# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:03:44 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 3-[(3,4-dichlorobenzyl)sulfanyl]-N-(methylsulfonyl)thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)NC(=O)c1sccc1SCc2ccc(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
 NX2  NX2  3-[(3,4-dichlorobenzyl)sulfanyl]-N-(methylsulfonyl)thiophene-2-carboxamide  ligand  33  22  .  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_NX2
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
 NX2  C1    C   CR5   0   0.004  -1.2590   1.7047  -0.0312
 NX2  C2    C   CR15  0  -0.169  -1.1981   3.1223  -0.1281
 NX2  C3    C   CR15  0  -0.432  -2.4281   3.6920  -0.2522
 NX2  S4    S   S2    0   0.266  -3.6835   2.5468  -0.2612
 NX2  C5    C   CR5   0  -0.356  -2.5623   1.2452  -0.0802
 NX2  S6    S   S2    0   0.121   0.1195   0.6473   0.1292
 NX2  C7    C   CH2   0  -0.666   1.4981   1.8399   0.2181
 NX2  C8    C   CR6   0   0.112   2.7454   1.0306   0.4021
 NX2  C9    C   CR16  0  -0.247   3.4430   0.5680  -0.7065
 NX2  C10   C   CR16  0  -0.200   4.3416  -0.0657   1.8381
 NX2  C11   C   CR16  0  -0.283   3.1993   0.6988   1.6744
 NX2  C12   C   CR6   0   0.023   4.5861  -0.1997  -0.5474
 NX2  C13   C   CR6   0  -0.014   5.0395  -0.5177   0.7280
 NX2  CL14  CL  CL    0  -0.093   6.4604  -1.4646   0.9452
 NX2  CL15  CL  CL    0  -0.094   5.4319  -0.7519  -1.9419
 NX2  C16   C   C     0   0.600  -2.9399  -0.1555  -0.0088
 NX2  N17   N   NC1   0  -0.857  -4.2872  -0.4343   0.0631
 NX2  O18   O   O     0  -0.439  -2.1046  -1.0401  -0.0058
 NX2  S19   S   S     0   1.361  -4.9179  -1.9909  -0.0308
 NX2  C20   C   CH3   0  -0.793  -4.4141  -2.7639   1.4797
 NX2  O21   O   OS    0  -0.652  -6.3545  -1.7882  -0.0124
 NX2  O22   O   OS    0  -0.638  -4.3042  -2.6727  -1.1513
 NX2  H2    H   HCR5  0   0.294  -0.2911   3.7064  -0.1122
 NX2  H3    H   HCR5  0   0.320  -2.6524   4.7435  -0.3467
 NX2  H7    H   HCH2  0   0.306   1.5447   2.4200  -0.7034
 NX2  H7A   H   HCH2  0   0.307   1.3481   2.5204   1.0560
 NX2  H9    H   HCR6  0   0.288   3.1001   0.8094  -1.7044
 NX2  H10   H   HCR6  0   0.292   4.6953  -0.3116   2.8297
 NX2  H11   H   HCR6  0   0.274   2.6638   1.0435   2.5495
 NX2  HN17  H   HNC1  0   0.444  -4.9755   0.2865   0.2455
 NX2  H20   H   HCH3  0   0.303  -4.8211  -2.2012   2.3158
 NX2  H20A  H   HCH3  0   0.315  -4.8214  -3.7741   1.4724
 NX2  H20B  H   HCH3  0   0.302  -3.3295  -2.8006   1.5274

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
 NX2  S6    C1    single    1.745  0.020  1.745
 NX2  C1    C5    aromatic  1.383  0.020  1.383
 NX2  C1    C2    aromatic  1.422  0.020  1.422
 NX2  C2    C3    aromatic  1.361  0.020  1.361
 NX2  C2    H2    single    0.930  0.020  1.080
 NX2  S4    C3    aromatic  1.699  0.020  1.699
 NX2  C3    H3    single    0.930  0.020  1.080
 NX2  C5    S4    aromatic  1.727  0.020  1.727
 NX2  C16   C5    single    1.452  0.020  1.452
