# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 05:31:52 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N~5~-D-lysyl-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@@H](N)C(=O)NCCC[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
 2YJ  2YJ  'N~5~-D-lysyl-L-ornithine '  L-peptide  41  18  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_2YJ
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
 2YJ  O2   O  O      0  -0.608   5.9208  -1.2748   1.0606
 2YJ  C10  C  C      0   0.404   5.2976  -1.3411  -0.0176
 2YJ  O1   O  OC    -1  -0.621   5.7929  -1.3467  -1.1630
 2YJ  C    C  CH1    0  -0.200   3.7559  -1.3576   0.0587
 2YJ  N    N  NH2    0  -0.801   3.3127  -1.8929   1.3352
 2YJ  C1   C  CH2    0  -0.432   3.2434   0.0579  -0.2636
 2YJ  C2   C  CH2    0  -0.435   1.7264   0.1572  -0.3490
 2YJ  C3   C  CH2    0  -0.278   1.2626   1.5651  -0.7090
 2YJ  N1   N  NH1    0  -0.628  -0.1764   1.6799  -0.8117
 2YJ  C4   C  C      0   0.553  -0.9820   1.8460   0.2484
 2YJ  O    O  O      0  -0.503  -0.5663   2.0503   1.3813
 2YJ  C5   C  CH1    0  -0.230  -2.4712   1.7098  -0.0403
 2YJ  N3   N  NH2    0  -0.789  -3.1961   2.6554   0.7869
 2YJ  C6   C  CH2    0  -0.419  -2.8572   0.2318   0.1417
 2YJ  C7   C  CH2    0  -0.432  -4.3168  -0.0543  -0.1890
 2YJ  C8   C  CH2    0  -0.423  -4.6489  -1.5401  -0.1373
 2YJ  C9   C  CH2    0  -0.271  -6.1074  -1.8263  -0.4603
 2YJ  N2   N  NH2    0  -0.801  -6.3817  -3.2561  -0.4199
 2YJ  H2   H  HCH1   0   0.199   3.3862  -2.0210  -0.7324
 2YJ  H3   H  HNH2   0   0.326   3.7943  -1.3996   2.0763
 2YJ  H4   H  HNH2   0   0.333   2.3223  -1.7307   1.4659
 2YJ  H6   H  HCH2   0   0.210   3.6142   0.7556   0.4970
 2YJ  H7   H  HCH2   0   0.213   3.6777   0.3754  -1.2166
 2YJ  H8   H  HCH2   0   0.219   1.3527  -0.5478  -1.0984
 2YJ  H9   H  HCH2   0   0.215   1.2691  -0.1235   0.6039
 2YJ  H10  H  HCH2   0   0.237   1.6210   2.2793   0.0339
 2YJ  H11  H  HCH2   0   0.244   1.6867   1.8659  -1.6678
 2YJ  H12  H  HNH1   0   0.399  -0.5957   1.4674  -1.7025
 2YJ  H13  H  HCH1   0   0.247  -2.6571   1.9787  -1.0861
 2YJ  H14  H  HNH2   0   0.353  -4.1877   2.5747   0.6024
 2YJ  H15  H  HNH2   0   0.340  -3.0680   2.4212   1.7643
 2YJ  H17  H  HCH2   0   0.222  -2.2199  -0.3841  -0.5013
 2YJ  H18  H  HCH2   0   0.226  -2.6452  -0.0720   1.1726
 2YJ  H19  H  HCH2   0   0.212  -4.9677   0.4811   0.5091
 2YJ  H20  H  HCH2   0   0.217  -4.5450   0.3365  -1.1869
 2YJ  H21  H  HCH2   0   0.212  -4.0101  -2.0763  -0.8483
 2YJ  H22  H  HCH2   0   0.214  -4.4141  -1.9412   0.8536
 2YJ  H23  H  HCH2   0   0.211  -6.7415  -1.3376   0.2848
 2YJ  H24  H  HCH2   0   0.186  -6.3540  -1.3599  -1.4256
 2YJ  H25  H  HNH2   0   0.345  -7.3636  -3.4158  -0.6058
