# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 14:37:34 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: pentanedial
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=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
 PTD  PTD  'pentanedial              '  ligand  15  7  .  2021-08-20  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PTD
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
 PTD  C1    C  C1    0   0.198  -0.2394  -0.4223  -2.4575
 PTD  C2    C  CH2   0  -0.529   0.5931  -0.1822  -1.2346
 PTD  C3    C  CH2   0  -0.443  -0.2678  -0.0199   0.0154
 PTD  C4    C  CH2   0  -0.527   0.5830   0.1194   1.2754
 PTD  C5    C  C1    0   0.191  -0.2586   0.3975   2.4864
 PTD  O1    O  O     0  -0.357  -0.0986   0.1308  -3.5169
 PTD  O5    O  O     0  -0.327  -0.1810  -0.1794   3.5365
 PTD  HC1   H  H     0   0.164  -1.0246  -1.1908  -2.3219
 PTD  HC21  H  HCH2  0   0.258   1.2376  -1.0615  -1.1157
 PTD  HC22  H  HCH2  0   0.247   1.2443   0.6804  -1.3858
 PTD  HC31  H  HCH2  0   0.238  -0.9094   0.8588  -0.0960
 PTD  HC32  H  HCH2  0   0.237  -0.9356  -0.8796   0.1197
 PTD  HC41  H  HCH2  0   0.246   1.1981  -0.7669   1.4400
 PTD  HC42  H  HCH2  0   0.252   1.2605   0.9731   1.1563
 PTD  HC5   H  H     0   0.151  -0.9867   1.2209   2.3415

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
 PTD  C1  C2    single  1.499  0.020  1.499
 PTD  C1  O1    double  1.203  0.020  1.203
 PTD  C1  HC1   single  0.930  0.020  1.080
 PTD  C2  C3    single  1.526  0.020  1.526
 PTD  C2  HC21  single  0.970  0.020  1.090
 PTD  C2  HC22  single  0.970  0.020  1.090
 PTD  C3  C4    single  1.527  0.020  1.527
 PTD  C3  HC31  single  0.970  0.020  1.090
 PTD  C3  HC32  single  0.970  0.020  1.090
 PTD  C4  C5    single  1.501  0.020  1.501
 PTD  C4  HC41  single  0.970  0.020  1.090
 PTD  C4  HC42  single  0.970  0.020  1.090
 PTD  C5  O5    double  1.201  0.020  1.201
 PTD  C5  HC5   single  0.930  0.020  1.080

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
 PTD  HC1   C1  O1    120.66  3.000
 PTD  HC1   C1  C2    113.91  3.000
 PTD  O1    C1  C2    125.43  3.000
 PTD  HC22  C2  HC21  107.35  3.000
 PTD  HC22  C2  C3    111.46  3.000
 PTD  HC21  C2  C3    109.15  3.000
 PTD  HC22  C2  C1    110.18  3.000
 PTD  HC21  C2  C1    106.64  3.000
 PTD  C3    C2  C1    111.83  3.000
 PTD  HC32  C3  HC31  106.45  3.000
 PTD  HC32  C3  C4    109.47  3.000
 PTD  HC31  C3  C4    109.74  3.000
 PTD  HC32  C3  C2    109.81  3.000
 PTD  HC31  C3  C2    109.44  3.000
 PTD  C4    C3  C2    111.79  3.000
 PTD  HC42  C4  HC41  107.49  3.000
 PTD  HC42  C4  C5    106.85  3.000
 PTD  HC41  C4  C5    110.17  3.000
 PTD  HC42  C4  C3    109.01  3.000
 PTD  HC41  C4  C3    111.38  3.000
 PTD  C5    C4  C3    111.73  3.000
 PTD  HC5   C5  O5    120.90  3.000
 PTD  HC5   C5  C4    113.61  3.000
 PTD  O5    C5  C4    125.49  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
 PTD  Var_01  C4  C3  C2  C1  175.70  30.0  3
 PTD  Var_02  C5  C4  C3  C2  175.07  30.0  3
 PTD  Var_03  O1  C1  C2  C3  133.69  30.0  2
 PTD  Var_04  O5  C5  C4  C3  131.28  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
 PTD  plan-1  C1   0.020
 PTD  plan-1  C2   0.020
 PTD  plan-1  O1   0.020
 PTD  plan-1  HC1  0.020
 PTD  plan-2  C4   0.020
 PTD  plan-2  C5   0.020
 PTD  plan-2  O5   0.020
 PTD  plan-2  HC5  0.020

