# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 11:40:33 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-(2-cyanophenyl)sulfanyl-~{N}-(3-sulfanylpropyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCCNC(=O)c1ccccc1Sc2ccccc2C#N
#
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
 T4Q  T4Q  2-(2-cyanophenyl)sulfanyl-~{N}-(3-sulfanylpropyl)benzamide  ligand  38  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T4Q
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
 T4Q  N1   N  NS    0  -0.240  13.9502  19.1953  -0.1661
 T4Q  C2   C  CH2   0  -0.312  18.5629  19.9120  -0.1199
 T4Q  C3   C  C     0   0.471  17.2818  19.2891   1.9350
 T4Q  C4   C  CR6   0  -0.017  17.8359  20.5032   2.6264
 T4Q  C6   C  CR16  0  -0.237  19.5383  21.5044   4.0082
 T4Q  C8   C  CR16  0  -0.220  17.5623  22.7537   3.4600
 T4Q  C11  C  CR16  0  -0.203  16.7576  23.1299  -0.1094
 T4Q  C15  C  CR6   0   0.047  15.4189  21.2368  -0.7395
 T4Q  N    N  NH1   0  -0.593  17.6462  19.1029   0.6574
 T4Q  C    C  CH2   0  -0.553  20.0850  18.0083  -0.8148
 T4Q  O    O  O     0  -0.461  16.5451  18.5298   2.5433
 T4Q  C1   C  CH2   0  -0.417  19.9893  19.3741  -0.1522
 T4Q  C10  C  CR6   0  -0.143  15.9371  22.0714   0.2566
 T4Q  C12  C  CR16  0  -0.225  17.0703  23.3432  -1.4432
 T4Q  C13  C  CR16  0  -0.247  16.5475  22.5180  -2.4313
 T4Q  C14  C  CR16  0  -0.235  15.7176  21.4681  -2.0830
 T4Q  C5   C  CR16  0  -0.256  19.0631  20.4270   3.2725
 T4Q  C7   C  CR16  0  -0.248  18.7880  22.6663   4.1056
 T4Q  C9   C  CR6   0  -0.171  17.0883  21.6777   2.7191
 T4Q  S    S  S2    0  -0.253  21.8315  17.4824  -0.8360
 T4Q  S1   S  S2    0   0.078  15.4892  21.7932   1.9493
 T4Q  H1   H  HCH2  0   0.264  18.1685  19.9792  -1.1357
 T4Q  H2   H  HCH2  0   0.271  18.5697  20.9266   0.2747
 T4Q  H3   H  HCR6  0   0.269  20.4938  21.4307   4.5103
 T4Q  H4   H  HCR6  0   0.278  16.9723  23.6583   3.5280
 T4Q  H5   H  HCR6  0   0.285  17.1565  23.7879   0.6515
 T4Q  H6   H  HNH1  0   0.401  17.2700  18.2766   0.2136
 T4Q  H7   H  HCH2  0   0.267  19.5000  17.2687  -0.2683
 T4Q  H8   H  HCH2  0   0.266  19.7081  18.0568  -1.8369
 T4Q  H9   H  HCH2  0   0.246  20.6033  20.0929  -0.7007
 T4Q  H10  H  HCH2  0   0.243  20.3864  19.3264   0.8647
 T4Q  H11  H  HCR6  0   0.279  17.7173  24.1674  -1.7122
 T4Q  H12  H  HCR6  0   0.279  16.7872  22.6914  -3.4713
 T4Q  H13  H  HCR6  0   0.286  15.3105  20.8145  -2.8426
 T4Q  H14  H  HCR6  0   0.272  19.6495  19.5186   3.2106
 T4Q  H15  H  HCR6  0   0.269  19.1534  23.5063   4.6812
 T4Q  H16  H  HSH1  0   0.223  21.6522  16.2855  -1.4056
 T4Q  C16  C  CSP   0   0.035  14.6054  20.1138  -0.3997

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
 T4Q  C13  C14  aromatic  1.383  0.020  1.383
 T4Q  C13  C12  aromatic  1.390  0.020  1.390
 T4Q  C14  C15  aromatic  1.396  0.020  1.396
 T4Q  C12  C11  aromatic  1.386  0.020  1.386
 T4Q  C2   N    single    1.449  0.020  1.449
 T4Q  C2   C1   single    1.525  0.020  1.525
 T4Q  C15  C16  single    1.428  0.020  1.428
 T4Q  C15  C10  aromatic  1.399  0.020  1.399
 T4Q  C    C1   single    1.521  0.020  1.521
 T4Q  C    S    single    1.824  0.020  1.824
