# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 01:22:26 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 4-amino-N-{1-[(3-chloro-2-fluorophenyl)amino]-6-methylisoquinolin-5-yl}thieno[3,2-d]pyrimidine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2c(Nc3cccc(Cl)c3F)nccc2c1NC(=O)c4csc5c(N)ncnc45
#
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
 V1Y  V1Y  4-amino-N-{1-[(3-chloro-2-fluorophenyl)amino]-6-methylisoquinolin-5-yl}thieno[3,2-d]pyrimidine-7-carboxamide  ligand  49  33  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_V1Y
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
 V1Y  C4    C   CR16  0  -0.297  -5.2010  12.5212  14.0414
 V1Y  C14   C   CR56  0  -0.318  -8.0228  20.5031  14.4534
 V1Y  C5    C   CR66  0  -0.081  -4.3673  13.5459  13.5549
 V1Y  C6    C   CR66  0   0.230  -4.8202  14.8842  13.6033
 V1Y  C11   C   CR5   0   0.008  -7.4178  18.5550  13.2948
 V1Y  C7    C   CR6   0   0.238  -6.1265  15.1473  14.0831
 V1Y  C9    C   C     0   0.525  -6.9519  17.1701  13.0321
 V1Y  C12   C   CR15  0  -0.504  -7.7600  19.3961  12.2825
 V1Y  C3    C   CR16  0  -0.319  -6.4473  12.8129  14.5257
 V1Y  C15   C   CR56  0   0.345  -7.5699  19.1940  14.5738
 V1Y  C17   C   CR16  0   0.066  -7.5410  19.4046  16.8072
 V1Y  C19   C   CR6   0   0.521  -8.2214  21.2495  15.6357
 V1Y  C2    C   CR6   0   0.071  -6.9393  14.1336  14.5432
 V1Y  C21   C   CR16  0  -0.422  -3.9252  15.9072  13.2037
 V1Y  C22   C   CR16  0  -0.073  -2.6813  15.5530  12.7787
 V1Y  C24   C   CR6   0   0.464  -3.0483  13.3158  13.0377
 V1Y  C26   C   CR6   0   0.178  -1.2888  11.7201  12.5246
 V1Y  C27   C   CR16  0  -0.296  -1.0407  10.9192  11.4153
 V1Y  C28   C   CR16  0  -0.271   0.2572  10.5832  11.0599
 V1Y  C29   C   CR16  0  -0.229   1.3345  11.0611  11.7885
 V1Y  C30   C   CR6   0  -0.242   1.0949  11.8597  12.8975
 V1Y  C31   C   CR6   0   0.615  -0.2007  12.1678  13.2674
 V1Y  F32   F   F     0  -0.285  -0.4108  12.8867  14.3674
 V1Y  N16   N   N     0  -0.514  -7.3217  18.6282  15.7679
 V1Y  N18   N   N     0  -0.463  -7.9683  20.6598  16.8057
 V1Y  N20   N   NH2   0  -0.819  -8.6585  22.5078  15.6454
 V1Y  N23   N   N     0  -0.458  -2.2485  14.2802  12.6720
 V1Y  N25   N   NH1   0  -0.764  -2.5900  12.0224  12.9292
 V1Y  N8    N   NH1   0  -0.788  -6.5899  16.4789  14.1336
 V1Y  O10   O   O     0  -0.456  -6.8994  16.7189  11.8997
 V1Y  S13   S   S2    0   0.285  -8.2619  20.9454  12.8007
 V1Y  CL33  CL  CL    0  -0.093   2.3975  12.4595  13.8549
 V1Y  H1    H   HCR6  0   0.255  -4.8663  11.4925  14.0596
 V1Y  H2    H   HCR5  0   0.319  -7.7400  19.1741  11.2257
 V1Y  H3    H   HCR6  0   0.261  -7.0746  12.0149  14.9020
 V1Y  H4    H   HCH3  0   0.255  -8.9135  14.9594  14.3254
 V1Y  H5    H   HCH3  0   0.253  -8.8365  13.5044  15.3195
 V1Y  H6    H   HCH3  0   0.254  -8.2817  15.0473  15.9589
 V1Y  H7    H   HCR6  0   0.262  -7.3494  18.9717  17.7830
 V1Y  H8    H   HCR6  0   0.252  -4.2015  16.9496  13.2604
