# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:40:38 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (E)-N~6~-(1-carboxyethylidene)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=NCCCC[C@H](N)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
 KPI  KPI  (E)-N~6~-(1-carboxyethylidene)-L-lysine  L-peptide  29  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_KPI
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
 KPI  OXT  O  OC    -1  -0.614  -24.4210  -17.3046   4.3566
 KPI  N    N  NH2    0  -0.794  -26.9960  -15.1036   3.3085
 KPI  CA   C  CH1    0  -0.187  -26.2740  -15.7900   4.3789
 KPI  CB   C  CH2    0  -0.411  -27.2554  -16.0818   5.5152
 KPI  CG   C  CH2    0  -0.426  -26.6345  -16.7250   6.7484
 KPI  CD   C  CH2    0  -0.420  -27.6140  -16.8388   7.9080
 KPI  CE   C  CH2    0  -0.304  -26.9963  -17.5111   9.1236
 KPI  NZ   N  N      0  -0.348  -27.9344  -17.5672  10.2237
 KPI  CX1  C  C      0   0.051  -27.5803  -18.1215  11.3096
 KPI  C1   C  CH3    0  -0.754  -26.2284  -18.7407  11.5277
 KPI  CX2  C  C      0   0.366  -28.6062  -18.1696  12.4657
 KPI  O1   O  OC    -1  -0.589  -28.2814  -18.8613  13.4509
 KPI  O2   O  O      0  -0.588  -29.6554  -17.5257  12.3084
 KPI  C    C  C      0   0.383  -25.5763  -17.0969   3.9317
 KPI  O    O  O      0  -0.612  -26.2478  -17.8500   3.1936
 KPI  HA   H  HCH1   0   0.191  -25.5136  -15.0999   4.7599
 KPI  HB   H  HCH2   0   0.207  -27.7346  -15.1406   5.8038
 KPI  HBA  H  HCH2   0   0.199  -28.0561  -16.7270   5.1347
 KPI  HG   H  HCH2   0   0.212  -26.2537  -17.7206   6.5033
 KPI  HGA  H  HCH2   0   0.203  -25.7650  -16.1390   7.0663
 KPI  HD   H  HCH2   0   0.208  -27.9696  -15.8429   8.1902
 KPI  HDA  H  HCH2   0   0.208  -28.4972  -17.4044   7.5936
 KPI  HE   H  HCH2   0   0.215  -26.6512  -18.5166   8.8457
 KPI  HEA  H  HCH2   0   0.216  -26.0896  -16.9641   9.4168
 KPI  H1   H  HCH3   0   0.252  -26.1345  -19.1647  12.5213
 KPI  H1A  H  HCH3   0   0.241  -26.0374  -19.5289  10.7947
 KPI  H1B  H  HCH3   0   0.241  -25.4380  -17.9983  11.3882
 KPI  H    H  HNH2   0   0.331  -26.3332  -14.8278   2.5927
 KPI  H2   H  HNH2   0   0.320  -27.5877  -15.7921   2.8552

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
 KPI  OXT  C    deloc   1.248  0.020  1.248
 KPI  N    CA   single  1.458  0.019  1.458
 KPI  CA   CB   single  1.530  0.020  1.530
 KPI  CA   C    single  1.525  0.021  1.525
 KPI  CB   CG   single  1.523  0.020  1.523
 KPI  CG   CD   single  1.522  0.020  1.522
 KPI  CD   CE   single  1.520  0.020  1.520
 KPI  CE   NZ   single  1.447  0.020  1.447
 KPI  NZ   CX1  double  1.270  0.020  1.270
 KPI  CX1  C1   single  1.503  0.020  1.503
 KPI  CX1  CX2  single  1.546  0.020  1.546
 KPI  CX2  O1   deloc   1.247  0.020  1.247
 KPI  CX2  O2   deloc   1.241  0.020  1.241
 KPI  C    O    deloc   1.231  0.020  1.231
 KPI  N    H    single  0.860  0.020  0.860
 KPI  N    H2   single  0.890  0.020  1.040
 KPI  CA   HA   single  0.970  0.020  0.970
