# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 22:22:15 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: N~6~-(4-methylpentyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCCNCCCC[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
 LYU  LYU  N~6~-(4-methylpentyl)-L-lysine  L-peptide  41  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_LYU
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
 LYU  N     N  NH2    0  -0.793   0.4814  21.5885  54.4210
 LYU  CA    C  CH1    0  -0.191   1.0773  21.9634  55.7031
 LYU  CB    C  CH2    0  -0.412   2.5337  22.3630  55.4577
 LYU  CG    C  CH2    0  -0.422   3.3574  22.6279  56.7119
 LYU  CD    C  CH2    0  -0.429   4.8179  22.9101  56.3854
 LYU  CE    C  CH2    0  -0.256   5.6708  23.1715  57.6178
 LYU  NZ    N  NH1    0  -0.594   7.0507  23.4211  57.2429
 LYU  C1'   C  CH2    0  -0.276   7.9300  23.8087  58.3286
 LYU  C2'   C  CH2    0  -0.448   8.1435  22.7849  59.4446
 LYU  C3'   C  CH2    0  -0.394   9.1731  23.2626  60.4613
 LYU  C4'   C  CH1    0  -0.228   9.5050  22.2573  61.5655
 LYU  C5'   C  CH3    0  -0.654   8.2982  21.9509  62.4468
 LYU  C6'   C  CH3    0  -0.648  10.6658  22.7646  62.4160
 LYU  C     C  C      0   0.384   0.3332  23.1044  56.4366
 LYU  O     O  O      0  -0.611  -0.0615  24.0503  55.7209
 LYU  HN    H  HNH2   0   0.331  -0.4478  21.2195  54.5893
 LYU  H2    H  HNH2   0   0.320   0.3230  22.4469  53.9036
 LYU  HA    H  HCH1   0   0.192   1.0741  21.0727  56.3410
 LYU  HB    H  HCH2   0   0.207   3.0099  21.5627  54.8815
 LYU  HBA   H  HCH2   0   0.200   2.5535  23.2528  54.8173
 LYU  HG    H  HCH2   0   0.213   2.9428  23.4724  57.2691
 LYU  HGA   H  HCH2   0   0.203   3.2913  21.7617  57.3788
 LYU  HD    H  HCH2   0   0.207   5.2357  22.0589  55.8353
 LYU  HDA   H  HCH2   0   0.209   4.8886  23.7728  55.7159
 LYU  HE    H  HCH2   0   0.207   5.2947  24.0588  58.1382
 LYU  HEA   H  HCH2   0   0.186   5.5492  22.3321  58.3199
 LYU  HNZ   H  HNH1   0   0.331   7.4241  22.5940  56.7910
 LYU  H1'   H  HCH2   0   0.216   8.9027  24.0610  57.8938
 LYU  H1'A  H  HCH2   0   0.208   7.5448  24.7374  58.7640
 LYU  H2'   H  HCH2   0   0.221   7.1919  22.5750  59.9395
 LYU  H2'A  H  HCH2   0   0.205   8.4779  21.8391  59.0023
 LYU  H3'   H  HCH2   0   0.211  10.0975  23.5163  59.9300
 LYU  H3'A  H  HCH2   0   0.203   8.8277  24.1958  60.9234
 LYU  H4'   H  HCH1   0   0.207   9.8204  21.3239  61.0833
 LYU  H5'   H  HCH3   0   0.223   8.5573  21.2425  63.2358
 LYU  H5'A  H  HCH3   0   0.210   7.9310  22.8607  62.9292
 LYU  H5'B  H  HCH3   0   0.226   7.4715  21.5198  61.8816
 LYU  H6'   H  HCH3   0   0.222  10.9336  22.0470  63.1934
 LYU  H6'A  H  HCH3   0   0.221  11.5556  22.9467  61.8107
 LYU  H6'B  H  HCH3   0   0.210  10.4033  23.7036  62.9095
