# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 08:45:16 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-[1,1-bis(oxidanylidene)thian-4-yl]-7-(3,4-dimethoxyphenyl)-5-methyl-4-oxidanylidene-thieno[3,2-c]pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC)C2=CN(C)C(=O)c3cc(sc23)C(=O)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
 TVU  TVU  N-[1,1-bis(oxidanylidene)thian-4-yl]-7-(3,4-dimethoxyphenyl)-5-methyl-4-oxidanylidene-thieno[3,2-c]pyridine-2-carboxamide  ligand  56  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TVU
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
 TVU  O5    O  OS    0  -0.681  -8.2378   1.5743  -0.1351
 TVU  S1    S  S     0   1.217  -6.8252   1.3992  -0.4727
 TVU  O4    O  OS    0  -0.687  -6.2891   2.1507  -1.6108
 TVU  C19   C  CH2   0  -0.622  -5.8127   1.7473   0.9587
 TVU  C18   C  CH2   0  -0.473  -4.3622   1.3617   0.7033
 TVU  C20   C  CH2   0  -0.623  -6.4688  -0.3341  -0.7234
 TVU  C21   C  CH2   0  -0.459  -4.9687  -0.5610  -0.8530
 TVU  C17   C  CH1   0  -0.061  -4.1977  -0.1266   0.3981
 TVU  N1    N  NH1   0  -0.671  -2.7859  -0.4191   0.2610
 TVU  C16   C  C     0   0.562  -2.2625  -1.6280   0.5398
 TVU  O3    O  O     0  -0.475  -2.9222  -2.5685   0.9558
 TVU  C14   C  CR5   0  -0.332  -0.8065  -1.7750   0.3232
 TVU  C13   C  CR15  0  -0.183  -0.1566  -2.9646   0.2247
 TVU  S     S  S2    0   0.267   0.2826  -0.4277   0.1771
 TVU  C15   C  CR56  0  -0.154   1.6250  -1.4763  -0.0426
 TVU  C12   C  CR56  0  -0.013   1.2350  -2.8041   0.0091
 TVU  C11   C  CR6   0   0.546   2.1933  -3.8791  -0.1076
 TVU  O2    O  O     0  -0.481   1.8967  -5.0657  -0.0664
 TVU  N     N  NR6   0  -0.535   3.5003  -3.4488  -0.2652
 TVU  C10   C  CH3   0  -0.547   4.5732  -4.4316  -0.3785
 TVU  C9    C  CR16  0   0.007   3.8568  -2.1343  -0.3061
 TVU  C8    C  CR6   0  -0.020   2.9835  -1.0974  -0.2021
 TVU  C4    C  CR6   0   0.048   3.4376   0.3037  -0.2268
 TVU  C3    C  CR16  0  -0.333   2.8078   1.2549  -1.0124
 TVU  C2    C  CR16  0  -0.370   3.2551   2.5744  -1.0227
 TVU  C5    C  CR16  0  -0.451   4.5356   0.6910   0.5529
 TVU  C6    C  CR6   0   0.335   4.9975   1.9947   0.5389
 TVU  O1    O  O2    0  -0.463   6.0435   2.4469   1.2514
 TVU  C7    C  CH3   0  -0.440   6.7578   1.5259   2.0513
 TVU  C1    C  CR6   0   0.305   4.3425   2.9589  -0.2575
 TVU  O     O  O2    0  -0.460   4.8493   4.2017  -0.1999
 TVU  C     C  CH3   0  -0.438   4.2153   5.2160  -0.9533
 TVU  H191  H  HCH2  0   0.328  -5.9204   2.8141   1.1627
 TVU  H192  H  HCH2  0   0.305  -6.2410   1.1896   1.7934
 TVU  H201  H  HCH2  0   0.304  -6.8881  -0.8708   0.1304
 TVU  H202  H  HCH2  0   0.327  -7.0092  -0.6358  -1.6226
 TVU  H181  H  HCH2  0   0.260  -3.9610   1.9634  -0.1167
