# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 20:46:29 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  33  17  .  2022-03-23  2022-03-23
;
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  OC    -1  -0.630  -4.6473   5.4918   0.1098
 NSK  O2    O  O      0  -0.609  -5.0658   4.2217  -1.6706
 NSK  C1    C  C      0   0.416  -4.3116   4.7178  -0.8108
 NSK  C2    C  CH2    0  -0.582  -2.8124   4.3780  -0.8867
 NSK  C3    C  CH2    0  -0.572  -2.4573   3.2542  -1.8468
 NSK  O3    O  O      0  -0.524  -0.2021   4.0222  -2.1266
 NSK  C4    C  C      0   0.562  -0.9641   3.0681  -2.0044
 NSK  N1    N  NH1    0  -0.625  -0.5324   1.7982  -1.9908
 NSK  C5    C  CH1    0  -0.189   0.8157   1.4324  -2.3540
 NSK  C6    C  C      0   0.410   1.0832   1.5579  -3.8778
 NSK  O4    O  O      0  -0.596   0.1113   1.7615  -4.6242
 NSK  C7    C  CH2    0  -0.452   1.1202   0.0169  -1.8651
 NSK  C8    C  CH2    0  -0.413   1.0238  -0.1489  -0.3534
 NSK  C9    C  CH2    0  -0.425   1.4003  -1.5506   0.1108
 NSK  C10   C  CH2    0  -0.271   1.2921  -1.7175   1.6186
 NSK  N2    N  NH2    0  -0.801   1.6438  -3.0719   2.0239
 NSK  O5    O  OC    -1  -0.620   2.2778   1.4217  -4.2130
 NSK  H21   H  HCH2   0   0.233  -2.2779   5.2880  -1.1767
 NSK  H22   H  HCH2   0   0.225  -2.4540   4.1394   0.1192
 NSK  H31   H  HCH2   0   0.251  -2.8610   3.4824  -2.8373
 NSK  H32   H  HCH2   0   0.233  -2.9327   2.3210  -1.5363
 NSK  HN1   H  HNH1   0   0.383  -1.2290   1.0706  -2.0108
 NSK  H5    H  HCH1   0   0.228   1.4984   2.1174  -1.8424
 NSK  H71   H  HCH2   0   0.216   0.4462  -0.6947  -2.3581
 NSK  H72   H  HCH2   0   0.231   2.1288  -0.2375  -2.1961
 NSK  H81   H  HCH2   0   0.213   0.0099   0.0824  -0.0129
 NSK  H82   H  HCH2   0   0.210   1.6803   0.5838   0.1293
 NSK  H91   H  HCH2   0   0.211   2.4216  -1.7864  -0.2044
 NSK  H92   H  HCH2   0   0.209   0.7482  -2.2824  -0.3801
 NSK  H101  H  HCH2   0   0.210   1.9857  -1.0250   2.1041
 NSK  H102  H  HCH2   0   0.185   0.2840  -1.4140   1.9376
 NSK  HN21  H  HNH2   0   0.336   0.9504  -3.7156   1.6618
 NSK  HN22  H  HNH2   0   0.344   1.5801  -3.1490   3.0312

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    deloc   1.249  0.020  1.249
 NSK  O2   C1    deloc   1.247  0.020  1.247
 NSK  C1   C2    single  1.539  0.020  1.539
 NSK  C2   C3    single  1.520  0.020  1.520
 NSK  C2   H21   single  0.970  0.020  1.090
 NSK  C2   H22   single  0.970  0.020  1.090
 NSK  C3   C4    single  1.513  0.020  1.513
 NSK  C3   H31   single  0.970  0.020  1.090
 NSK  C3   H32   single  0.970  0.020  1.090
 NSK  O3   C4    double  1.227  0.020  1.227
 NSK  C4   N1    single  1.341  0.020  1.341
 NSK  N1   C5    single  1.443  0.020  1.443
 NSK  N1   HN1   single  0.860  0.020  1.020
 NSK  C5   C6    single  1.552  0.020  1.552
 NSK  C5   C7    single  1.528  0.020  1.528
 NSK  C5   H5    single  0.970  0.020  1.090
 NSK  C6   O4    deloc   1.242  0.020  1.242
 NSK  C6   O5    deloc   1.248  0.020  1.248
