# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:50:51 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N~6~-benzyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNCc1ccccc1)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
 FQA  FQA  'N~6~-benzyl-L-lysine     '  L-peptide  37  17  .  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_FQA
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
 FQA  N    N  NH2   0  -0.759  -4.7835   1.7112  -0.3974
 FQA  CA   C  CH1   0  -0.211  -4.5839   0.2795  -0.3295
 FQA  C    C  C     0   0.549  -5.6660  -0.3288   0.5391
 FQA  O    O  O     0  -0.432  -6.3413   0.2844   1.3263
 FQA  CB   C  CH2   0  -0.432  -3.2083  -0.1813   0.1928
 FQA  CG   C  CH2   0  -0.419  -2.0466   0.3872  -0.6115
 FQA  CD   C  CH2   0  -0.430  -0.6981  -0.1084  -0.1054
 FQA  CE   C  CH2   0  -0.238   0.4683   0.4786  -0.8837
 FQA  NZ   N  NH1   0  -0.556   1.7384   0.0477  -0.3313
 FQA  CH   C  CH2   0  -0.330   2.8805   0.5683  -1.0592
 FQA  C1   C  CR6   0   0.117   4.1677   0.1833  -0.3814
 FQA  C2   C  CR16  0  -0.289   5.0913  -0.6475  -1.0060
 FQA  C3   C  CR16  0  -0.209   6.2721  -1.0092  -0.3659
 FQA  C4   C  CR16  0  -0.239   6.5408  -0.5415   0.9120
 FQA  C5   C  CR16  0  -0.212   5.6217   0.2877   1.5469
 FQA  C6   C  CR16  0  -0.256   4.4443   0.6415   0.9063
 FQA  O1   O  OH1   0  -0.575  -5.7661  -1.6419   0.3622
 FQA  H1   H  HNH2  0   0.333  -4.5254   2.1459   0.4807
 FQA  H2   H  HNH2  0   0.343  -4.1682   2.1026  -1.0980
 FQA  H4   H  HCH1  0   0.263  -4.7110  -0.1200  -1.3412
 FQA  H5   H  HCH2  0   0.217  -3.1028   0.1169   1.2420
 FQA  H6   H  HCH2  0   0.237  -3.1569  -1.2730   0.1726
 FQA  H7   H  HCH2  0   0.213  -2.1669   0.1216  -1.6672
 FQA  H8   H  HCH2  0   0.201  -2.0610   1.4800  -0.5636
 FQA  H9   H  HCH2  0   0.226  -0.5853   0.1482   0.9522
 FQA  H10  H  HCH2  0   0.205  -0.6626  -1.2018  -0.1649
 FQA  H11  H  HCH2  0   0.176   0.3589   0.2260  -1.9511
 FQA  H12  H  HCH2  0   0.204   0.4282   1.5716  -0.8258
 FQA  H13  H  HNH1  0   0.321   1.7795  -0.9653  -0.3420
 FQA  H15  H  HCH2  0   0.195   2.9071   0.2459  -2.1113
 FQA  H16  H  HCH2  0   0.224   2.7931   1.6593  -1.0779
 FQA  H17  H  HCR6  0   0.214   4.8856  -1.0186  -2.0034
 FQA  H18  H  HCR6  0   0.222   6.9793  -1.6580  -0.8667
 FQA  H19  H  HCR6  0   0.225   7.4595  -0.8199   1.4124
 FQA  H20  H  HCR6  0   0.224   5.8259   0.6588   2.5432
 FQA  H21  H  HCR6  0   0.224   3.7318   1.2853   1.4083
 FQA  H22  H  HOH1  0   0.452  -6.4313  -2.0067   0.9649

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
 FQA  C4  C5   aromatic  1.391  0.020  1.391
 FQA  C4  C3   aromatic  1.387  0.020  1.387
