# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 10:29:32 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C=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
 H1B  H1B  N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide  ligand  55  33  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H1B
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
 H1B  C01   C  CH3   0  -0.662   5.0091  -4.2500   1.4364
 H1B  C05   C  CH2   0  -0.323   4.5547  -4.0764  -0.0017
 H1B  N08   N  NR6   0  -0.528   3.3878  -3.1968  -0.1138
 H1B  C09   C  CR16  0   0.003   3.5928  -1.8758  -0.3627
 H1B  C11   C  CR6   0  -0.038   2.5958  -0.9553  -0.4586
 H1B  C12   C  CR6   0   0.061   2.8894   0.4611  -0.7398
 H1B  C13   C  CR16  0  -0.306   2.2001   1.1530  -1.7380
 H1B  C15   C  CR16  0  -0.221   2.4897   2.4805  -2.0026
 H1B  C17   C  CR16  0  -0.295   3.4780   3.1425  -1.2870
 H1B  C19   C  CR6   0  -0.173   4.1714   2.4596  -0.2985
 H1B  C20   C  CR16  0  -0.334   3.8747   1.1298  -0.0210
 H1B  C22   C  CT    0   1.054   5.2601   3.1213   0.4871
 H1B  F23   F  F     0  -0.301   5.3616   4.4282   0.2336
 H1B  F24   F  F     0  -0.313   5.0702   2.9902   1.8076
 H1B  F25   F  F     0  -0.315   6.4570   2.5769   0.2205
 H1B  C26   C  CR56  0  -0.156   1.2816  -1.4568  -0.2667
 H1B  S27   S  S2    0   0.278  -0.1834  -0.5548  -0.2589
 H1B  C28   C  CR5   0  -0.230  -1.1076  -1.9863   0.0682
 H1B  C29   C  CR15  0  -0.231  -0.3272  -3.0920   0.1801
 H1B  C31   C  CR56  0  -0.010   1.0502  -2.7974  -0.0094
 H1B  C32   C  CR6   0   0.557   2.1308  -3.7473   0.0868
 H1B  O33   O  O     0  -0.485   1.9848  -4.9392   0.3255
 H1B  C34   C  C     0   0.443  -2.5618  -1.8219   0.1941
 H1B  N35   N  NH2   0  -0.849  -3.2824  -2.9685   0.3130
 H1B  N37   N  N     0  -0.456  -2.9813  -0.6150   0.2181
 H1B  C39   C  CH1   0  -0.115  -4.3862  -0.3113   0.3093
 H1B  C41   C  CH2   0  -0.448  -4.5483   0.8881   1.2463
 H1B  C44   C  CH2   0  -0.625  -6.0003   1.3005   1.4406
 H1B  S47   S  S     0   1.216  -6.7429   1.7691  -0.1152
 H1B  O48   O  OS    0  -0.690  -5.9863   2.8937  -0.6733
 H1B  O49   O  OS    0  -0.685  -8.1876   1.9329   0.0553
 H1B  C50   C  CH2   0  -0.621  -6.4119   0.3206  -1.1082
 H1B  C53   C  CH2   0  -0.454  -4.9269  -0.0195  -1.0963
 H1B  H011  H  HCH3  0   0.234   5.3006  -3.2962   1.8767
 H1B  H012  H  HCH3  0   0.240   4.2265  -4.6900   2.0526
 H1B  H013  H  HCH3  0   0.244   5.8748  -4.9113   1.4683
 H1B  H051  H  HCH2  0   0.264   5.3500  -3.6391  -0.6036
 H1B  H052  H  HCH2  0   0.268   4.3044  -5.0349  -0.4503
 H1B  H09   H  HCR6  0   0.311   4.6255  -1.5908  -0.5107
