# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:31:43 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-[(1~{S})-2-oxidanylidenecyclopentyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H]1CCCC1=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
 7N0  7N0  '2-[(1~{S})-2-oxidanylidenecyclopentyl]ethanoic acid'  ligand  19  10  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7N0
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
 7N0  O3  O  O      0  -0.408  -0.1439  -1.6376   0.7907
 7N0  C4  C  C      0   0.408  -0.8940  -0.7724   0.4040
 7N0  C5  C  CH2    0  -0.561  -2.4010  -0.7826   0.5716
 7N0  C6  C  CH2    0  -0.457  -2.8856   0.4483  -0.1916
 7N0  C7  C  CH2    0  -0.436  -1.7001   1.4144  -0.1082
 7N0  C3  C  CH1    0  -0.351  -0.4790   0.5109  -0.2832
 7N0  C2  C  CH2    0  -0.566   0.8543   1.0550   0.1948
 7N0  C1  C  C      0   0.416   2.0811   0.2397  -0.2535
 7N0  O2  O  O      0  -0.615   2.0334  -0.2742  -1.3894
 7N0  O1  O  OC    -1  -0.626   3.0481   0.2048   0.5344
 7N0  H1  H  HCH2   0   0.272  -2.8378  -1.7288   0.2481
 7N0  H2  H  HCH2   0   0.270  -2.6095  -0.6850   1.6427
 7N0  H3  H  HCH2   0   0.231  -3.0782   0.1896  -1.2355
 7N0  H4  H  HCH2   0   0.242  -3.8058   0.8644   0.2168
 7N0  H5  H  HCH2   0   0.240  -1.7437   2.2067  -0.8557
 7N0  H6  H  HCH2   0   0.224  -1.6739   1.8931   0.8761
 7N0  H7  H  HCH1   0   0.270  -0.3907   0.2585  -1.3492
 7N0  H8  H  HCH2   0   0.238   0.9752   2.0686  -0.2068
 7N0  H9  H  HCH2   0   0.210   0.8467   1.1667   1.2825

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
 7N0  O3  C4  double  1.209  0.020  1.209
 7N0  C5  C4  single  1.516  0.020  1.516
 7N0  C5  C6  single  1.527  0.020  1.527
 7N0  C4  C3  single  1.514  0.020  1.514
 7N0  O2  C1  deloc   1.248  0.020  1.248
 7N0  O1  C1  deloc   1.248  0.020  1.248
 7N0  C1  C2  single  1.540  0.020  1.540
 7N0  C6  C7  single  1.532  0.020  1.532
 7N0  C3  C2  single  1.517  0.020  1.517
 7N0  C3  C7  single  1.529  0.020  1.529
 7N0  C5  H1  single  0.970  0.020  1.090
 7N0  C5  H2  single  0.970  0.020  1.090
 7N0  C6  H3  single  0.970  0.020  1.090
 7N0  C6  H4  single  0.970  0.020  1.090
 7N0  C7  H5  single  0.970  0.020  1.090
 7N0  C7  H6  single  0.970  0.020  1.090
 7N0  C3  H7  single  0.970  0.020  1.090
 7N0  C2  H8  single  0.970  0.020  1.090
 7N0  C2  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
 7N0  C3  C4  C5  109.17  3.000
 7N0  C3  C4  O3  125.59  3.000
 7N0  C5  C4  O3  125.21  3.000
 7N0  H2  C5  H1  106.91  3.000
 7N0  H2  C5  C6  110.88  3.000
 7N0  H1  C5  C6  115.07  3.000
 7N0  H2  C5  C4  107.25  3.000
 7N0  H1  C5  C4  111.77  3.000
 7N0  C6  C5  C4  104.76  3.000
 7N0  H4  C6  H3  107.44  3.000
 7N0  H4  C6  C7  113.11  3.000
 7N0  H3  C6  C7  109.74  3.000
 7N0  H4  C6  C5  112.86  3.000
 7N0  H3  C6  C5  110.03  3.000
 7N0  C7  C6  C5  103.63  3.000
 7N0  H6  C7  H5  107.44  3.000
 7N0  H6  C7  C3  110.01  3.000
 7N0  H5  C7  C3  112.52  3.000
 7N0  H6  C7  C6  110.07  3.000
 7N0  H5  C7  C6  112.96  3.000
 7N0  C3  C7  C6  103.84  3.000
 7N0  H7  C3  C2  108.50  3.000
 7N0  H7  C3  C7  108.11  3.000
 7N0  C2  C3  C7  116.99  3.000
 7N0  H7  C3  C4  105.52  3.000
 7N0  C7  C3  C4  103.30  3.000
 7N0  C2  C3  C4  113.70  3.000
 7N0  H9  C2  H8  105.70  3.000
 7N0  H9  C2  C1  110.44  3.000
 7N0  H8  C2  C1  107.15  3.000
 7N0  H9  C2  C3  110.12  3.000
 7N0  H8  C2  C3  108.23  3.000
 7N0  C1  C2  C3  114.74  3.000
 7N0  O1  C1  O2  126.37  3.000
 7N0  O1  C1  C2  116.64  3.000
 7N0  O2  C1  C2  116.92  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
 7N0  Var_01  C7  C6  C5  C4  -28.30  30.0  1
 7N0  Var_02  C3  C7  C6  C5   39.44  30.0  1
 7N0  Var_03  C3  C4  C5  C6    6.90  30.0  1
 7N0  Var_04  O2  C1  C2  C3   35.70  30.0  2

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
 7N0  chir_01  C3  C4  C2  C7  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
 7N0  plan-1  O3  0.020
 7N0  plan-1  C4  0.020
 7N0  plan-1  C5  0.020
 7N0  plan-1  C3  0.020
 7N0  plan-2  C2  0.020
 7N0  plan-2  C1  0.020
 7N0  plan-2  O2  0.020
 7N0  plan-2  O1  0.020

