# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:47:09 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 2-[(3,4-dichlorobenzyl)sulfanyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1SCc2ccc(Cl)c(Cl)c2
#
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
 NX5  NX5  '2-[(3,4-dichlorobenzyl)sulfanyl]benzoic acid'  ligand  28  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NX5
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
 NX5  C1    C   CR6    0  -0.130  -2.8320   0.5388  -0.0045
 NX5  S2    S   S2     0   0.086  -1.1995  -0.1386   0.1279
 NX5  C3    C   CH2    0  -0.675  -0.1582   1.3624   0.2354
 NX5  C4    C   CR6    0   0.124   1.2448   0.8639   0.4000
 NX5  C5    C   CR16   0  -0.252   2.0189   0.5742  -0.7172
 NX5  C6    C   CR16   0  -0.200   3.0604   0.1342   1.8126
 NX5  C7    C   CR16   0  -0.289   1.7765   0.6302   1.6645
 NX5  C8    C   CR6    0   0.022   3.3049   0.0771  -0.5747
 NX5  C9    C   CR6    0  -0.018   3.8300  -0.1455   0.6931
 NX5  CL10  CL  CL     0  -0.098   5.4265  -0.7614   0.8887
 NX5  CL11  CL  CL     0  -0.098   4.2396  -0.2588  -1.9829
 NX5  C12   C   CR16   0  -0.260  -3.0372   1.9202  -0.0697
 NX5  C13   C   CR16   0  -0.244  -4.3139   2.4515  -0.1676
 NX5  C14   C   CR16   0  -0.262  -5.4186   1.6149  -0.2015
 NX5  C15   C   CR16   0  -0.279  -5.2200   0.2458  -0.1370
 NX5  C16   C   CR6    0  -0.117  -3.9492  -0.3153  -0.0414
 NX5  C17   C   C      0   0.418  -3.8208  -1.8264   0.0109
 NX5  O18   O   OC    -1  -0.584  -4.8696  -2.4936   0.0418
 NX5  O19   O   O      0  -0.580  -2.6545  -2.2715   0.0149
 NX5  H3    H   HCH2   0   0.285  -0.2444   1.9668  -0.6686
 NX5  H3A   H   HCH2   0   0.287  -0.4466   1.9757   1.0901
 NX5  H5    H   HCR6   0   0.284   1.6220   0.7424  -1.7101
 NX5  H6    H   HCR6   0   0.289   3.4678  -0.0387   2.7990
 NX5  H7    H   HCR6   0   0.269   1.1875   0.8415   2.5478
 NX5  H12   H   HCR6   0   0.267  -2.2071   2.6097  -0.0506
 NX5  H13   H   HCR6   0   0.256  -4.4351   3.5262  -0.2167
 NX5  H14   H   HCR6   0   0.249  -6.4182   2.0225  -0.2783
 NX5  H15   H   HCR6   0   0.248  -6.0695  -0.4235  -0.1621

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
 NX5  S2    C1   single    1.772  0.020  1.772
 NX5  C1    C16  aromatic  1.407  0.020  1.407
 NX5  C1    C12  aromatic  1.398  0.020  1.398
 NX5  S2    C3   single    1.830  0.020  1.830
 NX5  C4    C3   single    1.498  0.020  1.498
 NX5  C3    H3   single    0.970  0.020  1.090
 NX5  C3    H3A  single    0.970  0.020  1.090
 NX5  C7    C4   aromatic  1.391  0.020  1.391
 NX5  C5    C4   aromatic  1.390  0.020  1.390
 NX5  C8    C5   aromatic  1.386  0.020  1.386
 NX5  C5    H5   single    0.930  0.020  1.080
 NX5  C9    C6   aromatic  1.387  0.020  1.387
 NX5  C6    C7   aromatic  1.384  0.020  1.384
 NX5  C6    H6   single    0.930  0.020  1.080
 NX5  C7    H7   single    0.930  0.020  1.080
 NX5  C9    C8   aromatic  1.390  0.020  1.390
 NX5  CL11  C8   single    1.723  0.020  1.723
 NX5  CL10  C9   single    1.722  0.020  1.722
 NX5  C12   C13  aromatic  1.386  0.020  1.386
 NX5  C12   H12  single    0.930  0.020  1.080
 NX5  C13   C14  aromatic  1.386  0.020  1.386
 NX5  C13   H13  single    0.930  0.020  1.080
 NX5  C15   C14  aromatic  1.385  0.020  1.385
 NX5  C14   H14  single    0.930  0.020  1.080
 NX5  C16   C15  aromatic  1.392  0.020  1.392
 NX5  C15   H15  single    0.930  0.020  1.080
 NX5  C17   C16  single    1.517  0.020  1.517
 NX5  O19   C17  deloc     1.248  0.020  1.248
 NX5  C17   O18  deloc     1.243  0.020  1.243

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
 NX5  C16   C1   C12  118.83  3.000
 NX5  C12   C1   S2   121.08  3.000
 NX5  C16   C1   S2   120.09  3.000
 NX5  C3    S2   C1   102.42  3.000
 NX5  H3A   C3   H3   108.47  3.000
 NX5  H3A   C3   C4   110.40  3.000
 NX5  H3    C3   C4   110.45  3.000
 NX5  H3A   C3   S2   110.91  3.000
 NX5  H3    C3   S2   111.15  3.000
