# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:55:19 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: N~6~-[(6R)-6,8-disulfanyloctanoyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)CCCC[C@@H](S)CCS)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
 LA2  LA2  N~6~-[(6R)-6,8-disulfanyloctanoyl]-L-lysine  L-peptide  48  21  .  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_LA2
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
 LA2  CB   C  CH2    0  -0.446  76.0204  84.4609  61.7182
 LA2  C    C  C      0   0.385  76.7627  86.6320  60.7161
 LA2  O    O  O      0  -0.618  75.9187  87.4293  61.1780
 LA2  N    N  NH2    0  -0.788  77.0888  84.4116  59.5189
 LA2  CA   C  CH1    0  -0.209  76.2430  85.2067  60.3983
 LA2  O1   O  O      0  -0.504  70.8801  82.4182  62.4052
 LA2  C1   C  C      0   0.543  70.7309  83.0885  61.3904
 LA2  NZ   N  NH1    0  -0.631  71.6838  83.9054  60.9113
 LA2  CE   C  CH2    0  -0.283  73.0039  84.0251  61.4928
 LA2  CD   C  CH2    0  -0.445  74.0207  83.0707  60.8735
 LA2  CG   C  CH2    0  -0.417  75.3702  83.0856  61.5883
 LA2  C2   C  CH2    0  -0.565  69.4429  83.0419  60.5953
 LA2  C3   C  CH2    0  -0.416  68.2102  83.2755  61.4635
 LA2  C4   C  CH2    0  -0.406  66.9145  83.0877  60.6857
 LA2  C5   C  CH2    0  -0.399  65.6864  83.3107  61.5564
 LA2  C6   C  CH1    0  -0.386  64.3502  83.1958  60.8326
 LA2  S6   S  S2     0  -0.230  64.1220  81.5605  60.0376
 LA2  C7   C  CH2    0  -0.398  63.1476  83.4888  61.7315
 LA2  C8   C  CH2    0  -0.561  63.1631  84.8394  62.4358
 LA2  S8   S  S2     0  -0.265  63.2404  86.1897  61.2085
 LA2  HB   H  HCH2   0   0.218  75.4232  85.0924  62.3800
 LA2  HBA  H  HCH2   0   0.215  76.9886  84.3421  62.2187
 LA2  OXT  O  OC    -1  -0.603  77.9731  86.8582  60.5164
 LA2  HN   H  HNH2   0   0.331  77.1217  84.8574  58.6096
 LA2  HNA  H  HNH2   0   0.320  78.0397  84.4789  59.8656
 LA2  HA   H  HCH1   0   0.207  75.2727  85.3204  59.9020
 LA2  HNZ  H  HNH1   0   0.395  71.5064  84.4028  60.0543
 LA2  HE   H  HCH2   0   0.242  73.3266  85.0600  61.3675
 LA2  HEA  H  HCH2   0   0.235  72.9271  83.8461  62.5659
 LA2  HD   H  HCH2   0   0.230  73.6167  82.0553  60.9033
 LA2  HDA  H  HCH2   0   0.218  74.1504  83.3175  59.8159
 LA2  HG   H  HCH2   0   0.218  76.0479  82.4076  61.0660
 LA2  HGA  H  HCH2   0   0.213  75.2410  82.6692  62.5927
 LA2  H2   H  HCH2   0   0.243  69.4575  83.7568  59.7688
 LA2  H2A  H  HCH2   0   0.256  69.3811  82.0475  60.1413
 LA2  H3   H  HCH2   0   0.224  68.2249  82.5862  62.3113
 LA2  H3A  H  HCH2   0   0.224  68.2455  84.2850  61.8843
 LA2  H4   H  HCH2   0   0.214  66.8887  83.7798  59.8369
 LA2  H4A  H  HCH2   0   0.219  66.8919  82.0814  60.2603
 LA2  H5   H  HCH2   0   0.223  65.6952  82.6150  62.4032
 LA2  H5A  H  HCH2   0   0.235  65.7487  84.3155  61.9866
 LA2  H6   H  HCH1   0   0.275  64.3497  83.8834  59.9804
 LA2  HS6  H  HSH1   0   0.213  64.1915  80.8298  61.1583
 LA2  H7   H  HCH2   0   0.250  62.2332  83.4030  61.1407
 LA2  H7A  H  HCH2   0   0.249  63.0893  82.7197  62.5076