 V1Y  H9    H   HCR6  0   0.257  -1.9680  16.3139  12.4840
 V1Y  H10   H   HCR6  0   0.278  -1.8777  10.5608  10.8298
 V1Y  H11   H   HCR6  0   0.272   0.4324   9.9567  10.1962
 V1Y  H12   H   HCR6  0   0.286   2.3497  10.8178  11.5070
 V1Y  H13   H   HNH2  0   0.410  -8.7402  22.9935  16.5232
 V1Y  H14   H   HNH2  0   0.416  -8.8128  23.0398  14.8066
 V1Y  H15   H   HNH1  0   0.413  -3.2746  11.3062  12.7419
 V1Y  H16   H   HNH1  0   0.426  -6.7406  16.9230  15.0403
 V1Y  C1    C   CH3   0  -0.723  -8.3146  14.4243  15.0631

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
 V1Y  C28  C27   aromatic  1.387  0.020  1.387
 V1Y  C28  C29   aromatic  1.386  0.020  1.386
 V1Y  C27  C26   aromatic  1.391  0.020  1.391
 V1Y  O10  C9    double    1.220  0.020  1.220
 V1Y  C29  C30   aromatic  1.387  0.020  1.387
 V1Y  C12  S13   aromatic  1.709  0.020  1.709
 V1Y  C12  C11   aromatic  1.360  0.020  1.360
 V1Y  C26  N25   single    1.396  0.020  1.396
 V1Y  C26  C31   aromatic  1.391  0.020  1.391
 V1Y  N23  C22   aromatic  1.349  0.020  1.349
 V1Y  N23  C24   aromatic  1.305  0.020  1.305
 V1Y  C22  C21   aromatic  1.361  0.020  1.361
 V1Y  S13  C14   aromatic  1.727  0.020  1.727
 V1Y  N25  C24   single    1.377  0.020  1.377
 V1Y  C24  C5    aromatic  1.435  0.020  1.435
 V1Y  C9   C11   single    1.485  0.020  1.485
 V1Y  C9   N8    single    1.350  0.020  1.350
 V1Y  C30  C31   aromatic  1.382  0.020  1.382
 V1Y  C30  CL33  single    1.724  0.020  1.724
 V1Y  C21  C6    aromatic  1.417  0.020  1.417
 V1Y  C11  C15   aromatic  1.438  0.020  1.438
 V1Y  C31  F32   single    1.331  0.020  1.331
 V1Y  C5   C6    aromatic  1.414  0.020  1.414
 V1Y  C5   C4    aromatic  1.408  0.020  1.408
 V1Y  C6   C7    aromatic  1.416  0.020  1.416
 V1Y  C4   C3    aromatic  1.369  0.020  1.369
 V1Y  C7   N8    single    1.411  0.020  1.411
 V1Y  C7   C2    aromatic  1.378  0.020  1.378
 V1Y  C3   C2    aromatic  1.409  0.020  1.409
 V1Y  C2   C1    single    1.499  0.020  1.499
 V1Y  C14  C15   aromatic  1.391  0.020  1.391
 V1Y  C14  C19   aromatic  1.412  0.020  1.412
 V1Y  C15  N16   aromatic  1.344  0.020  1.344
 V1Y  N20  C19   single    1.332  0.020  1.332
 V1Y  C19  N18   aromatic  1.334  0.020  1.334
 V1Y  N16  C17   aromatic  1.316  0.020  1.316
 V1Y  N18  C17   aromatic  1.326  0.020  1.326
 V1Y  C4   H1    single    0.930  0.020  1.080
 V1Y  C12  H2    single    0.930  0.020  1.080
 V1Y  C3   H3    single    0.930  0.020  1.080
 V1Y  C1   H4    single    0.970  0.020  1.090
 V1Y  C1   H5    single    0.970  0.020  1.090
 V1Y  C1   H6    single    0.970  0.020  1.090
 V1Y  C17  H7    single    0.930  0.020  1.080
 V1Y  C21  H8    single    0.930  0.020  1.080
 V1Y  C22  H9    single    0.930  0.020  1.080
 V1Y  C27  H10   single    0.930  0.020  1.080
 V1Y  C28  H11   single    0.930  0.020  1.080
 V1Y  C29  H12   single    0.930  0.020  1.080
 V1Y  N20  H13   single    0.860  0.020  1.020