 TVU  H182  H  HCH2  0   0.287  -3.7879   1.6162   1.5955
 TVU  H17   H  HCH1  0   0.265  -4.5706  -0.6980   1.2523
 TVU  H211  H  HCH2  0   0.282  -4.8097  -1.6265  -1.0243
 TVU  H212  H  HCH2  0   0.257  -4.5828  -0.0356  -1.7294
 TVU  H1    H  HNH1  0   0.405  -2.2362   0.2518  -0.2549
 TVU  H13   H  HCR5  0   0.279  -0.6522  -3.9218   0.2976
 TVU  H101  H  HCH3  0   0.277   4.1539  -5.4300  -0.3977
 TVU  H102  H  HCH3  0   0.266   5.1320  -4.2660  -1.2973
 TVU  H103  H  HCH3  0   0.266   5.2468  -4.3460   0.4718
 TVU  H9    H  HCR6  0   0.309   4.9148  -1.9561  -0.4438
 TVU  H3    H  HCR6  0   0.259   1.9793   0.9855  -1.6547
 TVU  H5    H  HCR6  0   0.283   5.0098  -0.0466   1.1870
 TVU  H2    H  HCR6  0   0.286   2.7419   3.2883  -1.6520
 TVU  H71C  H  HCH3  0   0.230   6.1330   1.0989   2.8405
 TVU  H72C  H  HCH3  0   0.229   7.1795   0.7114   1.4562
 TVU  H73C  H  HCH3  0   0.262   7.5703   2.0825   2.5108
 TVU  HC1   H  HCH3  0   0.230   3.1741   5.3575  -0.6512
 TVU  HC2   H  HCH3  0   0.261   4.7650   6.1335  -0.7589
 TVU  HC3   H  HCH3  0   0.229   4.2453   5.0082  -2.0263

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
 TVU  O5   S1    double    1.463  0.020  1.463
 TVU  S1   O4    double    1.465  0.020  1.465
 TVU  S1   C19   single    1.788  0.020  1.788
 TVU  S1   C20   single    1.787  0.020  1.787
 TVU  C19  C18   single    1.522  0.020  1.522
 TVU  C18  C17   single    1.528  0.020  1.528
 TVU  C20  C21   single    1.523  0.020  1.523
 TVU  C21  C17   single    1.532  0.020  1.532
 TVU  C17  N1    single    1.448  0.020  1.448
 TVU  N1   C16   single    1.347  0.020  1.347
 TVU  C16  O3    double    1.222  0.020  1.222
 TVU  C16  C14   single    1.479  0.020  1.479
 TVU  C14  C13   aromatic  1.359  0.020  1.359
 TVU  C14  S     aromatic  1.739  0.020  1.739
 TVU  C13  C12   aromatic  1.417  0.020  1.417
 TVU  S    C15   aromatic  1.717  0.020  1.717
 TVU  C15  C12   aromatic  1.385  0.020  1.385
 TVU  C15  C8    single    1.419  0.020  1.419
 TVU  C12  C11   single    1.445  0.020  1.445
 TVU  C11  O2    double    1.224  0.020  1.224
 TVU  C11  N     single    1.385  0.020  1.385
 TVU  N    C10   single    1.459  0.020  1.459
 TVU  N    C9    single    1.363  0.020  1.363
 TVU  C9   C8    double    1.360  0.020  1.360
 TVU  C8   C4    single    1.473  0.020  1.473
 TVU  C4   C3    aromatic  1.385  0.020  1.385
 TVU  C4   C5    aromatic  1.401  0.020  1.401
 TVU  C3   C2    aromatic  1.393  0.020  1.393
 TVU  C2   C1    aromatic  1.384  0.020  1.384
 TVU  C5   C6    aromatic  1.383  0.020  1.383
 TVU  C6   O1    single    1.344  0.020  1.344
 TVU  C6   C1    aromatic  1.412  0.020  1.412
 TVU  O1   C7    single    1.414  0.020  1.414
 TVU  C1   O     single    1.343  0.020  1.343