 FQA  C5  C6   aromatic  1.386  0.020  1.386
 FQA  C3  C2   aromatic  1.391  0.020  1.391
 FQA  C6  C1   aromatic  1.395  0.020  1.395
 FQA  C2  C1   aromatic  1.390  0.020  1.390
 FQA  C1  CH   single    1.505  0.020  1.505
 FQA  CH  NZ   single    1.451  0.020  1.451
 FQA  NZ  CE   single    1.451  0.020  1.451
 FQA  CE  CD   single    1.520  0.020  1.520
 FQA  CD  CG   single    1.523  0.020  1.523
 FQA  CG  CB   single    1.523  0.020  1.523
 FQA  CB  CA   single    1.530  0.020  1.530
 FQA  CA  C    single    1.525  0.021  1.525
 FQA  CA  N    single    1.458  0.019  1.458
 FQA  O   C    double    1.231  0.020  1.231
 FQA  C   O1   single    1.329  0.020  1.329
 FQA  N   H1   single    0.890  0.020  1.040
 FQA  N   H2   single    0.890  0.020  1.040
 FQA  CA  H4   single    0.970  0.020  1.090
 FQA  CB  H5   single    0.970  0.020  1.090
 FQA  CB  H6   single    0.970  0.020  1.090
 FQA  CG  H7   single    0.970  0.020  1.090
 FQA  CG  H8   single    0.970  0.020  1.090
 FQA  CD  H9   single    0.970  0.020  1.090
 FQA  CD  H10  single    0.970  0.020  1.090
 FQA  CE  H11  single    0.970  0.020  1.090
 FQA  CE  H12  single    0.970  0.020  1.090
 FQA  NZ  H13  single    0.890  0.020  1.040
 FQA  CH  H15  single    0.970  0.020  1.090
 FQA  CH  H16  single    0.970  0.020  1.090
 FQA  C2  H17  single    0.930  0.020  1.080
 FQA  C3  H18  single    0.930  0.020  1.080
 FQA  C4  H19  single    0.930  0.020  1.080
 FQA  C5  H20  single    0.930  0.020  1.080
 FQA  C6  H21  single    0.930  0.020  1.080
 FQA  O1  H22  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
 FQA  H2   N   H1   106.22  3.000
 FQA  H2   N   CA   109.36  3.000
 FQA  H1   N   CA   110.40  3.000
 FQA  H4   CA  CB   107.90  3.000
 FQA  H4   CA  C    107.47  3.000
 FQA  CB   CA  C    110.10  1.900
 FQA  H4   CA  N    107.55  3.000
 FQA  C    CA  N    111.00  2.800
 FQA  CB   CA  N    110.50  1.700
 FQA  O1   C   O    123.21  3.000
 FQA  O1   C   CA   111.98  3.000
 FQA  O    C   CA   120.80  1.700
 FQA  H6   CB  H5   106.55  3.000
 FQA  H6   CB  CG   109.10  3.000
 FQA  H5   CB  CG   109.30  3.000
 FQA  H6   CB  CA   109.52  3.000
 FQA  H5   CB  CA   109.20  3.000
 FQA  CG   CB  CA   112.96  3.000
 FQA  H8   CG  H7   106.44  3.000
 FQA  H8   CG  CD   108.79  3.000
 FQA  H7   CG  CD   109.79  3.000
 FQA  H8   CG  CB   109.86  3.000
 FQA  H7   CG  CB   109.56  3.000
 FQA  CD   CG  CB   112.23  3.000
 FQA  H10  CD  H9   106.46  3.000
 FQA  H10  CD  CE   109.43  3.000
 FQA  H9   CD  CE   108.98  3.000
 FQA  H10  CD  CG   109.59  3.000
 FQA  H9   CD  CG   109.64  3.000
 FQA  CE   CD  CG   112.55  3.000
 FQA  H12  CE  H11  106.04  3.000
 FQA  H12  CE  NZ   107.97  3.000
