# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:35:03 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: N~6~-[(2S)-4-hydroxy-4-methylpentan-2-yl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC(C)(C)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
 LLO  LLO  N~6~-[(2S)-4-hydroxy-4-methylpentan-2-yl]-L-lysine  L-peptide  42  17  .  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_LLO
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
 LLO  C     C  C      0   0.411  38.1841  -14.0513  18.9827
 LLO  N     N  NH2    0  -0.814  38.8586  -13.8616  16.6045
 LLO  O     O  O      0  -0.602  39.2351  -14.7117  19.1101
 LLO  O1    O  OH1    0  -0.675  28.9495  -10.5195  12.1526
 LLO  C8    C  CH3    0  -0.657  30.4610   -9.3860  13.5450
 LLO  CA    C  CH1    0  -0.219  37.9494  -13.3471  17.6205
 LLO  CB    C  CH2    0  -0.387  36.5010  -13.4806  17.1567
 LLO  CD    C  CH2    0  -0.430  34.7350  -12.8447  15.4520
 LLO  CE    C  CH2    0  -0.249  34.4325  -12.1169  14.1517
 LLO  CG    C  CH2    0  -0.422  36.1936  -12.7204  15.8731
 LLO  NZ    N  NH1    0  -0.603  33.0293  -12.2325  13.8032
 LLO  C12   C  CH2    0  -0.458  31.0863  -11.5802  12.4746
 LLO  C13   C  CH1    0  -0.067  32.6170  -11.4882  12.6189
 LLO  C14   C  CH3    0  -0.681  33.3177  -11.9221  11.3292
 LLO  C16   C  CH3    0  -0.675  30.8426   -9.4849  11.0720
 LLO  OXT   O  OC    -1  -0.608  37.3144  -13.8676  19.8574
 LLO  HN    H  HNH2   0   0.329  39.0225  -13.1577  15.8969
 LLO  HNA   H  HNH2   0   0.331  39.7496  -14.0472  17.0453
 LLO  HO1   H  HOH1   0   0.437  28.8319  -11.0700  11.3709
 LLO  H8    H  HCH3   0   0.226  31.4981   -9.1144  13.7398
 LLO  H8A   H  HCH3   0   0.229  29.8957   -8.4589  13.4334
 LLO  H8B   H  HCH3   0   0.227  30.0838   -9.9123  14.4237
 LLO  HA    H  HCH1   0   0.186  38.1224  -12.2724  17.8147
 LLO  HB    H  HCH2   0   0.193  36.2659  -14.5414  17.0120
 LLO  HBA   H  HCH2   0   0.202  35.8442  -13.1193  17.9504
 LLO  HD    H  HCH2   0   0.209  34.0873  -12.4526  16.2421
 LLO  HDA   H  HCH2   0   0.208  34.4782  -13.9043  15.3403
 LLO  HE    H  HCH2   0   0.206  34.6632  -11.0526  14.2709
 LLO  HEA   H  HCH2   0   0.185  35.1153  -12.4894  13.3729
 LLO  HG    H  HCH2   0   0.202  36.4404  -11.6610  16.0104
 LLO  HGA   H  HCH2   0   0.205  36.8342  -13.0795  15.0613
 LLO  HNZ   H  HNH1   0   0.330  32.7962  -13.2123  13.6753
 LLO  H12   H  HCH2   0   0.229  30.6800  -12.0682  13.3652
 LLO  H12A  H  HCH2   0   0.222  30.8396  -12.2298  11.6261
 LLO  H13   H  HCH1   0   0.219  32.8987  -10.4463  12.8113
 LLO  H14   H  HCH3   0   0.229  32.9660  -11.3416  10.4750
 LLO  H14A  H  HCH3   0   0.227  34.3991  -11.7946  11.3860
 LLO  H14B  H  HCH3   0   0.215  33.1125  -12.9750  11.1195
 LLO  H16   H  HCH3   0   0.225  31.8929   -9.2070  11.1686
