# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:19:52 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: N-(3-{5-[(1,5-dimethyl-1H-pyrazol-3-yl)amino]-6-oxo-1,6-dihydropyridazin-3-yl}-2,6-difluorophenyl)-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(NC2=CC(=NNC2=O)c3ccc(F)c(NC(=O)c4sc5CCCCc5c4)c3F)cc1C
#
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
 DY4  DY4  N-(3-{5-[(1,5-dimethyl-1H-pyrazol-3-yl)amino]-6-oxo-1,6-dihydropyridazin-3-yl}-2,6-difluorophenyl)-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide  ligand  57  35  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DY4
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
 DY4  C4    C  CR16  0  -0.368    3.2903   1.3551   0.2310
 DY4  C5    C  CR6   0   0.194    2.0941   1.0225   0.9187
 DY4  C6    C  CR6   0   0.505    4.4351  -0.3026   1.5849
 DY4  N1    N  NR5   0  -0.316    8.4930  -0.6493  -1.0028
 DY4  C7    C  CR6   0  -0.173    0.8436   1.7450   0.6141
 DY4  C8    C  CR6   0   0.547   -0.3558   1.0842   0.3887
 DY4  N2    N  N     0  -0.322    7.8632   0.4277  -0.5248
 DY4  C9    C  CR6   0  -0.001   -1.5373   1.7479   0.0856
 DY4  C10   C  C     0   0.547   -3.8036   1.1417   0.6446
 DY4  C11   C  CR5   0  -0.326   -4.9846   0.3610   0.2527
 DY4  C12   C  CR15  0  -0.212   -6.0881   0.1700   1.0355
 DY4  C13   C  CR5   0   0.193   -7.0861  -0.6237   0.4168
 DY4  C14   C  CR5   0  -0.233   -6.7226  -1.0250  -0.8402
 DY4  C15   C  CH2   0  -0.482   -7.5575  -1.8551  -1.7598
 DY4  N4    N  N     0  -0.237    2.0452   0.0909   1.8187
 DY4  C1    C  CH3   0  -0.519    9.9260  -0.6307  -1.1584
 DY4  C16   C  CH2   0  -0.449   -8.6914  -2.5154  -0.9758
 DY4  C17   C  CH2   0  -0.450   -9.3712  -1.5211  -0.0400
 DY4  C18   C  CH2   0  -0.492   -8.4016  -1.0112   1.0238
 DY4  C19   C  CR6   0   0.548   -1.4902   3.1346   0.0253
 DY4  C2    C  CR5   0   0.442    6.5969   0.0756  -0.4485
 DY4  C20   C  CR16  0  -0.430   -0.3278   3.8394   0.2568
 DY4  C21   C  CR16  0  -0.260    0.8304   3.1359   0.5410
 DY4  C22   C  CR15  0  -0.539    6.3996  -1.2490  -0.8700
 DY4  C23   C  CR5   0   0.413    7.6603  -1.6905  -1.2072
 DY4  C24   C  CH3   0  -0.747    8.1147  -3.0148  -1.7066
 DY4  C3    C  CR6   0   0.257    4.4533   0.7057   0.5226
 DY4  F1    F  F     0  -0.281   -0.3986  -0.2471   0.4227
 DY4  F2    F  F     0  -0.292   -2.6085   3.7907  -0.2789
 DY4  N5    N  NR16  0  -0.493    3.1868  -0.5316   2.0886
 DY4  N6    N  NH1   0  -0.759   -2.7170   1.0396  -0.1722
 DY4  O1    O  O     0  -0.473    5.4169  -0.8900   2.0159
 DY4  O2    O  O     0  -0.455   -3.8009   1.8396   1.6421
 DY4  S1    S  S2    0   0.233   -5.1712  -0.4318  -1.2714
 DY4  H4    H  HCR6  0   0.291    3.2682   2.1110  -0.5439
 DY4  H1    H  HCR5  0   0.268   -6.1832   0.5834   2.0305
 DY4  H2    H  HNH1  0   0.408    5.6368   1.8663  -0.6149
 DY4  H151  H  HCH2  0   0.258   -7.9698  -1.2220  -2.5517
 DY4  H152  H  HCH2  0   0.262   -6.9483  -2.6117  -2.2589