 NX2  S6    C7    single    1.825  0.020  1.825
 NX2  C8    C7    single    1.498  0.020  1.498
 NX2  C7    H7    single    0.970  0.020  1.090
 NX2  C7    H7A   single    0.970  0.020  1.090
 NX2  C11   C8    aromatic  1.391  0.020  1.391
 NX2  C9    C8    aromatic  1.389  0.020  1.389
 NX2  C12   C9    aromatic  1.386  0.020  1.386
 NX2  C9    H9    single    0.930  0.020  1.080
 NX2  C13   C10   aromatic  1.387  0.020  1.387
 NX2  C10   C11   aromatic  1.384  0.020  1.384
 NX2  C10   H10   single    0.930  0.020  1.080
 NX2  C11   H11   single    0.930  0.020  1.080
 NX2  C13   C12   aromatic  1.390  0.020  1.390
 NX2  CL15  C12   single    1.722  0.020  1.722
 NX2  CL14  C13   single    1.721  0.020  1.721
 NX2  O18   C16   double    1.217  0.020  1.217
 NX2  C16   N17   single    1.378  0.020  1.378
 NX2  S19   N17   single    1.682  0.020  1.682
 NX2  N17   HN17  single    0.860  0.020  1.020
 NX2  O21   S19   double    1.451  0.020  1.451
 NX2  C20   S19   single    1.770  0.020  1.770
 NX2  S19   O22   double    1.448  0.020  1.448
 NX2  C20   H20   single    0.970  0.020  1.090
 NX2  C20   H20A  single    0.970  0.020  1.090
 NX2  C20   H20B  single    0.970  0.020  1.090

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
 NX2  S6    C1   C5    123.13  3.000
 NX2  C5    C1   C2    111.66  3.000
 NX2  S6    C1   C2    125.20  3.000
 NX2  H2    C2   C3    122.30  3.000
 NX2  H2    C2   C1    125.08  3.000
 NX2  C3    C2   C1    112.62  3.000
 NX2  H3    C3   S4    120.17  3.000
 NX2  H3    C3   C2    127.12  3.000
 NX2  S4    C3   C2    112.71  3.000
 NX2  C5    S4   C3     91.59  3.000
 NX2  C16   C5   S4    124.27  3.000
 NX2  C16   C5   C1    124.32  3.000
 NX2  S4    C5   C1    111.41  3.000
 NX2  C7    S6   C1    101.84  3.000
 NX2  H7A   C7   H7    108.89  3.000
 NX2  H7A   C7   C8    110.94  3.000
 NX2  H7    C7   C8    110.84  3.000
 NX2  H7A   C7   S6    109.97  3.000
 NX2  H7    C7   S6    109.81  3.000
 NX2  C8    C7   S6    106.37  3.000
 NX2  C11   C8   C9    119.12  3.000
 NX2  C9    C8   C7    120.00  3.000
 NX2  C11   C8   C7    120.85  3.000
 NX2  H9    C9   C12   119.38  3.000
 NX2  H9    C9   C8    120.16  3.000
 NX2  C12   C9   C8    120.46  3.000
 NX2  H10   C10  C13   119.69  3.000
 NX2  H10   C10  C11   120.27  3.000
 NX2  C13   C10  C11   120.04  3.000
 NX2  H11   C11  C10   119.25  3.000
 NX2  H11   C11  C8    120.14  3.000
 NX2  C10   C11  C8    120.61  3.000
 NX2  CL15  C12  C13   120.62  3.000
 NX2  CL15  C12  C9    119.32  3.000
 NX2  C13   C12  C9    120.05  3.000
 NX2  CL14  C13  C12   120.71  3.000
 NX2  CL14  C13  C10   119.58  3.000
 NX2  C12   C13  C10   119.71  3.000
 NX2  O18   C16  N17   121.61  3.000
 NX2  N17   C16  C5    116.87  3.000
 NX2  O18   C16  C5    121.52  3.000
 NX2  HN17  N17  S19   114.43  3.000
 NX2  HN17  N17  C16   121.99  3.000
 NX2  S19   N17  C16   123.44  3.000
 NX2  O22   S19  O21   119.68  3.000
 NX2  O22   S19  C20   109.52  3.000
 NX2  O21   S19  C20   109.39  3.000
