# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 08:52:02 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N~6~-[(2R)-2-carboxy-5-oxotetrahydrofuran-2-yl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN[C@@]1(CCC(=O)O1)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
 KGC  KGC  N~6~-[(2R)-2-carboxy-5-oxotetrahydrofuran-2-yl]-L-lysine  L-peptide  35  19  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_KGC
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
 KGC  N     N  NH2    0  -0.801   4.9051   1.6367   0.2508
 KGC  CA    C  CH1    0  -0.201   4.6753   0.2145   0.4526
 KGC  CB    C  CH2    0  -0.426   3.4053  -0.3342  -0.2195
 KGC  CG    C  CH2    0  -0.428   2.1073   0.2657   0.3070
 KGC  CD    C  CH2    0  -0.430   0.8764  -0.2988  -0.3906
 KGC  CE    C  CH2    0  -0.278  -0.4237   0.2455   0.1805
 KGC  NZ    N  NH1    0  -0.627  -1.5577  -0.2418  -0.5936
 KGC  C11   C  CT     0   0.299  -2.8549  -0.0182  -0.0062
 KGC  C13   C  C      0   0.400  -3.2521   1.4868  -0.0329
 KGC  O15   O  O      0  -0.599  -3.7113   1.9131  -1.1061
 KGC  O14   O  OC    -1  -0.593  -3.0084   2.1340   1.0017
 KGC  O30   O  O2     0  -0.455  -3.7879  -0.7495  -0.8401
 KGC  C28   C  C      0   0.537  -4.7493  -1.3093  -0.1162
 KGC  O29   O  O      0  -0.448  -5.6661  -1.8980  -0.6283
 KGC  C27   C  CH2    0  -0.623  -4.4826  -1.0763   1.3481
 KGC  C12   C  CH2    0  -0.492  -3.0155  -0.6794   1.3605
 KGC  C     C  C      0   0.403   5.8808  -0.6057  -0.0534
 KGC  O1    O  O      0  -0.610   6.5609  -0.1092  -0.9740
 KGC  OXT   O  OC    -1  -0.622   6.0471  -1.7259   0.4707
 KGC  H     H  HNH2   0   0.325   5.1543   1.7841  -0.7193
 KGC  H2    H  HNH2   0   0.332   4.0533   2.1584   0.4152
 KGC  HA    H  HCH1   0   0.196   4.5749   0.0386   1.5305
 KGC  HB2   H  HCH2   0   0.206   3.4745  -0.1655  -1.3010
 KGC  HB3   H  HCH2   0   0.210   3.3711  -1.4188  -0.0773
 KGC  HG2   H  HCH2   0   0.212   2.0366   0.0823   1.3851
 KGC  HG3   H  HCH2   0   0.205   2.1120   1.3541   0.1835
 KGC  HD2   H  HCH2   0   0.214   0.9320  -0.0658  -1.4599
 KGC  HD3   H  HCH2   0   0.215   0.8713  -1.3902  -0.3140
 KGC  HE2   H  HCH2   0   0.233  -0.5289  -0.0916   1.2138
 KGC  HE3   H  HCH2   0   0.202  -0.3736   1.3424   0.2196
 KGC  HZ    H  HNH1   0   0.346  -1.5324   0.2017  -1.5065
 KGC  H271  H  HCH2   0   0.291  -5.1287  -0.2634   1.6940
 KGC  H272  H  HCH2   0   0.288  -4.7248  -1.9574   1.9399
 KGC  H121  H  HCH2   0   0.253  -2.3852  -1.5704   1.4109
 KGC  H122  H  HCH2   0   0.265  -2.7526  -0.0178   2.1800

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
 KGC  N    CA    single  1.458  0.019  1.458
 KGC  N    H     single  0.860  0.020  0.860
 KGC  N    H2    single  0.890  0.020  1.040
 KGC  CA   CB    single  1.530  0.020  1.530
 KGC  CA   C     single  1.525  0.021  1.525
 KGC  CA   HA    single  0.970  0.020  0.970
 KGC  CB   CG    single  1.524  0.020  1.524
 KGC  CB   HB2   single  0.970  0.020  1.090
 KGC  CB   HB3   single  0.970  0.020  1.090
 KGC  CG   CD    single  1.523  0.020  1.523
 KGC  CG   HG2   single  0.970  0.020  1.090
 KGC  CG   HG3   single  0.970  0.020  1.090
 KGC  CD   CE    single  1.521  0.020  1.521
 KGC  CD   HD2   single  0.970  0.020  1.090
 KGC  CD   HD3   single  0.970  0.020  1.090
 KGC  CE   NZ    single  1.457  0.020  1.457
 KGC  CE   HE2   single  0.970  0.020  1.090
 KGC  CE   HE3   single  0.970  0.020  1.090
 KGC  NZ   C11   single  1.441  0.020  1.441
 KGC  NZ   HZ    single  0.890  0.020  1.040
 KGC  C11  C12   single  1.527  0.020  1.527
 KGC  C11  C13   single  1.557  0.020  1.557
 KGC  C11  O30   single  1.449  0.020  1.449
 KGC  C13  O15   deloc   1.243  0.020  1.243
 KGC  C13  O14   deloc   1.244  0.020  1.244