 DY4  H12   H  HCH3  0   0.254   10.4310  -0.9083  -0.2327
 DY4  H13   H  HCH3  0   0.259   10.2218  -1.3267  -1.9393
 DY4  H11   H  HCH3  0   0.265   10.2396   0.3683  -1.4480
 DY4  H161  H  HCH2  0   0.245   -9.4127  -2.9387  -1.6766
 DY4  H162  H  HCH2  0   0.229   -8.2923  -3.3509  -0.3932
 DY4  H171  H  HCH2  0   0.227   -9.7511  -0.6766  -0.6228
 DY4  H172  H  HCH2  0   0.242  -10.2337  -1.9838   0.4423
 DY4  H181  H  HCH2  0   0.245   -8.2378  -1.7872   1.7781
 DY4  H182  H  HCH2  0   0.251   -8.8326  -0.1594   1.5549
 DY4  H20   H  HCR6  0   0.294   -0.3252   4.9195   0.2081
 DY4  H21   H  HCR6  0   0.287    1.7447   3.6854   0.7230
 DY4  H22   H  HCR5  0   0.266    5.4777  -1.8032  -0.9362
 DY4  H241  H  HCH3  0   0.259    8.8283  -3.4812  -1.0257
 DY4  H242  H  HCH3  0   0.266    7.2628  -3.6836  -1.8061
 DY4  H243  H  HCH3  0   0.258    8.5951  -2.9387  -2.6836
 DY4  H3    H  HNR6  0   0.427    3.1166  -1.2187   2.8278
 DY4  H5    H  HNH1  0   0.417   -2.6798   0.3248  -0.8837
 DY4  N3    N  NH1   0  -0.745    5.6448   1.0228  -0.0595

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
 DY4  C24  C23   single    1.487  0.020  1.487
 DY4  C23  N1    aromatic  1.349  0.020  1.349
 DY4  C23  C22   aromatic  1.378  0.020  1.378
 DY4  C1   N1    single    1.441  0.020  1.441
 DY4  N1   N2    aromatic  1.336  0.020  1.336
 DY4  C22  C2    aromatic  1.404  0.020  1.404
 DY4  N2   C2    aromatic  1.317  0.020  1.317
 DY4  C2   N3    single    1.398  0.020  1.398
 DY4  N3   C3    single    1.363  0.020  1.363
 DY4  C3   C4    double    1.364  0.020  1.364
 DY4  C3   C6    single    1.465  0.020  1.465
 DY4  C4   C5    single    1.419  0.020  1.419
 DY4  O1   C6    double    1.223  0.020  1.223
 DY4  C6   N5    single    1.365  0.020  1.365
 DY4  C21  C20   aromatic  1.385  0.020  1.385
 DY4  C21  C7    aromatic  1.393  0.020  1.393
 DY4  C5   C7    single    1.476  0.020  1.476
 DY4  C5   N4    double    1.296  0.020  1.296
 DY4  C20  C19   aromatic  1.379  0.020  1.379
 DY4  N5   N4    single    1.328  0.020  1.328
 DY4  C7   C8    aromatic  1.388  0.020  1.388
 DY4  C19  F2    single    1.332  0.020  1.332
 DY4  C19  C9    aromatic  1.389  0.020  1.389
 DY4  C8   C9    aromatic  1.389  0.020  1.389
 DY4  C8   F1    single    1.332  0.020  1.332
 DY4  C9   N6    single    1.400  0.020  1.400
 DY4  N6   C10   single    1.363  0.020  1.363
 DY4  O2   C10   double    1.217  0.020  1.217
 DY4  C10  C11   single    1.469  0.020  1.469
 DY4  C11  C12   aromatic  1.366  0.020  1.366
 DY4  C11  S1    aromatic  1.728  0.020  1.728
 DY4  C12  C13   aromatic  1.417  0.020  1.417
 DY4  S1   C14   aromatic  1.716  0.020  1.716
 DY4  C13  C14   aromatic  1.369  0.020  1.369
 DY4  C13  C18   single    1.500  0.020  1.500
 DY4  C14  C15   single    1.494  0.020  1.494
 DY4  C18  C17   single    1.527  0.020  1.527
 DY4  C15  C16   single    1.528  0.020  1.528
 DY4  C17  C16   single    1.525  0.020  1.525
 DY4  C4   H4    single    0.930  0.020  1.080
