# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:53:28 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: N-(4-aminobutyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCNCC(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
 NLY  NLY  'N-(4-aminobutyl)glycine  '  peptide  23  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NLY
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
 NLY  N    N  NH1    0  -0.599  -0.8863   0.1607  -0.1720
 NLY  CB   C  CH2    0  -0.241   0.3574  -0.5707  -0.0705
 NLY  CG   C  CH2    0  -0.445   1.5586   0.3621  -0.1011
 NLY  CD   C  CH2    0  -0.428   2.8834  -0.3800   0.0120
 NLY  CE   C  CH2    0  -0.271   4.0831   0.5547  -0.0167
 NLY  NZ   N  NH2    0  -0.801   5.3294  -0.1904   0.0966
 NLY  CA   C  CH2    0  -0.400  -2.0581  -0.6828  -0.0988
 NLY  C2   C  C      0   0.388  -3.3444   0.1026   0.2168
 NLY  O    O  O      0  -0.610  -3.2092   1.2217   0.7507
 NLY  H1   H  HNH1   0   0.325  -0.9489   0.8413   0.5752
 NLY  H3   H  HCH2   0   0.175   0.4064  -1.1962   0.8387
 NLY  H4   H  HCH2   0   0.204   0.4236  -1.2672  -0.9139
 NLY  H5   H  HCH2   0   0.213   1.5368   0.9441  -1.0282
 NLY  H6   H  HCH2   0   0.211   1.4732   1.0839   0.7191
 NLY  H7   H  HCH2   0   0.211   2.8993  -0.9584   0.9431
 NLY  H8   H  HCH2   0   0.213   2.9759  -1.1047  -0.8032
 NLY  H9   H  HCH2   0   0.211   4.0916   1.0934  -0.9686
 NLY  H10  H  HCH2   0   0.186   3.9558   1.3172   0.7659
 NLY  H11  H  HNH2   0   0.345   6.1116   0.4493   0.0393
 NLY  H12  H  HNH2   0   0.336   5.3850  -0.6028   1.0202
 NLY  H14  H  HCH2   0   0.210  -2.1835  -1.2245  -1.0419
 NLY  H15  H  HCH2   0   0.189  -1.9653  -1.4641   0.6790
 NLY  OXT  O  OC    -1  -0.622  -4.4176  -0.4691  -0.0529

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
 NLY  NZ  CE   single  1.456  0.020  1.456
 NLY  CE  CD   single  1.521  0.020  1.521
 NLY  CD  CG   single  1.523  0.020  1.523
 NLY  CG  CB   single  1.521  0.020  1.521
 NLY  CB  N    single  1.446  0.020  1.446
 NLY  N   CA   single  1.451  0.016  1.451
 NLY  CA  C2   single  1.540  0.020  1.540
 NLY  O   C2   deloc   1.247  0.020  1.247
 NLY  N   H1   single  0.890  0.020  1.040
 NLY  CB  H3   single  0.970  0.020  1.090
 NLY  CB  H4   single  0.970  0.020  1.090
 NLY  CG  H5   single  0.970  0.020  1.090
 NLY  CG  H6   single  0.970  0.020  1.090
 NLY  CD  H7   single  0.970  0.020  1.090
 NLY  CD  H8   single  0.970  0.020  1.090
 NLY  CE  H9   single  0.970  0.020  1.090
 NLY  CE  H10  single  0.970  0.020  1.090
 NLY  NZ  H11  single  0.890  0.020  1.040
 NLY  NZ  H12  single  0.890  0.020  1.040
 NLY  CA  H14  single  0.970  0.020  1.090
 NLY  CA  H15  single  0.970  0.020  1.090
 NLY  C2  OXT  deloc   1.246  0.020  1.246

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
 NLY  H1   N   CA   107.74  3.000
 NLY  H1   N   CB   109.96  3.000
 NLY  CA   N   CB   113.48  3.000
 NLY  H4   CB  H3   105.71  3.000
 NLY  H4   CB  CG   109.06  3.000
 NLY  H3   CB  CG   109.20  3.000
 NLY  H4   CB  N    108.62  3.000
 NLY  H3   CB  N    112.47  3.000
 NLY  CG   CB  N    111.56  3.000
 NLY  H6   CG  H5   106.38  3.000
 NLY  H6   CG  CD   109.46  3.000
 NLY  H5   CG  CD   109.83  3.000
 NLY  H6   CG  CB   109.10  3.000
 NLY  H5   CG  CB   109.11  3.000
 NLY  CD   CG  CB   112.75  3.000
 NLY  H8   CD  H7   106.38  3.000
 NLY  H8   CD  CE   109.03  3.000
 NLY  H7   CD  CE   109.19  3.000
 NLY  H8   CD  CG   109.93  3.000
 NLY  H7   CD  CG   109.44  3.000
 NLY  CE   CD  CG   112.67  3.000
 NLY  H10  CE  H9   106.18  3.000
 NLY  H10  CE  NZ   113.47  3.000
 NLY  H9   CE  NZ   108.24  3.000
 NLY  H10  CE  CD   108.74  3.000
 NLY  H9   CE  CD   108.98  3.000
 NLY  NZ   CE  CD   111.05  3.000
 NLY  H12  NZ  H11  105.46  3.000
 NLY  H12  NZ  CE   109.03  3.000
 NLY  H11  NZ  CE   109.49  3.000
 NLY  H15  CA  H14  105.41  3.000
 NLY  H15  CA  C2   106.63  3.000
 NLY  H14  CA  C2   109.47  3.000
 NLY  H15  CA  N    112.31  3.000
 NLY  H14  CA  N    109.75  3.000
 NLY  C2   CA  N    112.95  3.000
 NLY  OXT  C2  O    126.72  3.000
 NLY  OXT  C2  CA   116.19  3.000
 NLY  O    C2  CA   117.05  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
 NLY  Var_01  CD   CG  CB  N    179.68  30.0  1
 NLY  Var_02  O    C2  CA  N    -20.73  30.0  3
 NLY  Var_03  CE   CD  CG  CB  -179.91  30.0  1
 NLY  Var_04  C2   CA  N   CB   162.72  30.0  3
 NLY  Var_05  NZ   CE  CD  CG   179.87  30.0  1
 NLY  Var_06  CA   N   CB  CG  -177.91  30.0  3
 NLY  Var_07  H11  NZ  CE  CD   177.84  30.0  3

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
 NLY  plan-1  CA   0.020
 NLY  plan-1  C2   0.020
 NLY  plan-1  O    0.020
 NLY  plan-1  OXT  0.020