 V1Y  N20  H14   single    0.860  0.020  1.020
 V1Y  N25  H15   single    0.890  0.020  1.040
 V1Y  N8   H16   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
 V1Y  H1    C4   C3   118.58  3.000
 V1Y  H1    C4   C5   120.98  3.000
 V1Y  C3    C4   C5   120.43  3.000
 V1Y  S13   C14  C19  130.25  3.000
 V1Y  C19   C14  C15  118.09  3.000
 V1Y  S13   C14  C15  111.65  3.000
 V1Y  C24   C5   C6   117.29  3.000
 V1Y  C6    C5   C4   119.18  3.000
 V1Y  C24   C5   C4   123.51  3.000
 V1Y  C21   C6   C7   122.97  3.000
 V1Y  C7    C6   C5   118.88  3.000
 V1Y  C21   C6   C5   118.13  3.000
 V1Y  C15   C11  C12  111.15  3.000
 V1Y  C15   C11  C9   127.24  3.000
 V1Y  C12   C11  C9   121.61  3.000
 V1Y  N8    C7   C2   119.24  3.000
 V1Y  C2    C7   C6   121.36  3.000
 V1Y  N8    C7   C6   119.37  3.000
 V1Y  O10   C9   N8   123.81  3.000
 V1Y  N8    C9   C11  114.67  3.000
 V1Y  O10   C9   C11  121.51  3.000
 V1Y  H2    C12  S13  119.24  3.000
 V1Y  H2    C12  C11  126.63  3.000
 V1Y  S13   C12  C11  114.13  3.000
 V1Y  H3    C3   C2   118.96  3.000
 V1Y  H3    C3   C4   119.57  3.000
 V1Y  C2    C3   C4   121.47  3.000
 V1Y  N16   C15  C11  125.70  3.000
 V1Y  N16   C15  C14  122.23  3.000
 V1Y  C11   C15  C14  112.07  3.000
 V1Y  H7    C17  N18  115.83  3.000
 V1Y  H7    C17  N16  116.46  3.000
 V1Y  N18   C17  N16  127.70  3.000
 V1Y  N20   C19  N18  118.24  3.000
 V1Y  N18   C19  C14  118.28  3.000
 V1Y  N20   C19  C14  123.47  3.000
 V1Y  C1    C2   C3   120.42  3.000
 V1Y  C1    C2   C7   120.95  3.000
 V1Y  C3    C2   C7   118.63  3.000
 V1Y  H8    C21  C22  120.09  3.000
 V1Y  H8    C21  C6   121.37  3.000
 V1Y  C22   C21  C6   118.52  3.000
 V1Y  H9    C22  N23  115.46  3.000
 V1Y  H9    C22  C21  120.24  3.000
 V1Y  N23   C22  C21  124.30  3.000
 V1Y  N25   C24  N23  117.91  3.000
 V1Y  N25   C24  C5   119.01  3.000
 V1Y  N23   C24  C5   123.07  3.000
 V1Y  N25   C26  C31  120.31  3.000
 V1Y  C31   C26  C27  118.14  3.000
 V1Y  N25   C26  C27  121.49  3.000
 V1Y  H10   C27  C28  120.32  3.000
 V1Y  H10   C27  C26  118.96  3.000
 V1Y  C28   C27  C26  120.72  3.000
 V1Y  H11   C28  C29  119.60  3.000
 V1Y  H11   C28  C27  119.78  3.000
 V1Y  C29   C28  C27  120.62  3.000
 V1Y  H12   C29  C30  119.99  3.000
 V1Y  H12   C29  C28  121.03  3.000
 V1Y  C30   C29  C28  118.98  3.000
 V1Y  CL33  C30  C31  118.82  3.000
 V1Y  CL33  C30  C29  120.90  3.000
 V1Y  C31   C30  C29  120.27  3.000
 V1Y  F32   C31  C30  119.32  3.000
 V1Y  F32   C31  C26  119.45  3.000
 V1Y  C30   C31  C26  121.23  3.000
 V1Y  C17   N16  C15  114.99  3.000
 V1Y  C19   N18  C17  118.71  3.000
 V1Y  H14   N20  H13  117.38  3.000
 V1Y  H14   N20  C19  122.97  3.000
 V1Y  H13   N20  C19  119.27  3.000
 V1Y  C24   N23  C22  118.59  3.000
 V1Y  H15   N25  C26  115.17  3.000
 V1Y  H15   N25  C24  117.13  3.000
 V1Y  C26   N25  C24  122.47  3.000
 V1Y  H16   N8   C9   117.54  3.000
 V1Y  H16   N8   C7   119.41  3.000
 V1Y  C9    N8   C7   122.83  3.000