 H1B  H13   H  HCR6  0   0.271   1.4492   0.6468  -2.3314
 H1B  H20   H  HCR6  0   0.276   4.3982   0.6033   0.7682
 H1B  H15   H  HCR6  0   0.274   1.9511   3.0041  -2.7806
 H1B  H17   H  HCR6  0   0.276   3.6929   4.1780  -1.5106
 H1B  H29   H  HCR5  0   0.272  -0.6930  -4.0841   0.4035
 H1B  H351  H  HNH2  0   0.405  -2.8856  -3.8306  -0.0187
 H1B  H352  H  HNH2  0   0.406  -4.2838  -2.9290   0.2293
 H1B  H39   H  HCH1  0   0.215  -4.9871  -1.1294   0.7360
 H1B  H411  H  HCH2  0   0.272  -4.1429   0.6312   2.2264
 H1B  H412  H  HCH2  0   0.251  -3.9619   1.7304   0.8723
 H1B  H531  H  HCH2  0   0.255  -4.3497   0.7895  -1.5488
 H1B  H532  H  HCH2  0   0.272  -4.7878  -0.8980  -1.7294
 H1B  H441  H  HCH2  0   0.299  -6.6059   0.4868   1.8447
 H1B  H442  H  HCH2  0   0.323  -6.0993   2.1643   2.1005
 H1B  H501  H  HCH2  0   0.300  -7.0212  -0.4891  -0.7011
 H1B  H502  H  HCH2  0   0.323  -6.7707   0.5499  -2.1135

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
 H1B  C01  C05   single    1.518  0.020  1.518
 H1B  C05  N08   single    1.466  0.020  1.466
 H1B  N08  C09   single    1.360  0.020  1.360
 H1B  N08  C32   single    1.387  0.020  1.387
 H1B  C09  C11   double    1.360  0.020  1.360
 H1B  C11  C12   single    1.473  0.020  1.473
 H1B  C11  C26   single    1.420  0.020  1.420
 H1B  C12  C13   aromatic  1.397  0.020  1.397
 H1B  C12  C20   aromatic  1.391  0.020  1.391
 H1B  C13  C15   aromatic  1.384  0.020  1.384
 H1B  C15  C17   aromatic  1.388  0.020  1.388
 H1B  C17  C19   aromatic  1.387  0.020  1.387
 H1B  C19  C20   aromatic  1.391  0.020  1.391
 H1B  C19  C22   single    1.497  0.020  1.497
 H1B  C22  F23   single    1.335  0.020  1.335
 H1B  C22  F24   single    1.340  0.020  1.340
 H1B  C22  F25   single    1.342  0.020  1.342
 H1B  C26  S27   aromatic  1.720  0.020  1.720
 H1B  C26  C31   aromatic  1.385  0.020  1.385
 H1B  S27  C28   aromatic  1.735  0.020  1.735
 H1B  C28  C29   aromatic  1.358  0.020  1.358
 H1B  C28  C34   single    1.469  0.020  1.469
 H1B  C29  C31   aromatic  1.421  0.020  1.421
 H1B  C31  C32   single    1.442  0.020  1.442
 H1B  C32  O33   double    1.224  0.020  1.224
 H1B  C34  N35   single    1.359  0.020  1.359
 H1B  C34  N37   double    1.278  0.020  1.278
 H1B  N37  C39   single    1.440  0.020  1.440
 H1B  C39  C41   single    1.531  0.020  1.531
 H1B  C39  C53   single    1.534  0.020  1.534
 H1B  C41  C44   single    1.522  0.020  1.522
 H1B  C44  S47   single    1.786  0.020  1.786
 H1B  S47  O48   double    1.466  0.020  1.466
 H1B  S47  O49   double    1.464  0.020  1.464
 H1B  S47  C50   single    1.787  0.020  1.787
 H1B  C50  C53   single    1.523  0.020  1.523
