# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:52:15 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 1-[(2-aminopyridin-4-yl)methyl]-3-(2,4-dioxo-1,2-dihydrothieno[3,4-d]pyrimidin-3(4H)-yl)-5-(trifluoromethyl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(Cn2c3ccc(cc3c(N4C(=O)Nc5cscc5C4=O)c2C(O)=O)C(F)(F)F)ccn1
#
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
 054  054  '1-[(2-aminopyridin-4-yl)methyl]-3-(2,4-dioxo-1,2-dihydrothieno[3,4-d]pyrimidin-3(4H)-yl)-5-(trifluoromethyl)-1H-indole-2-carboxylic acid'  ligand  49  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_054
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
 054  C1    C  CR6   0  -0.208  -0.3380   3.4151  -0.4245
 054  C2    C  CR16  0  -0.277  -1.7238   3.4083  -0.1505
 054  C3    C  CR16  0  -0.290  -2.3420   2.3144   0.4037
 054  C4    C  CR16  0  -0.406   0.4464   2.3195  -0.1467
 054  C5    C  CR56  0   0.154  -0.1694   1.1983   0.4163
 054  C6    C  CR56  0   0.347  -1.5480   1.1993   0.6904
 054  N7    N  NR5   0  -0.614  -1.8879  -0.0062   1.2298
 054  C8    C  CR5   0   0.204  -0.7546  -0.7911   1.2931
 054  C9    C  CR5   0   0.246   0.3081  -0.0706   0.8126
 054  C10   C  C     0   0.544  -0.6594  -2.1849   1.7548
 054  O11   O  O     0  -0.425   0.4037  -2.7280   1.9335
 054  O12   O  OH1   0  -0.587  -1.8285  -2.7740   1.9241
 054  C13   C  CH2   0  -0.374  -3.2460  -0.3561   1.5827
 054  C14   C  CR6   0   0.191  -3.9901  -1.0868   0.4973
 054  C15   C  CT    0   1.053   0.2476   4.6495  -1.0284
 054  C16   C  CR16  0  -0.400  -5.2786  -1.5568   0.7688
 054  C17   C  CR16  0  -0.057  -5.9526  -2.2097  -0.2408
 054  N18   N  N     0  -0.463  -5.4589  -2.4203  -1.4584
 054  C19   C  CR6   0   0.465  -4.2351  -1.9695  -1.7192
 054  C20   C  CR16  0  -0.430  -3.4613  -1.2933  -0.7566
 054  N21   N  NR6   0  -0.725   1.6319  -0.5247   0.6672
 054  C22   C  CR6   0   0.675   2.4851  -0.3006   1.7552
 054  N23   N  NR16  0  -0.762   3.7474  -0.7779   1.6289
 054  C24   C  CR6   0   0.562   1.9305  -1.2420  -0.4917
 054  O25   O  O     0  -0.412   1.0963  -1.4202  -1.3488
 054  O26   O  O     0  -0.463   2.0977   0.2978   2.7340
 054  C27   C  CR15  0  -0.505   3.8819  -2.4248  -1.5616
 054  C28   C  CR56  0  -0.037   3.3005  -1.7190  -0.5447
 054  C29   C  CR56  0   0.460   4.1954  -1.4735   0.5288
 054  C30   C  CR15  0  -0.537   5.4378  -1.9887   0.3156
 054  S31   S  S2    0   0.289   5.5007  -2.7783  -1.2071
 054  F32   F  F     0  -0.315   0.0747   5.7208  -0.2388
 054  F33   F  F     0  -0.302   1.5594   4.5416  -1.2567
 054  F34   F  F     0  -0.315  -0.3315   4.9514  -2.2010
 054  N35   N  NH2   0  -0.833  -3.7608  -2.1482  -2.9841
 054  H2    H  HCR6  0   0.280  -2.3255   4.2774  -0.3827
 054  H3    H  HCR6  0   0.284  -3.4057   2.3311   0.5971
 054  H4    H  HCR6  0   0.268   1.5082   2.3047  -0.3535
 054  HO12  H  HOH1  0   0.497  -1.7043  -3.6869   2.2278
 054  H13   H  HCH2  0   0.306  -3.2523  -0.9338   2.5039
 054  H13A  H  HCH2  0   0.301  -3.7720   0.5701   1.8176
 054  H16   H  HCR6  0   0.257  -5.7345  -1.4210   1.7405
 054  H17   H  HCR6  0   0.257  -6.9518  -2.5927  -0.0622
 054  H20   H  HCR6  0   0.259  -2.4672  -0.9518  -1.0179
 054  HN23  H  HNR6  0   0.431   4.3740  -0.6022   2.4008
 054  H27   H  HCR5  0   0.319   3.4299  -2.7451  -2.4874
 054  H30   H  HCR5  0   0.317   6.3024  -1.9465   0.9593
 054  HN35  H  HNH2  0   0.383  -4.2232  -2.8474  -3.5417
 054  HN3A  H  HNH2  0   0.389  -2.7660  -2.0990  -3.1254

