# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:31:16 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC[C@H]1CCSS1
#
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
 LPB  LPB  '5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid'  ligand  25  12  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LPB
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
 LPB  O1   O  O      0  -0.609   4.7706   0.9261  -0.9134
 LPB  O2   O  OC    -1  -0.635   5.5924  -0.9306  -0.0019
 LPB  C1   C  C      0   0.409   4.6676  -0.1300  -0.2591
 LPB  C2   C  CH2    0  -0.581   3.2835  -0.5024   0.3003
 LPB  C3   C  CH2    0  -0.401   2.1436   0.4445  -0.0368
 LPB  C4   C  CH2    0  -0.419   0.8153  -0.0125   0.5566
 LPB  C5   C  CH2    0  -0.396  -0.3356   0.9293   0.2301
 LPB  C6   C  CH1    0  -0.368  -1.6554   0.5499   0.8896
 LPB  C7   C  CH2    0  -0.425  -2.7936   1.5258   0.5789
 LPB  C8   C  CH2    0  -0.563  -3.5228   1.1230  -0.6919
 LPB  S8   S  S2     0  -0.058  -4.0367  -0.5979  -0.4424
 LPB  S6   S  S2     0  -0.075  -2.1625  -1.1403   0.3119
 LPB  H21  H  HCH2   0   0.216   3.0370  -1.5134  -0.0452
 LPB  H22  H  HCH2   0   0.217   3.3734  -0.5932   1.3895
 LPB  H31  H  HCH2   0   0.204   2.3736   1.4500   0.3268
 LPB  H32  H  HCH2   0   0.203   2.0417   0.5323  -1.1224
 LPB  H41  H  HCH2   0   0.212   0.5881  -1.0199   0.1903
 LPB  H42  H  HCH2   0   0.211   0.9123  -0.0977   1.6447
 LPB  H51  H  HCH2   0   0.235  -0.0772   1.9362   0.5757
 LPB  H52  H  HCH2   0   0.227  -0.4717   0.9945  -0.8537
 LPB  H6   H  HCH1   0   0.288  -1.5158   0.4874   1.9706
 LPB  H71  H  HCH2   0   0.263  -3.5056   1.5410   1.4047
 LPB  H72  H  HCH2   0   0.267  -2.3855   2.5346   0.4803
 LPB  H81  H  HCH2   0   0.299  -4.4245   1.7143  -0.8527
 LPB  H82  H  HCH2   0   0.279  -2.8902   1.2006  -1.5769

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
 LPB  O1  C1   deloc   1.247  0.020  1.247
 LPB  O2  C1   deloc   1.250  0.020  1.250
 LPB  C1  C2   single  1.539  0.020  1.539
 LPB  C2  C3   single  1.520  0.020  1.520
 LPB  C2  H21  single  0.970  0.020  1.090
 LPB  C2  H22  single  0.970  0.020  1.090
 LPB  C3  C4   single  1.525  0.020  1.525
 LPB  C3  H31  single  0.970  0.020  1.090
 LPB  C3  H32  single  0.970  0.020  1.090
 LPB  C4  C5   single  1.522  0.020  1.522
 LPB  C4  H41  single  0.970  0.020  1.090
 LPB  C4  H42  single  0.970  0.020  1.090
 LPB  C5  C6   single  1.523  0.020  1.523
 LPB  C5  H51  single  0.970  0.020  1.090
 LPB  C5  H52  single  0.970  0.020  1.090
 LPB  C6  C7   single  1.531  0.020  1.531
 LPB  C6  S6   single  1.857  0.020  1.857
 LPB  C6  H6   single  0.970  0.020  1.090
 LPB  C7  C8   single  1.520  0.020  1.520
 LPB  C7  H71  single  0.970  0.020  1.090
 LPB  C7  H72  single  0.970  0.020  1.090
 LPB  C8  S8   single  1.813  0.020  1.813
 LPB  C8  H81  single  0.970  0.020  1.090
 LPB  C8  H82  single  0.970  0.020  1.090
 LPB  S8  S6   single  2.092  0.020  2.092

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
 LPB  C2   C1  O2   115.83  3.000
 LPB  C2   C1  O1   118.05  3.000
 LPB  O2   C1  O1   126.12  3.000
 LPB  H22  C2  H21  104.77  3.000
 LPB  H22  C2  C3   109.47  3.000
 LPB  H21  C2  C3   109.63  3.000
 LPB  H22  C2  C1   107.90  3.000
 LPB  H21  C2  C1   108.11  3.000
 LPB  C3   C2  C1   116.31  3.000
 LPB  H32  C3  H31  106.00  3.000
 LPB  H32  C3  C4   109.21  3.000
 LPB  H31  C3  C4   109.23  3.000
 LPB  H32  C3  C2   109.88  3.000
 LPB  H31  C3  C2   109.96  3.000
 LPB  C4   C3  C2   112.35  3.000
 LPB  H42  C4  H41  106.19  3.000
 LPB  H42  C4  C5   109.14  3.000
 LPB  H41  C4  C5   109.90  3.000
 LPB  H42  C4  C3   109.43  3.000
 LPB  H41  C4  C3   109.03  3.000
 LPB  C5   C4  C3   112.93  3.000
 LPB  H52  C5  H51  106.67  3.000
 LPB  H52  C5  C6   109.62  3.000
 LPB  H51  C5  C6   107.26  3.000
 LPB  H52  C5  C4   110.08  3.000
 LPB  H51  C5  C4   108.83  3.000
 LPB  C6   C5  C4   114.08  3.000
 LPB  H6   C6  S6   106.91  3.000
 LPB  H6   C6  C7   109.42  3.000
 LPB  S6   C6  C7   108.30  3.000
 LPB  H6   C6  C5   109.39  3.000
 LPB  S6   C6  C5   109.18  3.000
 LPB  C7   C6  C5   113.42  3.000
 LPB  H72  C7  H71  107.42  3.000
 LPB  H72  C7  C8   110.39  3.000
 LPB  H71  C7  C8   108.89  3.000
 LPB  H72  C7  C6   109.21  3.000
 LPB  H71  C7  C6   109.92  3.000
 LPB  C8   C7  C6   110.94  3.000
 LPB  H82  C8  H81  108.75  3.000
 LPB  H82  C8  S8   110.10  3.000
 LPB  H81  C8  S8   107.50  3.000
 LPB  H82  C8  C7   112.42  3.000
 LPB  H81  C8  C7   112.11  3.000
 LPB  S8   C8  C7   105.81  3.000
 LPB  S6   S8  C8    92.39  3.000
 LPB  S8   S6  C6    96.94  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
 LPB  Var_01  S8  C8  C7  C6    54.68  30.0  1
 LPB  Var_02  C6  C5  C4  C3  -176.00  30.0  3
 LPB  Var_03  C3  C2  C1  O1     1.80  30.0  3
 LPB  Var_04  C4  C3  C2  C1   179.77  30.0  3
 LPB  Var_05  C5  C4  C3  C2   179.83  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 LPB  chir_01  C6  C5  C7  S6  negativ

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
 LPB  plan-1  O1  0.020
 LPB  plan-1  O2  0.020
 LPB  plan-1  C1  0.020
 LPB  plan-1  C2  0.020

