# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:18:23 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: pentane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC
#
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
 LNK  LNK  'pentane                  '  ligand  17  5  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LNK
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
 LNK  C1   C  CH3   0  -0.662  -0.3324   0.0210   2.5187
 LNK  C2   C  CH2   0  -0.419   0.5276   0.0127   1.2622
 LNK  C3   C  CH2   0  -0.401  -0.3004   0.0064  -0.0170
 LNK  C4   C  CH2   0  -0.419   0.5421  -0.0011  -1.2869
 LNK  C5   C  CH3   0  -0.662  -0.3039  -0.0012  -2.5530
 LNK  H11  H  HCH3  0   0.225   0.2749   0.0252   3.4246
 LNK  H12  H  HCH3  0   0.215  -0.9754   0.9029   2.5485
 LNK  H13  H  HCH3  0   0.215  -0.9783  -0.8584   2.5581
 LNK  H21  H  HCH2  0   0.210   1.1873   0.8862   1.2625
 LNK  H22  H  HCH2  0   0.210   1.1848  -0.8626   1.2725
 LNK  H31  H  HCH2  0   0.205  -0.9616  -0.8677  -0.0161
 LNK  H32  H  HCH2  0   0.205  -0.9598   0.8823  -0.0254
 LNK  H41  H  HCH2  0   0.210   1.2041   0.8706  -1.2871
 LNK  H42  H  HCH2  0   0.210   1.1968  -0.8783  -1.2816
 LNK  H51  H  HCH3  0   0.225   0.3130  -0.0105  -3.4524
 LNK  H52  H  HCH3  0   0.215  -0.9550  -0.8768  -2.5897
 LNK  H23  H  HCH3  0   0.215  -0.9413   0.8841  -2.5988

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
 LNK  C1  C2   single  1.523  0.020  1.523
 LNK  C1  H11  single  0.970  0.020  1.090
 LNK  C1  H12  single  0.970  0.020  1.090
 LNK  C1  H13  single  0.970  0.020  1.090
 LNK  C2  C3   single  1.524  0.020  1.524
 LNK  C2  H21  single  0.970  0.020  1.090
 LNK  C2  H22  single  0.970  0.020  1.090
 LNK  C3  C4   single  1.524  0.020  1.524
 LNK  C3  H31  single  0.970  0.020  1.090
 LNK  C3  H32  single  0.970  0.020  1.090
 LNK  C4  C5   single  1.523  0.020  1.523
 LNK  C4  H41  single  0.970  0.020  1.090
 LNK  C4  H42  single  0.970  0.020  1.090
 LNK  C5  H51  single  0.970  0.020  1.090
 LNK  C5  H52  single  0.970  0.020  1.090
 LNK  C5  H23  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
 LNK  H13  C1  H12  107.54  3.000
 LNK  H13  C1  H11  107.61  3.000
 LNK  H12  C1  H11  107.59  3.000
 LNK  H13  C1  C2   111.07  3.000
 LNK  H12  C1  C2   111.07  3.000
 LNK  H11  C1  C2   111.77  3.000
 LNK  H22  C2  H21  106.04  3.000
 LNK  H22  C2  C3   109.32  3.000
 LNK  H21  C2  C3   109.33  3.000
 LNK  H22  C2  C1   109.61  3.000
 LNK  H21  C2  C1   109.62  3.000
 LNK  C3   C2  C1   112.70  3.000
 LNK  H32  C3  H31  105.92  3.000
 LNK  H32  C3  C4   109.27  3.000
 LNK  H31  C3  C4   109.28  3.000
 LNK  H32  C3  C2   109.27  3.000
 LNK  H31  C3  C2   109.29  3.000
 LNK  C4   C3  C2   113.53  3.000
 LNK  H42  C4  H41  106.05  3.000
 LNK  H42  C4  C5   109.65  3.000
 LNK  H41  C4  C5   109.63  3.000
 LNK  H42  C4  C3   109.30  3.000
 LNK  H41  C4  C3   109.30  3.000
 LNK  C5   C4  C3   112.69  3.000
 LNK  H23  C5  H52  107.50  3.000
 LNK  H23  C5  H51  107.61  3.000
 LNK  H52  C5  H51  107.62  3.000
 LNK  H23  C5  C4   111.05  3.000
 LNK  H52  C5  C4   111.06  3.000
 LNK  H51  C5  C4   111.80  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
 LNK  Var_01  C4   C3  C2  C1   179.96  30.0  3
 LNK  Var_02  C5   C4  C3  C2  -179.75  30.0  3
 LNK  Var_03  H11  C1  C2  C3   179.99  30.0  3
 LNK  Var_04  H51  C5  C4  C3  -179.78  30.0  3