 TVU  O    C     single    1.414  0.020  1.414
 TVU  C19  H191  single    0.970  0.020  1.090
 TVU  C19  H192  single    0.970  0.020  1.090
 TVU  C20  H201  single    0.970  0.020  1.090
 TVU  C20  H202  single    0.970  0.020  1.090
 TVU  C18  H181  single    0.970  0.020  1.090
 TVU  C18  H182  single    0.970  0.020  1.090
 TVU  C17  H17   single    0.970  0.020  1.090
 TVU  C21  H211  single    0.970  0.020  1.090
 TVU  C21  H212  single    0.970  0.020  1.090
 TVU  N1   H1    single    0.860  0.020  1.020
 TVU  C13  H13   single    0.930  0.020  1.080
 TVU  C10  H101  single    0.970  0.020  1.090
 TVU  C10  H102  single    0.970  0.020  1.090
 TVU  C10  H103  single    0.970  0.020  1.090
 TVU  C9   H9    single    0.930  0.020  1.080
 TVU  C3   H3    single    0.930  0.020  1.080
 TVU  C5   H5    single    0.930  0.020  1.080
 TVU  C2   H2    single    0.930  0.020  1.080
 TVU  C7   H71C  single    0.970  0.020  1.090
 TVU  C7   H72C  single    0.970  0.020  1.090
 TVU  C7   H73C  single    0.970  0.020  1.090
 TVU  C    HC1   single    0.970  0.020  1.090
 TVU  C    HC2   single    0.970  0.020  1.090
 TVU  C    HC3   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
 TVU  C20   S1   C19   100.85  3.000
 TVU  C20   S1   O4    108.39  3.000
 TVU  C19   S1   O4    108.35  3.000
 TVU  C20   S1   O5    109.94  3.000
 TVU  C19   S1   O5    109.81  3.000
 TVU  O4    S1   O5    118.11  3.000
 TVU  H192  C19  H191  108.53  3.000
 TVU  H192  C19  C18   111.89  3.000
 TVU  H191  C19  C18   111.90  3.000
 TVU  H192  C19  S1    106.89  3.000
 TVU  H191  C19  S1    106.51  3.000
 TVU  C18   C19  S1    110.86  3.000
 TVU  H182  C18  H181  106.96  3.000
 TVU  H182  C18  C17   109.50  3.000
 TVU  H181  C18  C17   110.28  3.000
 TVU  H182  C18  C19   107.77  3.000
 TVU  H181  C18  C19   109.64  3.000
 TVU  C17   C18  C19   112.50  3.000
 TVU  H202  C20  H201  108.55  3.000
 TVU  H202  C20  C21   112.11  3.000
 TVU  H201  C20  C21   111.81  3.000
 TVU  H202  C20  S1    106.55  3.000
 TVU  H201  C20  S1    106.88  3.000
 TVU  C21   C20  S1    110.66  3.000
 TVU  H212  C21  H211  107.00  3.000
 TVU  H212  C21  C17   109.93  3.000
 TVU  H211  C21  C17   109.38  3.000
 TVU  H212  C21  C20   110.16  3.000
 TVU  H211  C21  C20   107.61  3.000
 TVU  C17   C21  C20   112.58  3.000
 TVU  H17   C17  N1    107.51  3.000
 TVU  H17   C17  C21   108.55  3.000
 TVU  N1    C17  C21   110.85  3.000
 TVU  H17   C17  C18   108.43  3.000
 TVU  N1    C17  C18   108.69  3.000
 TVU  C21   C17  C18   112.64  3.000
 TVU  H1    N1   C16   119.40  3.000
 TVU  H1    N1   C17   116.43  3.000
 TVU  C16   N1   C17   122.73  3.000
 TVU  C14   C16  O3    120.32  3.000
 TVU  C14   C16  N1    116.20  3.000
 TVU  O3    C16  N1    123.48  3.000
