# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 14:43:39 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
 PEI  PEI  'pentanoic acid           '  ligand  16  7  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PEI
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
 PEI  C1   C  CH3    0  -0.661  -0.2914   0.0142   3.4624
 PEI  C2   C  CH2    0  -0.416   0.6037  -0.0071   2.2304
 PEI  C3   C  CH2    0  -0.397  -0.1883   0.0054   0.9277
 PEI  C4   C  CH2    0  -0.577   0.6992  -0.0033  -0.3064
 PEI  C5   C  C      0   0.408  -0.0304  -0.0002  -1.6613
 PEI  O1   O  OC    -1  -0.635   0.6814   0.2034  -2.6683
 PEI  O2   O  O      0  -0.611  -1.2590  -0.2143  -1.6616
 PEI  H11  H  HCH3   0   0.223   0.2884   0.0016   4.3863
 PEI  H12  H  HCH3   0   0.214  -0.9159   0.9097   3.4772
 PEI  H13  H  HCH3   0   0.214  -0.9574  -0.8507   3.4785
 PEI  H21  H  HCH2   0   0.205   1.2808   0.8530   2.2551
 PEI  H22  H  HCH2   0   0.205   1.2448  -0.8945   2.2576
 PEI  H31  H  HCH2   0   0.200  -0.8595  -0.8579   0.9068
 PEI  H32  H  HCH2   0   0.198  -0.8362   0.8881   0.9119
 PEI  H41  H  HCH2   0   0.210   1.3846   0.8510  -0.2763
 PEI  H42  H  HCH2   0   0.218   1.3498  -0.8871  -0.2790

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
 PEI  C1  C2   single  1.523  0.020  1.523
 PEI  C1  H11  single  0.970  0.020  1.090
 PEI  C1  H12  single  0.970  0.020  1.090
 PEI  C1  H13  single  0.970  0.020  1.090
 PEI  C2  C3   single  1.525  0.020  1.525
 PEI  C2  H21  single  0.970  0.020  1.090
 PEI  C2  H22  single  0.970  0.020  1.090
 PEI  C3  C4   single  1.520  0.020  1.520
 PEI  C3  H31  single  0.970  0.020  1.090
 PEI  C3  H32  single  0.970  0.020  1.090
 PEI  C4  C5   single  1.539  0.020  1.539
 PEI  C4  H41  single  0.970  0.020  1.090
 PEI  C4  H42  single  0.970  0.020  1.090
 PEI  C5  O1   deloc   1.250  0.020  1.250
 PEI  C5  O2   deloc   1.247  0.020  1.247

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
 PEI  H13  C1  H12  107.49  3.000
 PEI  H13  C1  H11  107.61  3.000
 PEI  H12  C1  H11  107.58  3.000
 PEI  H13  C1  C2   111.06  3.000
 PEI  H12  C1  C2   111.02  3.000
 PEI  H11  C1  C2   111.88  3.000
 PEI  H22  C2  H21  105.90  3.000
 PEI  H22  C2  C3   109.39  3.000
 PEI  H21  C2  C3   109.51  3.000
 PEI  H22  C2  C1   109.59  3.000
 PEI  H21  C2  C1   109.53  3.000
 PEI  C3   C2  C1   112.69  3.000
 PEI  H32  C3  H31  105.83  3.000
 PEI  H32  C3  C4   109.77  3.000
 PEI  H31  C3  C4   109.77  3.000
 PEI  H32  C3  C2   109.05  3.000
 PEI  H31  C3  C2   109.19  3.000
 PEI  C4   C3  C2   112.98  3.000
 PEI  H42  C4  H41  104.85  3.000
 PEI  H42  C4  C5   107.73  3.000
 PEI  H41  C4  C5   108.61  3.000
 PEI  H42  C4  C3   109.29  3.000
 PEI  H41  C4  C3   109.78  3.000
 PEI  C5   C4  C3   115.97  3.000
 PEI  O2   C5  O1   126.07  3.000
 PEI  O2   C5  C4   117.84  3.000
 PEI  O1   C5  C4   116.08  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
 PEI  Var_01  C4   C3  C2  C1  179.49  30.0  3
 PEI  Var_02  C5   C4  C3  C2  179.64  30.0  3
 PEI  Var_03  O1   C5  C4  C3  169.19  30.0  3
 PEI  Var_04  H11  C1  C2  C3  179.81  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
 PEI  plan-1  C4  0.020
 PEI  plan-1  C5  0.020
 PEI  plan-1  O1  0.020
 PEI  plan-1  O2  0.020

