# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 14:33:15 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N~2~-(3-carboxypropanoyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](NC(=O)CCC(O)=O)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
 NSK  NSK  N~2~-(3-carboxypropanoyl)-L-lysine  L-peptide  35  17  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NSK
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
 NSK  O1    O  OH1   0  -0.597  -4.6679   6.0169  -0.6640
 NSK  O2    O  O     0  -0.444  -5.1470   3.8693  -1.0217
 NSK  C1    C  C     0   0.556  -4.3419   4.7658  -0.9730
 NSK  C2    C  CH2   0  -0.578  -2.8703   4.6305  -1.2438
 NSK  C3    C  CH2   0  -0.592  -2.4762   3.2163  -1.6254
 NSK  O3    O  O     0  -0.493  -0.2649   4.0385  -2.1136
 NSK  C4    C  C     0   0.585  -0.9922   3.0842  -1.8850
 NSK  N1    N  NH1   0  -0.644  -0.5228   1.8222  -1.8470
 NSK  C5    C  CH1   0  -0.179   0.8381   1.5148  -2.1883
 NSK  C6    C  C     0   0.544   1.0802   1.7421  -3.6735
 NSK  O4    O  O     0  -0.434   0.2161   1.7775  -4.5099
 NSK  C7    C  CH2   0  -0.464   1.1699   0.0654  -1.8172
 NSK  C8    C  CH2   0  -0.421   1.0883  -0.1960  -0.3178
 NSK  C9    C  CH2   0  -0.427   1.4494  -1.6329   0.0368
 NSK  C10   C  CH2   0  -0.272   1.3805  -1.8976   1.5330
 NSK  N2    N  NH2   0  -0.801   1.7144  -3.2825   1.8350
 NSK  O5    O  OH1   0  -0.592   2.3739   1.8601  -3.9384
 NSK  HO1   H  HOH1  0   0.479  -5.6199   6.0792  -0.4960
 NSK  H21   H  HCH2  0   0.288  -2.5994   5.3390  -2.0298
 NSK  H22   H  HCH2  0   0.289  -2.3296   4.9584  -0.3515
 NSK  H31   H  HCH2  0   0.287  -3.0010   2.9069  -2.5344
 NSK  H32   H  HCH2  0   0.272  -2.7747   2.5080  -0.8501
 NSK  HN1   H  HNH1  0   0.405  -1.1791   1.0605  -1.7730
 NSK  H5    H  HCH1  0   0.284   1.5078   2.1757  -1.6309
 NSK  H71   H  HCH2  0   0.243   0.4965  -0.6090  -2.3563
 NSK  H72   H  HCH2  0   0.258   2.1797  -0.1589  -2.1668
 NSK  H81   H  HCH2  0   0.224   0.0833   0.0247   0.0527
 NSK  H82   H  HCH2  0   0.223   1.7648   0.4908   0.2012
 NSK  H91   H  HCH2  0   0.217   2.4564  -1.8640  -0.3234
 NSK  H92   H  HCH2  0   0.215   0.7682  -2.3163  -0.4823
 NSK  H101  H  HCH2  0   0.212   2.1037  -1.2540   2.0416
 NSK  H102  H  HCH2  0   0.188   0.3892  -1.5961   1.9026
 NSK  HN21  H  HNH2  0   0.337   0.9883  -3.8864   1.4687
 NSK  HN22  H  HNH2  0   0.345   1.6979  -3.4207   2.8375
 NSK  HO5   H  HOH1  0   0.484   2.5150   1.9515  -4.8929

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
 NSK  O1   C1    single  1.329  0.020  1.329
 NSK  O1   HO1   single  0.850  0.020  0.980
 NSK  O2   C1    double  1.206  0.020  1.206
 NSK  C1   C2    single  1.502  0.020  1.502
 NSK  C2   C3    single  1.517  0.020  1.517
 NSK  C2   H21   single  0.970  0.020  1.090
 NSK  C2   H22   single  0.970  0.020  1.090
 NSK  C3   C4    single  1.512  0.020  1.512
 NSK  C3   H31   single  0.970  0.020  1.090
 NSK  C3   H32   single  0.970  0.020  1.090
 NSK  O3   C4    double  1.221  0.020  1.221
 NSK  C4   N1    single  1.347  0.020  1.347
 NSK  N1   C5    single  1.436  0.020  1.436
 NSK  N1   HN1   single  0.860  0.020  1.020
 NSK  C5   C6    single  1.522  0.020  1.522
 NSK  C5   C7    single  1.532  0.020  1.532
 NSK  C5   H5    single  0.970  0.020  1.090
 NSK  C6   O4    double  1.203  0.020  1.203
 NSK  C6   O5    single  1.326  0.020  1.326
 NSK  C7   C8    single  1.524  0.020  1.524
 NSK  C7   H71   single  0.970  0.020  1.090
 NSK  C7   H72   single  0.970  0.020  1.090
 NSK  C8   C9    single  1.523  0.020  1.523
 NSK  C8   H81   single  0.970  0.020  1.090
 NSK  C8   H82   single  0.970  0.020  1.090
 NSK  C9   C10   single  1.521  0.020  1.521
 NSK  C9   H91   single  0.970  0.020  1.090
