# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:42:58 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: N~6~-[(2R)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)[C@H]1CCCC=N1)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
 2YF  2YF  N~6~-[(2R)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-L-lysine  L-peptide  38  18  .  2022-07-22  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_2YF
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
 2YF  O2   O  O      0  -0.608   6.8369   0.1358   1.0760
 2YF  C11  C  C      0   0.383   6.0345   0.6290   0.2588
 2YF  O1   O  OC    -1  -0.625   6.0453   1.8012  -0.1744
 2YF  C    C  CH1    0  -0.213   4.8922  -0.2756  -0.2674
 2YF  N    N  NH2    0  -0.785   5.0364  -1.6951   0.0197
 2YF  C1   C  CH2    0  -0.417   3.5515   0.2338   0.2675
 2YF  C2   C  CH2    0  -0.408   2.3418  -0.4561  -0.3474
 2YF  C3   C  CH2    0  -0.476   1.0251   0.0721   0.2050
 2YF  C4   C  CH2    0  -0.233  -0.1759  -0.6106  -0.4283
 2YF  N1   N  NH1    0  -0.643  -1.4109  -0.0995   0.1312
 2YF  C5   C  C      0   0.552  -2.6202  -0.5110  -0.2676
 2YF  O    O  O      0  -0.499  -2.7843  -1.3596  -1.1328
 2YF  C6   C  CH1    0  -0.229  -3.7997   0.1902   0.3934
 2YF  N2   N  N      0  -0.338  -4.7704  -0.8295   0.7483
 2YF  C10  C  C1     0  -0.051  -6.0024  -0.6016   0.5820
 2YF  C9   C  CH2    0  -0.511  -6.6415   0.6484   0.0603
 2YF  C8   C  CH2    0  -0.449  -5.6558   1.8045  -0.0086
 2YF  C7   C  CH2    0  -0.464  -4.3231   1.2910  -0.5312
 2YF  H2   H  HCH1   0   0.206   4.8682  -0.1638  -1.3586
 2YF  H3   H  HNH2   0   0.333   5.8764  -2.0339  -0.4342
 2YF  H4   H  HNH2   0   0.321   5.2326  -1.7926   1.0099
 2YF  H6   H  HCH2   0   0.204   3.5271   0.1073   1.3575
 2YF  H7   H  HCH2   0   0.217   3.4870   1.3090   0.0848
 2YF  H8   H  HCH2   0   0.207   2.3638  -0.3181  -1.4342
 2YF  H9   H  HCH2   0   0.219   2.4095  -1.5330  -0.1758
 2YF  H10  H  HCH2   0   0.226   0.9985  -0.0778   1.2895
 2YF  H11  H  HCH2   0   0.226   0.9606   1.1522   0.0382
 2YF  H12  H  HCH2   0   0.230  -0.1664  -0.4513  -1.5102
 2YF  H13  H  HCH2   0   0.229  -0.1132  -1.6911  -0.2685
 2YF  H14  H  HNH1   0   0.401  -1.3494   0.5791   0.8727
 2YF  H15  H  HCH1   0   0.263  -3.4650   0.6512   1.3310
 2YF  H16  H  H      0   0.244  -6.6847  -1.4080   0.8530
 2YF  H17  H  HCH2   0   0.259  -7.0546   0.4245  -0.9297
 2YF  H18  H  HCH2   0   0.261  -7.5032   0.8867   0.6886
 2YF  H19  H  HCH2   0   0.249  -6.0421   2.6012  -0.6453
 2YF  H20  H  HCH2   0   0.232  -5.5189   2.2342   0.9876
 2YF  H21  H  HCH2   0   0.250  -3.5876   2.0949  -0.5975
 2YF  H22  H  HCH2   0   0.237  -4.4542   0.8917  -1.5417

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
 2YF  N    C    single  1.455  0.020  1.455
 2YF  C2   C1   single  1.522  0.020  1.522
 2YF  C2   C3   single  1.522  0.020  1.522
 2YF  C    C1   single  1.531  0.020  1.531
 2YF  C    C11  single  1.549  0.020  1.549
 2YF  O2   C11  deloc   1.247  0.020  1.247
 2YF  C4   C3   single  1.520  0.020  1.520
 2YF  C4   N1   single  1.449  0.020  1.449
 2YF  N1   C5   single  1.338  0.020  1.338
 2YF  C11  O1   deloc   1.250  0.020  1.250
 2YF  C5   C6   single  1.523  0.020  1.523
 2YF  C5   O    double  1.223  0.020  1.223
 2YF  C6   C7   single  1.530  0.020  1.530
 2YF  C6   N2   single  1.452  0.020  1.452
 2YF  C7   C8   single  1.521  0.020  1.521
 2YF  N2   C10  double  1.264  0.020  1.264
 2YF  C8   C9   single  1.521  0.020  1.521
 2YF  C10  C9   single  1.498  0.020  1.498
 2YF  C    H2   single  0.970  0.020  1.090
 2YF  N    H3   single  0.890  0.020  1.040
 2YF  N    H4   single  0.890  0.020  1.040
 2YF  C1   H6   single  0.970  0.020  1.090
 2YF  C1   H7   single  0.970  0.020  1.090
 2YF  C2   H8   single  0.970  0.020  1.090
 2YF  C2   H9   single  0.970  0.020  1.090
 2YF  C3   H10  single  0.970  0.020  1.090
 2YF  C3   H11  single  0.970  0.020  1.090
 2YF  C4   H12  single  0.970  0.020  1.090
