# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 17:55:59 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 4,4'-disulfanediyldibenzene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(SSc2ccc(O)cc2O)c(O)c1
#
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
 D2S  D2S  4,4'-disulfanediyldibenzene-1,3-diol  ligand  28  18  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D2S
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
 D2S  C1   C  CR16  0  -0.506   4.0099   0.5384  -0.3124
 D2S  O1   O  OH1   0  -0.625   3.3370  -1.3307  -1.6623
 D2S  S1   S  S2    0   0.020   0.7609  -1.7885  -0.6705
 D2S  C2   C  CR6   0   0.411   3.0919  -0.4316  -0.6933
 D2S  S2   S  S2    0   0.021  -0.8020  -1.7900   0.6357
 D2S  C3   C  CR6   0  -0.262   1.8459  -0.5087  -0.0678
 D2S  O3   O  OH1   0  -0.632   4.5413   2.4025   1.0973
 D2S  C4   C  CR16  0  -0.203   1.5379   0.4012   0.9301
 D2S  C5   C  CR16  0  -0.358   2.4450   1.3739   1.3188
 D2S  C6   C  CR6   0   0.371   3.6869   1.4439   0.6944
 D2S  C7   C  CR16  0  -0.506  -4.0292   0.5717   0.3133
 D2S  C8   C  CR6   0   0.411  -3.1183  -0.4089   0.6827
 D2S  C9   C  CR6   0  -0.263  -1.8780  -0.4961   0.0472
 D2S  C10  C  CR16  0  -0.203  -1.5688   0.4144  -0.9497
 D2S  C11  C  CR16  0  -0.358  -2.4691   1.3978  -1.3274
 D2S  C12  C  CR6   0   0.371  -3.7053   1.4775  -0.6930
 D2S  H1   H  HCR6  0   0.288   4.9772   0.5835  -0.8033
 D2S  HO1  H  HOH1  0   0.484   4.2192  -1.2102  -2.0322
 D2S  HO3  H  HOH1  0   0.477   5.3570   2.3701   0.5851
 D2S  H4   H  HCR6  0   0.269   0.5754   0.3541   1.4228
 D2S  H5   H  HCR6  0   0.266   2.1886   2.0763   2.1008
 D2S  HO5  H  HOH1  0   0.477  -5.3641   2.4210  -0.5649
 D2S  H10  H  HCR6  0   0.269  -0.6106   0.3597  -1.4500
 D2S  H11  H  HCR6  0   0.266  -2.2116   2.1008  -2.1085
 D2S  H9   H  HOH1  0   0.484  -4.2450  -1.1862   2.0232
 D2S  H7   H  HCR6  0   0.288  -4.9920   0.6248   0.8120
 D2S  O4   O  OH1   0  -0.625  -3.3643  -1.3092   1.6505
 D2S  O5   O  OH1   0  -0.632  -4.5533   2.4463  -1.0851

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
 D2S  C1   C2   aromatic  1.389  0.020  1.389
 D2S  C1   C6   aromatic  1.392  0.020  1.392
 D2S  C1   H1   single    0.930  0.020  1.080
 D2S  O1   C2   single    1.344  0.020  1.344
 D2S  O1   HO1  single    0.850  0.020  0.980
 D2S  S1   S2   single    2.037  0.020  2.037
 D2S  S1   C3   single    1.783  0.020  1.783
 D2S  C2   C3   aromatic  1.396  0.020  1.396
 D2S  S2   C9   single    1.783  0.020  1.783
 D2S  C3   C4   aromatic  1.385  0.020  1.385
 D2S  O3   C6   single    1.346  0.020  1.346
 D2S  O3   HO3  single    0.850  0.020  0.980
 D2S  C4   C5   aromatic  1.386  0.020  1.386
 D2S  C4   H4   single    0.930  0.020  1.080
 D2S  O4   C8   single    1.344  0.020  1.344
 D2S  C5   C6   aromatic  1.392  0.020  1.392
 D2S  C5   H5   single    0.930  0.020  1.080
 D2S  O5   C12  single    1.346  0.020  1.346
 D2S  O5   HO5  single    0.850  0.020  0.980
 D2S  C7   C8   aromatic  1.388  0.020  1.388
 D2S  C7   C12  aromatic  1.392  0.020  1.392
 D2S  C8   C9   aromatic  1.396  0.020  1.396
 D2S  C9   C10  aromatic  1.385  0.020  1.385
 D2S  C10  C11  aromatic  1.386  0.020  1.386
 D2S  C10  H10  single    0.930  0.020  1.080
 D2S  C11  C12  aromatic  1.392  0.020  1.392
 D2S  C11  H11  single    0.930  0.020  1.080
 D2S  O4   H9   single    0.850  0.020  0.980
 D2S  C7   H7   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
 D2S  H1   C1   C6   120.44  3.000
 D2S  H1   C1   C2   119.61  3.000
 D2S  C6   C1   C2   119.95  3.000
 D2S  HO1  O1   C2   111.08  3.000
 D2S  C3   S1   S2   104.52  3.000
