# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 04:30:25 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: N~6~-[(2S)-4-(6-methoxynaphthalen-2-yl)-4-oxobutan-2-yl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2cc(ccc2c1)C(=O)C[C@H](C)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
 LLZ  LLZ  N~6~-[(2S)-4-(6-methoxynaphthalen-2-yl)-4-oxobutan-2-yl]-L-lysine  L-peptide  54  27  .  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_LLZ
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
 LLZ  C     C  C      0   0.414  -24.0680  12.3936   1.4224
 LLZ  N     N  NH2    0  -0.814  -23.2611  13.7768   3.3180
 LLZ  O     O  O      0  -0.602  -23.1261  12.9179   0.7938
 LLZ  C1    C  CR16   0  -0.286  -32.2535   7.9525  10.2088
 LLZ  O1    O  O      0  -0.394  -27.5739   9.9269  10.6569
 LLZ  C2    C  CR16   0  -0.375  -33.5264   7.6581   9.8055
 LLZ  C3    C  CR6    0   0.406  -34.0006   8.1294   8.5563
 LLZ  O3    O  O2     0  -0.464  -35.2387   7.8849   8.0991
 LLZ  C4    C  CR16   0  -0.427  -33.1749   8.8800   7.7476
 LLZ  C5    C  CR66   0   0.141  -31.8642   9.1887   8.1494
 LLZ  C6    C  CR66   0   0.117  -31.3869   8.7230   9.4032
 LLZ  C7    C  CR16   0  -0.332  -30.0766   9.0399   9.8086
 LLZ  C8    C  CR6    0  -0.043  -29.2367   9.7746   9.0041
 LLZ  C9    C  CR16   0  -0.287  -29.7167  10.2300   7.7483
 LLZ  CA    C  CH1    0  -0.223  -24.1553  12.6902   2.9423
 LLZ  CB    C  CH2    0  -0.413  -25.5855  13.0133   3.3754
 LLZ  CD    C  CH2    0  -0.435  -25.2312  12.2130   5.8060
 LLZ  CE    C  CH2    0  -0.297  -25.8961  10.8589   5.5918
 LLZ  CG    C  CH2    0  -0.442  -25.7418  13.3047   4.8683
 LLZ  NZ    N  NH1    0  -0.602  -25.4481   9.8562   6.5551
 LLZ  C10   C  CR16   0  -0.310  -30.9889   9.9547   7.3395
 LLZ  C12   C  CH2    0  -0.588  -26.8209  10.4957   8.4773
 LLZ  C13   C  CH1    0  -0.080  -26.4579   9.3770   7.4845
 LLZ  C14   C  CH3    0  -0.677  -25.9200   8.1542   8.2141
 LLZ  C31   C  CH3    0  -0.439  -36.1196   7.0954   8.8752
 LLZ  OXT   O  OC    -1  -0.608  -24.9295  11.6186   0.9606
 LLZ  HN    H  HNH2   0   0.330  -22.9679  13.6706   4.2804
 LLZ  HNA   H  HNH2   0   0.331  -22.4284  13.7118   2.7479
 LLZ  H4    H  HCR6   0   0.261  -33.5390   9.2374   6.7915
 LLZ  H7    H  HCR6   0   0.261  -29.7302   8.6785  10.7696
 LLZ  H9    H  HCR6   0   0.267  -29.0792  10.8193   7.1026
 LLZ  HA    H  HCH1   0   0.193  -23.8698  11.7418   3.4311
 LLZ  HB    H  HCH2   0   0.205  -25.9340  13.8877   2.8156
 LLZ  HBA   H  HCH2   0   0.206  -26.2373  12.1867   3.0892
 LLZ  HD    H  HCH2   0   0.223  -25.3924  12.5329   6.8397
 LLZ  HDA   H  HCH2   0   0.212  -24.1485  12.0916   5.6996
 LLZ  HE    H  HCH2   0   0.212  -26.9880  10.9780   5.6242
 LLZ  HEA   H  HCH2   0   0.232  -25.6735  10.5019   4.5828
 LLZ  HG    H  HCH2   0   0.215  -25.2328  14.2419   5.1103
 LLZ  HGA   H  HCH2   0   0.214  -26.8020  13.4824   5.0784
 LLZ  HNZ   H  HNH1   0   0.348  -25.0810   9.0569   6.0576
 LLZ  H10   H  HCR6   0   0.256  -31.3425  10.3218   6.3838
 LLZ  H12   H  HCH2   0   0.270  -27.1821  11.3723   7.9323
 LLZ  H12A  H  HCH2   0   0.259  -25.9196  10.7971   9.0141
 LLZ  H13   H  HCH1   0   0.210  -27.3755   9.0777   6.9525