 LLO  H16A  H  HCH3   0   0.224  30.7445  -10.0860  10.1644
 LLO  H16B  H  HCH3   0   0.232  30.2703   -8.5660  10.9331
 LLO  C11   C  CT     0   0.209  30.3406  -10.2496  12.2952

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
 LLO  C    O     deloc   1.231  0.020  1.231
 LLO  N    CA    single  1.458  0.019  1.458
 LLO  O1   C11   single  1.424  0.020  1.424
 LLO  CA   C     single  1.525  0.021  1.525
 LLO  CB   CA    single  1.530  0.020  1.530
 LLO  CE   CD    single  1.520  0.020  1.520
 LLO  CG   CB    single  1.523  0.020  1.523
 LLO  CG   CD    single  1.523  0.020  1.523
 LLO  NZ   CE    single  1.450  0.020  1.450
 LLO  C11  C8    single  1.524  0.020  1.524
 LLO  C11  C12   single  1.536  0.020  1.536
 LLO  C13  NZ    single  1.458  0.020  1.458
 LLO  C13  C12   single  1.540  0.020  1.540
 LLO  C14  C13   single  1.531  0.020  1.531
 LLO  C16  C11   single  1.527  0.020  1.527
 LLO  C    OXT   deloc   1.247  0.020  1.247
 LLO  N    HN    single  0.890  0.020  1.040
 LLO  N    HNA   single  0.890  0.020  1.040
 LLO  O1   HO1   single  0.850  0.020  0.980
 LLO  C8   H8    single  0.970  0.020  1.090
 LLO  C8   H8A   single  0.970  0.020  1.090
 LLO  C8   H8B   single  0.970  0.020  1.090
 LLO  CA   HA    single  0.970  0.020  0.970
 LLO  CB   HB    single  0.970  0.020  1.090
 LLO  CB   HBA   single  0.970  0.020  1.090
 LLO  CD   HD    single  0.970  0.020  1.090
 LLO  CD   HDA   single  0.970  0.020  1.090
 LLO  CE   HE    single  0.970  0.020  1.090
 LLO  CE   HEA   single  0.970  0.020  1.090
 LLO  CG   HG    single  0.970  0.020  1.090
 LLO  CG   HGA   single  0.970  0.020  1.090
 LLO  NZ   HNZ   single  0.890  0.020  1.040
 LLO  C12  H12   single  0.970  0.020  1.090
 LLO  C12  H12A  single  0.970  0.020  1.090
 LLO  C13  H13   single  0.970  0.020  1.090
 LLO  C14  H14   single  0.970  0.020  1.090
 LLO  C14  H14A  single  0.970  0.020  1.090
 LLO  C14  H14B  single  0.970  0.020  1.090
 LLO  C16  H16   single  0.970  0.020  1.090
 LLO  C16  H16A  single  0.970  0.020  1.090
 LLO  C16  H16B  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
 LLO  OXT   C    CA    116.33  3.000
 LLO  OXT   C    O     126.42  3.000
 LLO  CA    C    O     120.80  1.700
 LLO  HNA   N    HN    106.85  3.000
 LLO  HNA   N    CA    108.09  3.000
 LLO  HN    N    CA    110.07  3.000
 LLO  HO1   O1   C11   107.99  3.000
 LLO  H8B   C8   H8A   108.23  3.000
 LLO  H8B   C8   H8    107.77  3.000
 LLO  H8A   C8   H8    107.42  3.000
 LLO  H8B   C8   C11   111.08  3.000
 LLO  H8A   C8   C11   110.89  3.000
 LLO  H8    C8   C11   111.29  3.000
 LLO  HA    CA   CB    109.00  3.000
 LLO  HA    CA   N     110.00  3.000
 LLO  CB    CA   N     110.50  1.700
 LLO  HA    CA   C     109.00  3.000
 LLO  CB    CA   C     110.10  1.900
