# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:30:11 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: N~6~-(3-carboxypropanoyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)CCC(O)=O)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
 SLL  SLL  N~6~-(3-carboxypropanoyl)-L-lysine  L-peptide  33  17  .  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_SLL
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
 SLL  C    C  C      0   0.385  -13.2090  3.5685  -71.3085
 SLL  N    N  NH2    0  -0.807  -12.4155  5.7983  -72.0421
 SLL  O    O  O      0  -0.606  -14.0712  3.5034  -72.2059
 SLL  CA   C  CH1    0  -0.155  -12.7583  4.9856  -70.8771
 SLL  CB   C  CH2    0  -0.420  -13.8817  5.6877  -70.1159
 SLL  CD   C  CH2    0  -0.470  -15.3413  5.7786  -68.0506
 SLL  CE   C  CH2    0  -0.231  -15.8428  5.0268  -66.8291
 SLL  CG   C  CH2    0  -0.425  -14.3310  4.9666  -68.8510
 SLL  CK   C  CH2    0  -0.552  -18.5222  6.2859  -64.4524
 SLL  CL   C  CH2    0  -0.575  -19.9144  5.6664  -64.5156
 SLL  CP   C  C      0   0.413  -21.0264  6.5111  -63.8578
 SLL  CX   C  C      0   0.538  -17.4769  5.3585  -65.0287
 SLL  OX   O  O      0  -0.511  -17.2452  4.2561  -64.5431
 SLL  NZ   N  NH1    0  -0.639  -16.8275  5.8103  -66.1132
 SLL  OP1  O  O      0  -0.604  -20.6733  7.3792  -63.0354
 SLL  OP2  O  OC    -1  -0.616  -22.1938  6.2246  -64.1899
 SLL  OXT  O  OC    -1  -0.614  -12.6883  2.6100  -70.7009
 SLL  H    H  HNH2   0   0.329  -12.0386  6.6835  -71.7216
 SLL  H2   H  HNH2   0   0.333  -11.6613  5.3583  -72.5556
 SLL  HA   H  HCH1   0   0.166  -11.9101  4.8697  -70.1862
 SLL  HB   H  HCH2   0   0.207  -13.5469  6.6975  -69.8492
 SLL  HBA  H  HCH2   0   0.205  -14.7341  5.8136  -70.7906
 SLL  HD   H  HCH2   0   0.224  -16.1919  6.0351  -68.6911
 SLL  HDA  H  HCH2   0   0.226  -14.8886  6.7253  -67.7389
 SLL  HE   H  HCH2   0   0.224  -16.2815  4.0735  -67.1393
 SLL  HEA  H  HCH2   0   0.225  -15.0034  4.7865  -66.1699
 SLL  HG   H  HCH2   0   0.218  -14.7767  4.0020  -69.1108
 SLL  HGA  H  HCH2   0   0.211  -13.4625  4.7436  -68.2226
 SLL  HK   H  HCH2   0   0.232  -18.5163  7.2496  -64.9664
 SLL  HKA  H  HCH2   0   0.246  -18.2593  6.4852  -63.4120
 SLL  HL   H  HCH2   0   0.219  -20.1872  5.4597  -65.5544
 SLL  HLA  H  HCH2   0   0.230  -19.8974  4.6916  -64.0163
 SLL  HNZ  H  HNH1   0   0.396  -17.0761  6.7120  -66.4864

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
 SLL  C   O    deloc   1.231  0.020  1.231
 SLL  C   CA   single  1.525  0.021  1.525
 SLL  C   OXT  deloc   1.249  0.020  1.249
 SLL  N   CA   single  1.458  0.019  1.458
 SLL  CA  CB   single  1.530  0.020  1.530
 SLL  CB  CG   single  1.524  0.020  1.524
 SLL  CD  CE   single  1.519  0.020  1.519
 SLL  CD  CG   single  1.523  0.020  1.523
 SLL  CE  NZ   single  1.448  0.020  1.448
 SLL  CK  CL   single  1.525  0.020  1.525
 SLL  CK  CX   single  1.512  0.020  1.512
 SLL  CL  CP   single  1.544  0.020  1.544
 SLL  CP  OP1  deloc   1.247  0.020  1.247
 SLL  CP  OP2  deloc   1.247  0.020  1.247
 SLL  CX  OX   double  1.227  0.020  1.227
 SLL  CX  NZ   single  1.342  0.020  1.342
 SLL  N   H    single  0.860  0.020  0.860
 SLL  N   H2   single  0.890  0.020  1.040
 SLL  CA  HA   single  0.970  0.020  0.970
 SLL  CB  HB   single  0.970  0.020  1.090
 SLL  CB  HBA  single  0.970  0.020  1.090
 SLL  CD  HD   single  0.970  0.020  1.090
