# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:51:19 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N~6~-L-lysyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N)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
 2YG  2YG  'N~6~-L-lysyl-L-lysine    '  L-peptide  45  19  .  2022-03-10  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2YG
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
 2YG  O2   O  O     0  -0.441  -6.9113  -2.0447   0.0423
 2YG  C11  C  C     0   0.520  -6.4128  -1.0300  -0.3769
 2YG  O1   O  OH1   0  -0.594  -6.6773  -0.5313  -1.5797
 2YG  C    C  CH1   0  -0.207  -5.4045  -0.1807   0.3864
 2YG  N    N  NH2   0  -0.776  -5.3655  -0.4657   1.8001
 2YG  C1   C  CH2   0  -0.431  -4.0162  -0.3603  -0.2447
 2YG  C2   C  CH2   0  -0.410  -2.9699   0.5674   0.3581
 2YG  C3   C  CH2   0  -0.476  -1.6048   0.3965  -0.2960
 2YG  C4   C  CH2   0  -0.230  -0.5731   1.3341   0.3092
 2YG  N1   N  NH1   0  -0.640   0.7258   1.1389  -0.3025
 2YG  C5   C  C     0   0.531   1.8278   1.7799   0.1072
 2YG  O    O  O     0  -0.506   1.8131   2.6069   1.0116
 2YG  C6   C  CH1   0  -0.221   3.1292   1.3836  -0.5947
 2YG  N2   N  NH2   0  -0.776   4.0510   2.4889  -0.7483
 2YG  C7   C  CH2   0  -0.414   3.7751   0.2466   0.2058
 2YG  C8   C  CH2   0  -0.413   5.0346  -0.3144  -0.4397
 2YG  C9   C  CH2   0  -0.427   5.6234  -1.4781   0.3484
 2YG  C10  C  CH2   0  -0.271   6.9102  -2.0086  -0.2640
 2YG  N3   N  NH2   0  -0.801   7.4359  -3.1304   0.5027
 2YG  H1   H  HOH1  0   0.480  -7.3001  -1.1047  -2.0513
 2YG  H2   H  HCH1  0   0.265  -5.7015   0.8658   0.2567
 2YG  H3   H  HNH2  0   0.354  -6.2666  -0.2840   2.2228
 2YG  H4   H  HNH2  0   0.343  -5.1707  -1.4478   1.9526
 2YG  H6   H  HCH2  0   0.230  -3.7016  -1.4029  -0.1223
 2YG  H7   H  HCH2  0   0.241  -4.0802  -0.1800  -1.3202
 2YG  H8   H  HCH2  0   0.218  -3.3012   1.6051   0.2454
 2YG  H9   H  HCH2  0   0.228  -2.8877   0.3819   1.4309
 2YG  H10  H  HCH2  0   0.230  -1.2686  -0.6389  -0.1789
 2YG  H11  H  HCH2  0   0.230  -1.6844   0.5844  -1.3716
 2YG  H12  H  HCH2  0   0.229  -0.8951   2.3718   0.1787
 2YG  H13  H  HCH2  0   0.229  -0.5017   1.1589   1.3862
 2YG  H14  H  HNH1  0   0.398   0.7983   0.4895  -1.0693
 2YG  H15  H  HCH1  0   0.243   2.8911   1.0029  -1.5941
 2YG  H16  H  HNH2  0   0.349   3.6394   3.2064  -1.3325
 2YG  H17  H  HNH2  0   0.339   4.2077   2.9214   0.1548
 2YG  H19  H  HCH2  0   0.223   4.0069   0.6106   1.2130
 2YG  H20  H  HCH2  0   0.229   3.0410  -0.5554   0.3298
 2YG  H21  H  HCH2  0   0.209   4.8033  -0.6444  -1.4583
 2YG  H22  H  HCH2  0   0.219   5.7781   0.4801  -0.5356
 2YG  H23  H  HCH2  0   0.210   5.8213  -1.1556   1.3772
 2YG  H24  H  HCH2  0   0.212   4.8949  -2.2922   0.4142
 2YG  H25  H  HCH2  0   0.210   6.7055  -2.3584  -1.2800
 2YG  H26  H  HCH2  0   0.186   7.6230  -1.1767  -0.3645
 2YG  H27  H  HNH2  0   0.344   8.2841  -3.4659   0.0640
 2YG  H28  H  HNH2  0   0.336   7.7199  -2.8023   1.4181

