# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:40:27 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (E)-N~6~-(1-carboxy-2-hydroxyethylidene)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=C(CO)C(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
 KYQ  KYQ  (E)-N~6~-(1-carboxy-2-hydroxyethylidene)-L-lysine  L-peptide  30  16  .  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_KYQ
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
 KYQ  N     N  NH2    0  -0.794   0.0105  31.8116   -3.3745
 KYQ  CA    C  CH1    0  -0.188   0.7396  31.0770   -4.4068
 KYQ  CB    C  CH2    0  -0.414   0.6409  31.8596   -5.7186
 KYQ  CG    C  CH2    0  -0.421   1.1792  31.1290   -6.9417
 KYQ  CD    C  CH2    0  -0.433   1.0094  31.9331   -8.2240
 KYQ  CE    C  CH2    0  -0.330   1.4644  31.1512   -9.4548
 KYQ  NZ    N  N      0  -0.341   1.2885  31.9095  -10.6733
 KYQ  C11   C  C      0  -0.001   2.1552  32.7491  -11.0585
 KYQ  C12   C  C      0   0.419   1.8488  33.5474  -12.3451
 KYQ  O16   O  OC    -1  -0.551   0.8003  33.3041  -12.9439
 KYQ  O15   O  O      0  -0.605   2.7167  34.4037  -12.6655
 KYQ  C13   C  CH2    0  -0.226   3.4366  33.1089  -10.3251
 KYQ  O14   O  OH1    0  -0.692   4.5238  33.3503  -11.1775
 KYQ  C     C  C      0   0.384   2.2242  30.8081   -4.0623
 KYQ  O     O  O      0  -0.611   2.8408  31.7516   -3.5217
 KYQ  OXT   O  OC    -1  -0.613   2.6911  29.6927   -4.3726
 KYQ  HN    H  HNH2   0   0.331  -0.0110  31.2517   -2.5296
 KYQ  HNA   H  HNH2   0   0.320   0.5713  32.6204   -3.1272
 KYQ  HA    H  HCH1   0   0.192   0.2322  30.1166   -4.5489
 KYQ  HB    H  HCH2   0   0.209  -0.4118  32.1091   -5.8866
 KYQ  HBA   H  HCH2   0   0.200   1.1654  32.8156   -5.6009
 KYQ  HG    H  HCH2   0   0.217   2.2377  30.8910   -6.8098
 KYQ  HGA   H  HCH2   0   0.205   0.6624  30.1684   -7.0439
 KYQ  HD    H  HCH2   0   0.219  -0.0377  32.2243   -8.3507
 KYQ  HDA   H  HCH2   0   0.221   1.5822  32.8630   -8.1517
 KYQ  HE    H  HCH2   0   0.210   2.4979  30.8152   -9.3041
 KYQ  HEA   H  HCH2   0   0.227   0.8550  30.2472   -9.5345
 KYQ  H13   H  HCH2   0   0.201   3.2038  33.9841   -9.6953
 KYQ  H13A  H  HCH2   0   0.225   3.7216  32.3138   -9.6329
 KYQ  HO14  H  HOH1   0   0.438   4.1197  33.9012  -11.8861

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
 KYQ  CA   N     single  1.458  0.019  1.458
 KYQ  N    HN    single  0.890  0.020  1.040
 KYQ  N    HNA   single  0.890  0.020  1.040
 KYQ  CB   CA    single  1.530  0.020  1.530
 KYQ  CA   C     single  1.525  0.021  1.525
 KYQ  CA   HA    single  0.970  0.020  0.970
 KYQ  CG   CB    single  1.523  0.020  1.523
 KYQ  CB   HB    single  0.970  0.020  1.090
 KYQ  CB   HBA   single  0.970  0.020  1.090
 KYQ  CD   CG    single  1.523  0.020  1.523
 KYQ  CG   HG    single  0.970  0.020  1.090
 KYQ  CG   HGA   single  0.970  0.020  1.090
 KYQ  CE   CD    single  1.528  0.020  1.528
 KYQ  CD   HD    single  0.970  0.020  1.090
 KYQ  CD   HDA   single  0.970  0.020  1.090
 KYQ  NZ   CE    single  1.446  0.020  1.446
 KYQ  CE   HE    single  0.970  0.020  1.090
 KYQ  CE   HEA   single  0.970  0.020  1.090
 KYQ  C11  NZ    double  1.267  0.020  1.267
 KYQ  C12  C11   single  1.545  0.020  1.545
 KYQ  C13  C11   single  1.520  0.020  1.520
 KYQ  O15  C12   deloc   1.261  0.020  1.261
 KYQ  C12  O16   deloc   1.232  0.020  1.232
 KYQ  O14  C13   single  1.403  0.020  1.403
 KYQ  C13  H13   single  0.970  0.020  1.090
 KYQ  C13  H13A  single  0.970  0.020  1.090
 KYQ  O14  HO14  single  0.850  0.020  0.980
 KYQ  C    O     deloc   1.231  0.020  1.231
 KYQ  C    OXT   deloc   1.248  0.020  1.248

