# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 09:07:26 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-[1,1-bis(oxidanylidene)thian-4-yl]-5-methyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(c2cccc(c2)C(F)(F)F)c3sc(cc3C1=O)C(=N)NC4CC[S](=O)(=O)CC4
#
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
 5V2  5V2  N-[1,1-bis(oxidanylidene)thian-4-yl]-5-methyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide  ligand  52  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5V2
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
 5V2  C01   C  CH3   0  -0.484   4.2959   4.4794   0.4200
 5V2  N05   N  NR6   0  -0.531   3.2778   3.4429   0.3092
 5V2  C06   C  CR16  0   0.028   3.6272   2.1393   0.4788
 5V2  C08   C  CR6   0  -0.035   2.7499   1.1040   0.3922
 5V2  C09   C  CR6   0   0.066   3.1850  -0.2919   0.5756
 5V2  C10   C  CR16  0  -0.282   2.5148  -1.1389   1.4607
 5V2  C12   C  CR16  0  -0.189   2.9301  -2.4482   1.6308
 5V2  C14   C  CR16  0  -0.279   4.0233  -2.9372   0.9286
 5V2  C16   C  CR6   0  -0.159   4.6960  -2.0999   0.0509
 5V2  C17   C  CR16  0  -0.324   4.2764  -0.7863  -0.1299
 5V2  C19   C  CT    0   1.052   5.8793  -2.5796  -0.7304
 5V2  F20   F  F     0  -0.301   6.1388  -3.8739  -0.5305
 5V2  F21   F  F     0  -0.310   5.7019  -2.4136  -2.0490
 5V2  F22   F  F     0  -0.312   6.9910  -1.9016  -0.4095
 5V2  C23   C  CR56  0  -0.152   1.4096   1.4648   0.0986
 5V2  S24   S  S2    0   0.249   0.0843   0.3989  -0.1465
 5V2  C25   C  CR5   0  -0.248  -0.9866   1.7301  -0.4725
 5V2  C26   C  CR15  0  -0.164  -0.3448   2.9244  -0.4112
 5V2  C28   C  CR56  0  -0.009   1.0289   2.7833  -0.0820
 5V2  C29   C  CR6   0   0.556   1.9844   3.8582   0.0329
 5V2  O30   O  O     0  -0.434   1.7193   5.0446  -0.1021
 5V2  C31   C  C     0   0.401  -2.4063   1.5036  -0.8006
 5V2  N32   N  N     0  -0.579  -2.9843   2.3617  -1.5481
 5V2  N34   N  NH1   0  -0.657  -2.9198   0.3462  -0.2831
 5V2  C36   C  CH1   0  -0.083  -4.2981  -0.0512  -0.4526
 5V2  C38   C  CH2   0  -0.452  -4.3850  -1.5738  -0.3372
 5V2  C41   C  CH2   0  -0.609  -5.7868  -2.1026  -0.6039
 5V2  S44   S  S     0   1.215  -6.9607  -1.4292   0.5643
 5V2  O45   O  OS    0  -0.629  -8.3203  -1.7768   0.1523
 5V2  O46   O  OS    0  -0.641  -6.5309  -1.8005   1.9147
 5V2  C47   C  CH2   0  -0.604  -6.6879   0.3249   0.3492
 5V2  C50   C  CH2   0  -0.451  -5.2175   0.6677   0.5434
 5V2  H011  H  HCH3  0   0.261   4.3507   5.0583  -0.4992
 5V2  H012  H  HCH3  0   0.253   4.0747   5.1508   1.2471
 5V2  H013  H  HCH3  0   0.226   5.2586   4.0106   0.5962
 5V2  H06   H  HCR6  0   0.273   4.6687   1.9654   0.7108
 5V2  H10   H  HCR6  0   0.244   1.6783  -0.7673   2.0390
 5V2  H17   H  HCR6  0   0.251   4.7840  -0.1384  -0.8341
 5V2  H12   H  HCR6  0   0.245   2.4070  -3.0928   2.3237
 5V2  H14   H  HCR6  0   0.246   4.3336  -3.9620   1.0762
 5V2  H26   H  HCR5  0   0.266  -0.8357   3.8699  -0.5886
 5V2  H32   H  H     0   0.300  -3.9701   2.1633  -1.6850
 5V2  H34   H  HNH1  0   0.366  -2.4760  -0.0090   0.5517
 5V2  H36   H  HCH1  0   0.222  -4.6022   0.2159  -1.4705
 5V2  H381  H  HCH2  0   0.270  -3.7121  -2.0248  -1.0680
 5V2  H382  H  HCH2  0   0.252  -4.0465  -1.8996   0.6501
