# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 08:58:28 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: N~6~-glycyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=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
 Q3P  Q3P  'N~6~-glycyl-L-lysine     '  L-peptide  31  14  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_Q3P
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
 Q3P  C1    C  C     0   0.530  -4.0625  -0.0808  -0.0790
 Q3P  C4    C  CH2   0  -0.411  -5.1402   0.7426   0.6061
 Q3P  N     N  NH2   0  -0.784   3.5270  -1.7594   0.4302
 Q3P  CA    C  CH1   0  -0.219   3.4166  -0.4815  -0.2411
 Q3P  C     C  C     0   0.548   4.6338   0.3565   0.0919
 Q3P  O     O  O     0  -0.441   5.3445   0.1849   1.0495
 Q3P  CB    C  CH2   0  -0.436   2.1468   0.3280   0.0894
 Q3P  CG    C  CH2   0  -0.424   0.8723  -0.3516  -0.3941
 Q3P  CD    C  CH2   0  -0.472  -0.3807   0.3867   0.0577
 Q3P  CE    C  CH2   0  -0.231  -1.6467  -0.2633  -0.4758
 Q3P  NZ    N  NH1   0  -0.642  -2.8217   0.4169   0.0286
 Q3P  N5    N  NH2   0  -0.792  -6.4588   0.3593   0.1505
 Q3P  O2    O  O     0  -0.504  -4.3058  -1.1364  -0.6463
 Q3P  OXT   O  OH1   0  -0.595   4.8132   1.3411  -0.7825
 Q3P  H4    H  HCH2  0   0.239  -4.9830   0.6369   1.6903
 Q3P  H41   H  HCH2  0   0.252  -4.9799   1.8005   0.3847
 Q3P  H1    H  HNH2  0   0.357   2.7941  -2.3755   0.1053
 Q3P  HA    H  HCH1  0   0.268   3.4306  -0.6659  -1.3202
 Q3P  HB3   H  HCH2  0   0.230   2.1005   0.4758   1.1740
 Q3P  HB2   H  HCH2  0   0.237   2.2085   1.3227  -0.3591
 Q3P  HG3   H  HCH2  0   0.227   0.8918  -0.4155  -1.4868
 Q3P  HG2   H  HCH2  0   0.216   0.8251  -1.3806  -0.0256
 Q3P  HD3   H  HCH2  0   0.232  -0.4166   0.4052   1.1513
 Q3P  HD2   H  HCH2  0   0.232  -0.3346   1.4295  -0.2723
 Q3P  HE3   H  HCH2  0   0.228  -1.6377  -0.2502  -1.5704
 Q3P  HE2   H  HCH2  0   0.231  -1.6791  -1.3132  -0.1745
 Q3P  HZ3   H  HNH1  0   0.399  -2.6929   1.3085   0.4798
 Q3P  HN5   H  HNH2  0   0.344  -6.6539  -0.5912   0.4355
 Q3P  HN51  H  HNH2  0   0.353  -7.1444   0.9374   0.6180
 Q3P  HXT   H  HOH1  0   0.481   5.5667   1.8881  -0.5151
 Q3P  H2    H  HNH2  0   0.344   3.3759  -1.6423   1.4252

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
 Q3P  O    C     double  1.231  0.020  1.231
 Q3P  N    CA    single  1.458  0.019  1.458
 Q3P  C    CA    single  1.525  0.021  1.525
 Q3P  CA   CB    single  1.530  0.020  1.530
 Q3P  CB   CG    single  1.523  0.020  1.523
 Q3P  CE   NZ    single  1.448  0.020  1.448
 Q3P  CE   CD    single  1.520  0.020  1.520
 Q3P  CG   CD    single  1.523  0.020  1.523
 Q3P  O2   C1    double  1.223  0.020  1.223
 Q3P  NZ   C1    single  1.341  0.020  1.341
 Q3P  C1   C4    single  1.519  0.020  1.519
 Q3P  C4   N5    single  1.447  0.020  1.447
 Q3P  C    OXT   single  1.329  0.020  1.329
 Q3P  C4   H4    single  0.970  0.020  1.090
 Q3P  C4   H41   single  0.970  0.020  1.090
 Q3P  N    H2    single  0.890  0.020  1.040
 Q3P  N    H1    single  0.890  0.020  1.040
 Q3P  CA   HA    single  0.970  0.020  0.970
 Q3P  CB   HB3   single  0.970  0.020  1.090
 Q3P  CB   HB2   single  0.970  0.020  1.090
 Q3P  CG   HG3   single  0.970  0.020  1.090
 Q3P  CG   HG2   single  0.970  0.020  1.090