 LYU  OXT   O  OC    -1  -0.613   0.2114  23.0048  57.6748

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
 LYU  N    CA    single  1.458  0.019  1.458
 LYU  N    HN    single  0.890  0.020  1.040
 LYU  N    H2    single  0.890  0.020  1.040
 LYU  CA   CB    single  1.530  0.020  1.530
 LYU  CA   C     single  1.525  0.021  1.525
 LYU  CA   HA    single  0.970  0.020  0.970
 LYU  CB   CG    single  1.524  0.020  1.524
 LYU  CB   HB    single  0.970  0.020  1.090
 LYU  CB   HBA   single  0.970  0.020  1.090
 LYU  CG   HG    single  0.970  0.020  1.090
 LYU  CG   HGA   single  0.970  0.020  1.090
 LYU  CD   CG    single  1.523  0.020  1.523
 LYU  CD   CE    single  1.521  0.020  1.521
 LYU  CD   HD    single  0.970  0.020  1.090
 LYU  CD   HDA   single  0.970  0.020  1.090
 LYU  CE   HE    single  0.970  0.020  1.090
 LYU  CE   HEA   single  0.970  0.020  1.090
 LYU  NZ   CE    single  1.452  0.020  1.452
 LYU  NZ   C1'   single  1.450  0.020  1.450
 LYU  NZ   HNZ   single  0.890  0.020  1.040
 LYU  C1'  C2'   single  1.529  0.020  1.529
 LYU  C1'  H1'   single  0.970  0.020  1.090
 LYU  C1'  H1'A  single  0.970  0.020  1.090
 LYU  C2'  C3'   single  1.524  0.020  1.524
 LYU  C2'  H2'   single  0.970  0.020  1.090
 LYU  C2'  H2'A  single  0.970  0.020  1.090
 LYU  C3'  C4'   single  1.530  0.020  1.530
 LYU  C3'  H3'   single  0.970  0.020  1.090
 LYU  C3'  H3'A  single  0.970  0.020  1.090
 LYU  C4'  C6'   single  1.526  0.020  1.526
 LYU  C4'  C5'   single  1.525  0.020  1.525
 LYU  C4'  H4'   single  0.970  0.020  1.090
 LYU  C5'  H5'   single  0.970  0.020  1.090
 LYU  C5'  H5'A  single  0.970  0.020  1.090
 LYU  C5'  H5'B  single  0.970  0.020  1.090
 LYU  C6'  H6'   single  0.970  0.020  1.090
 LYU  C6'  H6'A  single  0.970  0.020  1.090
 LYU  C6'  H6'B  single  0.970  0.020  1.090
 LYU  C    O     deloc   1.231  0.020  1.231
 LYU  C    OXT   deloc   1.248  0.020  1.248

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
 LYU  H2    N    HN    104.44  3.000
 LYU  H2    N    CA    107.08  3.000
 LYU  HN    N    CA    108.73  3.000
 LYU  HA    CA   C     109.00  3.000
 LYU  HA    CA   CB    109.00  3.000
 LYU  C     CA   CB    110.10  1.900
 LYU  HA    CA   N     110.00  3.000
 LYU  C     CA   N     111.00  2.800
 LYU  CB    CA   N     110.50  1.700
 LYU  HBA   CB   HB    106.14  3.000
 LYU  HBA   CB   CG    109.26  3.000
 LYU  HB    CB   CG    108.96  3.000
 LYU  HBA   CB   CA    108.83  3.000
 LYU  HB    CB   CA    107.90  3.000
 LYU  CG    CB   CA    115.34  3.000
 LYU  HGA   CG   HG    106.12  3.000
 LYU  HGA   CG   CD    109.57  3.000
 LYU  HG    CG   CD    109.26  3.000
 LYU  CD    CG   CB    111.98  3.000
 LYU  HGA   CG   CB    109.34  3.000
 LYU  HG    CG   CB    110.41  3.000
