# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:47:57 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)c1ccccc1N)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
 KYN  KYN  '(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid'  L-peptide  26  15  .  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_KYN
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
 KYN  C     C  C      0   0.420  20.5631  -28.8060  8.5744
 KYN  N     N  NH2    0  -0.817  20.2797  -30.0626  6.4488
 KYN  OXT   O  OC    -1  -0.602  21.2583  -28.5918  9.5860
 KYN  C1    C  C      0   0.378  22.8050  -31.5168  6.9010
 KYN  O2    O  O      0  -0.412  22.1389  -32.5265  7.0331
 KYN  CA    C  CH1    0  -0.219  20.9041  -30.0859  7.7632
 KYN  CB    C  CH2    0  -0.572  22.4159  -30.2438  7.6181
 KYN  CG    C  CR6    0   0.285  25.1273  -30.7345  6.1083
 KYN  CZ    C  CR16   0  -0.275  24.8355  -32.4469  3.8871
 KYN  CD1   C  CR16   0  -0.323  26.1139  -30.8170  5.1103
 KYN  CD2   C  CR6    0  -0.067  23.9660  -31.5248  5.9667
 KYN  CE1   C  CR16   0  -0.244  25.9678  -31.6464  4.0195
 KYN  CE2   C  CR16   0  -0.275  23.8648  -32.3846  4.8649
 KYN  O     O  O      0  -0.595  19.5994  -28.1256  8.1711
 KYN  H     H  HNH2   0   0.332  20.0105  -30.9969  6.1723
 KYN  H2    H  HNH2   0   0.335  19.4288  -29.5202  6.5255
 KYN  HN1   H  HNH2   0   0.389  24.9229  -30.1040  8.0475
 KYN  HN1A  H  HNH2   0   0.389  26.2848  -29.5504  7.2645
 KYN  HA    H  HCH1   0   0.207  20.5354  -30.9218  8.3777
 KYN  HB    H  HCH2   0   0.261  22.8691  -30.2588  8.6148
 KYN  HBA   H  HCH2   0   0.245  22.8279  -29.3772  7.0972
 KYN  HE1   H  HCR6   0   0.257  26.7482  -31.6775  3.2696
 KYN  HE2   H  HCR6   0   0.254  22.9771  -32.9962  4.7693
 KYN  HZ    H  HCR6   0   0.248  24.7166  -33.1029  3.0356
 KYN  N1    N  NH2    0  -0.855  25.3378  -29.8783  7.1598
 KYN  HD1   H  HCR6   0   0.260  27.0113  -30.2179  5.2129

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
 KYN  CA   C     single    1.525  0.021  1.525
 KYN  O    C     deloc     1.231  0.020  1.231
 KYN  C    OXT   deloc     1.246  0.020  1.246
 KYN  N    CA    single    1.458  0.019  1.458
 KYN  N    H     single    0.860  0.020  0.860
 KYN  N    H2    single    0.890  0.020  1.040
 KYN  CD2  C1    single    1.490  0.020  1.490
 KYN  O2   C1    double    1.217  0.020  1.217
 KYN  C1   CB    single    1.512  0.020  1.512
 KYN  CG   N1    single    1.372  0.020  1.372
 KYN  N1   HN1   single    0.890  0.020  1.040
 KYN  N1   HN1A  single    0.890  0.020  1.040
 KYN  CB   CA    single    1.530  0.020  1.530
 KYN  CA   HA    single    0.970  0.020  0.970
 KYN  CB   HB    single    0.970  0.020  1.090
 KYN  CB   HBA   single    0.970  0.020  1.090
 KYN  CD1  CG    aromatic  1.406  0.020  1.406
 KYN  CD2  CG    aromatic  1.412  0.020  1.412
 KYN  CZ   CE1   aromatic  1.393  0.020  1.393
 KYN  CZ   CE2   aromatic  1.379  0.020  1.379
 KYN  CZ   HZ    single    0.930  0.020  1.080
 KYN  CE1  CD1   aromatic  1.378  0.020  1.378
 KYN  CD1  HD1   single    0.930  0.020  1.080
 KYN  CE2  CD2   aromatic  1.401  0.020  1.401
 KYN  CE1  HE1   single    0.930  0.020  1.080
 KYN  CE2  HE2   single    0.930  0.020  1.080

