# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 09:06:04 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: N~6~,N~6~-diethyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)CCCC[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
 ELY  ELY  N~6~,N~6~-diethyl-L-lysine  L-peptide  35  14  .  2016-04-22  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_ELY
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
 ELY  C     C  C      0   0.417   7.1353  47.6924  20.7073
 ELY  N     N  NH2    0  -0.815   8.0256  49.0759  22.5610
 ELY  O     O  O      0  -0.607   6.3108  46.8382  20.3260
 ELY  CA    C  CH1    0  -0.228   7.3116  47.8469  22.2407
 ELY  CB    C  CH2    0  -0.398   5.9702  47.8045  22.9739
 ELY  CD    C  CH2    0  -0.439   6.8658  46.8719  25.1905
 ELY  CE    C  CH2    0  -0.251   6.9098  47.0879  26.6991
 ELY  CG    C  CH2    0  -0.431   6.0698  47.9675  24.4892
 ELY  NZ    N  NT     0  -0.410   7.5841  46.0243  27.4264
 ELY  CH1   C  CH2    0  -0.278   9.0239  46.0449  27.2218
 ELY  CH2   C  CH2    0  -0.316   7.1872  45.9702  28.8242
 ELY  CT1   C  CH3    0  -0.684   9.7504  44.8729  27.8617
 ELY  CT2   C  CH3    0  -0.682   7.6285  47.1337  29.7122
 ELY  OXT   O  OC    -1  -0.603   7.8582  48.4026  19.9784
 ELY  H     H  HNH2   0   0.329   8.5350  48.9658  23.4281
 ELY  H2    H  HNH2   0   0.331   8.7122  49.2331  21.8350
 ELY  HA    H  HCH1   0   0.194   7.8840  46.9540  22.5480
 ELY  HB2   H  HCH2   0   0.201   5.3289  48.5996  22.5793
 ELY  HB3   H  HCH2   0   0.201   5.4734  46.8600  22.7437
 ELY  HD2   H  HCH2   0   0.207   6.4193  45.8946  24.9815
 ELY  HD3   H  HCH2   0   0.222   7.8802  46.8404  24.7848
 ELY  HE2   H  HCH2   0   0.182   7.3516  48.0784  26.9024
 ELY  HE3   H  HCH2   0   0.217   5.8792  47.1388  27.0632
 ELY  HG2   H  HCH2   0   0.206   6.5075  48.9426  24.7257
 ELY  HG3   H  HCH2   0   0.214   5.0567  47.9899  24.9041
 ELY  HH1   H  HCH2   0   0.230   9.2113  46.0090  26.1473
 ELY  HH1A  H  HCH2   0   0.185   9.4791  46.9872  27.5704
 ELY  HH2   H  HCH2   0   0.227   6.0966  45.8981  28.8509
 ELY  HH2A  H  HCH2   0   0.230   7.5521  45.0357  29.2575
 ELY  HT1   H  HCH3   0   0.232  10.7886  44.8579  27.5292
 ELY  HT1A  H  HCH3   0   0.224   9.7609  44.9270  28.9506
 ELY  HT1B  H  HCH3   0   0.221   9.2935  43.9250  27.5736
 ELY  HT2   H  HCH3   0   0.227   7.2412  46.9970  30.7228
 ELY  HT2A  H  HCH3   0   0.221   8.7148  47.2033  29.7872
 ELY  HT2B  H  HCH3   0   0.224   7.2575  48.0922  29.3465

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
 ELY  OXT  C     deloc   1.248  0.020  1.248
 ELY  C    O     deloc   1.231  0.020  1.231
 ELY  C    CA    single  1.525  0.021  1.525
 ELY  N    CA    single  1.458  0.019  1.458
 ELY  N    H     single  0.860  0.020  0.860
 ELY  N    H2    single  0.890  0.020  1.040
 ELY  CA   CB    single  1.530  0.020  1.530
 ELY  CA   HA    single  0.970  0.020  0.970
 ELY  CB   CG    single  1.527  0.020  1.527
 ELY  CB   HB2   single  0.970  0.020  1.090
 ELY  CB   HB3   single  0.970  0.020  1.090
 ELY  CG   CD    single  1.525  0.020  1.525
 ELY  CD   CE    single  1.525  0.020  1.525
 ELY  CD   HD2   single  0.970  0.020  1.090
 ELY  CD   HD3   single  0.970  0.020  1.090
 ELY  CE   NZ    single  1.454  0.020  1.454
 ELY  CE   HE2   single  0.970  0.020  1.090
 ELY  CE   HE3   single  0.970  0.020  1.090
 ELY  CG   HG2   single  0.970  0.020  1.090
 ELY  CG   HG3   single  0.970  0.020  1.090
 ELY  CH1  NZ    single  1.454  0.020  1.454
 ELY  NZ   CH2   single  1.454  0.020  1.454