 LLZ  H14   H  HCH3   0   0.233  -26.6699   7.7116   8.8697
 LLZ  H14A  H  HCH3   0   0.236  -25.6238   7.3830   7.5007
 LLZ  H14B  H  HCH3   0   0.226  -25.0480   8.4122   8.8173
 LLZ  H31   H  HCH3   0   0.261  -37.0456   7.0260   8.3099
 LLZ  H31A  H  HCH3   0   0.232  -35.7318   6.0866   9.0367
 LLZ  H31B  H  HCH3   0   0.231  -36.3350   7.5523   9.8442
 LLZ  C11   C  C      0   0.384  -27.8584  10.0664   9.4834
 LLZ  H1    H  HCR6   0   0.265  -31.8985   7.5884  11.1653
 LLZ  H2    H  HCR6   0   0.286  -34.1569   7.0640  10.4526

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
 LLZ  C    CA    single    1.525  0.021  1.525
 LLZ  C    OXT   deloc     1.247  0.020  1.247
 LLZ  N    HN    single    0.890  0.020  1.040
 LLZ  N    HNA   single    0.890  0.020  1.040
 LLZ  O    C     deloc     1.231  0.020  1.231
 LLZ  C1   H1    single    0.930  0.020  1.080
 LLZ  C2   C1    aromatic  1.367  0.020  1.367
 LLZ  C2   H2    single    0.930  0.020  1.080
 LLZ  C3   C2    aromatic  1.417  0.020  1.417
 LLZ  O3   C3    single    1.342  0.020  1.342
 LLZ  O3   C31   single    1.415  0.020  1.415
 LLZ  C4   C3    aromatic  1.378  0.020  1.378
 LLZ  C4   C5    aromatic  1.405  0.020  1.405
 LLZ  C4   H4    single    0.930  0.020  1.080
 LLZ  C5   C6    aromatic  1.420  0.020  1.420
 LLZ  C6   C1    aromatic  1.412  0.020  1.412
 LLZ  C6   C7    aromatic  1.408  0.020  1.408
 LLZ  C7   H7    single    0.930  0.020  1.080
 LLZ  C8   C7    aromatic  1.376  0.020  1.376
 LLZ  C8   C11   single    1.488  0.020  1.488
 LLZ  C9   C8    aromatic  1.419  0.020  1.419
 LLZ  C9   H9    single    0.930  0.020  1.080
 LLZ  CA   N     single    1.458  0.019  1.458
 LLZ  CA   CB    single    1.530  0.020  1.530
 LLZ  CA   HA    single    0.970  0.020  0.970
 LLZ  CB   CG    single    1.529  0.020  1.529
 LLZ  CB   HB    single    0.970  0.020  1.090
 LLZ  CB   HBA   single    0.970  0.020  1.090
 LLZ  CD   CE    single    1.524  0.020  1.524
 LLZ  CD   HD    single    0.970  0.020  1.090
 LLZ  CD   HDA   single    0.970  0.020  1.090
 LLZ  CE   NZ    single    1.461  0.020  1.461
 LLZ  CE   HE    single    0.970  0.020  1.090
 LLZ  CE   HEA   single    0.970  0.020  1.090
 LLZ  CG   CD    single    1.527  0.020  1.527
 LLZ  CG   HG    single    0.970  0.020  1.090
 LLZ  CG   HGA   single    0.970  0.020  1.090
 LLZ  NZ   C13   single    1.454  0.020  1.454
 LLZ  NZ   HNZ   single    0.890  0.020  1.040
 LLZ  C10  C5    aromatic  1.417  0.020  1.417
 LLZ  C10  C9    aromatic  1.364  0.020  1.364
 LLZ  C10  H10   single    0.930  0.020  1.080
 LLZ  C11  O1    double    1.216  0.020  1.216
 LLZ  C12  C11   single    1.508  0.020  1.508
 LLZ  C12  H12   single    0.970  0.020  1.090
 LLZ  C12  H12A  single    0.970  0.020  1.090
 LLZ  C13  C12   single    1.539  0.020  1.539
 LLZ  C13  C14   single    1.522  0.020  1.522
 LLZ  C13  H13   single    0.970  0.020  1.090
 LLZ  C14  H14   single    0.970  0.020  1.090
 LLZ  C14  H14A  single    0.970  0.020  1.090
 LLZ  C14  H14B  single    0.970  0.020  1.090
 LLZ  C31  H31   single    0.970  0.020  1.090
 LLZ  C31  H31A  single    0.970  0.020  1.090
