523  0.020  1.523
 TLY  CD  CE   single  1.519  0.020  1.519
 TLY  CD  CG   single  1.523  0.020  1.523
 TLY  CE  NZ   single  1.450  0.020  1.450
 TLY  CX  SX   double  1.670  0.020  1.670
 TLY  CX  CY   single  1.501  0.020  1.501
 TLY  CX  NZ   single  1.318  0.020  1.318
 TLY  N   H    single  0.860  0.020  0.860
 TLY  N   H2   single  0.890  0.020  1.040
 TLY  CA  HA   single  0.970  0.020  0.970
 TLY  CB  HB   single  0.970  0.020  1.090
 TLY  CB  HBA  single  0.970  0.020  1.090
 TLY  CD  HD   single  0.970  0.020  1.090
 TLY  CD  HDA  single  0.970  0.020  1.090
 TLY  CE  HE   single  0.970  0.020  1.090
 TLY  CE  HEA  single  0.970  0.020  1.090
 TLY  CG  HG   single  0.970  0.020  1.090
 TLY  CG  HGA  single  0.970  0.020  1.090
 TLY  CY  HY   single  0.970  0.020  1.090
 TLY  CY  HYA  single  0.970  0.020  1.090
 TLY  CY  HYB  single  0.970  0.020  1.090
 TLY  NZ  HNZ  single  0.860  0.020  1.020

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
 TLY  OXT  C   CA   115.88  3.000
 TLY  OXT  C   O    126.70  3.000
 TLY  CA   C   O    120.80  1.700
 TLY  H2   N   H    105.44  3.000
 TLY  H2   N   CA   109.75  3.000
 TLY  H    N   CA   114.00  3.000
 TLY  HA   CA  CB   109.00  3.000
 TLY  HA   CA  N    110.00  3.000
 TLY  CB   CA  N    110.50  1.700
 TLY  HA   CA  C    109.00  3.000
 TLY  CB   CA  C    110.10  1.900
 TLY  N    CA  C    111.00  2.800
 TLY  HBA  CB  HB   106.09  3.000
 TLY  HBA  CB  CG   109.69  3.000
 TLY  HB   CB  CG   108.54  3.000
 TLY  HBA  CB  CA   108.74  3.000
 TLY  HB   CB  CA   108.33  3.000
 TLY  CG   CB  CA   115.06  3.000
 TLY  HDA  CD  HD   106.70  3.000
 TLY  HDA  CD  CG   109.54  3.000
 TLY  HD   CD  CG   109.57  3.000
 TLY  HDA  CD  CE   109.60  3.000
 TLY  HD   CD  CE   109.35  3.000
 TLY  CG   CD  CE   111.94  3.000
 TLY  HEA  CE  HE   106.60  3.000
 TLY  HEA  CE  NZ   109.22  3.000
 TLY  HE   CE  NZ   108.82  3.000
 TLY  HEA  CE  CD   110.70  3.000
 TLY  HE   CE  CD   110.60  3.000
 TLY  NZ   CE  CD   110.80  3.000
 TLY  HGA  CG  HG   106.20  3.000
 TLY  HGA  CG  CD   109.37  3.000
 TLY  HG   CG  CD   109.29  3.000
 TLY  HGA  CG  CB   109.74  3.000
 TLY  HG   CG  CB   110.20  3.000
 TLY  CD   CG  CB   111.88  3.000
 TLY  NZ   CX  CY   116.06  3.000
 TLY  NZ   CX  SX   123.07  3.000
 TLY  CY   CX  SX   120.86  3.000
 TLY  HYB  CY  HYA  108.49  3.000
 TLY  HYB  CY  HY   108.67  3.000
 TLY  HYA  CY  HY   107.22  3.000
 TLY  HYB  CY  CX   113.11  3.000
 TLY  HYA  CY  CX   109.47  3.000
 TLY  HY   CY  CX   109.69  3.000
 TLY  HNZ  NZ  CX   117.88  3.000
 TLY  HNZ  NZ  CE   116.89  3.000
 TLY  CX   NZ  CE   125.22  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
 TLY  Var_01  CD  CG  CB  CA  174.30  30.0  3
 TLY  Var_02  CE  CD  CG  CB  177.58  30.0  1
 TLY  Var_03  CX  NZ  CE  CD  174.10  30.0  3
 TLY  Var_04  SX  CX  NZ  CE   -0.38  30.0  1
 TLY  Var_05  NZ  CE  CD  CG  179.24  30.0  3
 TLY  Var_06  HY  CY  CX  SX  -55.78  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
 TLY  chir_01  CA  C  N  CB  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
 TLY  plan-1  C    0.020
 TLY  plan-1  O    0.020
 TLY  plan-1  CA   0.020
 TLY  plan-1  OXT  0.020
 TLY  plan-2  CX   0.020
 TLY  plan-2  SX   0.020
 TLY  plan-2  CY   0.020
 TLY  plan-2  NZ   0.020

