# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:30:41 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 2-oxidanylidenehexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(=O)C(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
 7N5  7N5  '2-oxidanylidenehexanoic acid'  ligand  18  9  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7N5
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
 7N5  C4  C  CH2    0  -0.546   0.4244  -0.4666   0.0191
 7N5  C2  C  CH2    0  -0.419   2.9458  -0.6174  -0.0083
 7N5  C3  C  CH2    0  -0.406   1.7330   0.3052   0.0309
 7N5  C5  C  C      0   0.236  -0.8149   0.3859   0.0565
 7N5  C1  C  CH3    0  -0.662   4.2618   0.1478  -0.0063
 7N5  C6  C  C      0   0.344  -2.1894  -0.3449  -0.0046
 7N5  O7  O  O      0  -0.579  -2.1389  -1.5866   0.0209
 7N5  O8  O  OC    -1  -0.585  -3.1848   0.3895  -0.0712
 7N5  O9  O  O      0  -0.400  -0.7660   1.5921   0.1323
 7N5  H1  H  HCH2   0   0.253   0.3642  -1.1115  -0.8644
 7N5  H2  H  HCH2   0   0.255   0.3777  -1.1615   0.8649
 7N5  H3  H  HCH2   0   0.212   2.9135  -1.2963   0.8495
 7N5  H4  H  HCH2   0   0.212   2.8912  -1.2522  -0.8982
 7N5  H5  H  HCH2   0   0.214   1.7723   0.9869  -0.8238
 7N5  H6  H  HCH2   0   0.214   1.7883   0.9353   0.9235
 7N5  H7  H  HCH3   0   0.216   4.3331   0.8101  -0.8714
 7N5  H8  H  HCH3   0   0.216   4.3550   0.7662   0.8886
 7N5  H9  H  HCH3   0   0.226   5.1199  -0.5246  -0.0339

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
 7N5  O7  C6  deloc   1.243  0.020  1.243
 7N5  C6  O8  deloc   1.239  0.020  1.239
 7N5  C6  C5  single  1.558  0.020  1.558
 7N5  C4  C5  single  1.505  0.020  1.505
 7N5  C4  C3  single  1.519  0.020  1.519
 7N5  C5  O9  double  1.210  0.020  1.210
 7N5  C2  C3  single  1.524  0.020  1.524
 7N5  C2  C1  single  1.522  0.020  1.522
 7N5  C4  H1  single  0.970  0.020  1.090
 7N5  C4  H2  single  0.970  0.020  1.090
 7N5  C2  H3  single  0.970  0.020  1.090
 7N5  C2  H4  single  0.970  0.020  1.090
 7N5  C3  H5  single  0.970  0.020  1.090
 7N5  C3  H6  single  0.970  0.020  1.090
 7N5  C1  H7  single  0.970  0.020  1.090
 7N5  C1  H8  single  0.970  0.020  1.090
 7N5  C1  H9  single  0.970  0.020  1.090

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
 7N5  H2  C4  H1  104.29  3.000
 7N5  H2  C4  C5  107.76  3.000
 7N5  H1  C4  C5  107.96  3.000
 7N5  H2  C4  C3  110.67  3.000
 7N5  H1  C4  C3  110.65  3.000
 7N5  C5  C4  C3  114.92  3.000
 7N5  H4  C2  H3  106.02  3.000
 7N5  H4  C2  C1  109.62  3.000
 7N5  H3  C2  C1  109.65  3.000
 7N5  H4  C2  C3  109.41  3.000
 7N5  H3  C2  C3  109.38  3.000
 7N5  C1  C2  C3  112.55  3.000
 7N5  H6  C3  H5  106.07  3.000
 7N5  H6  C3  C2  109.23  3.000
 7N5  H5  C3  C2  109.18  3.000
 7N5  H6  C3  C4  110.03  3.000
 7N5  H5  C3  C4  109.97  3.000
 7N5  C2  C3  C4  112.18  3.000
 7N5  O9  C5  C6  120.39  3.000
 7N5  O9  C5  C4  122.22  3.000
 7N5  C6  C5  C4  117.39  3.000
 7N5  H9  C1  H8  107.62  3.000
 7N5  H9  C1  H7  107.61  3.000
 7N5  H8  C1  H7  107.48  3.000
 7N5  H9  C1  C2  111.73  3.000
 7N5  H8  C1  C2  111.08  3.000
 7N5  H7  C1  C2  111.12  3.000
 7N5  O8  C6  O7  128.75  3.000
 7N5  O8  C6  C5  115.65  3.000
 7N5  O7  C6  C5  115.59  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
 7N5  Var_01  O7  C6  C5  C4    5.15  30.0  2
 7N5  Var_02  C1  C2  C3  C4  179.61  30.0  1
 7N5  Var_03  C5  C4  C3  C2  179.99  30.0  1
 7N5  Var_04  C6  C5  C4  C3  177.88  30.0  3
 7N5  Var_05  H7  C1  C2  C3  -59.83  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
 7N5  plan-1  C4  0.020
 7N5  plan-1  C5  0.020
 7N5  plan-1  C6  0.020
 7N5  plan-1  O9  0.020
 7N5  plan-2  C5  0.020
 7N5  plan-2  C6  0.020
 7N5  plan-2  O7  0.020
 7N5  plan-2  O8  0.020

