# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 06:57:19 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(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
 LEA  LEA  'pentanoic acid           '  ligand  17  7  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LEA
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
 LEA  C2   C  C     0   0.549  -1.6437  -0.0986   0.0237
 LEA  O2   O  OH1   0  -0.599  -2.6914   0.7216   0.0588
 LEA  C3   C  CH2   0  -0.578  -0.3435   0.6561   0.0285
 LEA  C4   C  CH2   0  -0.412   0.8878  -0.2347   0.0068
 LEA  C5   C  CH2   0  -0.421   2.1767   0.5786   0.0148
 LEA  C6   C  CH3   0  -0.662   3.4172  -0.3032  -0.0079
 LEA  O1   O  O     0  -0.446  -1.7540  -1.2990  -0.0088
 LEA  HO2  H  HOH1  0   0.478  -3.5127   0.2080   0.0547
 LEA  H31  H  HCH2  0   0.275  -0.3418   1.3329  -0.8323
 LEA  H32  H  HCH2  0   0.274  -0.3310   1.3069   0.9089
 LEA  H41  H  HCH2  0   0.224   0.8777  -0.9044   0.8710
 LEA  H42  H  HCH2  0   0.224   0.8693  -0.8735  -0.8805
 LEA  H51  H  HCH2  0   0.216   2.1881   1.2521  -0.8477
 LEA  H52  H  HCH2  0   0.216   2.1971   1.2202   0.9012
 LEA  H61  H  HCH3  0   0.218   3.4451  -0.9641   0.8604
 LEA  H62  H  HCH3  0   0.218   3.4367  -0.9306  -0.9009
 LEA  H63  H  HCH3  0   0.228   4.3319   0.2902  -0.0009

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
 LEA  C2  O2   single  1.331  0.020  1.331
 LEA  C2  C3   single  1.503  0.020  1.503
 LEA  C2  O1   double  1.206  0.020  1.206
 LEA  O2  HO2  single  0.850  0.020  0.980
 LEA  C3  C4   single  1.520  0.020  1.520
 LEA  C3  H31  single  0.970  0.020  1.090
 LEA  C3  H32  single  0.970  0.020  1.090
 LEA  C4  C5   single  1.524  0.020  1.524
 LEA  C4  H41  single  0.970  0.020  1.090
 LEA  C4  H42  single  0.970  0.020  1.090
 LEA  C5  C6   single  1.522  0.020  1.522
 LEA  C5  H51  single  0.970  0.020  1.090
 LEA  C5  H52  single  0.970  0.020  1.090
 LEA  C6  H61  single  0.970  0.020  1.090
 LEA  C6  H62  single  0.970  0.020  1.090
 LEA  C6  H63  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
 LEA  O1   C2  C3   125.38  3.000
 LEA  O1   C2  O2   122.82  3.000
 LEA  C3   C2  O2   111.80  3.000
 LEA  HO2  O2  C2   109.91  3.000
 LEA  H32  C3  H31  105.34  3.000
 LEA  H32  C3  C4   110.52  3.000
 LEA  H31  C3  C4   110.47  3.000
 LEA  H32  C3  C2   108.11  3.000
 LEA  H31  C3  C2   108.00  3.000
 LEA  C4   C3  C2   113.98  3.000
 LEA  H42  C4  H41  106.46  3.000
 LEA  H42  C4  C5   109.28  3.000
 LEA  H41  C4  C5   109.30  3.000
 LEA  H42  C4  C3   109.89  3.000
 LEA  H41  C4  C3   109.89  3.000
 LEA  C5   C4  C3   111.86  3.000
 LEA  H52  C5  H51  106.10  3.000
 LEA  H52  C5  C6   109.66  3.000
 LEA  H51  C5  C6   109.65  3.000
 LEA  H52  C5  C4   109.44  3.000
 LEA  H51  C5  C4   109.46  3.000
 LEA  C6   C5  C4   112.34  3.000
 LEA  H63  C6  H62  107.65  3.000
 LEA  H63  C6  H61  107.64  3.000
 LEA  H62  C6  H61  107.59  3.000
 LEA  H63  C6  C5   111.61  3.000
 LEA  H62  C6  C5   111.08  3.000
 LEA  H61  C6  C5   111.08  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
 LEA  CONST_01  HO2  O2  C2  C3   180.00   0.0  0
 LEA  Var_01    C5   C4  C3  C2  -179.91  30.0  3
 LEA  Var_02    C4   C3  C2  O2   179.27  30.0  3
 LEA  Var_03    C6   C5  C4  C3  -179.96  30.0  3
 LEA  Var_04    H61  C6  C5  C4   -59.81  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
 LEA  plan-1  C2   0.020
 LEA  plan-1  O2   0.020
 LEA  plan-1  C3   0.020
 LEA  plan-1  O1   0.020
 LEA  plan-1  HO2  0.020

