# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 06:00:19 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 5-azanylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCC(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
 KFB  KFB  '5-azanylpentanoic acid   '  ligand  19  8  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KFB
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
 KFB  CA   C  CH2   0  -0.578   0.9062  -0.6577  -0.0274
 KFB  CB   C  CH2   0  -0.424  -0.2890   0.2805   0.0026
 KFB  CG   C  CH2   0  -0.427  -1.6050  -0.4857  -0.0340
 KFB  CD   C  CH2   0  -0.272  -2.8154   0.4349  -0.0119
 KFB  C    C  C     0   0.550   2.2351   0.0429   0.0226
 KFB  O    O  O     0  -0.446   2.3938   1.2375   0.0735
 KFB  O1   O  OH1   0  -0.598   3.2486  -0.8193   0.0039
 KFB  H4   H  HCH2  0   0.275   0.8609  -1.3624   0.8092
 KFB  H5   H  HCH2  0   0.226  -0.2515   0.8996   0.9033
 KFB  H6   H  HCH2  0   0.226  -0.2428   0.9674  -0.8470
 KFB  H7   H  HCH2  0   0.217  -1.6485  -1.1131  -0.9301
 KFB  H8   H  HCH2  0   0.215  -1.6540  -1.1673   0.8230
 KFB  H9   H  HCH2  0   0.188  -2.7349   1.1059   0.8559
 KFB  H11  H  HCH2  0   0.213  -2.7901   1.0763  -0.8972
 KFB  H12  H  HOH1  0   0.478   4.0904  -0.3405   0.0304
 KFB  N1   N  NH2   0  -0.801  -4.0528  -0.3323  -0.0391
 KFB  H1   H  HCH2  0   0.276   0.8844  -1.2776  -0.9297
 KFB  H2   H  HNH2  0   0.337  -4.1470  -0.8383   0.8335
 KFB  H3   H  HNH2  0   0.345  -4.8424   0.2998  -0.0710

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
 KFB  O   C    double  1.206  0.020  1.206
 KFB  C   CA   single  1.503  0.020  1.503
 KFB  CA  CB   single  1.520  0.020  1.520
 KFB  CB  CG   single  1.523  0.020  1.523
 KFB  CG  CD   single  1.521  0.020  1.521
 KFB  C   O1   single  1.331  0.020  1.331
 KFB  CA  H4   single  0.970  0.020  1.090
 KFB  CB  H5   single  0.970  0.020  1.090
 KFB  CB  H6   single  0.970  0.020  1.090
 KFB  CG  H7   single  0.970  0.020  1.090
 KFB  CG  H8   single  0.970  0.020  1.090
 KFB  CD  H9   single  0.970  0.020  1.090
 KFB  CD  N1   single  1.456  0.020  1.456
 KFB  CD  H11  single  0.970  0.020  1.090
 KFB  O1  H12  single  0.850  0.020  0.980
 KFB  CA  H1   single  0.970  0.020  1.090
 KFB  N1  H2   single  0.890  0.020  1.040
 KFB  N1  H3   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
 KFB  H1   CA  H4   105.33  3.000
 KFB  H1   CA  C    107.99  3.000
 KFB  H4   CA  C    108.13  3.000
 KFB  H1   CA  CB   110.50  3.000
 KFB  H4   CA  CB   110.47  3.000
 KFB  C    CA  CB   114.01  3.000
 KFB  H6   CB  H5   106.43  3.000
 KFB  H6   CB  CG   109.50  3.000
 KFB  H5   CB  CG   109.53  3.000
 KFB  H6   CB  CA   109.82  3.000
 KFB  H5   CB  CA   109.80  3.000
 KFB  CG   CB  CA   111.62  3.000
 KFB  H8   CG  H7   106.37  3.000
 KFB  H8   CG  CD   109.24  3.000
 KFB  H7   CG  CD   109.09  3.000
 KFB  H8   CG  CB   109.43  3.000
 KFB  H7   CG  CB   110.02  3.000
 KFB  CD   CG  CB   112.50  3.000
 KFB  N1   CD  H11  108.27  3.000
 KFB  H11  CD  H9   106.21  3.000
 KFB  N1   CD  H9   113.48  3.000
 KFB  H11  CD  CG   108.96  3.000
 KFB  N1   CD  CG   110.92  3.000
 KFB  H9   CD  CG   108.81  3.000
 KFB  O1   C   O    122.83  3.000
 KFB  O1   C   CA   111.77  3.000
 KFB  O    C   CA   125.40  3.000
 KFB  H12  O1  C    109.95  3.000
 KFB  H3   N1  H2   105.46  3.000
 KFB  H3   N1  CD   109.55  3.000
 KFB  H2   N1  CD   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
 KFB  CONST_01  H12  O1  C   CA   180.00   0.0  0
 KFB  Var_01    CD   CG  CB  CA  -179.71  30.0  3
 KFB  Var_02    O    C   CA  CB    -0.48  30.0  2
 KFB  Var_03    N1   CD  CG  CB  -179.63  30.0  3
 KFB  Var_04    C    CA  CB  CG  -179.34  30.0  1
 KFB  Var_05    H2   N1  CD  CG    67.90  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
 KFB  plan-1  CA   0.020
 KFB  plan-1  C    0.020
 KFB  plan-1  O    0.020
 KFB  plan-1  O1   0.020
 KFB  plan-1  H12  0.020