 DY4  C12  H1    single    0.930  0.020  1.080
 DY4  N3   H2    single    0.890  0.020  1.040
 DY4  C15  H151  single    0.970  0.020  1.090
 DY4  C15  H152  single    0.970  0.020  1.090
 DY4  C1   H12   single    0.970  0.020  1.090
 DY4  C1   H13   single    0.970  0.020  1.090
 DY4  C1   H11   single    0.970  0.020  1.090
 DY4  C16  H161  single    0.970  0.020  1.090
 DY4  C16  H162  single    0.970  0.020  1.090
 DY4  C17  H171  single    0.970  0.020  1.090
 DY4  C17  H172  single    0.970  0.020  1.090
 DY4  C18  H181  single    0.970  0.020  1.090
 DY4  C18  H182  single    0.970  0.020  1.090
 DY4  C20  H20   single    0.930  0.020  1.080
 DY4  C21  H21   single    0.930  0.020  1.080
 DY4  C22  H22   single    0.930  0.020  1.080
 DY4  C24  H241  single    0.970  0.020  1.090
 DY4  C24  H242  single    0.970  0.020  1.090
 DY4  C24  H243  single    0.970  0.020  1.090
 DY4  N5   H3    single    0.860  0.020  1.020
 DY4  N6   H5    single    0.860  0.020  1.020

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
 DY4  H4    C4   C3    120.19  3.000
 DY4  H4    C4   C5    119.55  3.000
 DY4  C3    C4   C5    120.24  3.000
 DY4  N4    C5   C7    117.59  3.000
 DY4  N4    C5   C4    122.45  3.000
 DY4  C7    C5   C4    119.95  3.000
 DY4  O1    C6   N5    121.57  3.000
 DY4  N5    C6   C3    113.22  3.000
 DY4  O1    C6   C3    125.20  3.000
 DY4  C23   N1   C1    127.40  3.000
 DY4  C1    N1   N2    119.79  3.000
 DY4  C23   N1   N2    112.67  3.000
 DY4  C21   C7   C8    117.31  3.000
 DY4  C8    C7   C5    122.18  3.000
 DY4  C21   C7   C5    120.51  3.000
 DY4  F1    C8   C9    117.12  3.000
 DY4  F1    C8   C7    119.96  3.000
 DY4  C9    C8   C7    122.90  3.000
 DY4  C2    N2   N1    104.99  3.000
 DY4  N6    C9   C19   121.72  3.000
 DY4  N6    C9   C8    121.02  3.000
 DY4  C19   C9   C8    117.25  3.000
 DY4  O2    C10  N6    122.15  3.000
 DY4  O2    C10  C11   121.68  3.000
 DY4  N6    C10  C11   116.17  3.000
 DY4  S1    C11  C12   110.73  3.000
 DY4  S1    C11  C10   124.47  3.000
 DY4  C12   C11  C10   124.80  3.000
 DY4  H1    C12  C13   123.62  3.000
 DY4  H1    C12  C11   123.00  3.000
 DY4  C13   C12  C11   113.38  3.000
 DY4  C18   C13  C14   121.93  3.000
 DY4  C18   C13  C12   125.85  3.000
 DY4  C14   C13  C12   112.22  3.000
 DY4  S1    C14  C15   122.87  3.000
 DY4  C15   C14  C13   125.44  3.000
 DY4  S1    C14  C13   111.68  3.000
 DY4  H152  C15  H151  106.28  3.000
 DY4  H152  C15  C16   110.43  3.000
 DY4  H151  C15  C16   109.97  3.000
 DY4  H152  C15  C14   110.76  3.000
 DY4  H151  C15  C14   109.54  3.000
 DY4  C16   C15  C14   109.81  3.000
 DY4  N5    N4   C5    116.46  3.000
 DY4  H11   C1   H13   108.58  3.000
 DY4  H11   C1   H12   109.06  3.000
 DY4  H13   C1   H12   108.72  3.000
 DY4  H11   C1   N1    109.13  3.000
 DY4  H13   C1   N1    109.86  3.000
 DY4  H12   C1   N1    111.44  3.000
 DY4  H162  C16  H161  106.67  3.000
 DY4  H162  C16  C17   109.49  3.000
 DY4  H161  C16  C17   110.63  3.000
