# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:38:06 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: (Z)-N~6~-(2-carboxy-1-methylethylidene)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(CC(O)=O)=NCCCC[C@H](N)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
 LCK  LCK  (Z)-N~6~-(2-carboxy-1-methylethylidene)-L-lysine  L-peptide  32  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_LCK
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
 LCK  OXT  O  OC    -1  -0.613  22.6664  42.2704  75.6058
 LCK  O2   O  O      0  -0.604  28.8086  39.2688  83.3247
 LCK  C4   C  C      0   0.432  28.8702  40.4067  82.8278
 LCK  O1   O  OC    -1  -0.593  28.2207  41.4164  83.1554
 LCK  C3   C  CH2    0  -0.703  29.8960  40.5726  81.6664
 LCK  C2   C  C      0   0.263  29.8878  41.9457  81.0658
 LCK  C1   C  CH3    0  -0.725  30.8543  42.9200  81.6697
 LCK  NZ   N  N      0  -0.383  29.1333  42.3412  80.1240
 LCK  CE   C  CH2    0  -0.303  28.1792  41.4135  79.5490
 LCK  CD   C  CH2    0  -0.420  27.3542  42.0768  78.4569
 LCK  CB   C  CH2    0  -0.422  25.5185  41.7467  76.7240
 LCK  CA   C  CH1    0  -0.195  24.4717  40.8020  76.1076
 LCK  N    N  NH2    0  -0.802  25.0240  39.6260  75.4511
 LCK  C    C  C      0   0.400  23.6079  41.6149  75.1160
 LCK  O    O  O      0  -0.606  23.9554  41.5861  73.9176
 LCK  H3   H  HCH2   0   0.246  30.8904  40.3462  82.0626
 LCK  H3A  H  HCH2   0   0.250  29.6904  39.8055  80.9149
 LCK  H1   H  HCH3   0   0.232  30.7672  43.9058  81.2165
 LCK  H1A  H  HCH3   0   0.237  30.6733  43.0071  82.7432
 LCK  H1B  H  HCH3   0   0.235  31.8815  42.5669  81.5525
 LCK  HE   H  HCH2   0   0.211  28.6869  40.5370  79.1244
 LCK  HEA  H  HCH2   0   0.213  27.5027  41.0214  80.3187
 LCK  HD   H  HCH2   0   0.208  26.8169  42.9336  78.8755
 LCK  HDA  H  HCH2   0   0.207  28.0242  42.4783  77.6895
 LCK  HG   H  HCH2   0   0.203  26.9219  40.2558  77.4199
 LCK  HGA  H  HCH2   0   0.207  25.7029  40.7028  78.5937
 LCK  HB   H  HCH2   0   0.205  25.0004  42.6167  77.1399
 LCK  HBA  H  HCH2   0   0.202  26.1717  42.1262  75.9293
 LCK  HA   H  HCH1   0   0.190  23.8231  40.4610  76.9236
 LCK  HN   H  HNH2   0   0.323  25.4736  39.9263  74.5947
 LCK  HNA  H  HNH2   0   0.332  25.7425  39.2037  76.0257
 LCK  CG   C  CH2    0  -0.427  26.3642  41.1096  77.8199

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
 LCK  OXT  C    deloc   1.247  0.020  1.247
 LCK  O2   C4   deloc   1.243  0.020  1.243
 LCK  C4   O1   deloc   1.245  0.020  1.245
 LCK  C4   C3   single  1.558  0.020  1.558
 LCK  C3   C2   single  1.499  0.020  1.499
 LCK  C3   H3   single  0.970  0.020  1.090
 LCK  C3   H3A  single  0.970  0.020  1.090
 LCK  C2   C1   single  1.499  0.020  1.499
 LCK  C2   NZ   double  1.270  0.020  1.270
 LCK  C1   H1   single  0.970  0.020  1.090
 LCK  C1   H1A  single  0.970  0.020  1.090
 LCK  C1   H1B  single  0.970  0.020  1.090
 LCK  NZ   CE   single  1.450  0.020  1.450
 LCK  CE   CD   single  1.521  0.020  1.521
 LCK  CE   HE   single  0.970  0.020  1.090
 LCK  CE   HEA  single  0.970  0.020  1.090
 LCK  CD   CG   single  1.524  0.020  1.524
 LCK  CD   HD   single  0.970  0.020  1.090
 LCK  CD   HDA  single  0.970  0.020  1.090
 LCK  CG   CB   single  1.524  0.020  1.524
