# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 05:02:18 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  18  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  -0.579   0.9252  -0.6724  -0.0704
 KFB  CB   C  CH2    0  -0.407  -0.2685   0.2675  -0.0109
 KFB  CG   C  CH2    0  -0.422  -1.5992  -0.4747  -0.0463
 KFB  CD   C  CH2    0  -0.271  -2.7996   0.4578   0.0052
 KFB  C    C  C      0   0.410   2.3148  -0.0116  -0.0430
 KFB  O    O  O      0  -0.610   2.3701   1.2319   0.0275
 KFB  O1   O  OC    -1  -0.635   3.2902  -0.7913  -0.0958
 KFB  H4   H  HCH2   0   0.216   0.8707  -1.3866   0.7599
 KFB  H5   H  HCH2   0   0.202  -0.2164   0.8761   0.8971
 KFB  H6   H  HCH2   0   0.201  -0.2257   0.9725  -0.8467
 KFB  H7   H  HCH2   0   0.206  -1.6619  -1.0858  -0.9532
 KFB  H8   H  HCH2   0   0.204  -1.6500  -1.1739   0.7970
 KFB  H9   H  HCH2   0   0.184  -2.7064   1.1075   0.8881
 KFB  H11  H  HCH2   0   0.208  -2.7713   1.1212  -0.8640
 KFB  N1   N  NH2    0  -0.801  -4.0487  -0.2912  -0.0335
 KFB  H1   H  HCH2   0   0.216   0.8603  -1.2901  -0.9743
 KFB  H2   H  HNH2   0   0.335  -4.1380  -0.8275   0.8214
 KFB  H3   H  HNH2   0   0.344  -4.8305   0.3516  -0.0311

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    deloc   1.247  0.020  1.247
 KFB  C   CA   single  1.539  0.020  1.539
 KFB  CA  CB   single  1.520  0.020  1.520
 KFB  CB  CG   single  1.524  0.020  1.524
 KFB  CG  CD   single  1.521  0.020  1.521
 KFB  C   O1   deloc   1.250  0.020  1.250
 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  1.457  0.020  1.457
 KFB  CD  H11  single  0.970  0.020  1.090
 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   104.73  3.000
 KFB  H1   CA  C    108.05  3.000
 KFB  H4   CA  C    108.12  3.000
 KFB  H1   CA  CB   109.51  3.000
 KFB  H4   CA  CB   109.52  3.000
 KFB  C    CA  CB   116.28  3.000
 KFB  H6   CB  H5   105.88  3.000
 KFB  H6   CB  CG   109.28  3.000
 KFB  H5   CB  CG   109.36  3.000
 KFB  H6   CB  CA   109.74  3.000
 KFB  H5   CB  CA   109.81  3.000
 KFB  CG   CB  CA   112.55  3.000
 KFB  H8   CG  H7   106.15  3.000
 KFB  H8   CG  CD   109.17  3.000
 KFB  H7   CG  CD   108.96  3.000
 KFB  H8   CG  CB   109.46  3.000
 KFB  H7   CG  CB   109.93  3.000
 KFB  CD   CG  CB   112.94  3.000
 KFB  N1   CD  H11  108.23  3.000
 KFB  H11  CD  H9   106.10  3.000
 KFB  N1   CD  H9   113.42  3.000
 KFB  H11  CD  CG   108.94  3.000
 KFB  N1   CD  CG   111.14  3.000
 KFB  H9   CD  CG   108.81  3.000
 KFB  O1   C   O    126.16  3.000
 KFB  O1   C   CA   115.85  3.000
 KFB  O    C   CA   117.99  3.000
 KFB  H3   N1  H2   105.43  3.000
 KFB  H3   N1  CD   109.61  3.000
 KFB  H2   N1  CD   108.98  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
 KFB  Var_01  CD  CG  CB  CA  -179.69  30.0  3
 KFB  Var_02  O   C   CA  CB     0.13  30.0  2
 KFB  Var_03  N1  CD  CG  CB   179.88  30.0  3
 KFB  Var_04  C   CA  CB  CG   179.87  30.0  1
 KFB  Var_05  H2  N1  CD  CG    67.06  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

