# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 09:45:44 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: N~6~-tetradecanoyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCC(=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
 MYK  MYK  N~6~-tetradecanoyl-L-lysine  L-peptide  64  25  .  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_MYK
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
 MYK  OXT  O  OC    -1  -0.615  -11.0018  32.6429  -40.0217
 MYK  C    C  C      0   0.384  -11.6239  32.3608  -41.0674
 MYK  N    N  NH2    0  -0.806  -13.9404  32.5464  -41.9543
 MYK  O    O  O      0  -0.605  -11.1587  32.3255  -42.2230
 MYK  CA   C  CH1    0  -0.155  -13.1142  31.9787  -40.8920
 MYK  CB   C  CH2    0  -0.423  -13.2762  30.4576  -40.9237
 MYK  CD   C  CH2    0  -0.470  -12.9014  28.2319  -39.7824
 MYK  CE   C  CH2    0  -0.231  -12.1894  27.5020  -38.6561
 MYK  CG   C  CH2    0  -0.423  -12.5730  29.7190  -39.7925
 MYK  CI   C  CH2    0  -0.418  -11.5828  21.4442  -38.7267
 MYK  CK   C  CH2    0  -0.421  -10.4544  20.6091  -39.3204
 MYK  CL   C  CH2    0  -0.421  -10.8115  19.1430  -39.5477
 MYK  CM   C  CH2    0  -0.416  -11.0476  18.3482  -38.2684
 MYK  CP   C  CH2    0  -0.408  -11.3416  16.8769  -38.5310
 MYK  CQ   C  CH2    0  -0.410  -12.0925  13.7919  -36.2532
 MYK  CR   C  CH2    0  -0.410  -11.5665  16.0703  -37.2586
 MYK  CS   C  CH2    0  -0.404  -12.4050  12.3256  -36.5215
 MYK  CT   C  CH2    0  -0.415  -11.2031  22.9110  -38.5738
 MYK  CU   C  CH2    0  -0.410  -11.8714  14.6018  -37.5242
 MYK  CV   C  CH3    0  -0.659  -12.9436  10.0511  -35.5322
 MYK  CW   C  CH2    0  -0.417  -12.6244  11.5128  -35.2517
 MYK  CX   C  C      0   0.535  -11.9339  25.2009  -37.8476
 MYK  OX   O  O      0  -0.505  -11.0930  25.5257  -37.0171
 MYK  CY   C  CH2    0  -0.556  -12.3540  23.7598  -38.0348
 MYK  NZ   N  NH1    0  -0.638  -12.5152  26.0907  -38.6660
 MYK  H    H  HNH2   0   0.329  -14.9143  32.3716  -41.7353
 MYK  H2   H  HNH2   0   0.332  -13.8437  33.5545  -41.9597
 MYK  HA   H  HCH1   0   0.167  -13.4268  32.3225  -39.8939
 MYK  HB   H  HCH2   0   0.208  -14.3468  30.2225  -40.8803
 MYK  HBA  H  HCH2   0   0.206  -12.9213  30.0855  -41.8903
 MYK  HD   H  HCH2   0   0.226  -12.6185  27.7854  -40.7411
 MYK  HDA  H  HCH2   0   0.225  -13.9832  28.0970  -39.6810
 MYK  HE   H  HCH2   0   0.227  -11.1084  27.6303  -38.7603
 MYK  HEA  H  HCH2   0   0.225  -12.4676  27.9458  -37.6951
 MYK  HG   H  HCH2   0   0.219  -11.4901  29.8458  -39.8727
