# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:35:08 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: O-(3-methylbutyl) trihydrogen thiodiphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCO[P](O)(=O)O[P](O)(S)=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
 IS3  IS3  'O-(3-methylbutyl) trihydrogen thiodiphosphate'  ligand  26  14  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IS3
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
 IS3  O    O  O2     0  -0.741   1.1991  -0.3306   0.0929
 IS3  C1   C  CH2    0  -0.138  -2.5059   0.3209  -0.0641
 IS3  O1   O  O2     0  -0.622  -1.1933  -0.2231  -0.0584
 IS3  P1   P  P      0   1.338   0.0132   0.7544   0.4743
 IS3  C2   C  CH2    0  -0.441  -3.5161  -0.8066   0.0270
 IS3  O2   O  OP    -1  -0.789  -0.0823   0.8979   1.9599
 IS3  P2   P  P      0   1.194   2.7341   0.1159  -0.2692
 IS3  C3   C  CH1    0  -0.243  -4.9676  -0.3239   0.0613
 IS3  O3   O  O      0  -0.800   0.1228   1.9635  -0.4008
 IS3  C4   C  CH3    0  -0.658  -5.3955   0.3221  -1.2536
 IS3  O4   O  O      0  -0.773   3.2003   1.2000   0.6473
 IS3  C5   C  CH3    0  -0.649  -5.9003  -1.4816   0.4038
 IS3  O5   O  OP    -1  -0.765   2.9149   0.2179  -1.7488
 IS3  S6   S  S2     0  -0.517   3.5498  -1.7691   0.3892
 IS3  H1   H  HCH2   0   0.198  -2.6585   1.0002   0.7840
 IS3  H1A  H  HCH2   0   0.207  -2.6529   0.9102  -0.9744
 IS3  H2   H  HCH2   0   0.215  -3.3844  -1.4958  -0.8151
 IS3  H2A  H  HCH2   0   0.224  -3.3106  -1.3796   0.9366
 IS3  H4   H  HCH3   0   0.226  -6.4337   0.6549  -1.2046
 IS3  H4A  H  HCH3   0   0.229  -4.7896   1.1911  -1.5133
 IS3  H4B  H  HCH3   0   0.214  -5.3171  -0.3931  -2.0764
 IS3  H5   H  HCH3   0   0.224  -5.6405  -1.9362   1.3614
 IS3  H5A  H  HCH3   0   0.224  -6.9377  -1.1477   0.4646
 IS3  H11  H  HCH1   0   0.215  -5.0568   0.4254   0.8576
 IS3  H12  H  HCH3   0   0.213  -5.8498  -2.2621  -0.3593
 IS3  H14  H  HSH1   0   0.216   4.7936  -1.5345  -0.0461

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
 IS3  O   P1   single  1.652  0.020  1.652
 IS3  O   P2   single  1.639  0.020  1.639
 IS3  C1  O1   single  1.421  0.020  1.421
 IS3  C1  C2   single  1.517  0.020  1.517
 IS3  C1  H1   single  0.970  0.020  1.090
 IS3  C1  H1A  single  0.970  0.020  1.090
 IS3  O1  P1   single  1.642  0.020  1.642
 IS3  P1  O2   deloc   1.496  0.020  1.496
 IS3  P1  O3   deloc   1.497  0.020  1.497
 IS3  C2  C3   single  1.530  0.020  1.530
 IS3  C2  H2   single  0.970  0.020  1.090
 IS3  C2  H2A  single  0.970  0.020  1.090
 IS3  P2  O4   deloc   1.494  0.020  1.494
 IS3  P2  O5   deloc   1.494  0.020  1.494
 IS3  P2  S6   single  2.157  0.020  2.157
 IS3  C3  C4   single  1.526  0.020  1.526
 IS3  C3  C5   single  1.526  0.020  1.526
 IS3  C4  H4   single  0.970  0.020  1.090
 IS3  C4  H4A  single  0.970  0.020  1.090
 IS3  C4  H4B  single  0.970  0.020  1.090
 IS3  C5  H5   single  0.970  0.020  1.090
 IS3  C5  H5A  single  0.970  0.020  1.090
 IS3  C3  H11  single  0.970  0.020  1.090
 IS3  C5  H12  single  0.970  0.020  1.090
 IS3  S6  H14  single  1.200  0.020  1.300

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
 IS3  P2   O   P1   122.98  3.000
 IS3  H1A  C1  H1   106.91  3.000
 IS3  H1A  C1  C2   111.15  3.000
 IS3  H1   C1  C2   108.74  3.000
 IS3  H1A  C1  O1   109.49  3.000
 IS3  H1   C1  O1   111.24  3.000
 IS3  C2   C1  O1   109.30  3.000
 IS3  P1   O1  C1   116.89  3.000
 IS3  O3   P1  O2   120.53  3.000
 IS3  O3   P1  O1   110.20  3.000
 IS3  O2   P1  O1   109.42  3.000
 IS3  O3   P1  O    110.06  3.000
 IS3  O2   P1  O    109.76  3.000
 IS3  O1   P1  O     93.53  3.000
 IS3  H2A  C2  H2   106.66  3.000
 IS3  H2A  C2  C3   108.94  3.000
 IS3  H2   C2  C3   109.25  3.000
 IS3  H2A  C2  C1   108.30  3.000
 IS3  H2   C2  C1   109.96  3.000
 IS3  C3   C2  C1   113.50  3.000
 IS3  S6   P2  O5   108.43  3.000
 IS3  S6   P2  O4   109.20  3.000
 IS3  O5   P2  O4   121.34  3.000
 IS3  S6   P2  O     92.79  3.000
 IS3  O5   P2  O    110.53  3.000
 IS3  O4   P2  O    110.75  3.000
 IS3  H11  C3  C5   107.80  3.000
 IS3  H11  C3  C4   108.26  3.000
 IS3  C5   C3  C4   110.07  3.000
 IS3  H11  C3  C2   107.99  3.000
 IS3  C5   C3  C2   110.22  3.000
 IS3  C4   C3  C2   112.34  3.000
 IS3  H4B  C4  H4A  107.59  3.000
 IS3  H4B  C4  H4   107.55  3.000
 IS3  H4A  C4  H4   107.23  3.000
 IS3  H4B  C4  C3   110.57  3.000
 IS3  H4A  C4  C3   112.75  3.000
 IS3  H4   C4  C3   110.92  3.000
 IS3  H12  C5  H5A  107.54  3.000
 IS3  H12  C5  H5   107.71  3.000
 IS3  H5A  C5  H5   107.74  3.000
 IS3  H12  C5  C3   110.92  3.000
 IS3  H5A  C5  C3   111.19  3.000
 IS3  H5   C5  C3   111.56  3.000
 IS3  H14  S6  P2    95.68  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
 IS3  Var_01  C4  C3  C2  C1    67.01  30.0  3
 IS3  Var_02  C3  C2  C1  O1   178.64  30.0  3
 IS3  Var_03  O4  P2  O   P1    41.55  30.0  3
 IS3  Var_04  C2  C1  O1  P1  -155.06  30.0  1
 IS3  Var_05  H4  C4  C3  C2   179.84  30.0  3
 IS3  Var_06  H5  C5  C3  C2    57.84  30.0  3