 5V2  H501  H  HCH2  0   0.256  -4.9080   0.4299   1.5640
 5V2  H502  H  HCH2  0   0.265  -5.1124   1.7483   0.4304
 5V2  H411  H  HCH2  0   0.269  -6.1412  -1.8332  -1.6009
 5V2  H412  H  HCH2  0   0.309  -5.8401  -3.1880  -0.5014
 5V2  H471  H  HCH2  0   0.268  -7.0413   0.5812  -0.6516
 5V2  H472  H  HCH2  0   0.308  -7.3258   0.8273   1.0788

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
 5V2  C01  N05   single    1.457  0.020  1.457
 5V2  N05  C06   single    1.360  0.020  1.360
 5V2  N05  C29   single    1.386  0.020  1.386
 5V2  C06  C08   double    1.360  0.020  1.360
 5V2  C08  C09   single    1.474  0.020  1.474
 5V2  C08  C23   single    1.419  0.020  1.419
 5V2  C09  C10   aromatic  1.396  0.020  1.396
 5V2  C09  C17   aromatic  1.390  0.020  1.390
 5V2  C10  C12   aromatic  1.384  0.020  1.384
 5V2  C12  C14   aromatic  1.388  0.020  1.388
 5V2  C14  C16   aromatic  1.387  0.020  1.387
 5V2  C16  C17   aromatic  1.391  0.020  1.391
 5V2  C16  C19   single    1.497  0.020  1.497
 5V2  C19  F20   single    1.335  0.020  1.335
 5V2  C19  F21   single    1.341  0.020  1.341
 5V2  C19  F22   single    1.341  0.020  1.341
 5V2  C23  S24   aromatic  1.718  0.020  1.718
 5V2  C23  C28   aromatic  1.384  0.020  1.384
 5V2  S24  C25   aromatic  1.739  0.020  1.739
 5V2  C25  C26   aromatic  1.357  0.020  1.357
 5V2  C25  C31   single    1.475  0.020  1.475
 5V2  C26  C28   aromatic  1.420  0.020  1.420
 5V2  C28  C29   single    1.443  0.020  1.443
 5V2  C29  O30   double    1.223  0.020  1.223
 5V2  C31  N32   double    1.276  0.020  1.276
 5V2  C31  N34   single    1.368  0.020  1.368
 5V2  N34  C36   single    1.444  0.020  1.444
 5V2  C36  C38   single    1.529  0.020  1.529
 5V2  C36  C50   single    1.534  0.020  1.534
 5V2  C38  C41   single    1.522  0.020  1.522
 5V2  C41  S44   single    1.788  0.020  1.788
 5V2  S44  O45   double    1.462  0.020  1.462
 5V2  S44  O46   double    1.465  0.020  1.465
 5V2  S44  C47   single    1.788  0.020  1.788
 5V2  C47  C50   single    1.522  0.020  1.522
 5V2  C01  H011  single    0.970  0.020  1.090
 5V2  C01  H012  single    0.970  0.020  1.090
 5V2  C01  H013  single    0.970  0.020  1.090
 5V2  C06  H06   single    0.930  0.020  1.080
 5V2  C10  H10   single    0.930  0.020  1.080
 5V2  C17  H17   single    0.930  0.020  1.080
 5V2  C12  H12   single    0.930  0.020  1.080
 5V2  C14  H14   single    0.930  0.020  1.080
 5V2  C26  H26   single    0.930  0.020  1.080
 5V2  N32  H32   single    0.890  0.020  1.040
 5V2  N34  H34   single    0.890  0.020  1.040
 5V2  C36  H36   single    0.970  0.020  1.090
 5V2  C38  H381  single    0.970  0.020  1.090
 5V2  C38  H382  single    0.970  0.020  1.090
 5V2  C50  H501  single    0.970  0.020  1.090
 5V2  C50  H502  single    0.970  0.020  1.090
 5V2  C41  H411  single    0.970  0.020  1.090
 5V2  C41  H412  single    0.970  0.020  1.090
 5V2  C47  H471  single    0.970  0.020  1.090
 5V2  C47  H472  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
 5V2  H013  C01  H012  108.87  3.000
 5V2  H013  C01  H011  108.81  3.000
 5V2  H012  C01  H011  108.93  3.000
 5V2  H013  C01  N05   108.96  3.000
 5V2  H012  C01  N05   110.77  3.000
 5V2  H011  C01  N05   110.46  3.000
