# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 05:39:28 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  30  14  .  2022-09-22  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_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   0.529  -4.1139  -0.0818  -0.0851
 Q3P  C4    C  CH2    0  -0.410  -5.1968   0.7924   0.5258
 Q3P  N     N  NH2    0  -0.801   3.6180  -1.7446   0.2144
 Q3P  CA    C  CH1    0  -0.204   3.4005  -0.4115  -0.3250
 Q3P  C     C  C      0   0.404   4.5991   0.5086  -0.0050
 Q3P  O     O  O      0  -0.607   5.3272   0.1924   0.9563
 Q3P  CB    C  CH2    0  -0.424   2.1115   0.2732   0.1583
 Q3P  CG    C  CH2    0  -0.424   0.8337  -0.4160  -0.3050
 Q3P  CD    C  CH2    0  -0.469  -0.4233   0.3038   0.1656
 Q3P  CE    C  CH2    0  -0.230  -1.6897  -0.3493  -0.3632
 Q3P  NZ    N  NH1    0  -0.641  -2.8632   0.3684   0.0912
 Q3P  N5    N  NH2    0  -0.791  -6.5075   0.4171   0.0423
 Q3P  O2    O  O      0  -0.505  -4.3644  -1.1321  -0.6596
 Q3P  OXT   O  OC    -1  -0.622   4.7159   1.5254  -0.7195
 Q3P  H4    H  HCH2   0   0.238  -5.0783   0.7349   1.6183
 Q3P  H41   H  HCH2   0   0.253  -5.0047   1.8351   0.2614
 Q3P  HA    H  HCH1   0   0.198   3.3314  -0.4938  -1.4170
 Q3P  HB3   H  HCH2   0   0.207   2.1254   0.3304   1.2532
 Q3P  HB2   H  HCH2   0   0.212   2.1010   1.3041  -0.2063
 Q3P  HG3   H  HCH2   0   0.215   0.8345  -0.4692  -1.3991
 Q3P  HG2   H  HCH2   0   0.209   0.8022  -1.4511   0.0508
 Q3P  HD3   H  HCH2   0   0.229  -0.4512   0.3201   1.2596
 Q3P  HD2   H  HCH2   0   0.227  -0.3872   1.3482  -0.1615
 Q3P  HE3   H  HCH2   0   0.226  -1.6615  -0.3753  -1.4572
 Q3P  HE2   H  HCH2   0   0.229  -1.7425  -1.3874  -0.0251
 Q3P  HZ3   H  HNH1   0   0.399  -2.7253   1.2575   0.5450
 Q3P  HN5   H  HNH2   0   0.344  -6.7321  -0.5167   0.3593
 Q3P  HN51  H  HNH2   0   0.353  -7.1951   1.0272   0.4638
 Q3P  H2    H  HNH2   0   0.326   3.9034  -1.6544   1.1815
 Q3P  H1    H  HNH2   0   0.331   2.7557  -2.2745   0.2119

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     deloc   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  1.524  0.020  1.524
 Q3P  CE  NZ    single  1.449  0.020  1.449
 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  1.520  0.020  1.520
 Q3P  C4  N5    single  1.447  0.020  1.447
 Q3P  C   OXT   deloc   1.248  0.020  1.248
 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

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   122.76  3.000
 Q3P  NZ    C1  C4   114.74  3.000
 Q3P  O2    C1  C4   122.47  3.000
 Q3P  H41   C4  H4   105.73  3.000
 Q3P  H41   C4  N5   109.02  3.000
 Q3P  H4    C4  N5   114.57  3.000
 Q3P  H41   C4  C1   109.05  3.000
 Q3P  H4    C4  C1   107.00  3.000
 Q3P  N5    C4  C1   111.22  3.000
 Q3P  H1    N   H2   106.81  3.000
 Q3P  H1    N   CA   110.58  3.000
 Q3P  H2    N   CA   108.35  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    126.39  3.000
 Q3P  OXT   C   CA   116.06  3.000
 Q3P  O     C   CA   120.80  1.700
 Q3P  HB2   CB  HB3  106.49  3.000
 Q3P  HB2   CB  CG   108.48  3.000
 Q3P  HB3   CB  CG   109.74  3.000
 Q3P  HB2   CB  CA   108.85  3.000
 Q3P  HB3   CB  CA   109.06  3.000
 Q3P  CG    CB  CA   113.95  3.000
 Q3P  HG2   CG  HG3  106.18  3.000
 Q3P  HG2   CG  CD   108.82  3.000
 Q3P  HG3   CG  CD   109.40  3.000
 Q3P  HG2   CG  CB   110.67  3.000
 Q3P  HG3   CG  CB   108.97  3.000
 Q3P  CD    CG  CB   112.61  3.000
 Q3P  HD2   CD  HD3  106.57  3.000
 Q3P  HD2   CD  CE   109.48  3.000
 Q3P  HD3   CD  CE   109.45  3.000
 Q3P  HD2   CD  CG   109.34  3.000
 Q3P  HD3   CD  CG   109.69  3.000
 Q3P  CE    CD  CG   112.15  3.000
 Q3P  HE2   CE  HE3  106.73  3.000
 Q3P  HE2   CE  NZ   109.53  3.000
 Q3P  HE3   CE  NZ   110.25  3.000
 Q3P  HE2   CE  CD   109.92  3.000
 Q3P  HE3   CE  CD   109.66  3.000
 Q3P  NZ    CE  CD   110.66  3.000
 Q3P  HZ3   NZ  CE   117.88  3.000
 Q3P  HZ3   NZ  C1   118.89  3.000
 Q3P  CE    NZ  C1   123.22  3.000
 Q3P  HN51  N5  HN5  105.99  3.000
 Q3P  HN51  N5  C4   108.68  3.000
 Q3P  HN5   N5  C4   109.63  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  Var_01    CD   CE  NZ  C1  -171.38  30.0  2
 Q3P  Var_02    CD   CG  CB  CA  -178.77  30.0  3
 Q3P  Var_03    CE   CD  CG  CB   176.96  30.0  3
 Q3P  Var_04    NZ   CE  CD  CG  -179.38  30.0  1
 Q3P  Var_05    N5   C4  C1  NZ   166.93  30.0  3
 Q3P  Var_06    HN5  N5  C4  C1    65.19  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