 H1B  C01  H011  single    0.970  0.020  1.090
 H1B  C01  H012  single    0.970  0.020  1.090
 H1B  C01  H013  single    0.970  0.020  1.090
 H1B  C05  H051  single    0.970  0.020  1.090
 H1B  C05  H052  single    0.970  0.020  1.090
 H1B  C09  H09   single    0.930  0.020  1.080
 H1B  C13  H13   single    0.930  0.020  1.080
 H1B  C20  H20   single    0.930  0.020  1.080
 H1B  C15  H15   single    0.930  0.020  1.080
 H1B  C17  H17   single    0.930  0.020  1.080
 H1B  C29  H29   single    0.930  0.020  1.080
 H1B  N35  H351  single    0.890  0.020  1.040
 H1B  N35  H352  single    0.890  0.020  1.040
 H1B  C39  H39   single    0.970  0.020  1.090
 H1B  C41  H411  single    0.970  0.020  1.090
 H1B  C41  H412  single    0.970  0.020  1.090
 H1B  C53  H531  single    0.970  0.020  1.090
 H1B  C53  H532  single    0.970  0.020  1.090
 H1B  C44  H441  single    0.970  0.020  1.090
 H1B  C44  H442  single    0.970  0.020  1.090
 H1B  C50  H501  single    0.970  0.020  1.090
 H1B  C50  H502  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
 H1B  H013  C01  H012  108.01  3.000
 H1B  H013  C01  H011  107.86  3.000
 H1B  H012  C01  H011  108.50  3.000
 H1B  H013  C01  C05   109.56  3.000
 H1B  H012  C01  C05   111.54  3.000
 H1B  H011  C01  C05   111.25  3.000
 H1B  H052  C05  H051  107.10  3.000
 H1B  H052  C05  N08   108.31  3.000
 H1B  H051  C05  N08   107.35  3.000
 H1B  H052  C05  C01   111.03  3.000
 H1B  H051  C05  C01   110.54  3.000
 H1B  N08   C05  C01   112.30  3.000
 H1B  C32   N08  C09   123.27  3.000
 H1B  C32   N08  C05   118.19  3.000
 H1B  C09   N08  C05   118.50  3.000
 H1B  H09   C09  C11   120.79  3.000
 H1B  H09   C09  N08   115.15  3.000
 H1B  C11   C09  N08   124.05  3.000
 H1B  C26   C11  C12   123.35  3.000
 H1B  C26   C11  C09   115.46  3.000
 H1B  C12   C11  C09   121.19  3.000
 H1B  C20   C12  C13   118.74  3.000
 H1B  C20   C12  C11   120.31  3.000
 H1B  C13   C12  C11   120.95  3.000
 H1B  H13   C13  C15   119.25  3.000
 H1B  H13   C13  C12   120.16  3.000
 H1B  C15   C13  C12   120.57  3.000
 H1B  H15   C15  C17   119.64  3.000
 H1B  H15   C15  C13   119.85  3.000
 H1B  C17   C15  C13   120.51  3.000
 H1B  H17   C17  C19   121.31  3.000
 H1B  H17   C17  C15   119.46  3.000
 H1B  C19   C17  C15   119.24  3.000
 H1B  C22   C19  C20   118.24  3.000
 H1B  C22   C19  C17   121.33  3.000
 H1B  C20   C19  C17   120.42  3.000
 H1B  H20   C20  C19   120.46  3.000
 H1B  H20   C20  C12   119.02  3.000
 H1B  C19   C20  C12   120.52  3.000
 H1B  F25   C22  F24   106.41  3.000
 H1B  F25   C22  F23   106.96  3.000
 H1B  F24   C22  F23   107.07  3.000
 H1B  F25   C22  C19   111.42  3.000
 H1B  F24   C22  C19   111.76  3.000