 5V2  C29   N05  C06   123.48  3.000
 5V2  C29   N05  C01   117.00  3.000
 5V2  C06   N05  C01   119.52  3.000
 5V2  H06   C06  C08   120.84  3.000
 5V2  H06   C06  N05   115.37  3.000
 5V2  C08   C06  N05   123.78  3.000
 5V2  C23   C08  C09   123.07  3.000
 5V2  C23   C08  C06   115.41  3.000
 5V2  C09   C08  C06   121.52  3.000
 5V2  C17   C09  C10   118.86  3.000
 5V2  C17   C09  C08   120.36  3.000
 5V2  C10   C09  C08   120.78  3.000
 5V2  H10   C10  C12   119.40  3.000
 5V2  H10   C10  C09   120.07  3.000
 5V2  C12   C10  C09   120.51  3.000
 5V2  H12   C12  C14   119.67  3.000
 5V2  H12   C12  C10   119.84  3.000
 5V2  C14   C12  C10   120.48  3.000
 5V2  H14   C14  C16   121.30  3.000
 5V2  H14   C14  C12   119.41  3.000
 5V2  C16   C14  C12   119.29  3.000
 5V2  C19   C16  C17   118.25  3.000
 5V2  C19   C16  C14   121.34  3.000
 5V2  C17   C16  C14   120.41  3.000
 5V2  H17   C17  C16   120.53  3.000
 5V2  H17   C17  C09   119.01  3.000
 5V2  C16   C17  C09   120.44  3.000
 5V2  F22   C19  F21   106.40  3.000
 5V2  F22   C19  F20   107.05  3.000
 5V2  F21   C19  F20   107.03  3.000
 5V2  F22   C19  C16   111.62  3.000
 5V2  F21   C19  C16   111.66  3.000
 5V2  F20   C19  C16   112.72  3.000
 5V2  C28   C23  S24   111.10  3.000
 5V2  C28   C23  C08   121.94  3.000
 5V2  S24   C23  C08   126.90  3.000
 5V2  C25   S24  C23    91.54  3.000
 5V2  C31   C25  C26   126.91  3.000
 5V2  C31   C25  S24   121.12  3.000
 5V2  C26   C25  S24   111.95  3.000
 5V2  H26   C26  C28   124.40  3.000
 5V2  H26   C26  C25   123.23  3.000
 5V2  C28   C26  C25   112.37  3.000
 5V2  C29   C28  C26   125.82  3.000
 5V2  C29   C28  C23   121.14  3.000
 5V2  C26   C28  C23   113.02  3.000
 5V2  O30   C29  C28   124.77  3.000
 5V2  O30   C29  N05   120.98  3.000
 5V2  C28   C29  N05   114.24  3.000
 5V2  N34   C31  N32   128.35  3.000
 5V2  N34   C31  C25   114.03  3.000
 5V2  N32   C31  C25   117.57  3.000
 5V2  H32   N32  C31   112.79  3.000
 5V2  H34   N34  C36   114.80  3.000
 5V2  H34   N34  C31   116.45  3.000
 5V2  C36   N34  C31   123.14  3.000
 5V2  H36   C36  C50   108.83  3.000
 5V2  H36   C36  C38   107.28  3.000
 5V2  C50   C36  C38   112.55  3.000
 5V2  H36   C36  N34   107.86  3.000
 5V2  C50   C36  N34   111.52  3.000
 5V2  C38   C36  N34   108.61  3.000
 5V2  H382  C38  H381  106.90  3.000
 5V2  H382  C38  C41   109.87  3.000
 5V2  H381  C38  C41   107.88  3.000
 5V2  H382  C38  C36   110.32  3.000
 5V2  H381  C38  C36   109.02  3.000
 5V2  C41   C38  C36   112.64  3.000
 5V2  H412  C41  H411  108.38  3.000
 5V2  H412  C41  S44   106.33  3.000
 5V2  H411  C41  S44   106.90  3.000
 5V2  H412  C41  C38   111.96  3.000
 5V2  H411  C41  C38   111.92  3.000
 5V2  S44   C41  C38   111.07  3.000
 5V2  C47   S44  O46   108.34  3.000
 5V2  C47   S44  O45   109.94  3.000
 5V2  O46   S44  O45   118.18  3.000
 5V2  C47   S44  C41   100.99  3.000
 5V2  O46   S44  C41   108.31  3.000
 5V2  O45   S44  C41   109.68  3.000
 5V2  H472  C47  H471  108.39  3.000
 5V2  H472  C47  C50   112.06  3.000
 5V2  H471  C47  C50   112.13  3.000
 5V2  H472  C47  S44   106.38  3.000
 5V2  H471  C47  S44   106.93  3.000
 5V2  C50   C47  S44   110.67  3.000
 5V2  H502  C50  H501  106.55  3.000