 LLZ  C31  H31B  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
 LLZ  OXT   C    CA    116.28  3.000
 LLZ  OXT   C    O     126.57  3.000
 LLZ  CA    C    O     120.80  1.700
 LLZ  HNA   N    HN    106.92  3.000
 LLZ  HNA   N    CA    108.19  3.000
 LLZ  HN    N    CA    110.19  3.000
 LLZ  H1    C1   C6    119.08  3.000
 LLZ  C6    C1   C2    121.38  3.000
 LLZ  H1    C1   C2    119.55  3.000
 LLZ  H2    C2   C3    121.02  3.000
 LLZ  C3    C2   C1    119.99  3.000
 LLZ  H2    C2   C1    118.99  3.000
 LLZ  C4    C3   O3    116.87  3.000
 LLZ  C4    C3   C2    119.87  3.000
 LLZ  O3    C3   C2    123.26  3.000
 LLZ  C31   O3   C3    119.28  3.000
 LLZ  H4    C4   C5    119.56  3.000
 LLZ  H4    C4   C3    119.73  3.000
 LLZ  C5    C4   C3    120.71  3.000
 LLZ  C10   C5   C6    118.30  3.000
 LLZ  C10   C5   C4    122.10  3.000
 LLZ  C6    C5   C4    119.60  3.000
 LLZ  C7    C6   C5    119.56  3.000
 LLZ  C7    C6   C1    121.99  3.000
 LLZ  C5    C6   C1    118.45  3.000
 LLZ  H7    C7   C8    120.10  3.000
 LLZ  C8    C7   C6    121.34  3.000
 LLZ  H7    C7   C6    118.55  3.000
 LLZ  C11   C8   C9    122.36  3.000
 LLZ  C9    C8   C7    118.83  3.000
 LLZ  C11   C8   C7    118.81  3.000
 LLZ  H9    C9   C10   118.71  3.000
 LLZ  C10   C9   C8    121.05  3.000
 LLZ  H9    C9   C8    120.23  3.000
 LLZ  HA    CA   CB    109.00  3.000
 LLZ  HA    CA   N     110.00  3.000
 LLZ  CB    CA   N     110.50  1.700
 LLZ  HA    CA   C     109.00  3.000
 LLZ  CB    CA   C     110.10  1.900
 LLZ  N     CA   C     111.00  2.800
 LLZ  HBA   CB   HB    106.30  3.000
 LLZ  HBA   CB   CG    109.84  3.000
 LLZ  HB    CB   CG    108.33  3.000
 LLZ  HBA   CB   CA    108.93  3.000
 LLZ  HB    CB   CA    108.76  3.000
 LLZ  CG    CB   CA    114.36  3.000
 LLZ  HDA   CD   HD    105.66  3.000
 LLZ  HDA   CD   CG    110.50  3.000
 LLZ  HD    CD   CG    108.78  3.000
 LLZ  CG    CD   CE    113.77  3.000
 LLZ  HDA   CD   CE    108.63  3.000
 LLZ  HD    CD   CE    109.17  3.000
 LLZ  HEA   CE   HE    105.36  3.000
 LLZ  HEA   CE   NZ    108.79  3.000
 LLZ  HE    CE   NZ    111.08  3.000
 LLZ  HEA   CE   CD    109.33  3.000
 LLZ  HE    CE   CD    109.46  3.000
 LLZ  NZ    CE   CD    112.54  3.000
 LLZ  HGA   CG   HG    105.60  3.000
 LLZ  HGA   CG   CD    108.78  3.000
 LLZ  HG    CG   CD    108.74  3.000
 LLZ  HGA   CG   CB    108.49  3.000
 LLZ  HG    CG   CB    109.38  3.000
 LLZ  CD    CG   CB    115.41  3.000
 LLZ  HNZ   NZ   C13   107.84  3.000
 LLZ  HNZ   NZ   CE    109.24  3.000
 LLZ  C13   NZ   CE    115.77  3.000
 LLZ  H10   C10  C9    120.03  3.000
 LLZ  H10   C10  C5    119.06  3.000
 LLZ  C9    C10  C5    120.91  3.000
 LLZ  H12A  C12  H12   107.24  3.000
 LLZ  H12A  C12  C13   108.86  3.000
 LLZ  H12   C12  C13   109.82  3.000
 LLZ  C13   C12  C11   112.69  3.000
 LLZ  H12A  C12  C11   108.58  3.000
 LLZ  H12   C12  C11   109.48  3.000
 LLZ  H13   C13  C14   107.91  3.000
 LLZ  H13   C13  C12   108.21  3.000
 LLZ  C14   C13  C12   110.98  3.000
 LLZ  H13   C13  NZ    111.05  3.000
 LLZ  C14   C13  NZ    109.01  3.000
 LLZ  C12   C13  NZ    109.67  3.000
 LLZ  H14B  C14  H14A  108.15  3.000
 LLZ  H14B  C14  H14   108.26  3.000
 LLZ  H14A  C14  H14   107.04  3.000