 LLO  N     CA   C     111.00  2.800
 LLO  HBA   CB   HB    106.69  3.000
 LLO  HBA   CB   CG    109.03  3.000
 LLO  HB    CB   CG    109.18  3.000
 LLO  HBA   CB   CA    108.72  3.000
 LLO  HB    CB   CA    109.16  3.000
 LLO  CG    CB   CA    113.82  3.000
 LLO  HDA   CD   HD    106.34  3.000
 LLO  HDA   CD   CG    109.36  3.000
 LLO  HD    CD   CG    109.75  3.000
 LLO  HDA   CD   CE    109.21  3.000
 LLO  HD    CD   CE    109.16  3.000
 LLO  CG    CD   CE    112.82  3.000
 LLO  HEA   CE   HE    105.97  3.000
 LLO  HEA   CE   NZ    113.77  3.000
 LLO  HE    CE   NZ    107.90  3.000
 LLO  HEA   CE   CD    108.64  3.000
 LLO  HE    CE   CD    109.27  3.000
 LLO  NZ    CE   CD    111.09  3.000
 LLO  HGA   CG   HG    106.14  3.000
 LLO  HGA   CG   CD    109.18  3.000
 LLO  HG    CG   CD    109.21  3.000
 LLO  HGA   CG   CB    110.07  3.000
 LLO  HG    CG   CB    109.35  3.000
 LLO  CD    CG   CB    112.68  3.000
 LLO  HNZ   NZ   C13   108.99  3.000
 LLO  HNZ   NZ   CE    109.23  3.000
 LLO  C13   NZ   CE    115.34  3.000
 LLO  H12A  C12  H12   106.38  3.000
 LLO  H12A  C12  C13   109.36  3.000
 LLO  H12   C12  C13   108.63  3.000
 LLO  H12A  C12  C11   108.28  3.000
 LLO  H12   C12  C11   107.53  3.000
 LLO  C13   C12  C11   116.21  3.000
 LLO  H13   C13  C14   107.44  3.000
 LLO  H13   C13  C12   109.18  3.000
 LLO  C14   C13  C12   111.04  3.000
 LLO  H13   C13  NZ    105.66  3.000
 LLO  C14   C13  NZ    114.21  3.000
 LLO  C12   C13  NZ    109.06  3.000
 LLO  H14B  C14  H14A  107.99  3.000
 LLO  H14B  C14  H14   107.57  3.000
 LLO  H14A  C14  H14   107.35  3.000
 LLO  H14B  C14  C13   110.42  3.000
 LLO  H14A  C14  C13   112.15  3.000
 LLO  H14   C14  C13   111.18  3.000
 LLO  H16B  C16  H16A  108.08  3.000
 LLO  H16B  C16  H16   107.57  3.000
 LLO  H16A  C16  H16   107.47  3.000
 LLO  H16B  C16  C11   110.55  3.000
 LLO  H16A  C16  C11   111.11  3.000
 LLO  H16   C16  C11   111.91  3.000
 LLO  C16   C11  C12   111.57  3.000
 LLO  C16   C11  C8    110.31  3.000
 LLO  C12   C11  C8    110.90  3.000
 LLO  C16   C11  O1    109.62  3.000
 LLO  C12   C11  O1    108.77  3.000
 LLO  C8    C11  O1    105.47  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
 LLO  Var_01  C13  C12  C11  O1   178.90  30.0  3
 LLO  Var_02  CD   CG   CB   CA  -178.66  30.0  1
 LLO  Var_03  CE   CD   CG   CB  -178.51  30.0  3
 LLO  Var_04  C13  NZ   CE   CD   175.87  30.0  1
 LLO  Var_05  NZ   CE   CD   CG  -178.63  30.0  1
 LLO  Var_06  H8   C8   C11  O1  -179.51  30.0  3
 LLO  Var_07  H16  C16  C11  O1   176.65  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
 LLO  chir_01  CA   N   C    CB   positiv
 LLO  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
 LLO  plan-1  C    0.020
 LLO  plan-1  O    0.020
 LLO  plan-1  CA   0.020
 LLO  plan-1  OXT  0.020