 H1B  F23   C22  C19   112.85  3.000
 H1B  C31   C26  S27   111.37  3.000
 H1B  C31   C26  C11   121.46  3.000
 H1B  S27   C26  C11   127.13  3.000
 H1B  C28   S27  C26    91.25  3.000
 H1B  C34   C28  C29   130.77  3.000
 H1B  C34   C28  S27   116.82  3.000
 H1B  C29   C28  S27   112.41  3.000
 H1B  H29   C29  C31   123.08  3.000
 H1B  H29   C29  C28   124.75  3.000
 H1B  C31   C29  C28   112.16  3.000
 H1B  C32   C31  C29   125.51  3.000
 H1B  C32   C31  C26   121.66  3.000
 H1B  C29   C31  C26   112.80  3.000
 H1B  O33   C32  C31   124.40  3.000
 H1B  O33   C32  N08   121.51  3.000
 H1B  C31   C32  N08   114.09  3.000
 H1B  N37   C34  N35   128.38  3.000
 H1B  N37   C34  C28   115.62  3.000
 H1B  N35   C34  C28   115.97  3.000
 H1B  H352  N35  H351  113.53  3.000
 H1B  H352  N35  C34   119.17  3.000
 H1B  H351  N35  C34   119.02  3.000
 H1B  C39   N37  C34   121.37  3.000
 H1B  H39   C39  C53   107.70  3.000
 H1B  H39   C39  C41   106.69  3.000
 H1B  C53   C39  C41   111.99  3.000
 H1B  H39   C39  N37   113.59  3.000
 H1B  C53   C39  N37   109.02  3.000
 H1B  C41   C39  N37   107.90  3.000
 H1B  H412  C41  H411  106.83  3.000
 H1B  H412  C41  C44   110.30  3.000
 H1B  H411  C41  C44   107.67  3.000
 H1B  H412  C41  C39   109.74  3.000
 H1B  H411  C41  C39   109.02  3.000
 H1B  C44   C41  C39   113.05  3.000
 H1B  H442  C44  H441  108.41  3.000
 H1B  H442  C44  S47   106.33  3.000
 H1B  H441  C44  S47   106.70  3.000
 H1B  H442  C44  C41   112.22  3.000
 H1B  H441  C44  C41   112.00  3.000
 H1B  S47   C44  C41   110.88  3.000
 H1B  C50   S47  O49   109.77  3.000
 H1B  C50   S47  O48   108.35  3.000
 H1B  O49   S47  O48   117.89  3.000
 H1B  C50   S47  C44   101.20  3.000
 H1B  O49   S47  C44   109.76  3.000
 H1B  O48   S47  C44   108.56  3.000
 H1B  H502  C50  H501  108.40  3.000
 H1B  H502  C50  C53   111.99  3.000
 H1B  H501  C50  C53   112.05  3.000
 H1B  H502  C50  S47   106.29  3.000
 H1B  H501  C50  S47   106.89  3.000
 H1B  C53   C50  S47   110.92  3.000
 H1B  H532  C53  H531  106.77  3.000
 H1B  H532  C53  C50   107.42  3.000
 H1B  H531  C53  C50   110.28  3.000
 H1B  H532  C53  C39   109.47  3.000
 H1B  H531  C53  C39   109.53  3.000
 H1B  C50   C53  C39   113.16  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
 H1B  CONST_01  C17   C15  C13  C12    0.00   0.0  0
 H1B  CONST_02  C17   C19  C20  C12    0.00   0.0  0
 H1B  CONST_03  C19   C20  C12  C13    0.00   0.0  0
 H1B  CONST_04  C19   C17  C15  C13    0.00   0.0  0
 H1B  CONST_05  C20   C12  C13  C15    0.00   0.0  0
 H1B  CONST_06  C20   C19  C17  C15    0.00   0.0  0
 H1B  CONST_07  C29   C28  S27  C26    0.00   0.0  0