 DY4  H162  C16  C15   109.42  3.000
 DY4  H161  C16  C15   109.18  3.000
 DY4  C17   C16  C15   111.33  3.000
 DY4  H172  C17  H171  106.75  3.000
 DY4  H172  C17  C18   109.61  3.000
 DY4  H171  C17  C18   109.50  3.000
 DY4  H172  C17  C16   110.31  3.000
 DY4  H171  C17  C16   109.34  3.000
 DY4  C18   C17  C16   111.23  3.000
 DY4  H182  C18  H181  106.06  3.000
 DY4  H182  C18  C17   110.40  3.000
 DY4  H181  C18  C17   109.78  3.000
 DY4  H182  C18  C13   109.96  3.000
 DY4  H181  C18  C13   109.32  3.000
 DY4  C17   C18  C13   111.18  3.000
 DY4  F2    C19  C20   119.63  3.000
 DY4  F2    C19  C9    118.25  3.000
 DY4  C20   C19  C9    122.12  3.000
 DY4  C22   C2   N3    128.83  3.000
 DY4  N3    C2   N2    119.34  3.000
 DY4  C22   C2   N2    111.72  3.000
 DY4  H20   C20  C21   120.98  3.000
 DY4  H20   C20  C19   120.34  3.000
 DY4  C21   C20  C19   118.68  3.000
 DY4  H21   C21  C20   118.90  3.000
 DY4  H21   C21  C7    119.36  3.000
 DY4  C20   C21  C7    121.74  3.000
 DY4  H22   C22  C23   127.08  3.000
 DY4  H22   C22  C2    128.60  3.000
 DY4  C23   C22  C2    104.32  3.000
 DY4  C24   C23  C22   130.36  3.000
 DY4  C22   C23  N1    106.29  3.000
 DY4  C24   C23  N1    123.36  3.000
 DY4  H243  C24  H242  107.81  3.000
 DY4  H243  C24  H241  107.50  3.000
 DY4  H242  C24  H241  107.85  3.000
 DY4  H243  C24  C23   111.91  3.000
 DY4  H242  C24  C23   109.82  3.000
 DY4  H241  C24  C23   111.78  3.000
 DY4  N3    C3   C6    118.72  3.000
 DY4  C6    C3   C4    118.19  3.000
 DY4  N3    C3   C4    122.91  3.000
 DY4  H3    N5   N4    114.03  3.000
 DY4  H3    N5   C6    116.54  3.000
 DY4  N4    N5   C6    129.22  3.000
 DY4  H5    N6   C10   120.33  3.000
 DY4  H5    N6   C9    117.20  3.000
 DY4  C10   N6   C9    121.56  3.000
 DY4  C14   S1   C11    91.98  3.000
 DY4  H2    N3   C3    114.96  3.000
 DY4  H2    N3   C2    114.72  3.000
 DY4  C3    N3   C2    123.80  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
 DY4  CONST_01  C2    C22  C23  N1     0.00   0.0  0
 DY4  CONST_02  C22   C2   N2   N1     0.00   0.0  0
 DY4  CONST_03  C19   C20  C21  C7     0.00   0.0  0
 DY4  CONST_04  C19   C9   C8   C7     0.00   0.0  0
 DY4  CONST_05  C20   C21  C7   C8     0.00   0.0  0
 DY4  CONST_06  C20   C19  C9   C8     0.00   0.0  0
 DY4  CONST_07  C22   C23  N1   N2     0.00   0.0  0
 DY4  CONST_08  C23   C22  C2   N2     0.00   0.0  0
 DY4  CONST_09  C21   C20  C19  C9     0.00   0.0  0
 DY4  CONST_10  C21   C7   C8   C9     0.00   0.0  0
 DY4  CONST_11  C14   C13  C12  C11    0.00   0.0  0
 DY4  CONST_12  C13   C14  S1   C11    0.00   0.0  0
 DY4  CONST_13  C14   S1   C11  C12    0.00   0.0  0
 DY4  CONST_14  S1    C14  C13  C12    0.00   0.0  0
 DY4  CONST_15  S1    C11  C12  C13    0.00   0.0  0
 DY4  CONST_16  C23   N1   N2   C2     0.00   0.0  0
 DY4  CONST_17  C20   C21  C7   C5   180.00   0.0  0
 DY4  CONST_18  C9    C8   C7   C5   180.00   0.0  0
 DY4  CONST_19  C3    C6   N5   N4     0.00   0.0  0
 DY4  CONST_20  F1    C8   C7   C5     0.00   0.0  0