 LCK  CG   HG   single  0.970  0.020  1.090
 LCK  CG   HGA  single  0.970  0.020  1.090
 LCK  CB   CA   single  1.530  0.020  1.530
 LCK  CB   HB   single  0.970  0.020  1.090
 LCK  CB   HBA  single  0.970  0.020  1.090
 LCK  CA   N    single  1.458  0.019  1.458
 LCK  CA   C    single  1.525  0.021  1.525
 LCK  CA   HA   single  0.970  0.020  0.970
 LCK  N    HN   single  0.890  0.020  1.040
 LCK  N    HNA  single  0.890  0.020  1.040
 LCK  C    O    deloc   1.231  0.020  1.231

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
 LCK  C3   C4  O1   116.96  3.000
 LCK  C3   C4  O2   115.34  3.000
 LCK  O1   C4  O2   127.70  3.000
 LCK  H3A  C3  H3   105.94  3.000
 LCK  H3A  C3  C2   111.49  3.000
 LCK  H3   C3  C2   109.85  3.000
 LCK  H3A  C3  C4   108.29  3.000
 LCK  H3   C3  C4   107.84  3.000
 LCK  C2   C3  C4   113.11  3.000
 LCK  NZ   C2  C1   118.64  3.000
 LCK  NZ   C2  C3   125.86  3.000
 LCK  C1   C2  C3   115.50  3.000
 LCK  H1B  C1  H1A  106.68  3.000
 LCK  H1B  C1  H1   108.86  3.000
 LCK  H1A  C1  H1   108.89  3.000
 LCK  H1B  C1  C2   110.66  3.000
 LCK  H1A  C1  C2   109.93  3.000
 LCK  H1   C1  C2   111.67  3.000
 LCK  CE   NZ  C2   119.07  3.000
 LCK  HEA  CE  HE   105.73  3.000
 LCK  HEA  CE  CD   108.97  3.000
 LCK  HE   CE  CD   108.74  3.000
 LCK  HEA  CE  NZ   110.86  3.000
 LCK  HE   CE  NZ   111.09  3.000
 LCK  CD   CE  NZ   111.27  3.000
 LCK  HDA  CD  HD   106.34  3.000
 LCK  HDA  CD  CG   109.72  3.000
 LCK  HD   CD  CG   109.75  3.000
 LCK  HDA  CD  CE   109.34  3.000
 LCK  HD   CD  CE   109.45  3.000
 LCK  CG   CD  CE   112.07  3.000
 LCK  HBA  CB  HB   106.39  3.000
 LCK  HBA  CB  CA   109.11  3.000
 LCK  HB   CB  CA   108.55  3.000
 LCK  HBA  CB  CG   109.60  3.000
 LCK  HB   CB  CG   108.77  3.000
 LCK  CA   CB  CG   114.14  3.000
 LCK  HA   CA  C    109.00  3.000
 LCK  HA   CA  N    110.00  3.000
 LCK  C    CA  N    111.00  2.800
 LCK  HA   CA  CB   109.00  3.000
 LCK  C    CA  CB   110.10  1.900
 LCK  N    CA  CB   110.50  1.700
 LCK  HNA  N   HN   106.77  3.000
 LCK  HNA  N   CA   110.51  3.000
 LCK  HN   N   CA   108.07  3.000
 LCK  O    C   CA   120.80  1.700
 LCK  O    C   OXT  126.82  3.000
 LCK  CA   C   OXT  116.50  3.000
 LCK  HGA  CG  HG   106.00  3.000
 LCK  HGA  CG  CB   109.15  3.000
 LCK  HG   CG  CB   110.23  3.000
 LCK  HGA  CG  CD   109.42  3.000
 LCK  HG   CG  CD   108.46  3.000
 LCK  CB   CG  CD   113.32  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
 LCK  Var_01  C2  C3  C4  O2   177.55  30.0  3
 LCK  Var_02  C1  C2  C3  C4    91.68  30.0  3
 LCK  Var_03  CD  CE  NZ  C2   178.99  30.0  3
 LCK  Var_04  CG  CD  CE  NZ   178.84  30.0  3
 LCK  Var_05  CB  CG  CD  CE   179.80  30.0  3
 LCK  Var_06  CA  CB  CG  CD  -177.60  30.0  3
 LCK  Var_07  H1  C1  C2  C3  -177.61  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
 LCK  chir_01  CA  CB  N  C  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
 LCK  plan-1  O2   0.020
 LCK  plan-1  C4   0.020
 LCK  plan-1  O1   0.020
 LCK  plan-1  C3   0.020
 LCK  plan-2  OXT  0.020
 LCK  plan-2  CA   0.020
 LCK  plan-2  C    0.020
 LCK  plan-2  O    0.020
 LCK  plan-3  C3   0.020
 LCK  plan-3  C2   0.020
 LCK  plan-3  C1   0.020
 LCK  plan-3  NZ   0.020
 LCK  plan-3  CE   0.020