 2YF  C4   H13  single  0.970  0.020  1.090
 2YF  N1   H14  single  0.860  0.020  1.020
 2YF  C6   H15  single  0.970  0.020  1.090
 2YF  C10  H16  single  0.930  0.020  1.080
 2YF  C9   H17  single  0.970  0.020  1.090
 2YF  C9   H18  single  0.970  0.020  1.090
 2YF  C8   H19  single  0.970  0.020  1.090
 2YF  C8   H20  single  0.970  0.020  1.090
 2YF  C7   H21  single  0.970  0.020  1.090
 2YF  C7   H22  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
 2YF  C    C11  O1   115.87  3.000
 2YF  O1   C11  O2   126.34  3.000
 2YF  C    C11  O2   117.78  3.000
 2YF  H2   C    C1   107.12  3.000
 2YF  H2   C    N    107.32  3.000
 2YF  C1   C    N    110.02  3.000
 2YF  H2   C    C11  107.12  3.000
 2YF  C1   C    C11  109.44  3.000
 2YF  N    C    C11  115.44  3.000
 2YF  H4   N    H3   104.17  3.000
 2YF  H4   N    C    107.79  3.000
 2YF  H3   N    C    108.66  3.000
 2YF  H7   C1   H6   106.15  3.000
 2YF  H7   C1   C2   109.37  3.000
 2YF  H6   C1   C2   109.34  3.000
 2YF  H7   C1   C    108.71  3.000
 2YF  H6   C1   C    109.15  3.000
 2YF  C2   C1   C    113.83  3.000
 2YF  H9   C2   H8   106.18  3.000
 2YF  H9   C2   C3   109.79  3.000
 2YF  H8   C2   C3   109.48  3.000
 2YF  H9   C2   C1   109.52  3.000
 2YF  H8   C2   C1   109.12  3.000
 2YF  C3   C2   C1   112.55  3.000
 2YF  H11  C3   H10  106.53  3.000
 2YF  H11  C3   C4   109.47  3.000
 2YF  H10  C3   C4   109.39  3.000
 2YF  H11  C3   C2   109.75  3.000
 2YF  H10  C3   C2   109.44  3.000
 2YF  C4   C3   C2   112.11  3.000
 2YF  H13  C4   H12  106.73  3.000
 2YF  H13  C4   N1   109.92  3.000
 2YF  H12  C4   N1   109.75  3.000
 2YF  H13  C4   C3   109.73  3.000
 2YF  H12  C4   C3   109.88  3.000
 2YF  N1   C4   C3   110.75  3.000
 2YF  H14  N1   C5   118.80  3.000
 2YF  H14  N1   C4   118.03  3.000
 2YF  C5   N1   C4   123.14  3.000
 2YF  C6   C5   O    121.50  3.000
 2YF  O    C5   N1   123.06  3.000
 2YF  C6   C5   N1   115.40  3.000
 2YF  H15  C6   C7   108.57  3.000
 2YF  H15  C6   N2   106.87  3.000
 2YF  C7   C6   N2   115.11  3.000
 2YF  H15  C6   C5   109.15  3.000
 2YF  N2   C6   C5   107.49  3.000
 2YF  C7   C6   C5   109.50  3.000
 2YF  C10  N2   C6   119.53  3.000
 2YF  H16  C10  C9   115.90  3.000
 2YF  H16  C10  N2   116.35  3.000
 2YF  C9   C10  N2   127.76  3.000
 2YF  H18  C9   H17  105.47  3.000
 2YF  H18  C9   C8   111.80  3.000
 2YF  H17  C9   C8   111.02  3.000
 2YF  H18  C9   C10  108.56  3.000
 2YF  H17  C9   C10  107.75  3.000
 2YF  C8   C9   C10  111.94  3.000
 2YF  H20  C8   H19  106.80  3.000
 2YF  H20  C8   C7   109.63  3.000
 2YF  H19  C8   C7   110.88  3.000
 2YF  H20  C8   C9   109.79  3.000
 2YF  H19  C8   C9   110.62  3.000
 2YF  C7   C8   C9   109.08  3.000
 2YF  H22  C7   H21  107.06  3.000
 2YF  H22  C7   C8   109.61  3.000
 2YF  H21  C7   C8   111.26  3.000
 2YF  H22  C7   C6   109.66  3.000
 2YF  H21  C7   C6   109.64  3.000
 2YF  C8   C7   C6   109.58  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
 2YF  CONST_01  C6   C5   N1   C4   180.00   0.0  0
 2YF  CONST_02  H14  N1   C5   C6     0.00   0.0  0
 2YF  CONST_03  O    C5   N1   C4     0.00   0.0  0
 2YF  Var_01    C9   C8   C7   C6   -58.74  30.0  1
 2YF  Var_02    C9   C10  N2   C6    -1.04  30.0  1
 2YF  Var_03    C8   C9   C10  N2   -11.93  30.0  1
 2YF  Var_04    C7   C8   C9   C10   41.34  30.0  1
 2YF  Var_05    C3   C2   C1   C    179.99  30.0  1
 2YF  Var_06    C4   C3   C2   C1   179.26  30.0  3
 2YF  Var_07    N1   C4   C3   C2   179.21  30.0  2
 2YF  Var_08    C5   N1   C4   C3   178.68  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
 2YF  chir_01  C   N   C1  C11  negativ
 2YF  chir_02  C6  C5  C7  N2   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
 2YF  plan-1  C4   0.020
 2YF  plan-1  N1   0.020
 2YF  plan-1  C5   0.020
 2YF  plan-1  O    0.020
 2YF  plan-1  C6   0.020
 2YF  plan-1  H14  0.020
 2YF  plan-2  O2   0.020
 2YF  plan-2  C11  0.020
 2YF  plan-2  O1   0.020
 2YF  plan-2  C    0.020