 LLZ  H14B  C14  C13   110.94  3.000
 LLZ  H14A  C14  C13   110.50  3.000
 LLZ  H14   C14  C13   111.80  3.000
 LLZ  H31B  C31  H31A  108.96  3.000
 LLZ  H31B  C31  H31   108.66  3.000
 LLZ  H31A  C31  H31   108.68  3.000
 LLZ  H31B  C31  O3    112.08  3.000
 LLZ  H31A  C31  O3    112.03  3.000
 LLZ  H31   C31  O3    106.31  3.000
 LLZ  C12   C11  C8    118.57  3.000
 LLZ  C12   C11  O1    121.06  3.000
 LLZ  C8    C11  O1    120.35  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
 LLZ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 LLZ  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 LLZ  CONST_03  C10  C5   C6   C1    180.00   0.0  0
 LLZ  CONST_04  C8   C7   C6   C1    180.00   0.0  0
 LLZ  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 LLZ  CONST_06  C7   C6   C1   C2    180.00   0.0  0
 LLZ  CONST_07  C5   C4   C3   C2      0.00   0.0  0
 LLZ  CONST_08  C6   C1   C2   C3      0.00   0.0  0
 LLZ  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 LLZ  CONST_10  C10  C5   C4   C3    180.00   0.0  0
 LLZ  CONST_11  C7   C6   C5   C4    180.00   0.0  0
 LLZ  CONST_12  C9   C10  C5   C4    180.00   0.0  0
 LLZ  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 LLZ  CONST_14  C8   C9   C10  C5      0.00   0.0  0
 LLZ  CONST_15  C9   C10  C5   C6      0.00   0.0  0
 LLZ  CONST_16  C9   C8   C7   C6      0.00   0.0  0
 LLZ  CONST_17  C10  C5   C6   C7      0.00   0.0  0
 LLZ  CONST_18  C10  C9   C8   C7      0.00   0.0  0
 LLZ  CONST_19  O3   C3   C2   C1    180.00   0.0  0
 LLZ  CONST_20  C5   C4   C3   O3    180.00   0.0  0
 LLZ  CONST_21  C11  C8   C7   C6    180.00   0.0  0
 LLZ  CONST_22  C11  C8   C9   C10   180.00   0.0  0
 LLZ  CONST_23  H7   C7   C6   C1      0.00   0.0  0
 LLZ  CONST_24  H4   C4   C3   C2    180.00   0.0  0
 LLZ  CONST_25  H1   C1   C2   C3    180.00   0.0  0
 LLZ  CONST_26  H2   C2   C3   C4    180.00   0.0  0
 LLZ  CONST_27  H10  C10  C5   C4      0.00   0.0  0
 LLZ  CONST_28  H9   C9   C10  C5    180.00   0.0  0
 LLZ  Var_01    C7   C8   C11  O1    -16.13  30.0  2
 LLZ  Var_02    C13  C12  C11  C8    -67.02  30.0  2
 LLZ  Var_03    H31  C31  O3   C3   -179.49  30.0  3
 LLZ  Var_04    CD   CG   CB   CA    -55.43  30.0  3
 LLZ  Var_05    CE   CD   CG   CB    -58.25  30.0  3
 LLZ  Var_06    C13  NZ   CE   CD    114.09  30.0  3
 LLZ  Var_07    NZ   CE   CD   CG   -176.48  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
 LLZ  chir_01  CA   C   N    CB   negativ
 LLZ  chir_02  C13  NZ  C14  C12  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
 LLZ  plan-1  C1   0.020
 LLZ  plan-1  C2   0.020
 LLZ  plan-1  C3   0.020
 LLZ  plan-1  O3   0.020
 LLZ  plan-1  C4   0.020
 LLZ  plan-1  C5   0.020
 LLZ  plan-1  C6   0.020
 LLZ  plan-1  C7   0.020
 LLZ  plan-1  C8   0.020
 LLZ  plan-1  C9   0.020
 LLZ  plan-1  C10  0.020
 LLZ  plan-1  H4   0.020
 LLZ  plan-1  H7   0.020
 LLZ  plan-1  H9   0.020
 LLZ  plan-1  H10  0.020
 LLZ  plan-1  C11  0.020
 LLZ  plan-1  H1   0.020
 LLZ  plan-1  H2   0.020
 LLZ  plan-2  O1   0.020
 LLZ  plan-2  C8   0.020
 LLZ  plan-2  C12  0.020
 LLZ  plan-2  C11  0.020
 LLZ  plan-3  C    0.020
 LLZ  plan-3  O    0.020
 LLZ  plan-3  CA   0.020
 LLZ  plan-3  OXT  0.020