 ELY  CH1  CT1   single  1.520  0.020  1.520
 ELY  CH1  HH1   single  0.970  0.020  1.090
 ELY  CH1  HH1A  single  0.970  0.020  1.090
 ELY  CH2  CT2   single  1.529  0.020  1.529
 ELY  CH2  HH2   single  0.970  0.020  1.090
 ELY  CH2  HH2A  single  0.970  0.020  1.090
 ELY  CT1  HT1   single  0.970  0.020  1.090
 ELY  CT1  HT1A  single  0.970  0.020  1.090
 ELY  CT1  HT1B  single  0.970  0.020  1.090
 ELY  CT2  HT2   single  0.970  0.020  1.090
 ELY  CT2  HT2A  single  0.970  0.020  1.090
 ELY  CT2  HT2B  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
 ELY  OXT   C    CA    117.05  3.000
 ELY  CA    C    O     120.80  1.700
 ELY  OXT   C    O     126.45  3.000
 ELY  H2    N    H     106.88  3.000
 ELY  H2    N    CA    107.81  3.000
 ELY  H     N    CA    114.00  3.000
 ELY  HA    CA   CB    109.00  3.000
 ELY  HA    CA   N     110.00  3.000
 ELY  CB    CA   N     110.50  1.700
 ELY  HA    CA   C     109.00  3.000
 ELY  CB    CA   C     110.10  1.900
 ELY  N     CA   C     111.00  2.800
 ELY  HB3   CB   HB2   106.60  3.000
 ELY  HB3   CB   CG    109.34  3.000
 ELY  HB2   CB   CG    108.55  3.000
 ELY  HB3   CB   CA    108.79  3.000
 ELY  HB2   CB   CA    108.71  3.000
 ELY  CG    CB   CA    114.55  3.000
 ELY  HD3   CD   HD2   106.38  3.000
 ELY  HD3   CD   CG    109.54  3.000
 ELY  HD2   CD   CG    109.92  3.000
 ELY  HD3   CD   CE    110.15  3.000
 ELY  HD2   CD   CE    109.10  3.000
 ELY  CG    CD   CE    111.61  3.000
 ELY  HE3   CE   HE2   105.91  3.000
 ELY  HE3   CE   NZ    107.72  3.000
 ELY  HE2   CE   NZ    112.25  3.000
 ELY  HE3   CE   CD    107.98  3.000
 ELY  HE2   CE   CD    108.73  3.000
 ELY  NZ    CE   CD    113.87  3.000
 ELY  HG3   CG   HG2   105.66  3.000
 ELY  HG3   CG   CD    108.86  3.000
 ELY  HG2   CG   CD    109.38  3.000
 ELY  HG3   CG   CB    108.53  3.000
 ELY  HG2   CG   CB    109.61  3.000
 ELY  CD    CG   CB    114.43  3.000
 ELY  CH2   NZ   CH1   113.95  3.000
 ELY  CH2   NZ   CE    112.42  3.000
 ELY  CH1   NZ   CE    112.23  3.000
 ELY  HH1A  CH1  HH1   105.57  3.000
 ELY  HH1A  CH1  CT1   109.18  3.000
 ELY  HH1   CH1  CT1   107.87  3.000
 ELY  HH1A  CH1  NZ    112.10  3.000
 ELY  HH1   CH1  NZ    107.94  3.000
 ELY  CT1   CH1  NZ    113.76  3.000
 ELY  HH2A  CH2  HH2   105.49  3.000
 ELY  HH2A  CH2  CT2   108.91  3.000
 ELY  HH2   CH2  CT2   108.91  3.000
 ELY  HH2A  CH2  NZ    108.77  3.000
 ELY  HH2   CH2  NZ    107.35  3.000
 ELY  CT2   CH2  NZ    116.83  3.000
 ELY  HT1B  CT1  HT1A  108.11  3.000
 ELY  HT1B  CT1  HT1   107.84  3.000
 ELY  HT1A  CT1  HT1   107.22  3.000
 ELY  HT1B  CT1  CH1   111.01  3.000
 ELY  HT1A  CT1  CH1   112.75  3.000
 ELY  HT1   CT1  CH1   109.71  3.000
 ELY  HT2B  CT2  HT2A  107.79  3.000
 ELY  HT2B  CT2  HT2   107.45  3.000
 ELY  HT2A  CT2  HT2   107.32  3.000
 ELY  HT2B  CT2  CH2   112.07  3.000
 ELY  HT2A  CT2  CH2   112.08  3.000
 ELY  HT2   CT2  CH2   109.90  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
 ELY  Var_01  CD   CG   CB   CA   -61.96  30.0  3
 ELY  Var_02  CE   CD   CG   CB  -179.30  30.0  3
 ELY  Var_03  CH1  NZ   CE   CD    72.00  30.0  3
 ELY  Var_04  CT1  CH1  NZ   CE  -174.67  30.0  2
 ELY  Var_05  CT2  CH2  NZ   CE   -68.35  30.0  3
 ELY  Var_06  NZ   CE   CD   CG   176.25  30.0  3
 ELY  Var_07  HT1  CT1  CH1  NZ   170.39  30.0  3
 ELY  Var_08  HT2  CT2  CH2  NZ   177.93  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
 ELY  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
 ELY  plan-1  C    0.020
 ELY  plan-1  O    0.020
 ELY  plan-1  CA   0.020
 ELY  plan-1  OXT  0.020