 TVU  S     C14  C13   111.88  3.000
 TVU  S     C14  C16   123.49  3.000
 TVU  C13   C14  C16   124.63  3.000
 TVU  H13   C13  C12   124.12  3.000
 TVU  H13   C13  C14   123.45  3.000
 TVU  C12   C13  C14   112.42  3.000
 TVU  C15   S    C14    91.56  3.000
 TVU  C8    C15  C12   121.98  3.000
 TVU  C8    C15  S     126.83  3.000
 TVU  C12   C15  S     111.13  3.000
 TVU  C11   C12  C15   121.58  3.000
 TVU  C11   C12  C13   125.40  3.000
 TVU  C15   C12  C13   113.00  3.000
 TVU  N     C11  O2    122.25  3.000
 TVU  N     C11  C12   113.83  3.000
 TVU  O2    C11  C12   123.92  3.000
 TVU  C9    N    C10   117.06  3.000
 TVU  C9    N    C11   123.36  3.000
 TVU  C10   N    C11   119.57  3.000
 TVU  H103  C10  H102  109.27  3.000
 TVU  H103  C10  H101  109.03  3.000
 TVU  H102  C10  H101  108.92  3.000
 TVU  H103  C10  N     109.96  3.000
 TVU  H102  C10  N     109.92  3.000
 TVU  H101  C10  N     109.72  3.000
 TVU  H9    C9   C8    120.82  3.000
 TVU  H9    C9   N     114.74  3.000
 TVU  C8    C9   N     124.43  3.000
 TVU  C4    C8   C9    121.74  3.000
 TVU  C4    C8   C15   123.43  3.000
 TVU  C9    C8   C15   114.82  3.000
 TVU  C5    C4   C3    118.82  3.000
 TVU  C5    C4   C8    119.68  3.000
 TVU  C3    C4   C8    121.50  3.000
 TVU  H3    C3   C2    118.49  3.000
 TVU  H3    C3   C4    120.91  3.000
 TVU  C2    C3   C4    120.57  3.000
 TVU  H2    C2   C1    120.75  3.000
 TVU  H2    C2   C3    118.50  3.000
 TVU  C1    C2   C3    120.74  3.000
 TVU  H5    C5   C6    120.13  3.000
 TVU  H5    C5   C4    118.75  3.000
 TVU  C6    C5   C4    121.10  3.000
 TVU  C1    C6   O1    115.49  3.000
 TVU  C1    C6   C5    119.63  3.000
 TVU  O1    C6   C5    124.87  3.000
 TVU  C7    O1   C6    118.29  3.000
 TVU  H73C  C7   H72C  108.86  3.000
 TVU  H73C  C7   H71C  108.78  3.000
 TVU  H72C  C7   H71C  108.81  3.000
 TVU  H73C  C7   O1    106.46  3.000
 TVU  H72C  C7   O1    111.86  3.000
 TVU  H71C  C7   O1    111.97  3.000
 TVU  O     C1   C6    115.63  3.000
 TVU  O     C1   C2    125.24  3.000
 TVU  C6    C1   C2    119.13  3.000
 TVU  C     O    C1    118.15  3.000
 TVU  HC3   C    HC2   108.78  3.000
 TVU  HC3   C    HC1   108.78  3.000
 TVU  HC2   C    HC1   108.84  3.000
 TVU  HC3   C    O     111.98  3.000
 TVU  HC2   C    O     106.47  3.000
 TVU  HC1   C    O     111.89  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
 TVU  CONST_01  C15   C12  C13  C14     0.00   0.0  0
 TVU  CONST_02  C12   C15  S    C14     0.00   0.0  0
 TVU  CONST_03  C15   S    C14  C13     0.00   0.0  0
 TVU  CONST_04  S     C15  C12  C13     0.00   0.0  0
 TVU  CONST_05  C12   C13  C14  S       0.00   0.0  0
 TVU  CONST_06  C1    C2   C3   C4      0.00   0.0  0
 TVU  CONST_07  C1    C6   C5   C4      0.00   0.0  0