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
 054  C1   C2    aromatic  1.413  0.020  1.413
 054  C1   C15   single    1.494  0.020  1.494
 054  C2   C3    aromatic  1.373  0.020  1.373
 054  C2   H2    single    0.930  0.020  1.080
 054  C3   H3    single    0.930  0.020  1.080
 054  C4   C1    aromatic  1.376  0.020  1.376
 054  C4   C5    aromatic  1.398  0.020  1.398
 054  C4   H4    single    0.930  0.020  1.080
 054  C5   C6    aromatic  1.406  0.020  1.406
 054  C6   C3    aromatic  1.399  0.020  1.399
 054  N7   C6    aromatic  1.364  0.020  1.364
 054  N7   C8    aromatic  1.380  0.020  1.380
 054  C8   C9    aromatic  1.371  0.020  1.371
 054  C9   C5    aromatic  1.412  0.020  1.412
 054  C9   N21   single    1.407  0.020  1.407
 054  C10  C8    single    1.471  0.020  1.471
 054  O11  C10   double    1.207  0.020  1.207
 054  O12  C10   single    1.320  0.020  1.320
 054  O12  HO12  single    0.850  0.020  0.980
 054  C13  N7    single    1.446  0.020  1.446
 054  C13  H13   single    0.970  0.020  1.090
 054  C13  H13A  single    0.970  0.020  1.090
 054  C14  C13   single    1.505  0.020  1.505
 054  C14  C20   aromatic  1.376  0.020  1.376
 054  C15  F32   single    1.342  0.020  1.342
 054  C15  F33   single    1.336  0.020  1.336
 054  C15  F34   single    1.342  0.020  1.342
 054  C16  C14   aromatic  1.398  0.020  1.398
 054  C16  H16   single    0.930  0.020  1.080
 054  C17  C16   aromatic  1.378  0.020  1.378
 054  C17  N18   aromatic  1.331  0.020  1.331
 054  C17  H17   single    0.930  0.020  1.080
 054  N18  C19   aromatic  1.330  0.020  1.330
 054  C19  N35   single    1.363  0.020  1.363
 054  C19  C20   aromatic  1.408  0.020  1.408
 054  C20  H20   single    0.930  0.020  1.080
 054  N21  C24   single    1.395  0.020  1.395
 054  C22  N21   single    1.401  0.020  1.401
 054  C22  N23   single    1.355  0.020  1.355
 054  N23  C29   single    1.376  0.020  1.376
 054  N23  HN23  single    0.860  0.020  1.020
 054  C24  C28   single    1.452  0.020  1.452
 054  C24  O25   double    1.209  0.020  1.209
 054  O26  C22   double    1.211  0.020  1.211
 054  C27  H27   single    0.930  0.020  1.080
 054  C28  C27   aromatic  1.368  0.020  1.368
 054  C29  C28   aromatic  1.419  0.020  1.419
 054  C29  C30   aromatic  1.362  0.020  1.362
 054  C30  S31   aromatic  1.716  0.020  1.716
 054  C30  H30   single    0.930  0.020  1.080
 054  S31  C27   aromatic  1.694  0.020  1.694
 054  N35  HN35  single    0.890  0.020  1.040
 054  N35  HN3A  single    0.890  0.020  1.040

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
 054  C15   C1   C4    121.08  3.000
 054  C4    C1   C2    121.08  3.000
 054  C15   C1   C2    117.84  3.000
 054  H2    C2   C3    118.42  3.000
 054  H2    C2   C1    120.00  3.000
 054  C3    C2   C1    121.58  3.000
 054  H3    C3   C6    122.29  3.000
 054  C6    C3   C2    117.53  3.000
 054  H3    C3   C2    120.18  3.000
 054  H4    C4   C5    119.90  3.000
 054  H4    C4   C1    122.13  3.000
 054  C5    C4   C1    117.97  3.000
 054  C9    C5   C6    106.12  3.000
 054  C9    C5   C4    133.21  3.000
 054  C6    C5   C4    120.67  3.000
 054  N7    C6   C5    108.72  3.000
 054  N7    C6   C3    130.12  3.000
 054  C5    C6   C3    121.16  3.000
 054  C13   N7   C8    128.49  3.000
 054  C13   N7   C6    122.99  3.000
 054  C8    N7   C6    108.43  3.000
 054  C10   C8   C9    123.90  3.000
 054  C10   C8   N7    127.32  3.000
 054  C9    C8   N7    108.76  3.000