 LYU  HDA   CD   HD    106.29  3.000
 LYU  HDA   CD   CE    108.90  3.000
 LYU  HD    CD   CE    109.04  3.000
 LYU  HDA   CD   CG    109.83  3.000
 LYU  HD    CD   CG    109.22  3.000
 LYU  CE    CD   CG    113.32  3.000
 LYU  HEA   CE   HE    106.06  3.000
 LYU  HEA   CE   NZ    113.63  3.000
 LYU  HE    CE   NZ    108.05  3.000
 LYU  NZ    CE   CD    110.68  3.000
 LYU  HEA   CE   CD    108.88  3.000
 LYU  HE    CE   CD    109.36  3.000
 LYU  HNZ   NZ   C1'   109.17  3.000
 LYU  HNZ   NZ   CE    108.96  3.000
 LYU  C1'   NZ   CE    115.41  3.000
 LYU  H1'A  C1'  H1'   105.95  3.000
 LYU  H1'A  C1'  C2'   109.06  3.000
 LYU  H1'   C1'  C2'   108.66  3.000
 LYU  H1'A  C1'  NZ    108.11  3.000
 LYU  H1'   C1'  NZ    107.64  3.000
 LYU  C2'   C1'  NZ    116.88  3.000
 LYU  H2'A  C2'  H2'   106.41  3.000
 LYU  H2'A  C2'  C3'   109.49  3.000
 LYU  H2'   C2'  C3'   110.27  3.000
 LYU  H2'A  C2'  C1'   109.01  3.000
 LYU  H2'   C2'  C1'   109.72  3.000
 LYU  C3'   C2'  C1'   111.80  3.000
 LYU  H3'A  C3'  H3'   105.84  3.000
 LYU  H3'A  C3'  C4'   108.86  3.000
 LYU  H3'   C3'  C4'   108.61  3.000
 LYU  H3'A  C3'  C2'   109.57  3.000
 LYU  H3'   C3'  C2'   108.60  3.000
 LYU  C4'   C3'  C2'   114.97  3.000
 LYU  H4'   C4'  C6'   108.01  3.000
 LYU  H4'   C4'  C5'   108.10  3.000
 LYU  C6'   C4'  C5'   110.28  3.000
 LYU  H4'   C4'  C3'   107.71  3.000
 LYU  C5'   C4'  C3'   112.17  3.000
 LYU  C6'   C4'  C3'   110.42  3.000
 LYU  H5'B  C5'  H5'A  107.65  3.000
 LYU  H5'B  C5'  H5'   107.34  3.000
 LYU  H5'A  C5'  H5'   107.51  3.000
 LYU  H5'B  C5'  C4'   112.32  3.000
 LYU  H5'A  C5'  C4'   110.70  3.000
 LYU  H5'   C5'  C4'   111.10  3.000
 LYU  H6'B  C6'  H6'A  107.63  3.000
 LYU  H6'B  C6'  H6'   107.59  3.000
 LYU  H6'A  C6'  H6'   107.74  3.000
 LYU  H6'B  C6'  C4'   110.77  3.000
 LYU  H6'A  C6'  C4'   111.50  3.000
 LYU  H6'   C6'  C4'   111.41  3.000
 LYU  OXT   C    O     126.69  3.000
 LYU  OXT   C    CA    117.28  3.000
 LYU  O     C    CA    120.80  1.700

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
 LYU  Var_01  CD   CG   CB   CA    175.45  30.0  3
 LYU  Var_02  CE   CD   CG   CB   -179.68  30.0  1
 LYU  Var_03  NZ   CE   CD   CG    179.49  30.0  3
 LYU  Var_04  C1'  NZ   CE   CD    174.36  30.0  1
 LYU  Var_05  C2'  C1'  NZ   CE     63.07  30.0  3
 LYU  Var_06  C3'  C2'  C1'  NZ    175.24  30.0  3
 LYU  Var_07  C4'  C3'  C2'  C1'  -176.51  30.0  3
 LYU  Var_08  C6'  C4'  C3'  C2'   172.81  30.0  3
 LYU  Var_09  H6'  C6'  C4'  C3'  -178.50  30.0  3
 LYU  Var_10  H5'  C5'  C4'  C3'  -179.27  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
 LYU  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
 LYU  plan-1  CA   0.020
 LYU  plan-1  C    0.020
 LYU  plan-1  O    0.020
 LYU  plan-1  OXT  0.020