 MYK  HGA  H  HCH2   0   0.210  -12.8615  30.1598  -38.8325
 MYK  HI   H  HCH2   0   0.209  -12.4676  21.3621  -39.3676
 MYK  HIA  H  HCH2   0   0.218  -11.8758  21.0482  -37.7497
 MYK  HK   H  HCH2   0   0.217  -10.1561  21.0545  -40.2745
 MYK  HKA  H  HCH2   0   0.207   -9.5746  20.6696  -38.6700
 MYK  HL   H  HCH2   0   0.206  -11.7013  19.0799  -40.1838
 MYK  HLA  H  HCH2   0   0.215  -10.0038  18.6666  -40.1124
 MYK  HM   H  HCH2   0   0.205  -10.1655  18.4339  -37.6237
 MYK  HMA  H  HCH2   0   0.212  -11.8786  18.7811  -37.7026
 MYK  HP   H  HCH2   0   0.205  -12.2249  16.7936  -39.1738
 MYK  HPA  H  HCH2   0   0.205  -10.5136  16.4364  -39.0976
 MYK  HQ   H  HCH2   0   0.205  -12.9112  14.2375  -35.6773
 MYK  HQA  H  HCH2   0   0.205  -11.2027  13.8636  -35.6181
 MYK  HR   H  HCH2   0   0.205  -10.6805  16.1476  -36.6189
 MYK  HRA  H  HCH2   0   0.205  -12.3902  16.5141  -36.6885
 MYK  HS   H  HCH2   0   0.205  -13.2961  12.2547  -37.1551
 MYK  HSA  H  HCH2   0   0.205  -11.5878  11.8798  -37.0996
 MYK  HT   H  HCH2   0   0.223  -10.3419  22.9962  -37.9060
 MYK  HTA  H  HCH2   0   0.222  -10.8852  23.3076  -39.5433
 MYK  HU   H  HCH2   0   0.205  -11.0496  14.1587  -38.0977
 MYK  HUA  H  HCH2   0   0.205  -12.7593  14.5259  -38.1615
 MYK  HV   H  HCH3   0   0.224  -13.0988   9.4889  -34.6107
 MYK  HVA  H  HCH3   0   0.215  -13.8489   9.9554  -36.1346
 MYK  HVB  H  HCH3   0   0.214  -12.1327   9.5688  -36.0811
 MYK  HW   H  HCH2   0   0.209  -11.7322  11.5802  -34.6216
 MYK  HWA  H  HCH2   0   0.209  -13.4378  11.9610  -34.6725
 MYK  HY   H  HCH2   0   0.241  -13.2138  23.6797  -38.7044
 MYK  HYA  H  HCH2   0   0.252  -12.6707  23.3714  -37.0633
 MYK  HNZ  H  HNH1   0   0.398  -13.2037  25.7674  -39.3259

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
 MYK  OXT  C    deloc   1.249  0.020  1.249
 MYK  C    O    deloc   1.231  0.020  1.231
 MYK  C    CA   single  1.525  0.021  1.525
 MYK  N    CA   single  1.458  0.019  1.458
 MYK  CA   CB   single  1.530  0.020  1.530
 MYK  CB   CG   single  1.523  0.020  1.523
 MYK  CD   CE   single  1.519  0.020  1.519
 MYK  CD   CG   single  1.523  0.020  1.523
 MYK  CE   NZ   single  1.448  0.020  1.448
 MYK  CI   CK   single  1.524  0.020  1.524
 MYK  CI   CT   single  1.523  0.020  1.523
 MYK  CK   CL   single  1.526  0.020  1.526
 MYK  CL   CM   single  1.524  0.020  1.524
 MYK  CM   CP   single  1.523  0.020  1.523
 MYK  CP   CR   single  1.523  0.020  1.523
 MYK  CQ   CS   single  1.523  0.020  1.523
 MYK  CQ   CU   single  1.523  0.020  1.523