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
 KYN  O     C    CA   120.80  1.700
 KYN  O     C    OXT  126.88  3.000
 KYN  CA    C    OXT  116.31  3.000
 KYN  H2    N    H    106.99  3.000
 KYN  H2    N    CA   107.51  3.000
 KYN  H     N    CA   114.00  3.000
 KYN  CD2   C1   CB   120.15  3.000
 KYN  CB    C1   O2   120.42  3.000
 KYN  CD2   C1   O2   119.34  3.000
 KYN  HA    CA   CB   109.00  3.000
 KYN  HA    CA   N    110.00  3.000
 KYN  CB    CA   N    110.50  1.700
 KYN  HA    CA   C    109.00  3.000
 KYN  CB    CA   C    110.10  1.900
 KYN  N     CA   C    111.00  2.800
 KYN  HBA   CB   HB   106.80  3.000
 KYN  HBA   CB   CA   109.69  3.000
 KYN  HB    CB   CA   108.94  3.000
 KYN  HBA   CB   C1   110.18  3.000
 KYN  HB    CB   C1   108.28  3.000
 KYN  CA    CB   C1   112.76  3.000
 KYN  CD2   CG   CD1  118.25  3.000
 KYN  CD2   CG   N1   123.52  3.000
 KYN  CD1   CG   N1   118.23  3.000
 KYN  HZ    CZ   CE2  120.55  3.000
 KYN  HZ    CZ   CE1  120.85  3.000
 KYN  CE2   CZ   CE1  118.60  3.000
 KYN  HD1   CD1  CE1  119.70  3.000
 KYN  HD1   CD1  CG   118.78  3.000
 KYN  CE1   CD1  CG   121.52  3.000
 KYN  CE2   CD2  CG   118.80  3.000
 KYN  CE2   CD2  C1   116.10  3.000
 KYN  CG    CD2  C1   125.10  3.000
 KYN  HE1   CE1  CD1  119.28  3.000
 KYN  HE1   CE1  CZ   120.23  3.000
 KYN  CD1   CE1  CZ   120.49  3.000
 KYN  HE2   CE2  CD2  118.40  3.000
 KYN  HE2   CE2  CZ   119.28  3.000
 KYN  CD2   CE2  CZ   122.30  3.000
 KYN  HN1A  N1   HN1  111.66  3.000
 KYN  HN1A  N1   CG   115.26  3.000
 KYN  HN1   N1   CG   118.24  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
 KYN  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 KYN  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 KYN  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 KYN  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 KYN  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 KYN  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 KYN  CONST_07  CD1  CG   CD2  C1    180.00   0.0  0
 KYN  CONST_08  CZ   CE2  CD2  C1    180.00   0.0  0
 KYN  CONST_09  CE1  CD1  CG   N1    180.00   0.0  0
 KYN  CONST_10  CE2  CD2  CG   N1    180.00   0.0  0
 KYN  CONST_11  HE1  CE1  CD1  CG    180.00   0.0  0
 KYN  CONST_12  HE2  CE2  CD2  CG    180.00   0.0  0
 KYN  CONST_13  HD1  CD1  CE1  CZ    180.00   0.0  0
 KYN  CONST_14  HZ   CZ   CE1  CD1   180.00   0.0  0
 KYN  Var_01    CG   CD2  C1   O2   -150.72  30.0  2
 KYN  Var_02    CD2  C1   CB   CA    143.05  30.0  2

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
 KYN  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
 KYN  plan-1  C1    0.020
 KYN  plan-1  CG    0.020
 KYN  plan-1  CZ    0.020
 KYN  plan-1  CD1   0.020
 KYN  plan-1  CD2   0.020
 KYN  plan-1  CE1   0.020
 KYN  plan-1  CE2   0.020
 KYN  plan-1  HE1   0.020
 KYN  plan-1  HE2   0.020
 KYN  plan-1  HZ    0.020
 KYN  plan-1  N1    0.020
 KYN  plan-1  HD1   0.020
 KYN  plan-2  CG    0.020
 KYN  plan-2  HN1   0.020
 KYN  plan-2  HN1A  0.020
 KYN  plan-2  N1    0.020
 KYN  plan-3  C1    0.020
 KYN  plan-3  O2    0.020
 KYN  plan-3  CB    0.020
 KYN  plan-3  CD2   0.020
 KYN  plan-4  C     0.020
 KYN  plan-4  OXT   0.020
 KYN  plan-4  CA    0.020
 KYN  plan-4  O     0.020