 KGC  O30  C28   single  1.327  0.020  1.327
 KGC  C28  C27   single  1.506  0.020  1.506
 KGC  C28  O29   double  1.204  0.020  1.204
 KGC  C27  C12   single  1.520  0.020  1.520
 KGC  C27  H271  single  0.970  0.020  1.090
 KGC  C27  H272  single  0.970  0.020  1.090
 KGC  C12  H121  single  0.970  0.020  1.090
 KGC  C12  H122  single  0.970  0.020  1.090
 KGC  C    O1    deloc   1.247  0.020  1.247
 KGC  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
 KGC  H2    N    H     106.71  3.000
 KGC  H2    N    CA    110.39  3.000
 KGC  H     N    CA    114.00  3.000
 KGC  HA    CA   C     109.00  3.000
 KGC  HA    CA   CB    109.00  3.000
 KGC  C     CA   CB    110.10  1.900
 KGC  HA    CA   N     110.00  3.000
 KGC  C     CA   N     111.00  2.800
 KGC  CB    CA   N     110.50  1.700
 KGC  HB3   CB   HB2   106.41  3.000
 KGC  HB3   CB   CG    108.58  3.000
 KGC  HB2   CB   CG    109.50  3.000
 KGC  HB3   CB   CA    108.82  3.000
 KGC  HB2   CB   CA    108.90  3.000
 KGC  CG    CB   CA    114.33  3.000
 KGC  HG3   CG   HG2   106.10  3.000
 KGC  HG3   CG   CD    108.66  3.000
 KGC  HG2   CG   CD    109.66  3.000
 KGC  HG3   CG   CB    110.40  3.000
 KGC  HG2   CG   CB    109.20  3.000
 KGC  CD    CG   CB    112.60  3.000
 KGC  HD3   CD   HD2   106.30  3.000
 KGC  HD3   CD   CE    109.07  3.000
 KGC  HD2   CD   CE    109.50  3.000
 KGC  HD3   CD   CG    109.96  3.000
 KGC  HD2   CD   CG    109.09  3.000
 KGC  CE    CD   CG    112.72  3.000
 KGC  HE3   CE   HE2   106.20  3.000
 KGC  HE3   CE   NZ    112.85  3.000
 KGC  HE2   CE   NZ    108.94  3.000
 KGC  HE3   CE   CD    109.37  3.000
 KGC  HE2   CE   CD    109.10  3.000
 KGC  NZ    CE   CD    110.25  3.000
 KGC  HZ    NZ   C11   108.73  3.000
 KGC  HZ    NZ   CE    108.19  3.000
 KGC  C11   NZ   CE    115.59  3.000
 KGC  C12   C11  O30   103.23  3.000
 KGC  O30   C11  C13   108.28  3.000
 KGC  C12   C11  C13   114.03  3.000
 KGC  O30   C11  NZ    105.46  3.000
 KGC  C13   C11  NZ    111.87  3.000
 KGC  C12   C11  NZ    113.10  3.000
 KGC  O14   C13  O15   127.73  3.000
 KGC  O14   C13  C11   116.01  3.000
 KGC  O15   C13  C11   116.15  3.000
 KGC  C28   O30  C11   111.42  3.000
 KGC  C27   C28  O29   128.60  3.000
 KGC  O29   C28  O30   121.73  3.000
 KGC  C27   C28  O30   109.67  3.000
 KGC  H272  C27  H271  107.34  3.000
 KGC  H272  C27  C12   114.94  3.000
 KGC  H271  C27  C12   111.92  3.000
 KGC  H272  C27  C28   111.33  3.000
 KGC  H271  C27  C28   108.52  3.000
 KGC  C12   C27  C28   102.66  3.000
 KGC  H122  C12  H121  108.81  3.000
 KGC  H122  C12  C27   113.52  3.000
 KGC  H121  C12  C27   110.14  3.000
 KGC  H122  C12  C11   112.73  3.000
 KGC  H121  C12  C11   109.50  3.000
 KGC  C27   C12  C11   101.97  3.000
 KGC  OXT   C    O1    126.48  3.000
 KGC  OXT   C    CA    116.32  3.000
 KGC  O1    C    CA    117.15  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
 KGC  Var_01  C28  C27  C12  C11   29.60  30.0  1
 KGC  Var_02  C27  C28  O30  C11   -4.20  30.0  1
 KGC  Var_03  C12  C27  C28  O30  -16.99  30.0  1
 KGC  Var_04  C11  NZ   CE   CD   168.25  30.0  3
 KGC  Var_05  CD   CG   CB   CA   179.66  30.0  3
 KGC  Var_06  CE   CD   CG   CB   177.09  30.0  3
 KGC  Var_07  NZ   CE   CD   CG   175.35  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
 KGC  chir_01  CA   N    CB   C    negativ
 KGC  chir_02  C11  O30  C12  C13  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
 KGC  plan-1  C11  0.020
 KGC  plan-1  C13  0.020
 KGC  plan-1  O15  0.020
 KGC  plan-1  O14  0.020
 KGC  plan-2  CA   0.020
 KGC  plan-2  C    0.020
 KGC  plan-2  O1   0.020
 KGC  plan-2  OXT  0.020
 KGC  plan-3  O30  0.020
 KGC  plan-3  C28  0.020
 KGC  plan-3  O29  0.020
 KGC  plan-3  C27  0.020