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
 2YG  N    C    single  1.443  0.020  1.443
 2YG  C2   C1   single  1.523  0.020  1.523
 2YG  C2   C3   single  1.523  0.020  1.523
 2YG  C    C1   single  1.536  0.020  1.536
 2YG  C    C11  single  1.523  0.020  1.523
 2YG  C4   C3   single  1.520  0.020  1.520
 2YG  C4   N1   single  1.449  0.020  1.449
 2YG  O2   C11  double  1.206  0.020  1.206
 2YG  N1   C5   single  1.339  0.020  1.339
 2YG  C11  O1   single  1.329  0.020  1.329
 2YG  C5   C6   single  1.531  0.020  1.531
 2YG  C5   O    double  1.226  0.020  1.226
 2YG  N2   C6   single  1.447  0.020  1.447
 2YG  C7   C6   single  1.533  0.020  1.533
 2YG  C7   C8   single  1.522  0.020  1.522
 2YG  C8   C9   single  1.524  0.020  1.524
 2YG  C9   C10  single  1.521  0.020  1.521
 2YG  C10  N3   single  1.457  0.020  1.457
 2YG  O1   H1   single  0.850  0.020  0.980
 2YG  C    H2   single  0.970  0.020  1.090
 2YG  N    H3   single  0.890  0.020  1.040
 2YG  N    H4   single  0.890  0.020  1.040
 2YG  C1   H6   single  0.970  0.020  1.090
 2YG  C1   H7   single  0.970  0.020  1.090
 2YG  C2   H8   single  0.970  0.020  1.090
 2YG  C2   H9   single  0.970  0.020  1.090
 2YG  C3   H10  single  0.970  0.020  1.090
 2YG  C3   H11  single  0.970  0.020  1.090
 2YG  C4   H12  single  0.970  0.020  1.090
 2YG  C4   H13  single  0.970  0.020  1.090
 2YG  N1   H14  single  0.860  0.020  1.020
 2YG  C6   H15  single  0.970  0.020  1.090
 2YG  N2   H16  single  0.890  0.020  1.040
 2YG  N2   H17  single  0.890  0.020  1.040
 2YG  C7   H19  single  0.970  0.020  1.090
 2YG  C7   H20  single  0.970  0.020  1.090
 2YG  C8   H21  single  0.970  0.020  1.090
 2YG  C8   H22  single  0.970  0.020  1.090
 2YG  C9   H23  single  0.970  0.020  1.090
 2YG  C9   H24  single  0.970  0.020  1.090
 2YG  C10  H25  single  0.970  0.020  1.090
 2YG  C10  H26  single  0.970  0.020  1.090
 2YG  N3   H27  single  0.890  0.020  1.040
 2YG  N3   H28  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
 2YG  C    C11  O1   112.10  3.000
 2YG  O1   C11  O2   123.25  3.000
 2YG  C    C11  O2   124.65  3.000
 2YG  H1   O1   C11  110.27  3.000
 2YG  H2   C    C1   107.95  3.000
 2YG  H2   C    N    108.18  3.000
 2YG  C1   C    N    110.80  3.000
 2YG  H2   C    C11  107.08  3.000
 2YG  C1   C    C11  109.10  3.000
 2YG  N    C    C11  113.51  3.000
 2YG  H4   N    H3   106.40  3.000
 2YG  H4   N    C    110.14  3.000
 2YG  H3   N    C    110.48  3.000
 2YG  H7   C1   H6   106.48  3.000
 2YG  H7   C1   C2   109.24  3.000
 2YG  H6   C1   C2   109.77  3.000
 2YG  H7   C1   C    109.41  3.000
 2YG  H6   C1   C    108.96  3.000
 2YG  C2   C1   C    112.79  3.000
 2YG  H9   C2   H8   106.55  3.000
 2YG  H9   C2   C3   109.60  3.000
 2YG  H8   C2   C3   109.46  3.000
 2YG  H9   C2   C1   109.70  3.000
 2YG  H8   C2   C1   109.19  3.000
 2YG  C3   C2   C1   112.18  3.000
 2YG  H11  C3   H10  106.84  3.000