 V1Y  C12   S13  C14   91.00  3.000
 V1Y  H6    C1   H5   107.67  3.000
 V1Y  H6    C1   H4   106.96  3.000
 V1Y  H5    C1   H4   108.10  3.000
 V1Y  H6    C1   C2   111.57  3.000
 V1Y  H5    C1   C2   110.97  3.000
 V1Y  H4    C1   C2   111.37  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
 V1Y  CONST_01  N23   C24  C5   C4    180.00   0.0  0
 V1Y  CONST_02  C21   C6   C5   C4    180.00   0.0  0
 V1Y  CONST_03  C7    C6   C5   C4      0.00   0.0  0
 V1Y  CONST_04  C7    C2   C3   C4      0.00   0.0  0
 V1Y  CONST_05  C11   C12  S13  C14     0.00   0.0  0
 V1Y  CONST_06  C12   C11  C15  C14     0.00   0.0  0
 V1Y  CONST_07  C17   N16  C15  C14     0.00   0.0  0
 V1Y  CONST_08  C17   N18  C19  C14     0.00   0.0  0
 V1Y  CONST_09  C22   N23  C24  C5      0.00   0.0  0
 V1Y  CONST_10  C22   C21  C6   C5      0.00   0.0  0
 V1Y  CONST_11  C2    C7   C6   C5      0.00   0.0  0
 V1Y  CONST_12  C2    C3   C4   C5      0.00   0.0  0
 V1Y  CONST_13  N23   C22  C21  C6      0.00   0.0  0
 V1Y  CONST_14  N23   C24  C5   C6      0.00   0.0  0
 V1Y  CONST_15  C3    C4   C5   C6      0.00   0.0  0
 V1Y  CONST_16  C3    C2   C7   C6      0.00   0.0  0
 V1Y  CONST_17  S13   C14  C15  C11     0.00   0.0  0
 V1Y  CONST_18  C19   C14  C15  C11   180.00   0.0  0
 V1Y  CONST_19  C17   N16  C15  C11   180.00   0.0  0
 V1Y  CONST_20  C22   C21  C6   C7    180.00   0.0  0
 V1Y  CONST_21  C24   C5   C6   C7    180.00   0.0  0
 V1Y  CONST_22  C15   C14  S13  C12     0.00   0.0  0
 V1Y  CONST_23  C19   C14  S13  C12   180.00   0.0  0
 V1Y  CONST_24  N16   C15  C11  C12   180.00   0.0  0
 V1Y  CONST_25  C24   C5   C4   C3    180.00   0.0  0
 V1Y  CONST_26  S13   C12  C11  C15     0.00   0.0  0
 V1Y  CONST_27  N18   C19  C14  C15     0.00   0.0  0
 V1Y  CONST_28  N18   C17  N16  C15     0.00   0.0  0
 V1Y  CONST_29  N16   C15  C14  C19     0.00   0.0  0
 V1Y  CONST_30  N16   C17  N18  C19     0.00   0.0  0
 V1Y  CONST_31  C21   C6   C7   C2    180.00   0.0  0
 V1Y  CONST_32  C24   N23  C22  C21     0.00   0.0  0
 V1Y  CONST_33  C24   C5   C6   C21     0.00   0.0  0
 V1Y  CONST_34  C29   C28  C27  C26     0.00   0.0  0
 V1Y  CONST_35  C29   C30  C31  C26     0.00   0.0  0
 V1Y  CONST_36  C30   C29  C28  C27     0.00   0.0  0
 V1Y  CONST_37  C30   C31  C26  C27     0.00   0.0  0
 V1Y  CONST_38  C31   C26  C27  C28     0.00   0.0  0
 V1Y  CONST_39  C31   C30  C29  C28     0.00   0.0  0
 V1Y  CONST_40  S13   C14  C15  N16   180.00   0.0  0
 V1Y  CONST_41  S13   C14  C19  N18   180.00   0.0  0
 V1Y  CONST_42  N25   C24  C5   C4      0.00   0.0  0
 V1Y  CONST_43  C1    C2   C3   C4    180.00   0.0  0
 V1Y  CONST_44  C9    C11  C15  C14   180.00   0.0  0
 V1Y  CONST_45  N8    C7   C6   C5    180.00   0.0  0
 V1Y  CONST_46  N25   C24  C5   C6    180.00   0.0  0
 V1Y  CONST_47  C1    C2   C7   C6    180.00   0.0  0
 V1Y  CONST_48  S13   C12  C11  C9    180.00   0.0  0
 V1Y  CONST_49  N16   C15  C11  C9      0.00   0.0  0