 MYK  CR   CU   single  1.523  0.020  1.523
 MYK  CS   CW   single  1.524  0.020  1.524
 MYK  CT   CY   single  1.528  0.020  1.528
 MYK  CV   CW   single  1.522  0.020  1.522
 MYK  CX   OX   double  1.226  0.020  1.226
 MYK  CX   CY   single  1.513  0.020  1.513
 MYK  CX   NZ   single  1.341  0.020  1.341
 MYK  N    H    single  0.860  0.020  0.860
 MYK  N    H2   single  0.890  0.020  1.040
 MYK  CA   HA   single  0.970  0.020  0.970
 MYK  CB   HB   single  0.970  0.020  1.090
 MYK  CB   HBA  single  0.970  0.020  1.090
 MYK  CD   HD   single  0.970  0.020  1.090
 MYK  CD   HDA  single  0.970  0.020  1.090
 MYK  CE   HE   single  0.970  0.020  1.090
 MYK  CE   HEA  single  0.970  0.020  1.090
 MYK  CG   HG   single  0.970  0.020  1.090
 MYK  CG   HGA  single  0.970  0.020  1.090
 MYK  CI   HI   single  0.970  0.020  1.090
 MYK  CI   HIA  single  0.970  0.020  1.090
 MYK  CK   HK   single  0.970  0.020  1.090
 MYK  CK   HKA  single  0.970  0.020  1.090
 MYK  CL   HL   single  0.970  0.020  1.090
 MYK  CL   HLA  single  0.970  0.020  1.090
 MYK  CM   HM   single  0.970  0.020  1.090
 MYK  CM   HMA  single  0.970  0.020  1.090
 MYK  CP   HP   single  0.970  0.020  1.090
 MYK  CP   HPA  single  0.970  0.020  1.090
 MYK  CQ   HQ   single  0.970  0.020  1.090
 MYK  CQ   HQA  single  0.970  0.020  1.090
 MYK  CR   HR   single  0.970  0.020  1.090
 MYK  CR   HRA  single  0.970  0.020  1.090
 MYK  CS   HS   single  0.970  0.020  1.090
 MYK  CS   HSA  single  0.970  0.020  1.090
 MYK  CT   HT   single  0.970  0.020  1.090
 MYK  CT   HTA  single  0.970  0.020  1.090
 MYK  CU   HU   single  0.970  0.020  1.090
 MYK  CU   HUA  single  0.970  0.020  1.090
 MYK  CV   HV   single  0.970  0.020  1.090
 MYK  CV   HVA  single  0.970  0.020  1.090
 MYK  CV   HVB  single  0.970  0.020  1.090
 MYK  CW   HW   single  0.970  0.020  1.090
 MYK  CW   HWA  single  0.970  0.020  1.090
 MYK  CY   HY   single  0.970  0.020  1.090
 MYK  CY   HYA  single  0.970  0.020  1.090
 MYK  NZ   HNZ  single  0.860  0.020  1.020

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
 MYK  CA   C   O    120.80  1.700
 MYK  CA   C   OXT  116.12  3.000
 MYK  O    C   OXT  126.64  3.000
 MYK  H2   N   H    105.34  3.000
 MYK  H2   N   CA   109.69  3.000
 MYK  H    N   CA   114.00  3.000
 MYK  HA   CA  CB   109.00  3.000
 MYK  HA   CA  N    110.00  3.000
 MYK  CB   CA  N    110.50  1.700
 MYK  HA   CA  C    109.00  3.000
 MYK  CB   CA  C    110.10  1.900
 MYK  N    CA  C    111.00  2.800
 MYK  HBA  CB  HB   106.16  3.000