 NX5  C4    C3   S2   105.45  3.000
 NX5  C7    C4   C5   118.87  3.000
 NX5  C5    C4   C3   120.18  3.000
 NX5  C7    C4   C3   120.90  3.000
 NX5  H5    C5   C8   119.35  3.000
 NX5  H5    C5   C4   120.06  3.000
 NX5  C8    C5   C4   120.59  3.000
 NX5  H6    C6   C9   119.68  3.000
 NX5  H6    C6   C7   120.29  3.000
 NX5  C9    C6   C7   120.04  3.000
 NX5  H7    C7   C6   119.16  3.000
 NX5  H7    C7   C4   120.06  3.000
 NX5  C6    C7   C4   120.78  3.000
 NX5  CL11  C8   C9   120.61  3.000
 NX5  CL11  C8   C5   119.29  3.000
 NX5  C9    C8   C5   120.10  3.000
 NX5  CL10  C9   C8   120.73  3.000
 NX5  CL10  C9   C6   119.65  3.000
 NX5  C8    C9   C6   119.62  3.000
 NX5  H12   C12  C13  117.69  3.000
 NX5  H12   C12  C1   121.17  3.000
 NX5  C13   C12  C1   121.14  3.000
 NX5  H13   C13  C14  120.58  3.000
 NX5  H13   C13  C12  119.13  3.000
 NX5  C14   C13  C12  120.29  3.000
 NX5  H14   C14  C15  120.54  3.000
 NX5  H14   C14  C13  120.70  3.000
 NX5  C15   C14  C13  118.76  3.000
 NX5  H15   C15  C16  117.96  3.000
 NX5  H15   C15  C14  119.86  3.000
 NX5  C16   C15  C14  122.17  3.000
 NX5  C17   C16  C15  118.74  3.000
 NX5  C17   C16  C1   122.45  3.000
 NX5  C15   C16  C1   118.81  3.000
 NX5  O19   C17  O18  126.64  3.000
 NX5  O18   C17  C16  117.63  3.000
 NX5  O19   C17  C16  115.73  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
 NX5  CONST_01  C14   C15  C16  C1      0.00   0.0  0
 NX5  CONST_02  C14   C13  C12  C1      0.00   0.0  0
 NX5  CONST_03  C9    C6   C7   C4      0.00   0.0  0
 NX5  CONST_04  C9    C8   C5   C4      0.00   0.0  0
 NX5  CONST_05  C6    C7   C4   C5      0.00   0.0  0
 NX5  CONST_06  C6    C9   C8   C5      0.00   0.0  0
 NX5  CONST_07  C8    C5   C4   C7      0.00   0.0  0
 NX5  CONST_08  C8    C9   C6   C7      0.00   0.0  0
 NX5  CONST_09  C15   C16  C1   C12     0.00   0.0  0
 NX5  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 NX5  CONST_11  C16   C1   C12  C13     0.00   0.0  0
 NX5  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 NX5  CONST_13  C15   C16  C1   S2    180.00   0.0  0
 NX5  CONST_14  C13   C12  C1   S2    180.00   0.0  0
 NX5  CONST_15  C6    C7   C4   C3    180.00   0.0  0
 NX5  CONST_16  C8    C5   C4   C3    180.00   0.0  0
 NX5  CONST_17  CL11  C8   C5   C4    180.00   0.0  0
 NX5  CONST_18  CL10  C9   C8   C5    180.00   0.0  0
 NX5  CONST_19  CL11  C8   C9   C6    180.00   0.0  0
 NX5  CONST_20  CL10  C9   C6   C7    180.00   0.0  0
 NX5  CONST_21  C17   C16  C1   C12   180.00   0.0  0
 NX5  CONST_22  C17   C16  C15  C14   180.00   0.0  0
 NX5  CONST_23  H15   C15  C16  C1    180.00   0.0  0
 NX5  CONST_24  H13   C13  C12  C1    180.00   0.0  0
 NX5  CONST_25  H6    C6   C7   C4    180.00   0.0  0
 NX5  CONST_26  H7    C7   C4   C5    180.00   0.0  0
 NX5  CONST_27  H5    C5   C4   C7    180.00   0.0  0
 NX5  CONST_28  H14   C14  C13  C12   180.00   0.0  0
 NX5  CONST_29  H12   C12  C13  C14   180.00   0.0  0
 NX5  Var_01    C4    C3   S2   C1    178.03  30.0  3
 NX5  Var_02    O19   C17  C16  C1     -3.79  30.0  2
 NX5  Var_03    C7    C4   C3   S2    -89.74  30.0  3
 NX5  Var_04    C16   C1   S2   C3   -176.74  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
 NX5  plan-1  C1    0.020
 NX5  plan-1  S2    0.020
 NX5  plan-1  C12   0.020
 NX5  plan-1  C13   0.020
 NX5  plan-1  C14   0.020
 NX5  plan-1  C15   0.020
 NX5  plan-1  C16   0.020
 NX5  plan-1  C17   0.020
 NX5  plan-1  H12   0.020
 NX5  plan-1  H13   0.020
 NX5  plan-1  H14   0.020
 NX5  plan-1  H15   0.020
 NX5  plan-2  C3    0.020
 NX5  plan-2  C4    0.020
 NX5  plan-2  C5    0.020
 NX5  plan-2  C6    0.020
 NX5  plan-2  C7    0.020
 NX5  plan-2  C8    0.020
 NX5  plan-2  C9    0.020
 NX5  plan-2  CL10  0.020
 NX5  plan-2  CL11  0.020
 NX5  plan-2  H5    0.020
 NX5  plan-2  H6    0.020
 NX5  plan-2  H7    0.020
 NX5  plan-3  C16   0.020
 NX5  plan-3  C17   0.020
 NX5  plan-3  O18   0.020
 NX5  plan-3  O19   0.020

