# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 12:34:55 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  37  19  .  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_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  -0.786   5.0001   1.5021   0.4048
 KGC  CA    C  CH1   0  -0.215   4.6952   0.0896   0.4937
 KGC  CB    C  CH2   0  -0.436   3.4207  -0.3675  -0.2438
 KGC  CG    C  CH2   0  -0.432   2.1605   0.3055   0.2834
 KGC  CD    C  CH2   0  -0.432   0.9074  -0.1644  -0.4437
 KGC  CE    C  CH2   0  -0.278  -0.3544   0.4712   0.1210
 KGC  NZ    N  NH1   0  -0.632  -1.5141   0.0680  -0.6623
 KGC  C11   C  CT    0   0.327  -2.8149   0.1096  -0.0889
 KGC  C13   C  C     0   0.526  -3.5084   1.4856  -0.0991
 KGC  O15   O  O     0  -0.420  -4.6569   1.6574  -0.4115
 KGC  O14   O  OH1   0  -0.577  -2.6939   2.4368   0.3183
 KGC  O30   O  O2    0  -0.445  -3.6544  -0.7425  -0.8747
 KGC  C28   C  C     0   0.550  -4.5512  -1.3885  -0.1198
 KGC  O29   O  O     0  -0.424  -5.3937  -2.0846  -0.6119
 KGC  C27   C  CH2   0  -0.617  -4.2959  -1.0956   1.3344
 KGC  C12   C  CH2   0  -0.526  -2.9059  -0.4794   1.3276
 KGC  C     C  C     0   0.546   5.8720  -0.7037  -0.0348
 KGC  O1    O  O     0  -0.441   6.7181  -0.2678  -0.7737
 KGC  OXT   O  OH1   0  -0.595   5.8471  -1.9660   0.3794
 KGC  H     H  HNH2  0   0.344   4.9858   1.8039  -0.5623
 KGC  H2    H  HNH2  0   0.358   4.2787   2.0315   0.8757
 KGC  HA    H  HCH1  0   0.267   4.5757  -0.1595   1.5533
 KGC  HB2   H  HCH2  0   0.230   3.5315  -0.1567  -1.3132
 KGC  HB3   H  HCH2  0   0.235   3.3107  -1.4509  -0.1486
 KGC  HG2   H  HCH2  0   0.222   2.0631   0.1015   1.3553
 KGC  HG3   H  HCH2  0   0.217   2.2446   1.3913   0.1811
 KGC  HD2   H  HCH2  0   0.222   0.9955   0.0780  -1.5082
 KGC  HD3   H  HCH2  0   0.222   0.8196  -1.2527  -0.3789
 KGC  HE2   H  HCH2  0   0.243  -0.4836   0.1429   1.1531
 KGC  HE3   H  HCH2  0   0.218  -0.2295   1.5592   0.1558
 KGC  HZ    H  HNH1  0   0.367  -1.4970   0.5199  -1.5684
 KGC  HO14  H  HOH1  0   0.491  -3.1544   3.2901   0.3413
 KGC  H271  H  HCH2  0   0.305  -5.0616  -0.4068   1.6996
 KGC  H272  H  HCH2  0   0.305  -4.3698  -2.0034   1.9303
 KGC  H121  H  HCH2  0   0.289  -2.1474  -1.2570   1.4325
 KGC  H122  H  HCH2  0   0.291  -2.7496   0.2567   2.1135
 KGC  HXT   H  HOH1  0   0.481   6.5744  -2.4619  -0.0252

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  1.523  0.020  1.523
 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  1.522  0.020  1.522
 KGC  CD   HD2   single  0.970  0.020  1.090
 KGC  CD   HD3   single  0.970  0.020  1.090
 KGC  CE   NZ    single  1.456  0.020  1.456
 KGC  CE   HE2   single  0.970  0.020  1.090
 KGC  CE   HE3   single  0.970  0.020  1.090
 KGC  NZ   C11   single  1.422  0.020  1.422
 KGC  NZ   HZ    single  0.890  0.020  1.040
 KGC  C11  C12   single  1.537  0.020  1.537
 KGC  C11  C13   single  1.541  0.020  1.541
 KGC  C11  O30   single  1.431  0.020  1.431
 KGC  C13  O15   double  1.203  0.020  1.203
 KGC  C13  O14   single  1.320  0.020  1.320
 KGC  O14  HO14  single  0.850  0.020  0.980
 KGC  O30  C28   single  1.338  0.020  1.338
 KGC  C28  C27   single  1.505  0.020  1.505