 T4Q  C16  N1   triple    1.152  0.020  1.152
 T4Q  C11  C10  aromatic  1.388  0.020  1.388
 T4Q  N    C3   single    1.341  0.020  1.341
 T4Q  C10  S1   single    1.773  0.020  1.773
 T4Q  C3   O    double    1.220  0.020  1.220
 T4Q  C3   C4   single    1.503  0.020  1.503
 T4Q  S1   C9   single    1.778  0.020  1.778
 T4Q  C4   C9   aromatic  1.395  0.020  1.395
 T4Q  C4   C5   aromatic  1.389  0.020  1.389
 T4Q  C9   C8   aromatic  1.390  0.020  1.390
 T4Q  C5   C6   aromatic  1.388  0.020  1.388
 T4Q  C8   C7   aromatic  1.388  0.020  1.388
 T4Q  C6   C7   aromatic  1.387  0.020  1.387
 T4Q  C2   H1   single    0.970  0.020  1.090
 T4Q  C2   H2   single    0.970  0.020  1.090
 T4Q  C6   H3   single    0.930  0.020  1.080
 T4Q  C8   H4   single    0.930  0.020  1.080
 T4Q  C11  H5   single    0.930  0.020  1.080
 T4Q  N    H6   single    0.860  0.020  1.020
 T4Q  C    H7   single    0.970  0.020  1.090
 T4Q  C    H8   single    0.970  0.020  1.090
 T4Q  C1   H9   single    0.970  0.020  1.090
 T4Q  C1   H10  single    0.970  0.020  1.090
 T4Q  C12  H11  single    0.930  0.020  1.080
 T4Q  C13  H12  single    0.930  0.020  1.080
 T4Q  C14  H13  single    0.930  0.020  1.080
 T4Q  C5   H14  single    0.930  0.020  1.080
 T4Q  C7   H15  single    0.930  0.020  1.080
 T4Q  S    H16  single    1.200  0.020  1.300

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
 T4Q  H2   C2   H1   106.38  3.000
 T4Q  H2   C2   C1   109.30  3.000
 T4Q  H1   C2   C1   109.87  3.000
 T4Q  H2   C2   N    109.27  3.000
 T4Q  H1   C2   N    107.76  3.000
 T4Q  C1   C2   N    113.97  3.000
 T4Q  O    C3   N    123.53  3.000
 T4Q  O    C3   C4   119.72  3.000
 T4Q  N    C3   C4   116.75  3.000
 T4Q  C9   C4   C5   119.25  3.000
 T4Q  C5   C4   C3   119.69  3.000
 T4Q  C9   C4   C3   120.86  3.000
 T4Q  H3   C6   C7   120.16  3.000
 T4Q  H3   C6   C5   119.69  3.000
 T4Q  C7   C6   C5   120.15  3.000
 T4Q  H4   C8   C9   119.65  3.000
 T4Q  H4   C8   C7   120.32  3.000
 T4Q  C9   C8   C7   120.03  3.000
 T4Q  H5   C11  C12  119.98  3.000
 T4Q  H5   C11  C10  119.75  3.000
 T4Q  C12  C11  C10  120.28  3.000
 T4Q  C16  C15  C14  118.78  3.000
 T4Q  C16  C15  C10  120.72  3.000
 T4Q  C14  C15  C10  120.48  3.000
 T4Q  H6   N    C3   115.51  3.000
 T4Q  H6   N    C2   117.16  3.000
 T4Q  C3   N    C2   127.25  3.000
 T4Q  H8   C    H7   108.34  3.000
 T4Q  H8   C    S    109.44  3.000
 T4Q  H7   C    S    108.91  3.000
 T4Q  H8   C    C1   110.28  3.000
 T4Q  H7   C    C1   110.93  3.000
 T4Q  S    C    C1   108.91  3.000
 T4Q  H10  C1   H9   106.96  3.000
 T4Q  H10  C1   C    110.08  3.000
 T4Q  H9   C1   C    109.67  3.000
 T4Q  H10  C1   C2   109.61  3.000
 T4Q  H9   C1   C2   107.71  3.000
 T4Q  C    C1   C2   112.63  3.000
 T4Q  S1   C10  C15  119.51  3.000
 T4Q  S1   C10  C11  121.37  3.000
 T4Q  C15  C10  C11  119.08  3.000
 T4Q  H11  C12  C13  120.04  3.000
 T4Q  H11  C12  C11  119.43  3.000
 T4Q  C13  C12  C11  120.52  3.000
 T4Q  H12  C13  C14  119.81  3.000
 T4Q  H12  C13  C12  120.35  3.000
 T4Q  C14  C13  C12  119.84  3.000
 T4Q  H13  C14  C13  120.51  3.000
 T4Q  H13  C14  C15  119.70  3.000