 FQA  H11  CE  NZ   112.81  3.000
 FQA  H12  CE  CD   109.27  3.000
 FQA  H11  CE  CD   109.33  3.000
 FQA  NZ   CE  CD   111.23  3.000
 FQA  H13  NZ  CH   108.75  3.000
 FQA  H13  NZ  CE   109.16  3.000
 FQA  CH   NZ  CE   113.05  3.000
 FQA  H16  CH  H15  106.11  3.000
 FQA  H16  CH  C1   109.33  3.000
 FQA  H15  CH  C1   109.57  3.000
 FQA  H16  CH  NZ   107.66  3.000
 FQA  H15  CH  NZ   113.17  3.000
 FQA  C1   CH  NZ   110.83  3.000
 FQA  C6   C1  C2   118.65  3.000
 FQA  C2   C1  CH   121.25  3.000
 FQA  C6   C1  CH   120.10  3.000
 FQA  H17  C2  C3   119.70  3.000
 FQA  H17  C2  C1   119.47  3.000
 FQA  C3   C2  C1   120.84  3.000
 FQA  H18  C3  C4   120.12  3.000
 FQA  H18  C3  C2   119.84  3.000
 FQA  C4   C3  C2   120.04  3.000
 FQA  H19  C4  C5   120.20  3.000
 FQA  H19  C4  C3   120.23  3.000
 FQA  C5   C4  C3   119.57  3.000
 FQA  H20  C5  C6   119.86  3.000
 FQA  H20  C5  C4   119.98  3.000
 FQA  C6   C5  C4   120.15  3.000
 FQA  H21  C6  C5   119.74  3.000
 FQA  H21  C6  C1   119.51  3.000
 FQA  C5   C6  C1   120.75  3.000
 FQA  H22  O1  C    109.93  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
 FQA  CONST_01  C4   C5  C6  C1     0.00   0.0  0
 FQA  CONST_02  C4   C3  C2  C1     0.00   0.0  0
 FQA  CONST_03  C5   C4  C3  C2     0.00   0.0  0
 FQA  CONST_04  C5   C6  C1  C2     0.00   0.0  0
 FQA  CONST_05  C6   C5  C4  C3     0.00   0.0  0
 FQA  CONST_06  C6   C1  C2  C3     0.00   0.0  0
 FQA  CONST_07  C5   C6  C1  CH   180.00   0.0  0
 FQA  CONST_08  C3   C2  C1  CH   180.00   0.0  0
 FQA  CONST_09  H20  C5  C6  C1   180.00   0.0  0
 FQA  CONST_10  H18  C3  C2  C1   180.00   0.0  0
 FQA  CONST_11  H19  C4  C3  C2   180.00   0.0  0
 FQA  CONST_12  H21  C6  C1  C2   180.00   0.0  0
 FQA  CONST_13  H17  C2  C3  C4   180.00   0.0  0
 FQA  CONST_14  H22  O1  C   CA   180.00   0.0  0
 FQA  Var_01    C6   C1  CH  NZ   -62.96  30.0  3
 FQA  Var_02    C1   CH  NZ  CE   175.44  30.0  1
 FQA  Var_03    CD   CG  CB  CA  -178.44  30.0  1
 FQA  Var_04    CE   CD  CG  CB  -178.74  30.0  1
 FQA  Var_05    NZ   CE  CD  CG   176.78  30.0  1
 FQA  Var_06    CH   NZ  CE  CD   179.05  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
 FQA  chir_01  CA  CB  C  N  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
 FQA  plan-1  CH   0.020
 FQA  plan-1  C1   0.020
 FQA  plan-1  C2   0.020
 FQA  plan-1  C3   0.020
 FQA  plan-1  C4   0.020
 FQA  plan-1  C5   0.020
 FQA  plan-1  C6   0.020
 FQA  plan-1  H17  0.020
 FQA  plan-1  H18  0.020
 FQA  plan-1  H19  0.020
 FQA  plan-1  H20  0.020
 FQA  plan-1  H21  0.020
 FQA  plan-2  CA   0.020
 FQA  plan-2  C    0.020
 FQA  plan-2  O    0.020
 FQA  plan-2  O1   0.020
 FQA  plan-2  H22  0.020