 KGC  C28  O29   double  1.199  0.020  1.199
 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    double  1.205  0.020  1.205
 KGC  C    OXT   single  1.329  0.020  1.329
 KGC  OXT  HXT   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
 KGC  H2    N    H     106.16  3.000
 KGC  H2    N    CA    109.39  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   106.61  3.000
 KGC  HB3   CB   CG    108.95  3.000
 KGC  HB2   CB   CG    109.67  3.000
 KGC  HB3   CB   CA    109.59  3.000
 KGC  HB2   CB   CA    109.04  3.000
 KGC  CG    CB   CA    112.80  3.000
 KGC  HG3   CG   HG2   106.44  3.000
 KGC  HG3   CG   CD    108.96  3.000
 KGC  HG2   CG   CD    109.66  3.000
 KGC  HG3   CG   CB    110.04  3.000
 KGC  HG2   CG   CB    109.27  3.000
 KGC  CD    CG   CB    112.29  3.000
 KGC  HD3   CD   HD2   106.51  3.000
 KGC  HD3   CD   CE    109.09  3.000
 KGC  HD2   CD   CE    109.57  3.000
 KGC  HD3   CD   CG    110.17  3.000
 KGC  HD2   CD   CG    109.24  3.000
 KGC  CE    CD   CG    112.10  3.000
 KGC  HE3   CE   HE2   106.39  3.000
 KGC  HE3   CE   NZ    112.51  3.000
 KGC  HE2   CE   NZ    109.35  3.000
 KGC  HE3   CE   CD    109.39  3.000
 KGC  HE2   CE   CD    108.88  3.000
 KGC  NZ    CE   CD    110.19  3.000
 KGC  HZ    NZ   C11   111.29  3.000
 KGC  HZ    NZ   CE    110.14  3.000
 KGC  C11   NZ   CE    120.23  3.000
 KGC  C12   C11  O30   104.07  3.000
 KGC  O30   C11  C13   105.31  3.000
 KGC  C12   C11  C13   108.77  3.000
 KGC  O30   C11  NZ    107.32  3.000
 KGC  C13   C11  NZ    115.79  3.000
 KGC  C12   C11  NZ    114.49  3.000
 KGC  O14   C13  O15   124.64  3.000
 KGC  O14   C13  C11   111.33  3.000
 KGC  O15   C13  C11   124.00  3.000
 KGC  HO14  O14  C13   110.41  3.000
 KGC  C28   O30  C11   111.76  3.000
 KGC  C27   C28  O29   128.97  3.000
 KGC  O29   C28  O30   121.32  3.000
 KGC  C27   C28  O30   109.71  3.000
 KGC  H272  C27  H271  107.17  3.000
 KGC  H272  C27  C12   113.74  3.000
 KGC  H271  C27  C12   112.75  3.000
 KGC  H272  C27  C28   110.80  3.000
 KGC  H271  C27  C28   109.06  3.000
 KGC  C12   C27  C28   103.27  3.000
 KGC  H122  C12  H121  108.22  3.000
 KGC  H122  C12  C27   113.72  3.000
 KGC  H121  C12  C27   110.25  3.000
 KGC  H122  C12  C11   113.45  3.000
 KGC  H121  C12  C11   108.70  3.000
 KGC  C27   C12  C11   102.34  3.000
 KGC  OXT   C    O1    123.23  3.000
 KGC  OXT   C    CA    111.98  3.000
 KGC  O1    C    CA    124.76  3.000
 KGC  HXT   OXT  C     110.00  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  CONST_01  HO14  O14  C13  C11   180.00   0.0  0
 KGC  CONST_02  HXT   OXT  C    CA    180.00   0.0  0
 KGC  Var_01    C28   C27  C12  C11    25.96  30.0  1
 KGC  Var_02    C27   C28  O30  C11    -5.11  30.0  1
 KGC  Var_03    C12   C27  C28  O30   -14.23  30.0  1
 KGC  Var_04    C11   NZ   CE   CD    157.03  30.0  3
 KGC  Var_05    CD    CG   CB   CA   -179.44  30.0  3
 KGC  Var_06    CE    CD   CG   CB    177.86  30.0  3
 KGC  Var_07    NZ    CE   CD   CG    176.00  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-1  HO14  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-2  HXT   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

