# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:28:32 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 3-{[(2,4-dichlorobenzyl)sulfanyl]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(CSCc2ccc(Cl)cc2Cl)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
 056  056  '3-{[(2,4-dichlorobenzyl)sulfanyl]methyl}benzoic acid'  ligand  32  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_056
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
 056  O17   O   OH1   0  -0.593  -6.5205  -1.2233   1.3649
 056  C16   C   C     0   0.535  -5.4191  -1.3859   0.6464
 056  O18   O   O     0  -0.438  -5.0438  -2.4622   0.2463
 056  C12   C   CR6   0  -0.065  -4.7019  -0.1127   0.3851
 056  C11   C   CR16  0  -0.299  -3.5452  -0.1597  -0.3895
 056  C10   C   CR6   0   0.123  -2.8350   0.9974  -0.6789
 056  C15   C   CR16  0  -0.276  -3.2880   2.2111  -0.1669
 056  C14   C   CR16  0  -0.227  -4.4379   2.2660   0.6062
 056  C13   C   CR16  0  -0.272  -5.1491   1.1088   0.8851
 056  S8    S   S2    0   0.008  -0.1743   0.7591  -0.3458
 056  C6    C   CR16  0  -0.148   4.0850  -0.9632   0.2550
 056  C9    C   CH2   0  -0.621  -1.5787   0.9350  -1.4923
 056  C1    C   CR6   0  -0.103   2.9083  -0.7510  -0.4468
 056  CL1   CL  CL    0  -0.110   1.9734  -2.1358  -0.8950
 056  C2    C   CR6   0   0.195   2.4749   0.5269  -0.7953
 056  C7    C   CH2   0  -0.618   1.2016   0.7701  -1.5403
 056  C3    C   CR16  0  -0.312   3.2628   1.6008  -0.3898
 056  C4    C   CR16  0  -0.185   4.4413   1.4231   0.3154
 056  C5    C   CR6   0  -0.063   4.8412   0.1346   0.6298
 056  CL2   CL  CL    0  -0.114   6.3104  -0.1172   1.5067
 056  H6    H   HCR6  0   0.303   4.4028  -1.9662   0.5032
 056  H4    H   HCR6  0   0.287   5.0360   2.2760   0.6118
 056  H3    H   HCR6  0   0.277   2.9451   2.6056  -0.6375
 056  H71C  H   HCH2  0   0.287   1.0269   0.0028  -2.2949
 056  H72C  H   HCH2  0   0.295   1.2356   1.7382  -2.0409
 056  H91C  H   HCH2  0   0.288  -1.5944   0.0836  -2.1740
 056  H92C  H   HCH2  0   0.289  -1.4481   1.8439  -2.0815
 056  H15   H   HCR6  0   0.265  -2.7401   3.1212  -0.3800
 056  H11   H   HCR6  0   0.265  -3.1971  -1.1092  -0.7767
 056  H14   H   HCR6  0   0.268  -4.7845   3.2157   0.9907
 056  H13   H   HCR6  0   0.270  -6.0440   1.1690   1.4884
 056  H17   H   HOH1  0   0.488  -6.9525  -2.0790   1.5049

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
 056  CL2  C5    single    1.729  0.020  1.729
 056  C5   C6    aromatic  1.385  0.020  1.385
 056  C5   C4    aromatic  1.385  0.020  1.385
 056  C6   C1    aromatic  1.386  0.020  1.386
 056  C1   CL1   single    1.730  0.020  1.730
 056  C1   C2    aromatic  1.394  0.020  1.394
 056  C4   C3    aromatic  1.385  0.020  1.385
 056  C3   C2    aromatic  1.392  0.020  1.392
 056  C2   C7    single    1.495  0.020  1.495
 056  C7   S8    single    1.822  0.020  1.822
 056  S8   C9    single    1.821  0.020  1.821
 056  C9   C10   single    1.498  0.020  1.498
 056  C10  C15   aromatic  1.393  0.020  1.393
 056  C10  C11   aromatic  1.388  0.020  1.388
 056  C15  C14   aromatic  1.387  0.020  1.387
 056  C14  C13   aromatic  1.387  0.020  1.387
 056  C13  C12   aromatic  1.394  0.020  1.394
 056  C12  C11   aromatic  1.393  0.020  1.393
 056  C12  C16   single    1.484  0.020  1.484
 056  C16  O17   single    1.325  0.020  1.325
 056  C16  O18   double    1.208  0.020  1.208
 056  C6   H6    single    0.930  0.020  1.080
 056  C4   H4    single    0.930  0.020  1.080
 056  C3   H3    single    0.930  0.020  1.080
 056  C7   H71C  single    0.970  0.020  1.090
 056  C7   H72C  single    0.970  0.020  1.090
 056  C9   H91C  single    0.970  0.020  1.090
 056  C9   H92C  single    0.970  0.020  1.090
 056  C15  H15   single    0.930  0.020  1.080
 056  C11  H11   single    0.930  0.020  1.080
 056  C14  H14   single    0.930  0.020  1.080
 056  C13  H13   single    0.930  0.020  1.080
 056  O17  H17   single    0.850  0.020  0.980