 LA2  H8   H  HCH2   0   0.282  62.2505  84.9444  63.0214
 LA2  H8A  H  HCH2   0   0.269  64.0081  84.9240  63.1176
 LA2  HS8  H  HSH1   0   0.223  63.2310  87.2100  62.0730

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
 LA2  CB  CG   single  1.527  0.020  1.527
 LA2  CB  HB   single  0.970  0.020  1.090
 LA2  CB  HBA  single  0.970  0.020  1.090
 LA2  C   CA   single  1.525  0.021  1.525
 LA2  C   OXT  deloc   1.247  0.020  1.247
 LA2  O   C    deloc   1.231  0.020  1.231
 LA2  N   CA   single  1.458  0.019  1.458
 LA2  N   HN   single  0.890  0.020  1.040
 LA2  N   HNA  single  0.890  0.020  1.040
 LA2  CA  CB   single  1.530  0.020  1.530
 LA2  CA  HA   single  0.970  0.020  0.970
 LA2  C1  O1   double  1.225  0.020  1.225
 LA2  NZ  C1   single  1.344  0.020  1.344
 LA2  NZ  CE   single  1.447  0.020  1.447
 LA2  NZ  HNZ  single  0.860  0.020  1.020
 LA2  CE  HE   single  0.970  0.020  1.090
 LA2  CE  HEA  single  0.970  0.020  1.090
 LA2  CD  CE   single  1.526  0.020  1.526
 LA2  CD  CG   single  1.527  0.020  1.527
 LA2  CD  HD   single  0.970  0.020  1.090
 LA2  CD  HDA  single  0.970  0.020  1.090
 LA2  CG  HG   single  0.970  0.020  1.090
 LA2  CG  HGA  single  0.970  0.020  1.090
 LA2  C2  C1   single  1.514  0.020  1.514
 LA2  C2  C3   single  1.526  0.020  1.526
 LA2  C2  H2   single  0.970  0.020  1.090
 LA2  C2  H2A  single  0.970  0.020  1.090
 LA2  C3  H3   single  0.970  0.020  1.090
 LA2  C3  H3A  single  0.970  0.020  1.090
 LA2  C4  C3   single  1.523  0.020  1.523
 LA2  C4  C5   single  1.522  0.020  1.522
 LA2  C4  H4   single  0.970  0.020  1.090
 LA2  C4  H4A  single  0.970  0.020  1.090
 LA2  C5  H5   single  0.970  0.020  1.090
 LA2  C5  H5A  single  0.970  0.020  1.090
 LA2  C6  C5   single  1.524  0.020  1.524
 LA2  C6  C7   single  1.530  0.020  1.530
 LA2  C6  H6   single  0.970  0.020  1.090
 LA2  S6  C6   single  1.833  0.020  1.833
 LA2  S6  HS6  single  1.200  0.020  1.300
 LA2  C7  C8   single  1.523  0.020  1.523
 LA2  C7  H7   single  0.970  0.020  1.090
 LA2  C7  H7A  single  0.970  0.020  1.090
 LA2  C8  H8   single  0.970  0.020  1.090
 LA2  C8  H8A  single  0.970  0.020  1.090
 LA2  S8  C8   single  1.826  0.020  1.826
 LA2  S8  HS8  single  1.200  0.020  1.300

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
 LA2  HBA  CB  HB  105.59  3.000
 LA2  HBA  CB  CG  108.50  3.000
 LA2  HB   CB  CG  109.85  3.000
 LA2  HBA  CB  CA  108.52  3.000
 LA2  HB   CB  CA  108.66  3.000
 LA2  CG   CB  CA  115.28  3.000
 LA2  OXT  C   CA  117.34  3.000
 LA2  OXT  C   O   126.79  3.000
 LA2  CA   C   O   120.80  1.700
 LA2  HNA  N   HN  104.31  3.000
 LA2  HNA  N   CA  107.56  3.000
 LA2  HN   N   CA  108.70  3.000
 LA2  HA   CA  N   110.00  3.000
 LA2  HA   CA  C   109.00  3.000
 LA2  N    CA  C   111.00  2.800
 LA2  HA   CA  CB  109.00  3.000
 LA2  N    CA  CB  110.50  1.700
 LA2  C    CA  CB  110.10  1.900
 LA2  C2   C1  NZ  115.77  3.000
 LA2  C2   C1  O1  121.44  3.000
 LA2  NZ   C1  O1  122.79  3.000
 LA2  HNZ  NZ  CE  117.51  3.000
 LA2  HNZ  NZ  C1  118.62  3.000
 LA2  CE   NZ  C1  123.63  3.000
 LA2  HEA  CE  HE  106.82  3.000