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
 KYQ  HNA   N    HN   104.40  3.000
 KYQ  HNA   N    CA   107.28  3.000
 KYQ  HN    N    CA   108.76  3.000
 KYQ  HA    CA   C    109.00  3.000
 KYQ  HA    CA   CB   109.00  3.000
 KYQ  C     CA   CB   110.10  1.900
 KYQ  HA    CA   N    110.00  3.000
 KYQ  C     CA   N    111.00  2.800
 KYQ  CB    CA   N    110.50  1.700
 KYQ  HBA   CB   HB   106.12  3.000
 KYQ  HBA   CB   CG   109.59  3.000
 KYQ  HB    CB   CG   109.02  3.000
 KYQ  HBA   CB   CA   108.83  3.000
 KYQ  HB    CB   CA   108.06  3.000
 KYQ  CG    CB   CA   114.85  3.000
 KYQ  HGA   CG   HG   106.09  3.000
 KYQ  HGA   CG   CD   109.38  3.000
 KYQ  HG    CG   CD   108.94  3.000
 KYQ  HGA   CG   CB   109.20  3.000
 KYQ  HG    CG   CB   110.48  3.000
 KYQ  CD    CG   CB   112.55  3.000
 KYQ  HDA   CD   HD   106.40  3.000
 KYQ  HDA   CD   CE   109.40  3.000
 KYQ  HD    CD   CE   109.15  3.000
 KYQ  HDA   CD   CG   109.55  3.000
 KYQ  HD    CD   CG   110.16  3.000
 KYQ  CE    CD   CG   112.02  3.000
 KYQ  HEA   CE   HE   106.37  3.000
 KYQ  HEA   CE   NZ   107.72  3.000
 KYQ  HE    CE   NZ   113.02  3.000
 KYQ  HEA   CE   CD   108.42  3.000
 KYQ  HE    CE   CD   109.07  3.000
 KYQ  NZ    CE   CD   111.98  3.000
 KYQ  C11   NZ   CE   121.37  3.000
 KYQ  C13   C11  C12  116.54  3.000
 KYQ  C13   C11  NZ   125.95  3.000
 KYQ  C12   C11  NZ   117.40  3.000
 KYQ  O15   C12  O16  126.63  3.000
 KYQ  O16   C12  C11  118.14  3.000
 KYQ  O15   C12  C11  115.22  3.000
 KYQ  H13A  C13  H13  105.72  3.000
 KYQ  H13A  C13  O14  107.95  3.000
 KYQ  H13   C13  O14  111.97  3.000
 KYQ  H13A  C13  C11  110.71  3.000
 KYQ  H13   C13  C11  106.59  3.000
 KYQ  O14   C13  C11  113.64  3.000
 KYQ  HO14  O14  C13  102.45  3.000
 KYQ  OXT   C    O    126.68  3.000
 KYQ  OXT   C    CA   117.31  3.000
 KYQ  O     C    CA   120.80  1.700

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
 KYQ  Var_01  C12  C11  NZ   CE  -177.72   0.0  2
 KYQ  Var_02  CD   CG   CB   CA   177.92  30.0  1
 KYQ  Var_03  CE   CD   CG   CB  -176.06  30.0  1
 KYQ  Var_04  NZ   CE   CD   CG   179.33  30.0  2
 KYQ  Var_05  O15  C12  C11  NZ   177.65  30.0  2
 KYQ  Var_06  O14  C13  C11  NZ   143.21  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
 KYQ  chir_01  CA  N  CB  C  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
 KYQ  plan-1  C11  0.020
 KYQ  plan-1  C12  0.020
 KYQ  plan-1  O16  0.020
 KYQ  plan-1  O15  0.020
 KYQ  plan-2  CA   0.020
 KYQ  plan-2  C    0.020
 KYQ  plan-2  O    0.020
 KYQ  plan-2  OXT  0.020
 KYQ  plan-3  CE   0.020
 KYQ  plan-3  NZ   0.020
 KYQ  plan-3  C11  0.020
 KYQ  plan-3  C12  0.020
 KYQ  plan-3  C13  0.020