 V1Y  CONST_50  N8    C7   C2   C3    180.00   0.0  0
 V1Y  CONST_51  N20   C19  C14  C15   180.00   0.0  0
 V1Y  CONST_52  N20   C19  N18  C17   180.00   0.0  0
 V1Y  CONST_53  N8    C7   C6   C21     0.00   0.0  0
 V1Y  CONST_54  N25   C24  N23  C22   180.00   0.0  0
 V1Y  CONST_55  CL33  C30  C31  C26   180.00   0.0  0
 V1Y  CONST_56  F32   C31  C26  C27   180.00   0.0  0
 V1Y  CONST_57  N25   C26  C27  C28   180.00   0.0  0
 V1Y  CONST_58  CL33  C30  C29  C28   180.00   0.0  0
 V1Y  CONST_59  F32   C31  C30  C29   180.00   0.0  0
 V1Y  CONST_60  N25   C26  C31  C30   180.00   0.0  0
 V1Y  CONST_61  S13   C14  C19  N20     0.00   0.0  0
 V1Y  CONST_62  H2    C12  S13  C14   180.00   0.0  0
 V1Y  CONST_63  H8    C21  C6   C5    180.00   0.0  0
 V1Y  CONST_64  H3    C3   C4   C5    180.00   0.0  0
 V1Y  CONST_65  H9    C22  C21  C6    180.00   0.0  0
 V1Y  CONST_66  H1    C4   C5   C6    180.00   0.0  0
 V1Y  CONST_67  H7    C17  N16  C15   180.00   0.0  0
 V1Y  CONST_68  H11   C28  C27  C26   180.00   0.0  0
 V1Y  CONST_69  H12   C29  C28  C27   180.00   0.0  0
 V1Y  CONST_70  H10   C27  C28  C29   180.00   0.0  0
 V1Y  CONST_71  C7    N8   C9   C11   180.00   0.0  0
 V1Y  CONST_74  H13   N20  C19  C14   180.00   0.0  0
 V1Y  CONST_75  H14   N20  C19  C14     0.00   0.0  0
 V1Y  CONST_77  O10   C9   N8   C7      0.00   0.0  0
 V1Y  Var_01    C26   N25  C24  C5   -175.43  30.0  1
 V1Y  Var_02    C27   C26  N25  C24  -122.17  30.0  3
 V1Y  Var_03    O10   C9   C11  C12    -2.41  30.0  2
 V1Y  Var_04    H4    C1   C2   C7     55.69  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
 V1Y  plan-1  C26   0.020
 V1Y  plan-1  C27   0.020
 V1Y  plan-1  C28   0.020
 V1Y  plan-1  C29   0.020
 V1Y  plan-1  C30   0.020
 V1Y  plan-1  C31   0.020
 V1Y  plan-1  F32   0.020
 V1Y  plan-1  N25   0.020
 V1Y  plan-1  CL33  0.020
 V1Y  plan-1  H10   0.020
 V1Y  plan-1  H11   0.020
 V1Y  plan-1  H12   0.020
 V1Y  plan-2  C14   0.020
 V1Y  plan-2  C11   0.020
 V1Y  plan-2  C9    0.020
 V1Y  plan-2  C12   0.020
 V1Y  plan-2  C15   0.020
 V1Y  plan-2  C17   0.020
 V1Y  plan-2  C19   0.020
 V1Y  plan-2  N16   0.020
 V1Y  plan-2  N18   0.020
 V1Y  plan-2  N20   0.020
 V1Y  plan-2  S13   0.020
 V1Y  plan-2  H2    0.020
 V1Y  plan-2  H7    0.020
 V1Y  plan-3  C4    0.020
 V1Y  plan-3  C5    0.020
 V1Y  plan-3  C6    0.020
 V1Y  plan-3  C7    0.020
 V1Y  plan-3  C3    0.020
 V1Y  plan-3  C2    0.020
 V1Y  plan-3  C21   0.020
 V1Y  plan-3  C22   0.020
 V1Y  plan-3  C24   0.020
 V1Y  plan-3  N23   0.020
 V1Y  plan-3  N25   0.020
 V1Y  plan-3  N8    0.020
 V1Y  plan-3  H1    0.020
 V1Y  plan-3  H3    0.020
 V1Y  plan-3  H8    0.020
 V1Y  plan-3  H9    0.020
 V1Y  plan-3  C1    0.020
 V1Y  plan-4  C11   0.020
 V1Y  plan-4  C7    0.020
 V1Y  plan-4  C9    0.020
 V1Y  plan-4  N8    0.020
 V1Y  plan-4  O10   0.020
 V1Y  plan-4  H16   0.020
 V1Y  plan-5  C19   0.020
 V1Y  plan-5  N20   0.020
 V1Y  plan-5  H13   0.020
 V1Y  plan-5  H14   0.020