 KPI  CB   HB   single  0.970  0.020  1.090
 KPI  CB   HBA  single  0.970  0.020  1.090
 KPI  CG   HG   single  0.970  0.020  1.090
 KPI  CG   HGA  single  0.970  0.020  1.090
 KPI  CD   HD   single  0.970  0.020  1.090
 KPI  CD   HDA  single  0.970  0.020  1.090
 KPI  CE   HE   single  0.970  0.020  1.090
 KPI  CE   HEA  single  0.970  0.020  1.090
 KPI  C1   H1   single  0.970  0.020  1.090
 KPI  C1   H1A  single  0.970  0.020  1.090
 KPI  C1   H1B  single  0.970  0.020  1.090

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
 KPI  H2   N    H    104.50  3.000
 KPI  H2   N    CA   107.24  3.000
 KPI  H    N    CA   114.00  3.000
 KPI  HA   CA   C    109.00  3.000
 KPI  HA   CA   CB   109.00  3.000
 KPI  C    CA   CB   110.10  1.900
 KPI  HA   CA   N    110.00  3.000
 KPI  C    CA   N    111.00  2.800
 KPI  CB   CA   N    110.50  1.700
 KPI  HBA  CB   HB   106.13  3.000
 KPI  HBA  CB   CG   109.28  3.000
 KPI  HB   CB   CG   109.15  3.000
 KPI  HBA  CB   CA   108.84  3.000
 KPI  HB   CB   CA   108.21  3.000
 KPI  CG   CB   CA   114.86  3.000
 KPI  HGA  CG   HG   106.00  3.000
 KPI  HGA  CG   CD   109.24  3.000
 KPI  HG   CG   CD   109.07  3.000
 KPI  HGA  CG   CB   109.43  3.000
 KPI  HG   CG   CB   110.18  3.000
 KPI  CD   CG   CB   112.70  3.000
 KPI  HDA  CD   HD   106.38  3.000
 KPI  HDA  CD   CE   109.20  3.000
 KPI  HD   CD   CE   109.16  3.000
 KPI  HDA  CD   CG   109.81  3.000
 KPI  HD   CD   CG   109.73  3.000
 KPI  CE   CD   CG   112.38  3.000
 KPI  HEA  CE   HE   105.30  3.000
 KPI  HEA  CE   NZ   110.58  3.000
 KPI  HE   CE   NZ   111.13  3.000
 KPI  HEA  CE   CD   109.18  3.000
 KPI  HE   CE   CD   109.27  3.000
 KPI  NZ   CE   CD   111.20  3.000
 KPI  CX1  NZ   CE   119.10  3.000
 KPI  CX2  CX1  C1   118.39  3.000
 KPI  CX2  CX1  NZ   117.90  3.000
 KPI  C1   CX1  NZ   123.71  3.000
 KPI  H1B  C1   H1A  106.12  3.000
 KPI  H1B  C1   H1   108.65  3.000
 KPI  H1A  C1   H1   108.50  3.000
 KPI  H1B  C1   CX1  110.62  3.000
 KPI  H1A  C1   CX1  110.91  3.000
 KPI  H1   C1   CX1  111.84  3.000
 KPI  O2   CX2  O1   127.46  3.000
 KPI  O2   CX2  CX1  116.74  3.000
 KPI  O1   CX2  CX1  115.80  3.000
 KPI  O    C    CA   120.80  1.700
 KPI  O    C    OXT  126.72  3.000
 KPI  CA   C    OXT  117.35  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
 KPI  Var_01  C1  CX1  NZ   CE    -0.35   0.0  2
 KPI  Var_02  CD  CG   CB   CA   173.02  30.0  3
 KPI  Var_03  CE  CD   CG   CB   178.66  30.0  3
 KPI  Var_04  NZ  CE   CD   CG   178.15  30.0  3
 KPI  Var_05  O1  CX2  CX1  NZ   171.56  30.0  2
 KPI  Var_06  H1  C1   CX1  NZ  -179.59  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
 KPI  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
 KPI  plan-1  CX1  0.020
 KPI  plan-1  CX2  0.020
 KPI  plan-1  O1   0.020
 KPI  plan-1  O2   0.020
 KPI  plan-2  OXT  0.020
 KPI  plan-2  CA   0.020
 KPI  plan-2  C    0.020
 KPI  plan-2  O    0.020
 KPI  plan-3  CE   0.020
 KPI  plan-3  NZ   0.020
 KPI  plan-3  CX1  0.020
 KPI  plan-3  C1   0.020
 KPI  plan-3  CX2  0.020

