# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 02:31:58 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  24  10  .  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_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  -0.8913   0.1970   0.0078
 NLY  CB   C  CH2   0  -0.249   0.3507  -0.5537  -0.0151
 NLY  CG   C  CH2   0  -0.448   1.5533   0.3761  -0.0100
 NLY  CD   C  CH2   0  -0.429   2.8754  -0.3792  -0.0284
 NLY  CE   C  CH2   0  -0.271   4.0790   0.5509  -0.0280
 NLY  NZ   N  NH2   0  -0.801   5.3235  -0.2052  -0.0379
 NLY  CA   C  CH2   0  -0.380  -2.0481  -0.6596   0.0253
 NLY  C2   C  C     0   0.517  -3.3286   0.1353   0.0385
 NLY  O    O  O     0  -0.440  -3.3989   1.3356   0.1060
 NLY  H1   H  HNH1  0   0.345  -0.9012   0.7916   0.8280
 NLY  H3   H  HCH2  0   0.191   0.4326  -1.2599   0.8275
 NLY  H4   H  HCH2  0   0.218   0.3672  -1.1629  -0.9250
 NLY  H5   H  HCH2  0   0.219   1.4932   1.0444  -0.8746
 NLY  H6   H  HCH2  0   0.216   1.5110   1.0150   0.8795
 NLY  H7   H  HCH2  0   0.213   2.9302  -1.0400   0.8441
 NLY  H8   H  HCH2  0   0.215   2.9240  -1.0264  -0.9099
 NLY  H9   H  HCH2  0   0.212   4.0489   1.1723  -0.9273
 NLY  H10  H  HCH2  0   0.187   3.9925   1.2408   0.8244
 NLY  H11  H  HNH2  0   0.345   6.1065   0.4343  -0.0852
 NLY  H12  H  HNH2  0   0.337   5.4235  -0.6898   0.8461
 NLY  H14  H  HCH2  0   0.272  -2.0484  -1.2879  -0.8715
 NLY  H15  H  HCH2  0   0.245  -2.0797  -1.3604   0.8759
 NLY  OXT  O  OH1   0  -0.596  -4.3905  -0.6610  -0.0191
 NLY  H2   H  HOH1  0   0.483  -5.2031  -0.1340   0.0038

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  1.520  0.020  1.520
 NLY  CB   N    single  1.451  0.020  1.451
 NLY  N    CA   single  1.451  0.016  1.451
 NLY  CA   C2   single  1.507  0.020  1.507
 NLY  O    C2   double  1.204  0.020  1.204
 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  single  1.329  0.020  1.329
 NLY  OXT  H2   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
 NLY  H1   N    CA   109.37  3.000
 NLY  H1   N    CB   108.95  3.000
 NLY  CA   N    CB   112.34  3.000
 NLY  H4   CB   H3   106.12  3.000
 NLY  H4   CB   CG   109.34  3.000
 NLY  H3   CB   CG   109.30  3.000
 NLY  H4   CB   N    108.28  3.000
 NLY  H3   CB   N    112.50  3.000
 NLY  CG   CB   N    111.13  3.000
 NLY  H6   CG   H5   106.45  3.000
 NLY  H6   CG   CD   109.42  3.000
 NLY  H5   CG   CD   109.93  3.000
 NLY  H6   CG   CB   109.20  3.000
 NLY  H5   CG   CB   109.11  3.000
 NLY  CD   CG   CB   112.54  3.000
 NLY  H8   CD   H7   106.40  3.000
 NLY  H8   CD   CE   109.07  3.000
 NLY  H7   CD   CE   109.20  3.000
 NLY  H8   CD   CG   109.97  3.000
 NLY  H7   CD   CG   109.44  3.000
 NLY  CE   CD   CG   112.56  3.000
 NLY  H10  CE   H9   106.18  3.000
 NLY  H10  CE   NZ   113.46  3.000
 NLY  H9   CE   NZ   108.24  3.000
 NLY  H10  CE   CD   108.75  3.000
 NLY  H9   CE   CD   108.99  3.000
 NLY  NZ   CE   CD   111.02  3.000
 NLY  H12  NZ   H11  105.47  3.000
 NLY  H12  NZ   CE   109.07  3.000
 NLY  H11  NZ   CE   109.48  3.000
 NLY  H15  CA   H14  105.49  3.000
 NLY  H15  CA   C2   107.70  3.000
 NLY  H14  CA   C2   108.03  3.000
 NLY  H15  CA   N    114.25  3.000
 NLY  H14  CA   N    109.37  3.000
 NLY  C2   CA   N    111.65  3.000
 NLY  OXT  C2   O    123.59  3.000
 NLY  OXT  C2   CA   111.26  3.000
 NLY  O    C2   CA   125.15  3.000
 NLY  H2   OXT  C2   110.08  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  CONST_01  H2   OXT  C2  CA   180.00   0.0  0
 NLY  Var_01    CD   CG   CB  N    179.79  30.0  1
 NLY  Var_02    O    C2   CA  N     -4.12  30.0  3
 NLY  Var_03    CE   CD   CG  CB   179.81  30.0  1
 NLY  Var_04    C2   CA   N   CB  -179.57  30.0  3
 NLY  Var_05    NZ   CE   CD  CG   179.66  30.0  1
 NLY  Var_06    CA   N    CB  CG  -179.06  30.0  3
 NLY  Var_07    H11  NZ   CE  CD   177.13  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
 NLY  plan-1  H2   0.020