 LA2  HEA  CE  CD  110.10  3.000
 LA2  HE   CE  CD  110.46  3.000
 LA2  CD   CE  NZ  113.14  3.000
 LA2  HEA  CE  NZ  108.51  3.000
 LA2  HE   CE  NZ  107.58  3.000
 LA2  HDA  CD  HD  106.24  3.000
 LA2  HDA  CD  CG  110.22  3.000
 LA2  HD   CD  CG  108.84  3.000
 LA2  HDA  CD  CE  109.29  3.000
 LA2  HD   CD  CE  108.88  3.000
 LA2  CG   CD  CE  113.13  3.000
 LA2  HGA  CG  HG  106.02  3.000
 LA2  HGA  CG  CD  108.75  3.000
 LA2  HG   CG  CD  108.57  3.000
 LA2  HGA  CG  CB  108.35  3.000
 LA2  HG   CG  CB  109.62  3.000
 LA2  CD   CG  CB  115.14  3.000
 LA2  H2A  C2  H2  106.34  3.000
 LA2  H2A  C2  C3  109.24  3.000
 LA2  H2   C2  C3  109.94  3.000
 LA2  H2A  C2  C1  107.08  3.000
 LA2  H2   C2  C1  111.44  3.000
 LA2  C3   C2  C1  112.56  3.000
 LA2  H3A  C3  H3  106.45  3.000
 LA2  H3A  C3  C4  109.73  3.000
 LA2  H3   C3  C4  109.26  3.000
 LA2  C4   C3  C2  112.20  3.000
 LA2  H3A  C3  C2  109.52  3.000
 LA2  H3   C3  C2  109.52  3.000
 LA2  H4A  C4  H4  106.24  3.000
 LA2  H4A  C4  C5  109.93  3.000
 LA2  H4   C4  C5  109.37  3.000
 LA2  H4A  C4  C3  109.27  3.000
 LA2  H4   C4  C3  109.75  3.000
 LA2  C5   C4  C3  112.11  3.000
 LA2  H5A  C5  H5  106.18  3.000
 LA2  H5A  C5  C6  107.80  3.000
 LA2  H5   C5  C6  109.04  3.000
 LA2  C6   C5  C4  115.14  3.000
 LA2  H5A  C5  C4  108.26  3.000
 LA2  H5   C5  C4  110.03  3.000
 LA2  H6   C6  C7  109.67  3.000
 LA2  H6   C6  S6  102.86  3.000
 LA2  C7   C6  S6  109.14  3.000
 LA2  S6   C6  C5  112.49  3.000
 LA2  H6   C6  C5  108.83  3.000
 LA2  C7   C6  C5  113.31  3.000
 LA2  HS6  S6  C6   96.74  3.000
 LA2  H7A  C7  H7  106.49  3.000
 LA2  H7A  C7  C8  107.21  3.000
 LA2  H7   C7  C8  109.16  3.000
 LA2  H7A  C7  C6  108.91  3.000
 LA2  H7   C7  C6  108.99  3.000
 LA2  C8   C7  C6  115.69  3.000
 LA2  H8A  C8  H8  107.81  3.000
 LA2  H8A  C8  S8  109.30  3.000
 LA2  H8   C8  S8  108.99  3.000
 LA2  S8   C8  C7  110.20  3.000
 LA2  H8A  C8  C7  111.49  3.000
 LA2  H8   C8  C7  108.99  3.000
 LA2  HS8  S8  C8   97.43  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
 LA2  CONST_01  CE   NZ  C1  O1     0.00   0.0  0
 LA2  CONST_02  C2   C1  NZ  CE   180.00   0.0  0
 LA2  CONST_03  HNZ  NZ  C1  O1   180.00   0.0  0
 LA2  Var_01    CE   CD  CG  CB   -54.70  30.0  1
 LA2  Var_02    CD   CG  CB  CA   -56.53  30.0  3
 LA2  Var_03    C3   C2  C1  O1    51.61  30.0  1
 LA2  Var_04    CD   CE  NZ  C1    91.45  30.0  3
 LA2  Var_05    C4   C3  C2  C1  -174.21  30.0  3
 LA2  Var_06    CG   CD  CE  NZ  -173.60  30.0  1
 LA2  Var_07    C5   C4  C3  C2   179.56  30.0  2
 LA2  Var_08    C6   C5  C4  C3   177.61  30.0  3
 LA2  Var_09    S8   C8  C7  C6    58.95  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
 LA2  chir_01  CA  C   N   CB  negativ
 LA2  chir_02  C6  C5  C7  S6  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
 LA2  plan-1  O1   0.020
 LA2  plan-1  C1   0.020
 LA2  plan-1  NZ   0.020
 LA2  plan-1  CE   0.020
 LA2  plan-1  C2   0.020
 LA2  plan-1  HNZ  0.020
 LA2  plan-2  C    0.020
 LA2  plan-2  O    0.020
 LA2  plan-2  CA   0.020
 LA2  plan-2  OXT  0.020