 SLL  CD  HDA  single  0.970  0.020  1.090
 SLL  CE  HE   single  0.970  0.020  1.090
 SLL  CE  HEA  single  0.970  0.020  1.090
 SLL  CG  HG   single  0.970  0.020  1.090
 SLL  CG  HGA  single  0.970  0.020  1.090
 SLL  CK  HK   single  0.970  0.020  1.090
 SLL  CK  HKA  single  0.970  0.020  1.090
 SLL  CL  HL   single  0.970  0.020  1.090
 SLL  CL  HLA  single  0.970  0.020  1.090
 SLL  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
 SLL  OXT  C   CA   116.46  3.000
 SLL  OXT  C   O    126.78  3.000
 SLL  CA   C   O    120.80  1.700
 SLL  H2   N   H    105.22  3.000
 SLL  H2   N   CA   109.71  3.000
 SLL  H    N   CA   114.00  3.000
 SLL  HA   CA  CB   109.00  3.000
 SLL  HA   CA  N    110.00  3.000
 SLL  CB   CA  N    110.50  1.700
 SLL  HA   CA  C    109.00  3.000
 SLL  CB   CA  C    110.10  1.900
 SLL  N    CA  C    111.00  2.800
 SLL  HBA  CB  HB   106.36  3.000
 SLL  HBA  CB  CG   109.67  3.000
 SLL  HB   CB  CG   108.90  3.000
 SLL  HBA  CB  CA   108.57  3.000
 SLL  HB   CB  CA   108.65  3.000
 SLL  CG   CB  CA   114.39  3.000
 SLL  HDA  CD  HD   106.56  3.000
 SLL  HDA  CD  CG   109.65  3.000
 SLL  HD   CD  CG   109.42  3.000
 SLL  HDA  CD  CE   109.60  3.000
 SLL  HD   CD  CE   109.25  3.000
 SLL  CG   CD  CE   112.18  3.000
 SLL  HEA  CE  HE   106.69  3.000
 SLL  HEA  CE  NZ   110.05  3.000
 SLL  HE   CE  NZ   109.81  3.000
 SLL  HEA  CE  CD   109.87  3.000
 SLL  HE   CE  CD   109.60  3.000
 SLL  NZ   CE  CD   110.75  3.000
 SLL  HGA  CG  HG   106.25  3.000
 SLL  HGA  CG  CD   109.45  3.000
 SLL  HG   CG  CD   108.94  3.000
 SLL  HGA  CG  CB   109.81  3.000
 SLL  HG   CG  CB   109.89  3.000
 SLL  CD   CG  CB   112.30  3.000
 SLL  HKA  CK  HK   106.63  3.000
 SLL  HKA  CK  CX   107.99  3.000
 SLL  HK   CK  CX   110.99  3.000
 SLL  HKA  CK  CL   109.48  3.000
 SLL  HK   CK  CL   110.11  3.000
 SLL  CX   CK  CL   111.48  3.000
 SLL  HLA  CL  HL   105.59  3.000
 SLL  HLA  CL  CP   107.69  3.000
 SLL  HL   CL  CP   109.18  3.000
 SLL  HLA  CL  CK   109.17  3.000
 SLL  HL   CL  CK   110.10  3.000
 SLL  CP   CL  CK   114.68  3.000
 SLL  OP2  CP  OP1  126.92  3.000
 SLL  OP2  CP  CL   115.79  3.000
 SLL  OP1  CP  CL   117.27  3.000
 SLL  NZ   CX  OX   122.07  3.000
 SLL  NZ   CX  CK   115.85  3.000
 SLL  OX   CX  CK   122.08  3.000
 SLL  HNZ  NZ  CX   118.78  3.000
 SLL  HNZ  NZ  CE   117.98  3.000
 SLL  CX   NZ  CE   123.12  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
 SLL  CONST_01  CK   CX  NZ  CE   180.00   0.0  0
 SLL  CONST_02  OX   CX  NZ  CE     0.00   0.0  0
 SLL  CONST_03  HNZ  NZ  CX  CK     0.00   0.0  0
 SLL  Var_01    CD   CG  CB  CA   173.75  30.0  3
 SLL  Var_02    CE   CD  CG  CB   176.97  30.0  1
 SLL  Var_03    CX   NZ  CE  CD   176.95  30.0  3
 SLL  Var_04    NZ   CE  CD  CG  -178.39  30.0  3
 SLL  Var_05    OP1  CP  CL  CK   -19.79  30.0  3
 SLL  Var_06    OX   CX  CK  CL   -61.95  30.0  3
 SLL  Var_07    CX   CK  CL  CP   175.99  30.0  1

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
 SLL  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
 SLL  plan-1  CE   0.020
 SLL  plan-1  CK   0.020
 SLL  plan-1  CX   0.020
 SLL  plan-1  OX   0.020
 SLL  plan-1  NZ   0.020
 SLL  plan-1  HNZ  0.020
 SLL  plan-2  C    0.020
 SLL  plan-2  O    0.020
 SLL  plan-2  CA   0.020
 SLL  plan-2  OXT  0.020
 SLL  plan-3  CL   0.020
 SLL  plan-3  CP   0.020
 SLL  plan-3  OP1  0.020
 SLL  plan-3  OP2  0.020