 TVU  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 TVU  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 TVU  CONST_10  C5    C4   C3   C2      0.00   0.0  0
 TVU  CONST_11  C5    C6   C1   C2      0.00   0.0  0
 TVU  CONST_12  C2    C3   C4   C8    180.00   0.0  0
 TVU  CONST_13  C6    C5   C4   C8    180.00   0.0  0
 TVU  CONST_14  C9    N    C11  C12     0.00   0.0  0
 TVU  CONST_15  C12   C13  C14  C16   180.00   0.0  0
 TVU  CONST_16  C15   S    C14  C16   180.00   0.0  0
 TVU  CONST_17  O1    C6   C5   C4    180.00   0.0  0
 TVU  CONST_18  O     C1   C2   C3    180.00   0.0  0
 TVU  CONST_19  O1    C6   C1   C2    180.00   0.0  0
 TVU  CONST_20  O     C1   C6   C5    180.00   0.0  0
 TVU  CONST_21  C10   N    C11  C12   180.00   0.0  0
 TVU  CONST_22  C9    N    C11  O2    180.00   0.0  0
 TVU  CONST_23  H13   C13  C14  S     180.00   0.0  0
 TVU  CONST_24  H3    C3   C4   C8      0.00   0.0  0
 TVU  CONST_25  H5    C5   C4   C8      0.00   0.0  0
 TVU  CONST_26  H2    C2   C3   C4    180.00   0.0  0
 TVU  CONST_27  C14   C16  N1   C17   180.00   0.0  0
 TVU  CONST_28  C10   N    C11  O2      0.00   0.0  0
 TVU  CONST_29  O3    C16  N1   C17     0.00   0.0  0
 TVU  CONST_30  H1    N1   C16  C14     0.00   0.0  0
 TVU  Var_01    C17   C18  C19  S1    -60.52  30.0  1
 TVU  Var_02    C17   C21  C20  S1     60.56  30.0  1
 TVU  Var_03    C21   C20  S1   C19   -54.98  30.0  1
 TVU  Var_04    C20   S1   C19  C18    55.02  30.0  1
 TVU  Var_05    C3    C4   C8   C15   -48.02  30.0  2
 TVU  Var_06    C13   C14  C16  N1   -162.93  30.0  2
 TVU  Var_07    C1    C6   O1   C7   -178.88  30.0  2
 TVU  Var_08    H101  C10  N    C11     4.47  30.0  3
 TVU  Var_09    H71C  C7   O1   C6    -63.00  30.0  3
 TVU  Var_10    HC1   C    O    C1     60.45  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
 TVU  chir_01  C17  C18  C21  N1  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
 TVU  plan-1  C8   0.020
 TVU  plan-1  C4   0.020
 TVU  plan-1  C3   0.020
 TVU  plan-1  C2   0.020
 TVU  plan-1  C5   0.020
 TVU  plan-1  C6   0.020
 TVU  plan-1  O1   0.020
 TVU  plan-1  C1   0.020
 TVU  plan-1  O    0.020
 TVU  plan-1  H3   0.020
 TVU  plan-1  H5   0.020
 TVU  plan-1  H2   0.020
 TVU  plan-2  C16  0.020
 TVU  plan-2  C14  0.020
 TVU  plan-2  C13  0.020
 TVU  plan-2  S    0.020
 TVU  plan-2  C15  0.020
 TVU  plan-2  C12  0.020
 TVU  plan-2  C11  0.020
 TVU  plan-2  O2   0.020
 TVU  plan-2  N    0.020
 TVU  plan-2  C10  0.020
 TVU  plan-2  C9   0.020
 TVU  plan-2  C8   0.020
 TVU  plan-2  C4   0.020
 TVU  plan-2  H13  0.020
 TVU  plan-2  H9   0.020
 TVU  plan-3  C17  0.020
 TVU  plan-3  N1   0.020
 TVU  plan-3  C16  0.020
 TVU  plan-3  O3   0.020
 TVU  plan-3  C14  0.020
 TVU  plan-3  H1   0.020