 T4Q  C13  C14  C15  119.79  3.000
 T4Q  H14  C5   C6   119.72  3.000
 T4Q  H14  C5   C4   119.86  3.000
 T4Q  C6   C5   C4   120.42  3.000
 T4Q  H15  C7   C8   119.79  3.000
 T4Q  H15  C7   C6   120.35  3.000
 T4Q  C8   C7   C6   119.86  3.000
 T4Q  S1   C9   C8   119.16  3.000
 T4Q  C8   C9   C4   120.29  3.000
 T4Q  S1   C9   C4   120.51  3.000
 T4Q  H16  S    C     97.73  3.000
 T4Q  C9   S1   C10  101.32  3.000
 T4Q  C15  C16  N1   180.00  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
 T4Q  CONST_01  C7   C8   C9   C4     0.00   0.0  0
 T4Q  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 T4Q  CONST_03  C9   C4   C5   C6     0.00   0.0  0
 T4Q  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 T4Q  CONST_05  C5   C4   C9   C8     0.00   0.0  0
 T4Q  CONST_06  C5   C6   C7   C8     0.00   0.0  0
 T4Q  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 T4Q  CONST_08  C14  C15  C10  C11    0.00   0.0  0
 T4Q  CONST_09  C12  C13  C14  C15    0.00   0.0  0
 T4Q  CONST_10  C12  C11  C10  C15    0.00   0.0  0
 T4Q  CONST_11  C13  C14  C15  C10    0.00   0.0  0
 T4Q  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 T4Q  CONST_13  C8   C9   C4   C3   180.00   0.0  0
 T4Q  CONST_14  C6   C5   C4   C3   180.00   0.0  0
 T4Q  CONST_15  C16  C15  C10  C11  180.00   0.0  0
 T4Q  CONST_16  S1   C10  C11  C12  180.00   0.0  0
 T4Q  CONST_17  C16  C15  C14  C13  180.00   0.0  0
 T4Q  CONST_18  S1   C10  C15  C14  180.00   0.0  0
 T4Q  CONST_19  S1   C9   C4   C5   180.00   0.0  0
 T4Q  CONST_20  S1   C9   C8   C7   180.00   0.0  0
 T4Q  CONST_21  H4   C8   C9   C4   180.00   0.0  0
 T4Q  CONST_22  H3   C6   C5   C4   180.00   0.0  0
 T4Q  CONST_23  H12  C13  C12  C11  180.00   0.0  0
 T4Q  CONST_24  H5   C11  C10  C15  180.00   0.0  0
 T4Q  CONST_25  H13  C14  C15  C10  180.00   0.0  0
 T4Q  CONST_26  H11  C12  C11  C10  180.00   0.0  0
 T4Q  CONST_27  H15  C7   C6   C5   180.00   0.0  0
 T4Q  CONST_28  H14  C5   C6   C7   180.00   0.0  0
 T4Q  CONST_29  C4   C3   N    C2     0.00   0.0  0
 T4Q  CONST_30  H6   N    C3   C4   180.00   0.0  0
 T4Q  CONST_31  O    C3   N    C2   180.00   0.0  0
 T4Q  Var_01    C9   C4   C3   N     97.11  30.0  2
 T4Q  Var_02    S    C    C1   C2   178.60  30.0  1
 T4Q  Var_03    C1   C2   N    C3    96.10  30.0  1
 T4Q  Var_04    C    C1   C2   N     62.89  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
 T4Q  plan-1  C3   0.020
 T4Q  plan-1  C4   0.020
 T4Q  plan-1  C6   0.020
 T4Q  plan-1  C8   0.020
 T4Q  plan-1  C5   0.020
 T4Q  plan-1  C7   0.020
 T4Q  plan-1  C9   0.020
 T4Q  plan-1  S1   0.020
 T4Q  plan-1  H3   0.020
 T4Q  plan-1  H4   0.020
 T4Q  plan-1  H14  0.020
 T4Q  plan-1  H15  0.020
 T4Q  plan-2  N1   0.020
 T4Q  plan-2  C11  0.020
 T4Q  plan-2  C15  0.020
 T4Q  plan-2  C10  0.020
 T4Q  plan-2  C12  0.020
 T4Q  plan-2  C13  0.020
 T4Q  plan-2  C14  0.020
 T4Q  plan-2  S1   0.020
 T4Q  plan-2  H5   0.020
 T4Q  plan-2  H11  0.020
 T4Q  plan-2  H12  0.020
 T4Q  plan-2  H13  0.020
 T4Q  plan-2  C16  0.020
 T4Q  plan-3  C2   0.020
 T4Q  plan-3  C3   0.020
 T4Q  plan-3  C4   0.020
 T4Q  plan-3  N    0.020
 T4Q  plan-3  O    0.020
 T4Q  plan-3  H6   0.020

