# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:36:18 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: pentanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC=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
 PTL  PTL  'pentanal                 '  ligand  16  6  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PTL
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
 PTL  C1   C  C1    0   0.167  15.3876  17.8726  13.0736
 PTL  O1   O  O     0  -0.380  14.7620  16.9562  13.5469
 PTL  C2   C  CH2   0  -0.563  16.5256  18.5805  13.7372
 PTL  C3   C  CH2   0  -0.421  16.8038  18.1936  15.1812
 PTL  C4   C  CH2   0  -0.420  15.7742  18.7299  16.1699
 PTL  C5   C  CH3   0  -0.659  16.1001  18.3481  17.6068
 PTL  H1   H  H     0   0.198  15.1546  18.2445  12.0585
 PTL  H21  H  HCH2  0   0.279  17.3998  18.3917  13.1011
 PTL  H22  H  HCH2  0   0.261  16.3468  19.6573  13.6368
 PTL  H31  H  HCH2  0   0.221  16.8691  17.1053  15.2674
 PTL  H32  H  HCH2  0   0.229  17.7894  18.5775  15.4568
 PTL  H41  H  HCH2  0   0.212  15.7290  19.8196  16.0815
 PTL  H42  H  HCH2  0   0.219  14.7789  18.3610  15.9125
 PTL  H51  H  HCH3  0   0.226  15.3654  18.7511  18.3046
 PTL  H52  H  HCH3  0   0.216  16.1152  17.2640  17.7321
 PTL  H53  H  HCH3  0   0.216  17.0800  18.7272  17.9024

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
 PTL  C1  O1   double  1.206  0.020  1.206
 PTL  C1  C2   single  1.496  0.020  1.496
 PTL  C1  H1   single  0.930  0.020  1.080
 PTL  C2  C3   single  1.521  0.020  1.521
 PTL  C2  H21  single  0.970  0.020  1.090
 PTL  C2  H22  single  0.970  0.020  1.090
 PTL  C3  C4   single  1.525  0.020  1.525
 PTL  C3  H31  single  0.970  0.020  1.090
 PTL  C3  H32  single  0.970  0.020  1.090
 PTL  C4  C5   single  1.522  0.020  1.522
 PTL  C4  H41  single  0.970  0.020  1.090
 PTL  C4  H42  single  0.970  0.020  1.090
 PTL  C5  H51  single  0.970  0.020  1.090
 PTL  C5  H52  single  0.970  0.020  1.090
 PTL  C5  H53  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
 PTL  H1   C1  C2   114.10  3.000
 PTL  H1   C1  O1   120.42  3.000
 PTL  C2   C1  O1   125.46  3.000
 PTL  H22  C2  H21  104.23  3.000
 PTL  H22  C2  C3   111.52  3.000
 PTL  H21  C2  C3   111.16  3.000
 PTL  H22  C2  C1   107.47  3.000
 PTL  H21  C2  C1   105.51  3.000
 PTL  C3   C2  C1   116.11  3.000
 PTL  H32  C3  H31  106.02  3.000
 PTL  H32  C3  C4   108.77  3.000
 PTL  H31  C3  C4   109.82  3.000
 PTL  H32  C3  C2   108.36  3.000
 PTL  H31  C3  C2   109.82  3.000
 PTL  C4   C3  C2   113.75  3.000
 PTL  H42  C4  H41  106.24  3.000
 PTL  H42  C4  C5   109.44  3.000
 PTL  H41  C4  C5   109.57  3.000
 PTL  H42  C4  C3   110.10  3.000
 PTL  H41  C4  C3   109.01  3.000
 PTL  C5   C4  C3   112.30  3.000
 PTL  H53  C5  H52  107.54  3.000
 PTL  H53  C5  H51  107.65  3.000
 PTL  H52  C5  H51  107.64  3.000
 PTL  H53  C5  C4   111.15  3.000
 PTL  H52  C5  C4   111.13  3.000
 PTL  H51  C5  C4   111.54  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
 PTL  Var_01  C4   C3  C2  C1   -73.25  30.0  3
 PTL  Var_02  C3   C2  C1  O1    -6.72  30.0  3
 PTL  Var_03  C5   C4  C3  C2  -178.80  30.0  3
 PTL  Var_04  H51  C5  C4  C3   179.08  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
 PTL  plan-1  C1  0.020
 PTL  plan-1  O1  0.020
 PTL  plan-1  C2  0.020
 PTL  plan-1  H1  0.020