 5V2  H502  C50  C47   107.63  3.000
 5V2  H501  C50  C47   110.11  3.000
 5V2  H502  C50  C36   109.80  3.000
 5V2  H501  C50  C36   109.55  3.000
 5V2  C47   C50  C36   112.98  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
 5V2  CONST_01  C14   C12  C10  C09     0.00   0.0  0
 5V2  CONST_02  C14   C16  C17  C09     0.00   0.0  0
 5V2  CONST_03  C16   C17  C09  C10     0.00   0.0  0
 5V2  CONST_04  C16   C14  C12  C10     0.00   0.0  0
 5V2  CONST_05  C17   C09  C10  C12     0.00   0.0  0
 5V2  CONST_06  C17   C16  C14  C12     0.00   0.0  0
 5V2  CONST_07  C26   C25  S24  C23     0.00   0.0  0
 5V2  CONST_08  C25   C26  C28  C23     0.00   0.0  0
 5V2  CONST_09  C26   C28  C23  S24     0.00   0.0  0
 5V2  CONST_10  C28   C26  C25  S24     0.00   0.0  0
 5V2  CONST_11  C28   C23  S24  C25     0.00   0.0  0
 5V2  CONST_12  C12   C10  C09  C08   180.00   0.0  0
 5V2  CONST_13  C16   C17  C09  C08   180.00   0.0  0
 5V2  CONST_14  C28   C29  N05  C06     0.00   0.0  0
 5V2  CONST_15  C19   C16  C17  C09   180.00   0.0  0
 5V2  CONST_16  C19   C16  C14  C12   180.00   0.0  0
 5V2  CONST_17  C31   C25  S24  C23   180.00   0.0  0
 5V2  CONST_18  C31   C25  C26  C28   180.00   0.0  0
 5V2  CONST_19  C28   C29  N05  C01   180.00   0.0  0
 5V2  CONST_20  O30   C29  N05  C06   180.00   0.0  0
 5V2  CONST_21  H10   C10  C09  C08     0.00   0.0  0
 5V2  CONST_22  H17   C17  C09  C08     0.00   0.0  0
 5V2  CONST_23  H12   C12  C10  C09   180.00   0.0  0
 5V2  CONST_24  H14   C14  C12  C10   180.00   0.0  0
 5V2  CONST_25  H26   C26  C28  C23   180.00   0.0  0
 5V2  CONST_26  O30   C29  N05  C01     0.00   0.0  0
 5V2  CONST_27  C36   N34  C31  C25   180.00   0.0  0
 5V2  CONST_28  C36   N34  C31  N32     0.00   0.0  0
 5V2  CONST_29  H32   N32  C31  C25   180.00   0.0  0
 5V2  Var_01    C10   C09  C08  C06   129.27  30.0  2
 5V2  Var_02    S44   C41  C38  C36   -60.30  30.0  1
 5V2  Var_03    S44   C47  C50  C36    60.22  30.0  1
 5V2  Var_04    C47   S44  C41  C38    54.74  30.0  1
 5V2  Var_05    C50   C47  S44  C41   -54.50  30.0  1
 5V2  Var_06    F20   C19  C16  C14     3.22  30.0  2
 5V2  Var_07    N32   C31  C25  S24  -151.03  30.0  2
 5V2  Var_08    H011  C01  N05  C06   121.85  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5V2  chir_01  C36  N34  C38  C50  negativ

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
 5V2  plan-1  C08  0.020
 5V2  plan-1  C09  0.020
 5V2  plan-1  C10  0.020
 5V2  plan-1  C12  0.020
 5V2  plan-1  C14  0.020
 5V2  plan-1  C16  0.020
 5V2  plan-1  C17  0.020
 5V2  plan-1  C19  0.020
 5V2  plan-1  H10  0.020
 5V2  plan-1  H17  0.020
 5V2  plan-1  H12  0.020
 5V2  plan-1  H14  0.020
 5V2  plan-2  C01  0.020
 5V2  plan-2  N05  0.020
 5V2  plan-2  C06  0.020
 5V2  plan-2  C08  0.020
 5V2  plan-2  C09  0.020
 5V2  plan-2  C23  0.020
 5V2  plan-2  S24  0.020
 5V2  plan-2  C25  0.020
 5V2  plan-2  C26  0.020
 5V2  plan-2  C28  0.020
 5V2  plan-2  C29  0.020
 5V2  plan-2  O30  0.020
 5V2  plan-2  C31  0.020
 5V2  plan-2  H06  0.020
 5V2  plan-2  H26  0.020
 5V2  plan-3  C25  0.020
 5V2  plan-3  C31  0.020
 5V2  plan-3  N32  0.020
 5V2  plan-3  N34  0.020
 5V2  plan-3  C36  0.020
 5V2  plan-3  H32  0.020
 5V2  plan-3  H34  0.020