 NSK  C9   H92   single  0.970  0.020  1.090
 NSK  C10  N2    single  1.456  0.020  1.456
 NSK  C10  H101  single  0.970  0.020  1.090
 NSK  C10  H102  single  0.970  0.020  1.090
 NSK  N2   HN21  single  0.890  0.020  1.040
 NSK  N2   HN22  single  0.890  0.020  1.040
 NSK  O5   HO5   single  0.850  0.020  0.980

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
 NSK  HO1   O1   C1    109.99  3.000
 NSK  C2    C1   O2    125.43  3.000
 NSK  C2    C1   O1    111.52  3.000
 NSK  O2    C1   O1    123.05  3.000
 NSK  H22   C2   H21   105.66  3.000
 NSK  H22   C2   C3    110.87  3.000
 NSK  H21   C2   C3    111.06  3.000
 NSK  H22   C2   C1    108.07  3.000
 NSK  H21   C2   C1    108.31  3.000
 NSK  C3    C2   C1    112.57  3.000
 NSK  H32   C3   H31   105.99  3.000
 NSK  H32   C3   C4    109.48  3.000
 NSK  H31   C3   C4    107.66  3.000
 NSK  H32   C3   C2    110.80  3.000
 NSK  H31   C3   C2    110.36  3.000
 NSK  C4    C3   C2    112.31  3.000
 NSK  N1    C4   O3    121.98  3.000
 NSK  N1    C4   C3    114.77  3.000
 NSK  O3    C4   C3    123.24  3.000
 NSK  HN1   N1   C5    118.20  3.000
 NSK  HN1   N1   C4    118.88  3.000
 NSK  C5    N1   C4    121.61  3.000
 NSK  H5    C5   C7    108.40  3.000
 NSK  H5    C5   C6    108.04  3.000
 NSK  C7    C5   C6    110.07  3.000
 NSK  H5    C5   N1    109.25  3.000
 NSK  C7    C5   N1    110.49  3.000
 NSK  C6    C5   N1    110.53  3.000
 NSK  O5    C6   O4    124.01  3.000
 NSK  O5    C6   C5    111.32  3.000
 NSK  O4    C6   C5    124.65  3.000
 NSK  H72   C7   H71   106.54  3.000
 NSK  H72   C7   C8    109.22  3.000
 NSK  H71   C7   C8    110.23  3.000
 NSK  H72   C7   C5    108.48  3.000
 NSK  H71   C7   C5    109.27  3.000
 NSK  C8    C7   C5    112.88  3.000
 NSK  H82   C8   H81   106.30  3.000
 NSK  H82   C8   C9    109.56  3.000
 NSK  H81   C8   C9    109.22  3.000
 NSK  H82   C8   C7    109.01  3.000
 NSK  H81   C8   C7    110.36  3.000
 NSK  C9    C8   C7    112.21  3.000
 NSK  H92   C9   H91   106.52  3.000
 NSK  H92   C9   C10   109.23  3.000
 NSK  H91   C9   C10   109.19  3.000
 NSK  H92   C9   C8    109.31  3.000
 NSK  H91   C9   C8    109.92  3.000
 NSK  C10   C9   C8    112.48  3.000
 NSK  H102  C10  H101  106.16  3.000
 NSK  H102  C10  N2    113.42  3.000
 NSK  H101  C10  N2    108.15  3.000
 NSK  H102  C10  C9    108.88  3.000
 NSK  H101  C10  C9    108.97  3.000
 NSK  N2    C10  C9    111.05  3.000
 NSK  HN22  N2   HN21  105.37  3.000
 NSK  HN22  N2   C10   109.37  3.000
 NSK  HN21  N2   C10   109.12  3.000
 NSK  HO5   O5   C6    110.31  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
 NSK  CONST_01  C5    N1   C4   C3   180.00   0.0  0
 NSK  CONST_02  C5    N1   C4   O3     0.00   0.0  0
 NSK  CONST_03  HN1   N1   C4   C3     0.00   0.0  0
 NSK  CONST_04  HO1   O1   C1   O2     0.00   0.0  0
 NSK  CONST_05  HO5   O5   C6   C5   180.00   0.0  0
 NSK  Var_01    C3    C2   C1   O1  -178.89  30.0  3
 NSK  Var_02    C4    C3   C2   C1  -179.50  30.0  3
 NSK  Var_03    O3    C4   C3   C2   -18.29  30.0  3
 NSK  Var_04    C9    C8   C7   C5  -178.79  30.0  3
 NSK  Var_05    C10   C9   C8   C7   179.55  30.0  3
 NSK  Var_06    N2    C10  C9   C8   179.28  30.0  3
 NSK  Var_07    HN21  N2   C10  C9   -67.52  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
 NSK  chir_01  C5  N1  C6  C7  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
 NSK  plan-1  C3   0.020
 NSK  plan-1  O3   0.020
 NSK  plan-1  C4   0.020
 NSK  plan-1  N1   0.020
 NSK  plan-1  C5   0.020
 NSK  plan-1  HN1  0.020
 NSK  plan-2  O1   0.020
 NSK  plan-2  O2   0.020
 NSK  plan-2  C1   0.020
 NSK  plan-2  C2   0.020
 NSK  plan-2  HO1  0.020
 NSK  plan-3  C5   0.020
 NSK  plan-3  C6   0.020
 NSK  plan-3  O4   0.020
 NSK  plan-3  O5   0.020
 NSK  plan-3  HO5  0.020