 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  1.524  0.020  1.524
 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  1.457  0.020  1.457
 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

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  C2    C1   O2    117.87  3.000
 NSK  C2    C1   O1    115.79  3.000
 NSK  O2    C1   O1    126.33  3.000
 NSK  H22   C2   H21   105.36  3.000
 NSK  H22   C2   C3    110.05  3.000
 NSK  H21   C2   C3    109.47  3.000
 NSK  H22   C2   C1    108.77  3.000
 NSK  H21   C2   C1    107.78  3.000
 NSK  C3    C2   C1    114.95  3.000
 NSK  H32   C3   H31   105.97  3.000
 NSK  H32   C3   C4    110.73  3.000
 NSK  H31   C3   C4    107.19  3.000
 NSK  H32   C3   C2    110.51  3.000
 NSK  H31   C3   C2    109.36  3.000
 NSK  C4    C3   C2    112.78  3.000
 NSK  N1    C4   O3    122.50  3.000
 NSK  N1    C4   C3    115.66  3.000
 NSK  O3    C4   C3    121.84  3.000
 NSK  HN1   N1   C5    117.24  3.000
 NSK  HN1   N1   C4    117.45  3.000
 NSK  C5    N1   C4    122.55  3.000
 NSK  H5    C5   C7    107.81  3.000
 NSK  H5    C5   C6    107.51  3.000
 NSK  C7    C5   C6    110.77  3.000
 NSK  H5    C5   N1    107.85  3.000
 NSK  C7    C5   N1    109.90  3.000
 NSK  C6    C5   N1    112.80  3.000
 NSK  O5    C6   O4    127.25  3.000
 NSK  O5    C6   C5    114.82  3.000
 NSK  O4    C6   C5    117.92  3.000
 NSK  H72   C7   H71   106.27  3.000
 NSK  H72   C7   C8    109.51  3.000
 NSK  H71   C7   C8    109.65  3.000
 NSK  H72   C7   C5    107.64  3.000
 NSK  H71   C7   C5    109.54  3.000
 NSK  C8    C7   C5    113.93  3.000
 NSK  H82   C8   H81   106.07  3.000
 NSK  H82   C8   C9    109.44  3.000
 NSK  H81   C8   C9    109.18  3.000
 NSK  H82   C8   C7    109.05  3.000
 NSK  H81   C8   C7    110.13  3.000
 NSK  C9    C8   C7    112.75  3.000
 NSK  H92   C9   H91   106.39  3.000
 NSK  H92   C9   C10   109.17  3.000
 NSK  H91   C9   C10   109.17  3.000
 NSK  H92   C9   C8    109.31  3.000
 NSK  H91   C9   C8    109.94  3.000
 NSK  C10   C9   C8    112.67  3.000
 NSK  H102  C10  H101  106.13  3.000
 NSK  H102  C10  N2    113.39  3.000
 NSK  H101  C10  N2    108.18  3.000
 NSK  H102  C10  C9    108.81  3.000
 NSK  H101  C10  C9    108.99  3.000
 NSK  N2    C10  C9    111.14  3.000
 NSK  HN22  N2   HN21  105.33  3.000
 NSK  HN22  N2   C10   109.42  3.000
 NSK  HN21  N2   C10   109.03  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  Var_01    C3    C2   C1   O1   169.67  30.0  3
 NSK  Var_02    C4    C3   C2   C1   173.34  30.0  3
 NSK  Var_03    O3    C4   C3   C2   -43.18  30.0  3
 NSK  Var_04    C9    C8   C7   C5  -177.12  30.0  3
 NSK  Var_05    C10   C9   C8   C7  -179.51  30.0  3
 NSK  Var_06    N2    C10  C9   C8   179.33  30.0  3
 NSK  Var_07    HN21  N2   C10  C9   -66.36  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
 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-3  C5   0.020
 NSK  plan-3  C6   0.020
 NSK  plan-3  O4   0.020
 NSK  plan-3  O5   0.020