 2YG  H11  C3   C4   109.55  3.000
 2YG  H10  C3   C4   109.42  3.000
 2YG  H11  C3   C2   109.72  3.000
 2YG  H10  C3   C2   109.59  3.000
 2YG  C4   C3   C2   111.60  3.000
 2YG  H13  C4   H12  106.78  3.000
 2YG  H13  C4   N1   109.61  3.000
 2YG  H12  C4   N1   109.95  3.000
 2YG  H13  C4   C3   109.74  3.000
 2YG  H12  C4   C3   109.74  3.000
 2YG  N1   C4   C3   110.94  3.000
 2YG  H14  N1   C5   118.83  3.000
 2YG  H14  N1   C4   118.21  3.000
 2YG  C5   N1   C4   122.96  3.000
 2YG  C6   C5   O    121.55  3.000
 2YG  O    C5   N1   122.61  3.000
 2YG  C6   C5   N1   115.81  3.000
 2YG  H15  C6   C7   108.06  3.000
 2YG  H15  C6   N2   107.87  3.000
 2YG  C7   C6   N2   110.70  3.000
 2YG  H15  C6   C5   108.87  3.000
 2YG  C7   C6   C5   108.10  3.000
 2YG  N2   C6   C5   113.10  3.000
 2YG  H17  N2   H16  105.93  3.000
 2YG  H17  N2   C6   109.25  3.000
 2YG  H16  N2   C6   110.08  3.000
 2YG  H20  C7   H19  106.33  3.000
 2YG  H20  C7   C8   109.45  3.000
 2YG  H19  C7   C8   109.70  3.000
 2YG  H20  C7   C6   108.67  3.000
 2YG  H19  C7   C6   108.82  3.000
 2YG  C8   C7   C6   113.60  3.000
 2YG  H22  C8   H21  106.33  3.000
 2YG  H22  C8   C9   109.74  3.000
 2YG  H21  C8   C9   109.41  3.000
 2YG  H22  C8   C7   109.41  3.000
 2YG  H21  C8   C7   109.30  3.000
 2YG  C9   C8   C7   112.45  3.000
 2YG  H24  C9   H23  106.41  3.000
 2YG  H24  C9   C10  109.15  3.000
 2YG  H23  C9   C10  109.14  3.000
 2YG  H24  C9   C8   109.99  3.000
 2YG  H23  C9   C8   109.30  3.000
 2YG  C10  C9   C8   112.66  3.000
 2YG  H26  C10  H25  106.15  3.000
 2YG  H26  C10  N3   113.36  3.000
 2YG  H25  C10  N3   108.07  3.000
 2YG  H26  C10  C9   108.74  3.000
 2YG  H25  C10  C9   109.11  3.000
 2YG  N3   C10  C9   111.23  3.000
 2YG  H28  N3   H27  105.32  3.000
 2YG  H28  N3   C10  109.11  3.000
 2YG  H27  N3   C10  109.24  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
 2YG  CONST_01  C6   C5   N1   C4   180.00   0.0  0
 2YG  CONST_02  O    C5   N1   C4     0.00   0.0  0
 2YG  CONST_03  H14  N1   C5   O    180.00   0.0  0
 2YG  CONST_04  H1   O1   C11  O2     0.00   0.0  0
 2YG  Var_01    C3   C2   C1   C   -178.91  30.0  1
 2YG  Var_02    C4   C3   C2   C1   179.64  30.0  3
 2YG  Var_03    N1   C4   C3   C2   178.73  30.0  1
 2YG  Var_04    C5   N1   C4   C3  -175.66  30.0  3
 2YG  Var_05    C9   C8   C7   C6  -177.74  30.0  3
 2YG  Var_06    C10  C9   C8   C7  -177.87  30.0  3
 2YG  Var_07    N3   C10  C9   C8  -179.23  30.0  3
 2YG  Var_08    H27  N3   C10  C9   179.36  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
 2YG  chir_01  C   N   C1  C11  negativ
 2YG  chir_02  C6  C5  N2  C7   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
 2YG  plan-1  C4   0.020
 2YG  plan-1  N1   0.020
 2YG  plan-1  C5   0.020
 2YG  plan-1  O    0.020
 2YG  plan-1  C6   0.020
 2YG  plan-1  H14  0.020
 2YG  plan-2  O2   0.020
 2YG  plan-2  C11  0.020
 2YG  plan-2  O1   0.020
 2YG  plan-2  C    0.020
 2YG  plan-2  H1   0.020