 MYK  HBA  CB  CG   109.95  3.000
 MYK  HB   CB  CG   108.50  3.000
 MYK  HBA  CB  CA   108.78  3.000
 MYK  HB   CB  CA   108.40  3.000
 MYK  CG   CB  CA   114.70  3.000
 MYK  HDA  CD  HD   106.63  3.000
 MYK  HDA  CD  CG   109.51  3.000
 MYK  HD   CD  CG   109.67  3.000
 MYK  HDA  CD  CE   109.58  3.000
 MYK  HD   CD  CE   109.40  3.000
 MYK  CG   CD  CE   111.90  3.000
 MYK  HEA  CE  HE   106.70  3.000
 MYK  HEA  CE  NZ   110.11  3.000
 MYK  HE   CE  NZ   109.63  3.000
 MYK  HEA  CE  CD   109.69  3.000
 MYK  HE   CE  CD   109.65  3.000
 MYK  NZ   CE  CD   110.96  3.000
 MYK  HGA  CG  HG   106.17  3.000
 MYK  HGA  CG  CD   109.30  3.000
 MYK  HG   CG  CD   109.11  3.000
 MYK  HGA  CG  CB   109.52  3.000
 MYK  HG   CG  CB   110.28  3.000
 MYK  CD   CG  CB   112.27  3.000
 MYK  HIA  CI  HI   106.20  3.000
 MYK  HIA  CI  CT   109.01  3.000
 MYK  HI   CI  CT   109.40  3.000
 MYK  HIA  CI  CK   110.35  3.000
 MYK  HI   CI  CK   109.20  3.000
 MYK  CT   CI  CK   112.48  3.000
 MYK  HKA  CK  HK   106.03  3.000
 MYK  HKA  CK  CL   109.23  3.000
 MYK  HK   CK  CL   108.97  3.000
 MYK  HKA  CK  CI   109.45  3.000
 MYK  HK   CK  CI   108.56  3.000
 MYK  CL   CK  CI   114.28  3.000
 MYK  HLA  CL  HL   105.94  3.000
 MYK  HLA  CL  CM   108.68  3.000
 MYK  HL   CL  CM   109.35  3.000
 MYK  HLA  CL  CK   108.80  3.000
 MYK  HL   CL  CK   109.38  3.000
 MYK  CM   CL  CK   114.34  3.000
 MYK  HMA  CM  HM   106.03  3.000
 MYK  HMA  CM  CP   108.94  3.000
 MYK  HM   CM  CP   109.41  3.000
 MYK  HMA  CM  CL   110.19  3.000
 MYK  HM   CM  CL   109.16  3.000
 MYK  CP   CM  CL   112.88  3.000
 MYK  HPA  CP  HP   105.98  3.000
 MYK  HPA  CP  CR   109.31  3.000
 MYK  HP   CP  CR   109.32  3.000
 MYK  HPA  CP  CM   109.37  3.000
 MYK  HP   CP  CM   109.28  3.000
 MYK  CR   CP  CM   113.33  3.000
 MYK  HQA  CQ  HQ   106.00  3.000
 MYK  HQA  CQ  CU   109.33  3.000
 MYK  HQ   CQ  CU   109.32  3.000
 MYK  HQA  CQ  CS   109.38  3.000
 MYK  HQ   CQ  CS   109.31  3.000
 MYK  CU   CQ  CS   113.24  3.000
 MYK  HRA  CR  HR   105.99  3.000
 MYK  HRA  CR  CU   109.32  3.000
 MYK  HR   CR  CU   109.38  3.000
 MYK  HRA  CR  CP   109.34  3.000
 MYK  HR   CR  CP   109.33  3.000
 MYK  CU   CR  CP   113.23  3.000
 MYK  HSA  CS  HS   105.97  3.000
 MYK  HSA  CS  CW   109.27  3.000
 MYK  HS   CS  CW   109.28  3.000
 MYK  HSA  CS  CQ   109.37  3.000
 MYK  HS   CS  CQ   109.33  3.000
 MYK  CW   CS  CQ   113.35  3.000
 MYK  HTA  CT  HT   106.50  3.000
 MYK  HTA  CT  CY   109.26  3.000
 MYK  HT   CT  CY   109.55  3.000
 MYK  HTA  CT  CI   109.42  3.000