 H1B  CONST_08  C28   C29  C31  C26    0.00   0.0  0
 H1B  CONST_09  C29   C31  C26  S27    0.00   0.0  0
 H1B  CONST_10  C31   C29  C28  S27    0.00   0.0  0
 H1B  CONST_11  C31   C26  S27  C28    0.00   0.0  0
 H1B  CONST_12  C15   C13  C12  C11  180.00   0.0  0
 H1B  CONST_13  C19   C20  C12  C11  180.00   0.0  0
 H1B  CONST_14  C31   C32  N08  C09    0.00   0.0  0
 H1B  CONST_15  C22   C19  C20  C12  180.00   0.0  0
 H1B  CONST_16  C22   C19  C17  C15  180.00   0.0  0
 H1B  CONST_17  C34   C28  S27  C26  180.00   0.0  0
 H1B  CONST_18  C34   C28  C29  C31  180.00   0.0  0
 H1B  CONST_19  C31   C32  N08  C05  180.00   0.0  0
 H1B  CONST_20  O33   C32  N08  C09  180.00   0.0  0
 H1B  CONST_21  H13   C13  C12  C11    0.00   0.0  0
 H1B  CONST_22  H20   C20  C12  C11    0.00   0.0  0
 H1B  CONST_23  H15   C15  C13  C12  180.00   0.0  0
 H1B  CONST_24  H17   C17  C15  C13  180.00   0.0  0
 H1B  CONST_25  H29   C29  C31  C26  180.00   0.0  0
 H1B  CONST_26  O33   C32  N08  C05    0.00   0.0  0
 H1B  CONST_27  C39   N37  C34  C28  180.00   0.0  0
 H1B  CONST_28  C39   N37  C34  N35    0.00   0.0  0
 H1B  CONST_30  H352  N35  C34  C28  180.00   0.0  0
 H1B  Var_01    C13   C12  C11  C09  130.97  30.0  2
 H1B  Var_02    S47   C44  C41  C39  -60.52  30.0  1
 H1B  Var_03    S47   C50  C53  C39   59.95  30.0  1
 H1B  Var_04    C50   S47  C44  C41   54.17  30.0  1
 H1B  Var_05    C53   C50  S47  C44  -53.90  30.0  1
 H1B  Var_06    C09   N08  C05  C01   94.11  30.0  3
 H1B  Var_07    F23   C22  C19  C17    7.08  30.0  2
 H1B  Var_08    N35   C34  C28  S27  173.49  30.0  2
 H1B  Var_09    H011  C01  C05  N08  -60.94  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
 H1B  chir_01  C39  N37  C41  C53  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
 H1B  plan-1  C11   0.020
 H1B  plan-1  C12   0.020
 H1B  plan-1  C13   0.020
 H1B  plan-1  C15   0.020
 H1B  plan-1  C17   0.020
 H1B  plan-1  C19   0.020
 H1B  plan-1  C20   0.020
 H1B  plan-1  C22   0.020
 H1B  plan-1  H13   0.020
 H1B  plan-1  H20   0.020
 H1B  plan-1  H15   0.020
 H1B  plan-1  H17   0.020
 H1B  plan-2  C05   0.020
 H1B  plan-2  N08   0.020
 H1B  plan-2  C09   0.020
 H1B  plan-2  C11   0.020
 H1B  plan-2  C12   0.020
 H1B  plan-2  C26   0.020
 H1B  plan-2  S27   0.020
 H1B  plan-2  C28   0.020
 H1B  plan-2  C29   0.020
 H1B  plan-2  C31   0.020
 H1B  plan-2  C32   0.020
 H1B  plan-2  O33   0.020
 H1B  plan-2  C34   0.020
 H1B  plan-2  H09   0.020
 H1B  plan-2  H29   0.020
 H1B  plan-3  C28   0.020
 H1B  plan-3  C34   0.020
 H1B  plan-3  N35   0.020
 H1B  plan-3  N37   0.020
 H1B  plan-3  C39   0.020
 H1B  plan-3  H351  0.020
 H1B  plan-3  H352  0.020

