# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 15:44:03 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  29  19  .  2021-08-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.105  -2.8350   0.5337  -0.0180
 NX5  S2    S   S2    0   0.108  -1.2038  -0.1222   0.1229
 NX5  C3    C   CH2   0  -0.675  -0.1642   1.3719   0.2401
 NX5  C4    C   CR6   0   0.117   1.2417   0.8750   0.3929
 NX5  C5    C   CR16  0  -0.247   2.0090   0.6005  -0.7325
 NX5  C6    C   CR16  0  -0.200   3.0721   0.1560   1.7883
 NX5  C7    C   CR16  0  -0.285   1.7825   0.6408   1.6528
 NX5  C8    C   CR6   0   0.023   3.3004   0.1147  -0.6018
 NX5  C9    C   CR6   0  -0.015   3.8360  -0.1098   0.6617
 NX5  CL10  CL  CL    0  -0.095   5.4390  -0.7107   0.8422
 NX5  CL11  CL  CL    0  -0.095   4.2285  -0.2033  -2.0174
 NX5  C12   C   CR16  0  -0.255  -3.0555   1.9121  -0.0695
 NX5  C13   C   CR16  0  -0.222  -4.3339   2.4319  -0.1774
 NX5  C14   C   CR16  0  -0.257  -5.4361   1.5922  -0.2380
 NX5  C15   C   CR16  0  -0.252  -5.2373   0.2262  -0.1894
 NX5  C16   C   CR6   0  -0.088  -3.9564  -0.3205  -0.0805
 NX5  C17   C   C     0   0.536  -3.7852  -1.7863  -0.0377
 NX5  O18   O   OH1   0  -0.593  -4.9290  -2.4555  -0.0592
 NX5  O19   O   O     0  -0.439  -2.7071  -2.3329   0.0118
 NX5  H3    H   HCH2  0   0.300  -0.2613   1.9810  -0.6590
 NX5  H3A   H   HCH2  0   0.302  -0.4561   1.9708   1.1030
 NX5  H5    H   HCR6  0   0.287   1.6038   0.7725  -1.7213
 NX5  H6    H   HCR6  0   0.291   3.4883  -0.0182   2.7709
 NX5  H7    H   HCR6  0   0.273   1.1981   0.8426   2.5412
 NX5  H12   H   HCR6  0   0.282  -2.2316   2.6071  -0.0310
 NX5  H13   H   HCR6  0   0.272  -4.4619   3.5058  -0.2142
 NX5  H14   H   HCR6  0   0.267  -6.4357   1.9950  -0.3242
 NX5  H15   H   HCR6  0   0.274  -6.0950  -0.4290  -0.2390
 NX5  HO18  H   HOH1  0   0.490  -4.7524  -3.4075  -0.0341

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    1.764  0.020  1.764
 NX5  C1    C16   aromatic  1.411  0.020  1.411
 NX5  C1    C12   aromatic  1.397  0.020  1.397
 NX5  S2    C3    single    1.824  0.020  1.824
 NX5  C4    C3    single    1.499  0.020  1.499
 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  1.389  0.020  1.389
 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  1.391  0.020  1.391
 NX5  CL11  C8    single    1.722  0.020  1.722
 NX5  CL10  C9    single    1.721  0.020  1.721
 NX5  C12   C13   aromatic  1.384  0.020  1.384
 NX5  C12   H12   single    0.930  0.020  1.080
 NX5  C13   C14   aromatic  1.387  0.020  1.387
 NX5  C13   H13   single    0.930  0.020  1.080
 NX5  C15   C14   aromatic  1.381  0.020  1.381
 NX5  C14   H14   single    0.930  0.020  1.080
 NX5  C16   C15   aromatic  1.397  0.020  1.397
 NX5  C15   H15   single    0.930  0.020  1.080
 NX5  C17   C16   single    1.476  0.020  1.476
 NX5  O19   C17   double    1.210  0.020  1.210
 NX5  C17   O18   single    1.325  0.020  1.325
 NX5  O18   HO18  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
 NX5  C16   C1   C12  118.05  3.000
 NX5  C12   C1   S2   121.06  3.000
 NX5  C16   C1   S2   120.89  3.000
 NX5  C3    S2   C1   103.16  3.000
 NX5  H3A   C3   H3   108.79  3.000
 NX5  H3A   C3   C4   110.64  3.000
 NX5  H3    C3   C4   110.65  3.000
 NX5  H3A   C3   S2   110.38  3.000
 NX5  H3    C3   S2   110.72  3.000
 NX5  C4    C3   S2   105.64  3.000
 NX5  C7    C4   C5   119.06  3.000
 NX5  C5    C4   C3   120.06  3.000
 NX5  C7    C4   C3   120.85  3.000
 NX5  H5    C5   C8   119.38  3.000
 NX5  H5    C5   C4   120.12  3.000
 NX5  C8    C5   C4   120.49  3.000
 NX5  H6    C6   C9   119.69  3.000
 NX5  H6    C6   C7   120.27  3.000
 NX5  C9    C6   C7   120.04  3.000
 NX5  H7    C7   C6   119.20  3.000
 NX5  H7    C7   C4   120.15  3.000
 NX5  C6    C7   C4   120.65  3.000
 NX5  CL11  C8   C9   120.62  3.000
 NX5  CL11  C8   C5   119.30  3.000
 NX5  C9    C8   C5   120.08  3.000
 NX5  CL10  C9   C8   120.68  3.000
 NX5  CL10  C9   C6   119.64  3.000
 NX5  C8    C9   C6   119.67  3.000
 NX5  H12   C12  C13  117.79  3.000
 NX5  H12   C12  C1   120.92  3.000
 NX5  C13   C12  C1   121.28  3.000
 NX5  H13   C13  C14  120.36  3.000
 NX5  H13   C13  C12  118.98  3.000
 NX5  C14   C13  C12  120.66  3.000
 NX5  H14   C14  C15  120.29  3.000
 NX5  H14   C14  C13  120.84  3.000
 NX5  C15   C14  C13  118.87  3.000
 NX5  H15   C15  C16  119.61  3.000
 NX5  H15   C15  C14  118.93  3.000
 NX5  C16   C15  C14  121.45  3.000
 NX5  C17   C16  C15  119.82  3.000
 NX5  C17   C16  C1   120.50  3.000
 NX5  C15   C16  C1   119.69  3.000
 NX5  O19   C17  O18  122.79  3.000
 NX5  O18   C17  C16  113.62  3.000
 NX5  O19   C17  C16  123.58  3.000
 NX5  HO18  O18  C17  109.79  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  CONST_30  HO18  O18  C17  C16   180.00   0.0  0
 NX5  Var_01    C4    C3   S2   C1    178.80  30.0  3
 NX5  Var_02    O19   C17  C16  C1     -2.21  30.0  3
 NX5  Var_03    C7    C4   C3   S2    -90.25  30.0  2
 NX5  Var_04    C16   C1   S2   C3   -177.50  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
 NX5  plan-3  HO18  0.020

