# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 03:00:23 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 4-oxidanylidene-4-(6-oxidanylidene-1~{H}-pyridin-3-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)C1=CNC(=O)C=C1
#
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
 6HY  6HY  '4-oxidanylidene-4-(6-oxidanylidene-1~{H}-pyridin-3-yl)butanoic acid'  ligand  22  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6HY
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
 6HY  O3  O  OC    -1  -0.629  -5.1589  -0.0734   0.0107
 6HY  C8  C  C      0   0.420  -4.0189   0.4356   0.0228
 6HY  O2  O  O      0  -0.606  -3.7524   1.6532   0.0295
 6HY  C3  C  CH2    0  -0.586  -2.8467  -0.5630   0.0282
 6HY  C   C  CH2    0  -0.576  -1.4704   0.0735   0.0273
 6HY  C1  C  C      0   0.375  -0.3311  -0.9113   0.0321
 6HY  O   O  O      0  -0.418  -0.5136  -2.1140   0.0358
 6HY  C2  C  CR6    0  -0.170   1.0453  -0.3670   0.0372
 6HY  C5  C  CR16   0  -0.141   1.3617   1.0200   0.0234
 6HY  C6  C  CR16   0  -0.452   2.6459   1.4579   0.0284
 6HY  C7  C  CR6    0   0.539   3.7537   0.5397   0.0500
 6HY  O1  O  O      0  -0.490   4.9410   0.8365   0.0558
 6HY  N   N  NR16   0  -0.653   3.3659  -0.7958   0.0610
 6HY  C4  C  CR16   0   0.092   2.1021  -1.2358   0.0551
 6HY  H2  H  HCH2   0   0.231  -2.9586  -1.2156   0.8991
 6HY  H3  H  HCH2   0   0.231  -2.9566  -1.2226  -0.8374
 6HY  H4  H  HCH2   0   0.262  -1.3511   0.7292  -0.8412
 6HY  H5  H  HCH2   0   0.262  -1.3533   0.7367   0.8902
 6HY  H6  H  HCR6   0   0.280   0.5682   1.7552   0.0080
 6HY  H7  H  HCR6   0   0.281   2.8722   2.5151   0.0164
 6HY  H9  H  HCR6   0   0.318   1.9764  -2.3089   0.0660
 6HY  H8  H  HNR6   0   0.430   4.1103  -1.4813   0.0763

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
 6HY  N   C4  single  1.338  0.020  1.338
 6HY  N   C7  single  1.391  0.020  1.391
 6HY  O1  C7  double  1.224  0.020  1.224
 6HY  C4  C2  double  1.368  0.020  1.368
 6HY  C7  C6  single  1.439  0.020  1.439
 6HY  O   C1  double  1.216  0.020  1.216
 6HY  C2  C1  single  1.480  0.020  1.480
 6HY  C2  C5  single  1.423  0.020  1.423
 6HY  C6  C5  double  1.357  0.020  1.357
 6HY  C1  C   single  1.506  0.020  1.506
 6HY  C   C3  single  1.516  0.020  1.516
 6HY  C3  C8  single  1.540  0.020  1.540
 6HY  C8  O2  deloc   1.246  0.020  1.246
 6HY  C8  O3  deloc   1.249  0.020  1.249
 6HY  C3  H2  single  0.970  0.020  1.090
 6HY  C3  H3  single  0.970  0.020  1.090
 6HY  C   H4  single  0.970  0.020  1.090
 6HY  C   H5  single  0.970  0.020  1.090
 6HY  C5  H6  single  0.930  0.020  1.080
 6HY  C6  H7  single  0.930  0.020  1.080
 6HY  C4  H9  single  0.930  0.020  1.080
 6HY  N   H8  single  0.860  0.020  1.020

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
 6HY  C3  C8  O2  118.08  3.000
 6HY  O2  C8  O3  126.41  3.000
 6HY  C3  C8  O3  115.52  3.000
 6HY  H3  C3  H2  105.07  3.000
 6HY  H3  C3  C   110.11  3.000
 6HY  H2  C3  C   110.11  3.000
 6HY  H3  C3  C8  108.16  3.000
 6HY  H2  C3  C8  108.17  3.000
 6HY  C   C3  C8  114.76  3.000
 6HY  H5  C   H4  104.53  3.000
 6HY  H5  C   C1  108.22  3.000
 6HY  H4  C   C1  108.17  3.000
 6HY  H5  C   C3  110.55  3.000
 6HY  H4  C   C3  110.54  3.000
 6HY  C1  C   C3  114.34  3.000
 6HY  C2  C1  O   120.20  3.000
 6HY  C2  C1  C   117.59  3.000
 6HY  O   C1  C   122.21  3.000
 6HY  C4  C2  C5  116.58  3.000
 6HY  C5  C2  C1  124.42  3.000
 6HY  C4  C2  C1  119.00  3.000
 6HY  H6  C5  C6  118.36  3.000
 6HY  H6  C5  C2  119.97  3.000
 6HY  C6  C5  C2  121.67  3.000
 6HY  H7  C6  C7  117.58  3.000
 6HY  H7  C6  C5  120.91  3.000
 6HY  C7  C6  C5  121.52  3.000
 6HY  N   C7  O1  120.22  3.000
 6HY  O1  C7  C6  126.31  3.000
 6HY  N   C7  C6  113.47  3.000
 6HY  H8  N   C4  118.16  3.000
 6HY  H8  N   C7  116.45  3.000
 6HY  C4  N   C7  125.38  3.000
 6HY  H9  C4  N   115.88  3.000
 6HY  H9  C4  C2  122.74  3.000
 6HY  N   C4  C2  121.38  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
 6HY  CONST_01  C4  N   C7  C6     0.00   0.0  0
 6HY  CONST_02  C4  N   C7  O1   180.00   0.0  0
 6HY  CONST_03  H8  N   C7  C6   180.00   0.0  0
 6HY  Var_01    C4  C2  C1  C    179.35  30.0  2
 6HY  Var_02    C2  C1  C   C3  -179.75  30.0  1
 6HY  Var_03    C   C3  C8  O3   179.35  30.0  2
 6HY  Var_04    C1  C   C3  C8  -179.98  30.0  2

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
 6HY  plan-1  C1  0.020
 6HY  plan-1  C2  0.020
 6HY  plan-1  C5  0.020
 6HY  plan-1  C6  0.020
 6HY  plan-1  C7  0.020
 6HY  plan-1  O1  0.020
 6HY  plan-1  N   0.020
 6HY  plan-1  C4  0.020
 6HY  plan-1  H6  0.020
 6HY  plan-1  H7  0.020
 6HY  plan-1  H9  0.020
 6HY  plan-1  H8  0.020
 6HY  plan-2  C   0.020
 6HY  plan-2  C1  0.020
 6HY  plan-2  O   0.020
 6HY  plan-2  C2  0.020
 6HY  plan-3  O3  0.020
 6HY  plan-3  C8  0.020
 6HY  plan-3  O2  0.020
 6HY  plan-3  C3  0.020