 Q3P  CD   HD3   single  0.970  0.020  1.090
 Q3P  CD   HD2   single  0.970  0.020  1.090
 Q3P  CE   HE3   single  0.970  0.020  1.090
 Q3P  CE   HE2   single  0.970  0.020  1.090
 Q3P  NZ   HZ3   single  0.860  0.020  1.020
 Q3P  N5   HN5   single  0.890  0.020  1.040
 Q3P  N5   HN51  single  0.890  0.020  1.040
 Q3P  OXT  HXT   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
 Q3P  O2    C1   NZ   122.79  3.000
 Q3P  NZ    C1   C4   114.77  3.000
 Q3P  O2    C1   C4   122.40  3.000
 Q3P  H41   C4   H4   105.76  3.000
 Q3P  H41   C4   N5   109.05  3.000
 Q3P  H4    C4   N5   114.52  3.000
 Q3P  H41   C4   C1   109.22  3.000
 Q3P  H4    C4   C1   106.91  3.000
 Q3P  N5    C4   C1   111.16  3.000
 Q3P  H1    N    H2   106.14  3.000
 Q3P  H1    N    CA   109.48  3.000
 Q3P  H2    N    CA   110.00  3.000
 Q3P  HA    CA   CB   109.00  3.000
 Q3P  HA    CA   C    109.00  3.000
 Q3P  CB    CA   C    110.10  1.900
 Q3P  HA    CA   N    110.00  3.000
 Q3P  CB    CA   N    110.50  1.700
 Q3P  C     CA   N    111.00  2.800
 Q3P  OXT   C    O    123.29  3.000
 Q3P  OXT   C    CA   111.94  3.000
 Q3P  O     C    CA   120.80  1.700
 Q3P  HB2   CB   HB3  106.61  3.000
 Q3P  HB2   CB   CG   108.85  3.000
 Q3P  HB3   CB   CG   109.82  3.000
 Q3P  HB2   CB   CA   110.09  3.000
 Q3P  HB3   CB   CA   108.53  3.000
 Q3P  CG    CB   CA   112.76  3.000
 Q3P  HG2   CG   HG3  106.39  3.000
 Q3P  HG2   CG   CD   108.70  3.000
 Q3P  HG3   CG   CD   109.82  3.000
 Q3P  HG2   CG   CB   110.42  3.000
 Q3P  HG3   CG   CB   109.15  3.000
 Q3P  CD    CG   CB   112.21  3.000
 Q3P  HD2   CD   HD3  106.65  3.000
 Q3P  HD2   CD   CE   109.67  3.000
 Q3P  HD3   CD   CE   109.31  3.000
 Q3P  HD2   CD   CG   109.74  3.000
 Q3P  HD3   CD   CG   109.37  3.000
 Q3P  CE    CD   CG   111.95  3.000
 Q3P  HE2   CE   HE3  106.70  3.000
 Q3P  HE2   CE   NZ   109.34  3.000
 Q3P  HE3   CE   NZ   110.45  3.000
 Q3P  HE2   CE   CD   109.80  3.000
 Q3P  HE3   CE   CD   109.81  3.000
 Q3P  NZ    CE   CD   110.65  3.000
 Q3P  HZ3   NZ   CE   117.90  3.000
 Q3P  HZ3   NZ   C1   118.85  3.000
 Q3P  CE    NZ   C1   123.25  3.000
 Q3P  HN51  N5   HN5  106.04  3.000
 Q3P  HN51  N5   C4   108.72  3.000
 Q3P  HN5   N5   C4   109.64  3.000
 Q3P  HXT   OXT  C    109.98  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
 Q3P  CONST_01  CE   NZ   C1  C4   180.00   0.0  0
 Q3P  CONST_02  O2   C1   NZ  CE     0.00   0.0  0
 Q3P  CONST_03  HZ3  NZ   C1  C4     0.00   0.0  0
 Q3P  CONST_04  HXT  OXT  C   CA   180.00   0.0  0
 Q3P  Var_01    CD   CE   NZ  C1  -167.54  30.0  1
 Q3P  Var_02    CD   CG   CB  CA   174.35  30.0  3
 Q3P  Var_03    CE   CD   CG  CB   177.63  30.0  3
 Q3P  Var_04    NZ   CE   CD  CG   176.92  30.0  1
 Q3P  Var_05    N5   C4   C1  NZ   164.38  30.0  3
 Q3P  Var_06    HN5  N5   C4  C1    65.32  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
 Q3P  chir_01  CA  N  C  CB  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
 Q3P  plan-1  C1   0.020
 Q3P  plan-1  C4   0.020
 Q3P  plan-1  CE   0.020
 Q3P  plan-1  NZ   0.020
 Q3P  plan-1  O2   0.020
 Q3P  plan-1  HZ3  0.020
 Q3P  plan-2  CA   0.020
 Q3P  plan-2  C    0.020
 Q3P  plan-2  O    0.020
 Q3P  plan-2  OXT  0.020
 Q3P  plan-2  HXT  0.020

