# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:57:53 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  20  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.401  -0.0655  -1.5712   0.7793
 7N0  C4   C  C     0   0.422  -0.8583  -0.7519   0.3801
 7N0  C5   C  CH2   0  -0.561  -2.3619  -0.8166   0.5323
 7N0  C6   C  CH2   0  -0.461  -2.8807   0.4265  -0.1904
 7N0  C7   C  CH2   0  -0.436  -1.7197   1.4226  -0.0944
 7N0  C3   C  CH1   0  -0.371  -0.4868   0.5464  -0.3082
 7N0  C2   C  CH2   0  -0.571   0.8362   1.1086   0.1777
 7N0  C1   C  C     0   0.550   2.0104   0.2499  -0.2107
 7N0  O2   O  O     0  -0.451   2.1182  -0.3201  -1.2686
 7N0  O1   O  OH1   0  -0.593   2.9569   0.2335   0.7204
 7N0  H1   H  HCH2  0   0.281  -2.7616  -1.7627   0.1642
 7N0  H2   H  HCH2  0   0.278  -2.5852  -0.7729   1.6034
 7N0  H3   H  HCH2  0   0.237  -3.0812   0.1950  -1.2387
 7N0  H4   H  HCH2  0   0.249  -3.8033   0.8105   0.2420
 7N0  H5   H  HCH2  0   0.252  -1.7898   2.2305  -0.8219
 7N0  H6   H  HCH2  0   0.234  -1.6911   1.8744   0.9018
 7N0  H7   H  HCH1  0   0.294  -0.4174   0.3161  -1.3801
 7N0  H8   H  HCH2  0   0.301   1.0035   2.0911  -0.2761
 7N0  H9   H  HCH2  0   0.270   0.8142   1.2683   1.2568
 7N0  H10  H  HOH1  0   0.478   3.7129  -0.2892   0.4129

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  1.208  0.020  1.208
 7N0  C5  C4   single  1.513  0.020  1.513
 7N0  C5  C6   single  1.529  0.020  1.529
 7N0  C4  C3   single  1.516  0.020  1.516
 7N0  O2  C1   double  1.206  0.020  1.206
 7N0  O1  C1   single  1.328  0.020  1.328
 7N0  C1  C2   single  1.506  0.020  1.506
 7N0  C6  C7   single  1.533  0.020  1.533
 7N0  C3  C2   single  1.517  0.020  1.517
 7N0  C3  C7   single  1.528  0.020  1.528
 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
 7N0  O1  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
 7N0  C3   C4  C5  109.02  3.000
 7N0  C3   C4  O3  124.77  3.000
 7N0  C5   C4  O3  126.16  3.000
 7N0  H2   C5  H1  106.85  3.000
 7N0  H2   C5  C6  111.15  3.000
 7N0  H1   C5  C6  114.92  3.000
 7N0  H2   C5  C4  107.42  3.000
 7N0  H1   C5  C4  111.55  3.000
 7N0  C6   C5  C4  104.77  3.000
 7N0  H4   C6  H3  107.48  3.000
 7N0  H4   C6  C7  112.82  3.000
 7N0  H3   C6  C7  109.69  3.000
 7N0  H4   C6  C5  112.74  3.000
 7N0  H3   C6  C5  110.10  3.000
 7N0  C7   C6  C5  103.99  3.000
 7N0  H6   C7  H5  107.67  3.000
 7N0  H6   C7  C3  110.07  3.000
 7N0  H5   C7  C3  112.57  3.000
 7N0  H6   C7  C6  110.19  3.000
 7N0  H5   C7  C6  113.03  3.000
 7N0  C3   C7  C6  103.29  3.000
 7N0  H7   C3  C2  109.58  3.000
 7N0  H7   C3  C7  107.92  3.000
 7N0  C2   C3  C7  116.51  3.000
 7N0  H7   C3  C4  106.20  3.000
 7N0  C7   C3  C4  103.29  3.000
 7N0  C2   C3  C4  112.68  3.000
 7N0  H9   C2  H8  106.36  3.000
 7N0  H9   C2  C1  110.75  3.000
 7N0  H8   C2  C1  106.59  3.000
 7N0  H9   C2  C3  110.70  3.000
 7N0  H8   C2  C3  109.45  3.000
 7N0  C1   C2  C3  112.71  3.000
 7N0  O1   C1  O2  123.05  3.000
 7N0  O1   C1  C2  112.46  3.000
 7N0  O2   C1  C2  124.43  3.000
 7N0  H10  O1  C1  109.89  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  CONST_01  H10  O1  C1  C2  180.00   0.0  0
 7N0  Var_01    C7   C6  C5  C4  -26.99  30.0  1
 7N0  Var_02    C3   C7  C6  C5   39.40  30.0  1
 7N0  Var_03    C3   C4  C5  C6    4.59  30.0  1
 7N0  Var_04    O2   C1  C2  C3   38.43  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
 7N0  plan-2  H10  0.020