 MYK  HT   CT  CI   109.44  3.000
 MYK  CY   CT  CI   112.49  3.000
 MYK  HUA  CU  HU   105.98  3.000
 MYK  HUA  CU  CR   109.30  3.000
 MYK  HU   CU  CR   109.33  3.000
 MYK  HUA  CU  CQ   109.32  3.000
 MYK  HU   CU  CQ   109.30  3.000
 MYK  CR   CU  CQ   113.34  3.000
 MYK  HVB  CV  HVA  107.45  3.000
 MYK  HVB  CV  HV   107.63  3.000
 MYK  HVA  CV  HV   107.64  3.000
 MYK  HVB  CV  CW   111.17  3.000
 MYK  HVA  CV  CW   111.09  3.000
 MYK  HV   CV  CW   111.67  3.000
 MYK  HWA  CW  HW   106.02  3.000
 MYK  HWA  CW  CV   109.56  3.000
 MYK  HW   CW  CV   109.65  3.000
 MYK  HWA  CW  CS   109.25  3.000
 MYK  HW   CW  CS   109.24  3.000
 MYK  CV   CW  CS   112.89  3.000
 MYK  NZ   CX  CY   115.85  3.000
 MYK  NZ   CX  OX   122.34  3.000
 MYK  CY   CX  OX   121.79  3.000
 MYK  HYA  CY  HY   106.89  3.000
 MYK  HYA  CY  CX   108.00  3.000
 MYK  HY   CY  CX   111.36  3.000
 MYK  HYA  CY  CT   109.53  3.000
 MYK  HY   CY  CT   109.61  3.000
 MYK  CX   CY  CT   111.32  3.000
 MYK  HNZ  NZ  CX   118.89  3.000
 MYK  HNZ  NZ  CE   118.11  3.000
 MYK  CX   NZ  CE   123.00  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
 MYK  CONST_01  OX   CX  NZ  CE     0.00   0.0  0
 MYK  CONST_02  CY   CX  NZ  CE   180.00   0.0  0
 MYK  CONST_03  HNZ  NZ  CX  OX   180.00   0.0  0
 MYK  Var_01    CD   CG  CB  CA   173.36  30.0  3
 MYK  Var_02    CE   CD  CG  CB   179.67  30.0  1
 MYK  Var_03    CX   NZ  CE  CD   174.25  30.0  3
 MYK  Var_04    NZ   CE  CD  CG  -179.97  30.0  3
 MYK  Var_05    CM   CL  CK  CI   -66.94  30.0  3
 MYK  Var_06    CX   CY  CT  CI   178.00  30.0  3
 MYK  Var_07    CY   CT  CI  CK   177.54  30.0  3
 MYK  Var_08    CP   CM  CL  CK  -177.49  30.0  3
 MYK  Var_09    CT   CI  CK  CL  -177.49  30.0  2
 MYK  Var_10    CR   CP  CM  CL   179.47  30.0  3
 MYK  Var_11    CU   CR  CP  CM   179.53  30.0  3
 MYK  Var_12    CQ   CU  CR  CP   179.82  30.0  3
 MYK  Var_13    CV   CW  CS  CQ   179.68  30.0  3
 MYK  Var_14    CS   CQ  CU  CR   179.67  30.0  1
 MYK  Var_15    OX   CX  CY  CT   -66.00  30.0  1
 MYK  Var_16    CW   CS  CQ  CU   179.91  30.0  3
 MYK  Var_17    HV   CV  CW  CS  -179.88  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
 MYK  chir_01  CA  C  N  CB  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
 MYK  plan-1  CE   0.020
 MYK  plan-1  CX   0.020
 MYK  plan-1  OX   0.020
 MYK  plan-1  CY   0.020
 MYK  plan-1  NZ   0.020
 MYK  plan-1  HNZ  0.020
 MYK  plan-2  OXT  0.020
 MYK  plan-2  C    0.020
 MYK  plan-2  O    0.020
 MYK  plan-2  CA   0.020

