# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:42:12 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 5-amino-N-hydroxypentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCC(=O)NO
#
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
 5XA  5XA  5-amino-N-hydroxypentanamide  ligand  21  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5XA
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
 5XA  O8   O  OH1   0  -0.545  -3.9065   0.0148   0.5313
 5XA  N7   N  NH1   0  -0.376  -2.6804   0.5966   0.4252
 5XA  C6   C  C     0   0.531  -1.6993  -0.0013  -0.2743
 5XA  O9   O  O     0  -0.484  -1.8720  -1.0116  -0.9353
 5XA  C5   C  CH2   0  -0.580  -0.3753   0.7238  -0.2005
 5XA  C4   C  CH2   0  -0.423   0.8012  -0.2286  -0.0178
 5XA  C3   C  CH2   0  -0.427   2.1355   0.5054  -0.0286
 5XA  C2   C  CH2   0  -0.271   3.3185  -0.4366   0.1317
 5XA  N1   N  NH2   0  -0.801   4.5769   0.2960   0.1048
 5XA  H1   H  HOH1  0   0.477  -4.4515   0.4017  -0.1662
 5XA  H2   H  HNH1  0   0.414  -2.5138   1.3628   1.0606
 5XA  H3   H  HCH2  0   0.268  -0.2562   1.2751  -1.1388
 5XA  H4   H  HCH2  0   0.251  -0.3801   1.4735   0.5947
 5XA  H5   H  HCH2  0   0.227   0.6903  -0.7732   0.9251
 5XA  H6   H  HCH2  0   0.227   0.7886  -0.9780  -0.8126
 5XA  H7   H  HCH2  0   0.214   2.2360   1.0564  -0.9709
 5XA  H8   H  HCH2  0   0.217   2.1602   1.2526   0.7706
 5XA  H9   H  HCH2  0   0.212   3.2409  -0.9461   1.0964
 5XA  H10  H  HCH2  0   0.188   3.2531  -1.2224  -0.6353
 5XA  H11  H  HNH2  0   0.345   5.3440  -0.3489   0.2462
 5XA  H12  H  HNH2  0   0.337   4.7159   0.6804  -0.8220

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
 5XA  N1  C2   single  1.456  0.020  1.456
 5XA  C2  C3   single  1.521  0.020  1.521
 5XA  C3  C4   single  1.523  0.020  1.523
 5XA  C4  C5   single  1.525  0.020  1.525
 5XA  C5  C6   single  1.511  0.020  1.511
 5XA  N7  C6   single  1.345  0.020  1.345
 5XA  N7  O8   single  1.361  0.020  1.361
 5XA  C6  O9   double  1.220  0.020  1.220
 5XA  O8  H1   single  0.850  0.020  0.980
 5XA  N7  H2   single  0.860  0.020  1.020
 5XA  C5  H3   single  0.970  0.020  1.090
 5XA  C5  H4   single  0.970  0.020  1.090
 5XA  C4  H5   single  0.970  0.020  1.090
 5XA  C4  H6   single  0.970  0.020  1.090
 5XA  C3  H7   single  0.970  0.020  1.090
 5XA  C3  H8   single  0.970  0.020  1.090
 5XA  C2  H9   single  0.970  0.020  1.090
 5XA  C2  H10  single  0.970  0.020  1.090
 5XA  N1  H11  single  0.890  0.020  1.040
 5XA  N1  H12  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
 5XA  H1   O8  N7   106.30  3.000
 5XA  H2   N7  C6   122.99  3.000
 5XA  H2   N7  O8   115.09  3.000
 5XA  C6   N7  O8   120.50  3.000
 5XA  C5   C6  O9   123.23  3.000
 5XA  O9   C6  N7   123.14  3.000
 5XA  C5   C6  N7   113.60  3.000
 5XA  H4   C5  H3   106.17  3.000
 5XA  H4   C5  C4   110.16  3.000
 5XA  H3   C5  C4   109.47  3.000
 5XA  H4   C5  C6   111.15  3.000
 5XA  H3   C5  C6   107.16  3.000
 5XA  C4   C5  C6   112.47  3.000
 5XA  H6   C4  H5   106.51  3.000
 5XA  H6   C4  C3   109.61  3.000
 5XA  H5   C4  C3   109.55  3.000
 5XA  H6   C4  C5   109.41  3.000
 5XA  H5   C4  C5   109.62  3.000
 5XA  C3   C4  C5   111.97  3.000
 5XA  H8   C3  H7   106.41  3.000
 5XA  H8   C3  C2   109.17  3.000
 5XA  H7   C3  C2   109.31  3.000
 5XA  H8   C3  C4   110.11  3.000
 5XA  H7   C3  C4   109.19  3.000
 5XA  C2   C3  C4   112.47  3.000
 5XA  H10  C2  H9   106.15  3.000
 5XA  H10  C2  N1   113.44  3.000
 5XA  H9   C2  N1   108.18  3.000
 5XA  H10  C2  C3   108.83  3.000
 5XA  H9   C2  C3   109.04  3.000
 5XA  N1   C2  C3   111.02  3.000
 5XA  H12  N1  H11  105.40  3.000
 5XA  H12  N1  C2   109.05  3.000
 5XA  H11  N1  C2   109.38  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
 5XA  CONST_01  C5   C6  N7  O8   180.00   0.0  0
 5XA  CONST_02  O9   C6  N7  O8     0.00   0.0  0
 5XA  CONST_03  H2   N7  C6  O9   180.00   0.0  0
 5XA  Var_01    C4   C5  C6  N7   137.58  30.0  1
 5XA  Var_02    C3   C4  C5  C6   176.58  30.0  1
 5XA  Var_03    C2   C3  C4  C5  -179.13  30.0  1
 5XA  Var_04    N1   C2  C3  C4   179.48  30.0  1
 5XA  Var_05    H11  N1  C2  C3   178.00  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
 5XA  plan-1  O8  0.020
 5XA  plan-1  N7  0.020
 5XA  plan-1  C6  0.020
 5XA  plan-1  O9  0.020
 5XA  plan-1  C5  0.020
 5XA  plan-1  H2  0.020