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
 056  H17   O17  C16   109.91  3.000
 056  C12   C16  O18   123.76  3.000
 056  O18   C16  O17   123.17  3.000
 056  C12   C16  O17   113.07  3.000
 056  C13   C12  C11   119.71  3.000
 056  C11   C12  C16   118.04  3.000
 056  C13   C12  C16   122.25  3.000
 056  H11   C11  C10   119.47  3.000
 056  H11   C11  C12   119.69  3.000
 056  C10   C11  C12   120.84  3.000
 056  C9    C10  C15   120.57  3.000
 056  C15   C10  C11   118.90  3.000
 056  C9    C10  C11   120.50  3.000
 056  H15   C15  C14   119.73  3.000
 056  H15   C15  C10   119.68  3.000
 056  C14   C15  C10   120.60  3.000
 056  H14   C14  C13   119.80  3.000
 056  H14   C14  C15   119.91  3.000
 056  C13   C14  C15   120.29  3.000
 056  H13   C13  C14   119.37  3.000
 056  H13   C13  C12   120.98  3.000
 056  C14   C13  C12   119.65  3.000
 056  C7    S8   C9     99.73  3.000
 056  H6    C6   C5    120.86  3.000
 056  H6    C6   C1    120.51  3.000
 056  C5    C6   C1    118.63  3.000
 056  H92C  C9   H91C  108.33  3.000
 056  H92C  C9   S8    109.16  3.000
 056  H91C  C9   S8    109.21  3.000
 056  H92C  C9   C10   111.03  3.000
 056  H91C  C9   C10   111.09  3.000
 056  S8    C9   C10   107.99  3.000
 056  C2    C1   CL1   120.08  3.000
 056  C2    C1   C6    122.06  3.000
 056  CL1   C1   C6    117.86  3.000
 056  C3    C2   C7    120.11  3.000
 056  C7    C2   C1    122.58  3.000
 056  C3    C2   C1    117.29  3.000
 056  H72C  C7   H71C  108.19  3.000
 056  H72C  C7   C2    110.28  3.000
 056  H71C  C7   C2    111.53  3.000
 056  H72C  C7   S8    109.26  3.000
 056  H71C  C7   S8    109.17  3.000
 056  C2    C7   S8    108.39  3.000
 056  H3    C3   C4    119.04  3.000
 056  H3    C3   C2    118.89  3.000
 056  C4    C3   C2    122.07  3.000
 056  H4    C4   C5    120.85  3.000
 056  H4    C4   C3    120.43  3.000
 056  C5    C4   C3    118.72  3.000
 056  CL2   C5   C4    119.72  3.000
 056  C4    C5   C6    121.22  3.000
 056  CL2   C5   C6    119.06  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
 056  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 056  CONST_02  C15  C10  C11  C12     0.00   0.0  0
 056  CONST_03  C14  C15  C10  C11     0.00   0.0  0
 056  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 056  CONST_05  C13  C14  C15  C10     0.00   0.0  0
 056  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 056  CONST_07  C3   C4   C5   C6      0.00   0.0  0
 056  CONST_08  C3   C2   C1   C6      0.00   0.0  0
 056  CONST_09  C4   C5   C6   C1      0.00   0.0  0
 056  CONST_10  C4   C3   C2   C1      0.00   0.0  0
 056  CONST_11  C5   C6   C1   C2      0.00   0.0  0
 056  CONST_12  C5   C4   C3   C2      0.00   0.0  0
 056  CONST_13  C14  C13  C12  C16   180.00   0.0  0
 056  CONST_14  C10  C11  C12  C16   180.00   0.0  0
 056  CONST_15  C9   C10  C11  C12   180.00   0.0  0
 056  CONST_16  C9   C10  C15  C14   180.00   0.0  0
 056  CONST_17  C7   C2   C1   C6    180.00   0.0  0
 056  CONST_18  CL2  C5   C6   C1    180.00   0.0  0
 056  CONST_19  C5   C6   C1   CL1   180.00   0.0  0
 056  CONST_20  C3   C2   C1   CL1   180.00   0.0  0
 056  CONST_21  C4   C3   C2   C7    180.00   0.0  0
 056  CONST_22  CL2  C5   C4   C3    180.00   0.0  0
 056  CONST_23  H14  C14  C13  C12   180.00   0.0  0
 056  CONST_24  H15  C15  C10  C11   180.00   0.0  0
 056  CONST_25  H13  C13  C12  C11   180.00   0.0  0
 056  CONST_26  H11  C11  C10  C15   180.00   0.0  0
 056  CONST_27  H4   C4   C5   C6    180.00   0.0  0
 056  CONST_28  H3   C3   C2   C1    180.00   0.0  0
 056  CONST_29  H6   C6   C1   C2    180.00   0.0  0
 056  CONST_30  H17  O17  C16  C12   180.00   0.0  0
 056  Var_01    C13  C12  C16  O17     1.43  30.0  2
 056  Var_02    S8   C9   C10  C11   -91.81  30.0  2
 056  Var_03    C1   C2   C7   S8     82.49  30.0  2
 056  Var_04    C2   C7   S8   C9   -175.70  30.0  1

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
 056  plan-1  C16  0.020
 056  plan-1  C12  0.020
 056  plan-1  C11  0.020
 056  plan-1  C10  0.020
 056  plan-1  C15  0.020
 056  plan-1  C14  0.020
 056  plan-1  C13  0.020
 056  plan-1  C9   0.020
 056  plan-1  H15  0.020
 056  plan-1  H11  0.020
 056  plan-1  H14  0.020
 056  plan-1  H13  0.020
 056  plan-2  C6   0.020
 056  plan-2  C1   0.020
 056  plan-2  CL1  0.020
 056  plan-2  C2   0.020
 056  plan-2  C7   0.020
 056  plan-2  C3   0.020
 056  plan-2  C4   0.020
 056  plan-2  C5   0.020
 056  plan-2  CL2  0.020
 056  plan-2  H6   0.020
 056  plan-2  H4   0.020
 056  plan-2  H3   0.020
 056  plan-3  O17  0.020
 056  plan-3  C16  0.020
 056  plan-3  O18  0.020
 056  plan-3  C12  0.020
 056  plan-3  H17  0.020