 2YJ  H26  H  HNH2   0   0.336  -5.8869  -3.7105  -1.1780

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
 2YJ  C5   N3   single  1.450  0.020  1.450
 2YJ  C5   C6   single  1.538  0.020  1.538
 2YJ  C5   C4   single  1.523  0.020  1.523
 2YJ  C7   C8   single  1.523  0.020  1.523
 2YJ  C7   C6   single  1.524  0.020  1.524
 2YJ  C8   C9   single  1.521  0.020  1.521
 2YJ  N1   C4   single  1.342  0.020  1.342
 2YJ  N1   C3   single  1.447  0.020  1.447
 2YJ  C4   O    double  1.224  0.020  1.224
 2YJ  C3   C2   single  1.525  0.020  1.525
 2YJ  N    C    single  1.453  0.020  1.453
 2YJ  C2   C1   single  1.523  0.020  1.523
 2YJ  C9   N2   single  1.456  0.020  1.456
 2YJ  C1   C    single  1.540  0.020  1.540
 2YJ  C    C10  single  1.544  0.020  1.544
 2YJ  O2   C10  deloc   1.247  0.020  1.247
 2YJ  C10  O1   deloc   1.248  0.020  1.248
 2YJ  C    H2   single  0.970  0.020  1.090
 2YJ  N    H3   single  0.890  0.020  1.040
 2YJ  N    H4   single  0.890  0.020  1.040
 2YJ  C1   H6   single  0.970  0.020  1.090
 2YJ  C1   H7   single  0.970  0.020  1.090
 2YJ  C2   H8   single  0.970  0.020  1.090
 2YJ  C2   H9   single  0.970  0.020  1.090
 2YJ  C3   H10  single  0.970  0.020  1.090
 2YJ  C3   H11  single  0.970  0.020  1.090
 2YJ  N1   H12  single  0.860  0.020  1.020
 2YJ  C5   H13  single  0.970  0.020  1.090
 2YJ  N3   H14  single  0.890  0.020  1.040
 2YJ  N3   H15  single  0.890  0.020  1.040
 2YJ  C6   H17  single  0.970  0.020  1.090
 2YJ  C6   H18  single  0.970  0.020  1.090
 2YJ  C7   H19  single  0.970  0.020  1.090
 2YJ  C7   H20  single  0.970  0.020  1.090
 2YJ  C8   H21  single  0.970  0.020  1.090
 2YJ  C8   H22  single  0.970  0.020  1.090
 2YJ  C9   H23  single  0.970  0.020  1.090
 2YJ  C9   H24  single  0.970  0.020  1.090
 2YJ  N2   H25  single  0.890  0.020  1.040
 2YJ  N2   H26  single  0.890  0.020  1.040

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
 2YJ  C    C10  O1   116.21  3.000
 2YJ  O1   C10  O2   126.54  3.000
 2YJ  C    C10  O2   117.19  3.000
 2YJ  H2   C    C1   107.03  3.000
 2YJ  H2   C    N    107.94  3.000
 2YJ  C1   C    N    114.89  3.000
 2YJ  H2   C    C10  107.91  3.000
 2YJ  C1   C    C10  108.20  3.000
 2YJ  N    C    C10  110.61  3.000
 2YJ  H4   N    H3   107.04  3.000
 2YJ  H4   N    C    110.66  3.000
 2YJ  H3   N    C    108.57  3.000
 2YJ  H7   C1   H6   106.57  3.000
 2YJ  H7   C1   C2   109.12  3.000
 2YJ  H6   C1   C2   109.52  3.000
 2YJ  H7   C1   C    108.48  3.000
 2YJ  H6   C1   C    109.10  3.000
 2YJ  C2   C1   C    113.79  3.000
 2YJ  H9   C2   H8   106.76  3.000
 2YJ  H9   C2   C3   108.39  3.000
 2YJ  H8   C2   C3   109.21  3.000
 2YJ  H9   C2   C1   110.55  3.000