 D2S  C3   C2   O1   116.65  3.000
 D2S  C3   C2   C1   120.37  3.000
 D2S  O1   C2   C1   122.98  3.000
 D2S  C9   S2   S1   104.53  3.000
 D2S  C4   C3   C2   119.00  3.000
 D2S  C4   C3   S1   125.44  3.000
 D2S  C2   C3   S1   115.55  3.000
 D2S  HO3  O3   C6   110.75  3.000
 D2S  H4   C4   C5   119.02  3.000
 D2S  H4   C4   C3   119.80  3.000
 D2S  C5   C4   C3   121.18  3.000
 D2S  H5   C5   C6   120.20  3.000
 D2S  H5   C5   C4   120.22  3.000
 D2S  C6   C5   C4   119.58  3.000
 D2S  C5   C6   O3   117.91  3.000
 D2S  C5   C6   C1   119.92  3.000
 D2S  O3   C6   C1   122.17  3.000
 D2S  H7   C7   C12  120.43  3.000
 D2S  H7   C7   C8   119.62  3.000
 D2S  C12  C7   C8   119.95  3.000
 D2S  C9   C8   C7   120.38  3.000
 D2S  C9   C8   O4   116.64  3.000
 D2S  C7   C8   O4   122.99  3.000
 D2S  C10  C9   C8   119.00  3.000
 D2S  C10  C9   S2   125.45  3.000
 D2S  C8   C9   S2   115.54  3.000
 D2S  H10  C10  C11  119.02  3.000
 D2S  H10  C10  C9   119.80  3.000
 D2S  C11  C10  C9   121.18  3.000
 D2S  H11  C11  C12  120.21  3.000
 D2S  H11  C11  C10  120.22  3.000
 D2S  C12  C11  C10  119.57  3.000
 D2S  C11  C12  C7   119.93  3.000
 D2S  C11  C12  O5   117.91  3.000
 D2S  C7   C12  O5   122.16  3.000
 D2S  H9   O4   C8   111.10  3.000
 D2S  HO5  O5   C12  110.73  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
 D2S  CONST_01  C4   C3   C2   C1    0.00   0.0  0
 D2S  CONST_02  C4   C5   C6   C1    0.00   0.0  0
 D2S  CONST_03  C5   C6   C1   C2    0.00   0.0  0
 D2S  CONST_04  C5   C4   C3   C2    0.00   0.0  0
 D2S  CONST_05  C6   C1   C2   C3    0.00   0.0  0
 D2S  CONST_06  C6   C5   C4   C3    0.00   0.0  0
 D2S  CONST_07  C10  C9   C8   C7    0.00   0.0  0
 D2S  CONST_08  C10  C11  C12  C7    0.00   0.0  0
 D2S  CONST_09  C11  C12  C7   C8    0.00   0.0  0
 D2S  CONST_10  C11  C10  C9   C8    0.00   0.0  0
 D2S  CONST_11  C12  C7   C8   C9    0.00   0.0  0
 D2S  CONST_12  C12  C11  C10  C9    0.00   0.0  0
 D2S  CONST_13  S1   C3   C2   C1  180.00   0.0  0
 D2S  CONST_14  C6   C1   C2   O1  180.00   0.0  0
 D2S  CONST_15  C4   C3   C2   O1  180.00   0.0  0
 D2S  CONST_16  C5   C4   C3   S1  180.00   0.0  0
 D2S  CONST_17  O3   C6   C1   C2  180.00   0.0  0
 D2S  CONST_18  C7   C8   C9   S2  180.00   0.0  0
 D2S  CONST_19  C11  C10  C9   S2  180.00   0.0  0
 D2S  CONST_20  C4   C5   C6   O3  180.00   0.0  0
 D2S  CONST_21  C12  C7   C8   O4  180.00   0.0  0
 D2S  CONST_22  C10  C9   C8   O4  180.00   0.0  0
 D2S  CONST_23  C8   C7   C12  O5  180.00   0.0  0
 D2S  CONST_24  C10  C11  C12  O5  180.00   0.0  0
 D2S  CONST_25  H5   C5   C6   C1  180.00   0.0  0
 D2S  CONST_26  H4   C4   C3   C2  180.00   0.0  0
 D2S  CONST_27  H1   C1   C2   C3  180.00   0.0  0
 D2S  CONST_28  H11  C11  C12  C7  180.00   0.0  0
 D2S  CONST_29  H10  C10  C9   C8  180.00   0.0  0
 D2S  CONST_30  H7   C7   C8   C9  180.00   0.0  0
 D2S  Var_01    C8   C9   S2   S1  172.14  30.0  2
 D2S  Var_02    C4   C3   S1   S2   -9.69  30.0  2

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
 D2S  plan-1  C1   0.020
 D2S  plan-1  O1   0.020
 D2S  plan-1  S1   0.020
 D2S  plan-1  C2   0.020
 D2S  plan-1  C3   0.020
 D2S  plan-1  O3   0.020
 D2S  plan-1  C4   0.020
 D2S  plan-1  C5   0.020
 D2S  plan-1  C6   0.020
 D2S  plan-1  H1   0.020
 D2S  plan-1  H4   0.020
 D2S  plan-1  H5   0.020
 D2S  plan-2  S2   0.020
 D2S  plan-2  C7   0.020
 D2S  plan-2  C8   0.020
 D2S  plan-2  C9   0.020
 D2S  plan-2  C10  0.020
 D2S  plan-2  C11  0.020
 D2S  plan-2  C12  0.020
 D2S  plan-2  H10  0.020
 D2S  plan-2  H11  0.020
 D2S  plan-2  H7   0.020
 D2S  plan-2  O4   0.020
 D2S  plan-2  O5   0.020