 NX2  O22   S19  N17   108.66  3.000
 NX2  C20   S19  N17   104.47  3.000
 NX2  O21   S19  N17   103.96  3.000
 NX2  H20B  C20  H20A  110.03  3.000
 NX2  H20B  C20  H20   110.95  3.000
 NX2  H20A  C20  H20   110.20  3.000
 NX2  H20B  C20  S19   109.65  3.000
 NX2  H20A  C20  S19   107.03  3.000
 NX2  H20   C20  S19   108.89  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
 NX2  CONST_01  C3    S4   C5   C1      0.00   0.0  0
 NX2  CONST_02  S4    C3   C2   C1      0.00   0.0  0
 NX2  CONST_03  S4    C5   C1   C2      0.00   0.0  0
 NX2  CONST_04  C5    S4   C3   C2      0.00   0.0  0
 NX2  CONST_05  C5    C1   C2   C3      0.00   0.0  0
 NX2  CONST_06  C13   C10  C11  C8      0.00   0.0  0
 NX2  CONST_07  C13   C12  C9   C8      0.00   0.0  0
 NX2  CONST_08  C10   C11  C8   C9      0.00   0.0  0
 NX2  CONST_09  C10   C13  C12  C9      0.00   0.0  0
 NX2  CONST_10  C12   C9   C8   C11     0.00   0.0  0
 NX2  CONST_11  C12   C13  C10  C11     0.00   0.0  0
 NX2  CONST_12  C16   C5   C1   C2    180.00   0.0  0
 NX2  CONST_13  S6    C1   C2   C3    180.00   0.0  0
 NX2  CONST_14  C16   C5   S4   C3    180.00   0.0  0
 NX2  CONST_15  S6    C1   C5   S4    180.00   0.0  0
 NX2  CONST_16  C10   C11  C8   C7    180.00   0.0  0
 NX2  CONST_17  C12   C9   C8   C7    180.00   0.0  0
 NX2  CONST_18  CL15  C12  C9   C8    180.00   0.0  0
 NX2  CONST_19  CL14  C13  C12  C9    180.00   0.0  0
 NX2  CONST_20  CL15  C12  C13  C10   180.00   0.0  0
 NX2  CONST_21  CL14  C13  C10  C11   180.00   0.0  0
 NX2  CONST_22  H3    C3   C2   C1    180.00   0.0  0
 NX2  CONST_23  H2    C2   C3   S4    180.00   0.0  0
 NX2  CONST_24  H10   C10  C11  C8    180.00   0.0  0
 NX2  CONST_25  H11   C11  C8   C9    180.00   0.0  0
 NX2  CONST_26  H9    C9   C8   C11   180.00   0.0  0
 NX2  CONST_27  S19   N17  C16  C5    180.00   0.0  0
 NX2  CONST_28  HN17  N17  C16  C5      0.00   0.0  0
 NX2  CONST_29  S19   N17  C16  O18     0.00   0.0  0
 NX2  Var_01    C8    C7   S6   C1    178.27  30.0  3
 NX2  Var_02    O18   C16  C5   C1     -5.95  30.0  2
 NX2  Var_03    C11   C8   C7   S6    -89.34  30.0  2
 NX2  Var_04    O21   S19  N17  C16  -175.83  30.0  1
 NX2  Var_05    H20   C20  S19  N17    59.68  30.0  3

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
 NX2  plan-1  C1    0.020
 NX2  plan-1  C2    0.020
 NX2  plan-1  C3    0.020
 NX2  plan-1  S4    0.020
 NX2  plan-1  C5    0.020
 NX2  plan-1  S6    0.020
 NX2  plan-1  C16   0.020
 NX2  plan-1  H2    0.020
 NX2  plan-1  H3    0.020
 NX2  plan-2  C7    0.020
 NX2  plan-2  C8    0.020
 NX2  plan-2  C9    0.020
 NX2  plan-2  C10   0.020
 NX2  plan-2  C11   0.020
 NX2  plan-2  C12   0.020
 NX2  plan-2  C13   0.020
 NX2  plan-2  CL14  0.020
 NX2  plan-2  CL15  0.020
 NX2  plan-2  H9    0.020
 NX2  plan-2  H10   0.020
 NX2  plan-2  H11   0.020
 NX2  plan-3  C5    0.020
 NX2  plan-3  C16   0.020
 NX2  plan-3  N17   0.020
 NX2  plan-3  O18   0.020
 NX2  plan-3  S19   0.020
 NX2  plan-3  HN17  0.020