 DY4  CONST_21  N3    C2   N2   N1   180.00   0.0  0
 DY4  CONST_22  N6    C9   C8   C7   180.00   0.0  0
 DY4  CONST_23  F2    C19  C9   C8   180.00   0.0  0
 DY4  CONST_24  C24   C23  N1   N2   180.00   0.0  0
 DY4  CONST_25  C13   C12  C11  C10  180.00   0.0  0
 DY4  CONST_26  C14   S1   C11  C10  180.00   0.0  0
 DY4  CONST_27  C23   C22  C2   N3   180.00   0.0  0
 DY4  CONST_28  C22   C23  N1   C1   180.00   0.0  0
 DY4  CONST_29  C2    N2   N1   C1   180.00   0.0  0
 DY4  CONST_30  F1    C8   C9   C19  180.00   0.0  0
 DY4  CONST_31  C24   C23  C22  C2   180.00   0.0  0
 DY4  CONST_32  N6    C9   C19  C20  180.00   0.0  0
 DY4  CONST_33  F2    C19  C20  C21  180.00   0.0  0
 DY4  CONST_34  F1    C8   C7   C21  180.00   0.0  0
 DY4  CONST_39  O1    C6   N5   N4   180.00   0.0  0
 DY4  CONST_40  H21   C21  C7   C5     0.00   0.0  0
 DY4  CONST_41  H22   C22  C23  N1   180.00   0.0  0
 DY4  CONST_42  H20   C20  C21  C7   180.00   0.0  0
 DY4  CONST_43  H1    C12  C13  C14  180.00   0.0  0
 DY4  CONST_44  H3    N5   C6   C3   180.00   0.0  0
 DY4  CONST_45  C11   C10  N6   C9   180.00   0.0  0
 DY4  CONST_50  O2    C10  N6   C9     0.00   0.0  0
 DY4  Var_01    C21   C7   C5   C4   -47.43  30.0  2
 DY4  Var_02    C17   C18  C13  C12  164.03  30.0  1
 DY4  Var_03    C16   C15  C14  C13  -15.70  30.0  1
 DY4  Var_04    C16   C17  C18  C13   46.20  30.0  1
 DY4  Var_05    C17   C16  C15  C14   45.52  30.0  1
 DY4  Var_06    C18   C17  C16  C15  -63.34  30.0  1
 DY4  Var_07    N6    C10  C11  C12  169.59  30.0  2
 DY4  Var_08    H241  C24  C23  N1    61.30  30.0  2
 DY4  Var_09    H12   C1   N1   N2    85.62  30.0  2

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
 DY4  plan-1  N1   0.020
 DY4  plan-1  N2   0.020
 DY4  plan-1  C1   0.020
 DY4  plan-1  C2   0.020
 DY4  plan-1  C22  0.020
 DY4  plan-1  C23  0.020
 DY4  plan-1  C24  0.020
 DY4  plan-1  H22  0.020
 DY4  plan-1  N3   0.020
 DY4  plan-2  C5   0.020
 DY4  plan-2  C7   0.020
 DY4  plan-2  C8   0.020
 DY4  plan-2  C9   0.020
 DY4  plan-2  C19  0.020
 DY4  plan-2  C20  0.020
 DY4  plan-2  C21  0.020
 DY4  plan-2  F1   0.020
 DY4  plan-2  F2   0.020
 DY4  plan-2  N6   0.020
 DY4  plan-2  H20  0.020
 DY4  plan-2  H21  0.020
 DY4  plan-3  C10  0.020
 DY4  plan-3  C11  0.020
 DY4  plan-3  C12  0.020
 DY4  plan-3  C13  0.020
 DY4  plan-3  C14  0.020
 DY4  plan-3  C15  0.020
 DY4  plan-3  C18  0.020
 DY4  plan-3  S1   0.020
 DY4  plan-3  H1   0.020
 DY4  plan-4  C4   0.020
 DY4  plan-4  C5   0.020
 DY4  plan-4  C6   0.020
 DY4  plan-4  C7   0.020
 DY4  plan-4  N4   0.020
 DY4  plan-4  C3   0.020
 DY4  plan-4  N5   0.020
 DY4  plan-4  O1   0.020
 DY4  plan-4  H4   0.020
 DY4  plan-4  H3   0.020
 DY4  plan-4  N3   0.020
 DY4  plan-5  C9   0.020
 DY4  plan-5  C10  0.020
 DY4  plan-5  C11  0.020
 DY4  plan-5  N6   0.020
 DY4  plan-5  O2   0.020
 DY4  plan-5  H5   0.020
 DY4  plan-6  C2   0.020
 DY4  plan-6  C3   0.020
 DY4  plan-6  H2   0.020
 DY4  plan-6  N3   0.020