 2YJ  H8   C2   C1   109.66  3.000
 2YJ  C3   C2   C1   112.11  3.000
 2YJ  H11  C3   H10  106.87  3.000
 2YJ  H11  C3   N1   107.60  3.000
 2YJ  H10  C3   N1   108.84  3.000
 2YJ  H11  C3   C2   110.11  3.000
 2YJ  H10  C3   C2   110.10  3.000
 2YJ  N1   C3   C2   113.10  3.000
 2YJ  H12  N1   C4   118.35  3.000
 2YJ  H12  N1   C3   117.38  3.000
 2YJ  C4   N1   C3   123.42  3.000
 2YJ  C5   C4   O    121.50  3.000
 2YJ  O    C4   N1   123.23  3.000
 2YJ  C5   C4   N1   115.23  3.000
 2YJ  H13  C5   C6   107.82  3.000
 2YJ  H13  C5   N3   107.44  3.000
 2YJ  C6   C5   N3   115.69  3.000
 2YJ  H13  C5   C4   108.96  3.000
 2YJ  C6   C5   C4   107.98  3.000
 2YJ  N3   C5   C4   108.80  3.000
 2YJ  H15  N3   H14  106.34  3.000
 2YJ  H15  N3   C5   109.65  3.000
 2YJ  H14  N3   C5   109.50  3.000
 2YJ  H18  C6   H17  106.50  3.000
 2YJ  H18  C6   C7   109.73  3.000
 2YJ  H17  C6   C7   108.94  3.000
 2YJ  H18  C6   C5   109.22  3.000
 2YJ  H17  C6   C5   108.96  3.000
 2YJ  C7   C6   C5   113.27  3.000
 2YJ  H20  C7   H19  106.42  3.000
 2YJ  H20  C7   C8   109.48  3.000
 2YJ  H19  C7   C8   109.02  3.000
 2YJ  H20  C7   C6   109.28  3.000
 2YJ  H19  C7   C6   109.84  3.000
 2YJ  C8   C7   C6   112.62  3.000
 2YJ  H22  C8   H21  106.44  3.000
 2YJ  H22  C8   C9   109.21  3.000
 2YJ  H21  C8   C9   109.21  3.000
 2YJ  H22  C8   C7   109.97  3.000
 2YJ  H21  C8   C7   109.16  3.000
 2YJ  C9   C8   C7   112.67  3.000
 2YJ  H24  C9   H23  106.16  3.000
 2YJ  H24  C9   N2   113.47  3.000
 2YJ  H23  C9   N2   108.10  3.000
 2YJ  H24  C9   C8   108.76  3.000
 2YJ  H23  C9   C8   109.10  3.000
 2YJ  N2   C9   C8   111.07  3.000
 2YJ  H26  N2   H25  105.41  3.000
 2YJ  H26  N2   C9   109.12  3.000
 2YJ  H25  N2   C9   109.42  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
 2YJ  CONST_01  C5   C4  N1  C3   180.00   0.0  0
 2YJ  CONST_02  O    C4  N1  C3     0.00   0.0  0
 2YJ  CONST_03  H12  N1  C4  O    180.00   0.0  0
 2YJ  Var_01    C3   C2  C1  C   -178.36  30.0  1
 2YJ  Var_02    N1   C3  C2  C1   179.30  30.0  1
 2YJ  Var_03    C4   N1  C3  C2    82.08  30.0  1
 2YJ  Var_04    C8   C7  C6  C5   174.34  30.0  1
 2YJ  Var_05    C9   C8  C7  C6   179.71  30.0  3
 2YJ  Var_06    N2   C9  C8  C7   179.17  30.0  3
 2YJ  Var_07    H25  N2  C9  C8   178.02  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
 2YJ  chir_01  C   N   C1  C10  negativ
 2YJ  chir_02  C5  N3  C6  C4   positiv

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
 2YJ  plan-1  C3   0.020
 2YJ  plan-1  N1   0.020
 2YJ  plan-1  C4   0.020
 2YJ  plan-1  O    0.020
 2YJ  plan-1  C5   0.020
 2YJ  plan-1  H12  0.020
 2YJ  plan-2  O2   0.020
 2YJ  plan-2  C10  0.020
 2YJ  plan-2  O1   0.020
 2YJ  plan-2  C    0.020

