# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:30:33 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  19  9  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.560   0.4103  -0.4795  -0.0030
 7N5  C2   C  CH2   0  -0.422   2.9259  -0.6384  -0.0150
 7N5  C3   C  CH2   0  -0.412   1.7189   0.2924   0.0006
 7N5  C5   C  C     0   0.294  -0.8098   0.3839   0.0189
 7N5  C1   C  CH3   0  -0.662   4.2436   0.1234  -0.0120
 7N5  C6   C  C     0   0.482  -2.1549  -0.3649   0.0100
 7N5  O7   O  O     0  -0.405  -2.2284  -1.5645  -0.0119
 7N5  O8   O  OH1   0  -0.571  -3.1731   0.4661   0.0295
 7N5  O9   O  O     0  -0.348  -0.8057   1.5859   0.0433
 7N5  H1   H  HCH2  0   0.281   0.3457  -1.1349  -0.8790
 7N5  H2   H  HCH2  0   0.281   0.3566  -1.1587   0.8558
 7N5  H3   H  HCH2  0   0.217   2.8827  -1.3038   0.8524
 7N5  H4   H  HCH2  0   0.217   2.8757  -1.2845  -0.8966
 7N5  H5   H  HCH2  0   0.227   1.7627   0.9561  -0.8675
 7N5  H6   H  HCH2  0   0.227   1.7697   0.9355   0.8834
 7N5  H7   H  HCH3  0   0.218   4.3249   0.7721  -0.8863
 7N5  H8   H  HCH3  0   0.218   4.3311   0.7542   0.8748
 7N5  H9   H  HCH3  0   0.229   5.0985  -0.5533  -0.0218
 7N5  H10  H  HOH1  0   0.493  -4.0099  -0.0245   0.0260

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   double  1.202  0.020  1.202
 7N5  C6  O8   single  1.314  0.020  1.314
 7N5  C6  C5   single  1.540  0.020  1.540
 7N5  C4  C5   single  1.495  0.020  1.495
 7N5  C4  C3   single  1.519  0.020  1.519
 7N5  C5  O9   double  1.202  0.020  1.202
 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
 7N5  O8  H10  single  0.850  0.020  0.980

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  104.64  3.000
 7N5  H2   C4  C5  107.85  3.000
 7N5  H1   C4  C5  108.00  3.000
 7N5  H2   C4  C3  110.80  3.000
 7N5  H1   C4  C3  110.88  3.000
 7N5  C5   C4  C3  114.18  3.000
 7N5  H4   C2  H3  106.13  3.000
 7N5  H4   C2  C1  109.69  3.000
 7N5  H3   C2  C1  109.69  3.000
 7N5  H4   C2  C3  109.42  3.000
 7N5  H3   C2  C3  109.39  3.000
 7N5  C1   C2  C3  112.33  3.000
 7N5  H6   C3  H5  106.39  3.000
 7N5  H6   C3  C2  109.31  3.000
 7N5  H5   C3  C2  109.31  3.000
 7N5  H6   C3  C4  109.92  3.000
 7N5  H5   C3  C4  109.94  3.000
 7N5  C2   C3  C4  111.83  3.000
 7N5  O9   C5  C6  119.30  3.000
 7N5  O9   C5  C4  125.10  3.000
 7N5  C6   C5  C4  115.60  3.000
 7N5  H9   C1  H8  107.64  3.000
 7N5  H9   C1  H7  107.65  3.000
 7N5  H8   C1  H7  107.53  3.000
 7N5  H9   C1  C2  111.60  3.000
 7N5  H8   C1  C2  111.11  3.000
 7N5  H7   C1  C2  111.12  3.000
 7N5  O8   C6  O7  125.72  3.000
 7N5  O8   C6  C5  111.67  3.000
 7N5  O7   C6  C5  122.61  3.000
 7N5  H10  O8  C6  110.39  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  CONST_01  H10  O8  C6  C5  180.00   0.0  0
 7N5  Var_01    O7   C6  C5  C4    0.07  30.0  2
 7N5  Var_02    C1   C2  C3  C4  179.98  30.0  1
 7N5  Var_03    C5   C4  C3  C2  179.71  30.0  1
 7N5  Var_04    C6   C5  C4  C3  179.75  30.0  3
 7N5  Var_05    H7   C1  C2  C3  -59.91  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
 7N5  plan-2  H10  0.020

