# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 17:51:23 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (3~{S})-3-azanylazepan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCCCNC1=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
 8F4  8F4  (3~{S})-3-azanylazepan-2-one  ligand  21  9  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8F4
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
 8F4  O    O  O     0  -0.500  -1.8335   1.3198  -0.5696
 8F4  C    C  C     0   0.490  -0.8381   0.8121  -0.0661
 8F4  NZ   N  NH1   0  -0.609   0.2997   1.5054   0.0973
 8F4  CE   C  CH2   0  -0.311   1.5620   1.0113   0.6138
 8F4  CD   C  CH2   0  -0.429   2.2194  -0.0466  -0.2635
 8F4  CG   C  CH2   0  -0.442   1.5702  -1.4205  -0.1600
 8F4  CB   C  CH2   0  -0.439   0.0903  -1.4844  -0.5187
 8F4  CA   C  CH1   0  -0.205  -0.8322  -0.6512   0.3862
 8F4  N    N  NH2   0  -0.778  -2.1562  -1.2374   0.4152
 8F4  H1   H  HNH1  0   0.391   0.2895   2.4523  -0.2501
 8F4  H2   H  HCH2  0   0.267   2.2146   1.8789   0.6926
 8F4  H3   H  HCH2  0   0.237   1.4358   0.6306   1.6326
 8F4  H4   H  HCH2  0   0.226   2.2223   0.3023  -1.3003
 8F4  H5   H  HCH2  0   0.236   3.2661  -0.1344   0.0379
 8F4  H6   H  HCH2  0   0.238   2.1128  -2.1187  -0.8016
 8F4  H7   H  HCH2  0   0.220   1.6959  -1.7894   0.8636
 8F4  H8   H  HCH2  0   0.228  -0.0617  -1.2031  -1.5662
 8F4  H9   H  HCH2  0   0.245  -0.2380  -2.5217  -0.4284
 8F4  H10  H  HCH1  0   0.251  -0.4353  -0.6953   1.4076
 8F4  H11  H  HNH2  0   0.345  -2.7537  -0.7043   1.0352
 8F4  H12  H  HNH2  0   0.338  -2.5795  -1.1511  -0.5013

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
 8F4  N   CA   single  1.448  0.020  1.448
 8F4  O   C    double  1.226  0.020  1.226
 8F4  CA  C    single  1.532  0.020  1.532
 8F4  CA  CB   single  1.538  0.020  1.538
 8F4  C   NZ   single  1.342  0.020  1.342
 8F4  NZ  CE   single  1.451  0.020  1.451
 8F4  CB  CG   single  1.524  0.020  1.524
 8F4  CG  CD   single  1.523  0.020  1.523
 8F4  CE  CD   single  1.524  0.020  1.524
 8F4  NZ  H1   single  0.860  0.020  1.020
 8F4  CE  H2   single  0.970  0.020  1.090
 8F4  CE  H3   single  0.970  0.020  1.090
 8F4  CD  H4   single  0.970  0.020  1.090
 8F4  CD  H5   single  0.970  0.020  1.090
 8F4  CG  H6   single  0.970  0.020  1.090
 8F4  CG  H7   single  0.970  0.020  1.090
 8F4  CB  H8   single  0.970  0.020  1.090
 8F4  CB  H9   single  0.970  0.020  1.090
 8F4  CA  H10  single  0.970  0.020  1.090
 8F4  N   H11  single  0.890  0.020  1.040
 8F4  N   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
 8F4  CA   C   NZ   117.02  3.000
 8F4  NZ   C   O    121.63  3.000
 8F4  CA   C   O    121.34  3.000
 8F4  H1   NZ  CE   116.82  3.000
 8F4  H1   NZ  C    115.75  3.000
 8F4  CE   NZ  C    127.23  3.000
 8F4  H3   CE  H2   106.19  3.000
 8F4  H3   CE  CD   110.13  3.000
 8F4  H2   CE  CD   109.66  3.000
 8F4  H3   CE  NZ   110.46  3.000
 8F4  H2   CE  NZ   106.02  3.000
 8F4  CD   CE  NZ   114.01  3.000
 8F4  H5   CD  H4   106.53  3.000
 8F4  H5   CD  CG   108.48  3.000
 8F4  H4   CD  CG   110.69  3.000
 8F4  H5   CD  CE   108.07  3.000
 8F4  H4   CD  CE   108.99  3.000
 8F4  CG   CD  CE   113.78  3.000
 8F4  H7   CG  H6   106.06  3.000
 8F4  H7   CG  CB   108.50  3.000
 8F4  H6   CG  CB   108.50  3.000
 8F4  H7   CG  CD   108.56  3.000
 8F4  H6   CG  CD   108.96  3.000
 8F4  CB   CG  CD   115.83  3.000
 8F4  H9   CB  H8   106.34  3.000
 8F4  H9   CB  CA   106.60  3.000
 8F4  H8   CB  CA   109.91  3.000
 8F4  H9   CB  CG   108.20  3.000
 8F4  H8   CB  CG   110.43  3.000
 8F4  CA   CB  CG   114.92  3.000
 8F4  H10  CA  N    107.21  3.000
 8F4  H10  CA  CB   108.01  3.000
 8F4  N    CA  CB   109.93  3.000
 8F4  H10  CA  C    108.35  3.000
 8F4  CB   CA  C    110.26  3.000
 8F4  N    CA  C    112.90  3.000
 8F4  H12  N   H11  105.21  3.000
 8F4  H12  N   CA   109.23  3.000
 8F4  H11  N   CA   109.79  3.000

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 8F4  chir_01  CA  N  C  CB  positiv

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
 8F4  plan-1  O   0.020
 8F4  plan-1  C   0.020
 8F4  plan-1  NZ  0.020
 8F4  plan-1  CE  0.020
 8F4  plan-1  CA  0.020
 8F4  plan-1  H1  0.020