 054  N21   C9   C8    126.58  3.000
 054  N21   C9   C5    125.38  3.000
 054  C8    C9   C5    107.96  3.000
 054  O12   C10  O11   124.08  3.000
 054  O12   C10  C8    113.93  3.000
 054  O11   C10  C8    121.98  3.000
 054  HO12  O12  C10   110.28  3.000
 054  H13A  C13  H13   105.42  3.000
 054  H13A  C13  C14   109.21  3.000
 054  H13   C13  C14   110.49  3.000
 054  C14   C13  N7    113.94  3.000
 054  H13A  C13  N7    107.46  3.000
 054  H13   C13  N7    109.93  3.000
 054  C20   C14  C16   118.72  3.000
 054  C16   C14  C13   118.60  3.000
 054  C20   C14  C13   122.67  3.000
 054  F34   C15  F33   107.01  3.000
 054  F34   C15  F32   106.19  3.000
 054  F33   C15  F32   106.95  3.000
 054  F34   C15  C1    111.71  3.000
 054  F33   C15  C1    112.79  3.000
 054  F32   C15  C1    111.80  3.000
 054  H16   C16  C17   120.75  3.000
 054  C17   C16  C14   117.88  3.000
 054  H16   C16  C14   121.37  3.000
 054  H17   C17  N18   115.88  3.000
 054  H17   C17  C16   119.80  3.000
 054  N18   C17  C16   124.32  3.000
 054  C19   N18  C17   117.85  3.000
 054  N35   C19  C20   120.42  3.000
 054  C20   C19  N18   122.30  3.000
 054  N35   C19  N18   117.24  3.000
 054  H20   C20  C19   119.40  3.000
 054  H20   C20  C14   121.67  3.000
 054  C19   C20  C14   118.93  3.000
 054  C24   N21  C22   126.66  3.000
 054  C22   N21  C9    116.18  3.000
 054  C24   N21  C9    116.95  3.000
 054  O26   C22  N23   123.18  3.000
 054  O26   C22  N21   120.80  3.000
 054  N23   C22  N21   116.01  3.000
 054  HN23  N23  C29   119.80  3.000
 054  HN23  N23  C22   116.46  3.000
 054  C29   N23  C22   123.75  3.000
 054  C28   C24  O25   125.22  3.000
 054  O25   C24  N21   121.12  3.000
 054  C28   C24  N21   113.66  3.000
 054  H27   C27  S31   121.19  3.000
 054  S31   C27  C28   110.99  3.000
 054  H27   C27  C28   127.82  3.000
 054  C29   C28  C27   112.57  3.000
 054  C29   C28  C24   120.70  3.000
 054  C27   C28  C24   126.73  3.000
 054  C30   C29  C28   113.04  3.000
 054  C30   C29  N23   127.82  3.000
 054  C28   C29  N23   119.13  3.000
 054  H30   C30  S31   121.20  3.000
 054  H30   C30  C29   128.54  3.000
 054  S31   C30  C29   110.27  3.000
 054  C30   S31  C27    93.13  3.000
 054  HN3A  N35  HN35  114.23  3.000
 054  HN3A  N35  C19   117.92  3.000
 054  HN35  N35  C19   116.45  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
 054  CONST_01  C6    C3   C2   C1      0.00   0.0  0
 054  CONST_02  C6    C5   C4   C1      0.00   0.0  0
 054  CONST_03  C9    C5   C4   C1    180.00   0.0  0
 054  CONST_04  C5    C4   C1   C2      0.00   0.0  0
 054  CONST_05  C5    C6   C3   C2      0.00   0.0  0
 054  CONST_06  N7    C6   C3   C2    180.00   0.0  0
 054  CONST_07  C4    C1   C2   C3      0.00   0.0  0
 054  CONST_08  C4    C5   C6   C3      0.00   0.0  0
 054  CONST_09  C9    C5   C6   C3    180.00   0.0  0
 054  CONST_10  C8    N7   C6   C3    180.00   0.0  0
 054  CONST_11  N7    C6   C5   C4    180.00   0.0  0
 054  CONST_12  C8    C9   C5   C4    180.00   0.0  0
 054  CONST_13  C8    N7   C6   C5      0.00   0.0  0
 054  CONST_14  N7    C8   C9   C5      0.00   0.0  0
 054  CONST_15  C8    C9   C5   C6      0.00   0.0  0
 054  CONST_16  C9    C8   N7   C6      0.00   0.0  0
 054  CONST_17  C9    C5   C6   N7      0.00   0.0  0
 054  CONST_18  N18   C19  C20  C14     0.00   0.0  0
 054  CONST_19  N18   C17  C16  C14     0.00   0.0  0
 054  CONST_20  C19   C20  C14  C16     0.00   0.0  0
 054  CONST_21  C19   N18  C17  C16     0.00   0.0  0
 054  CONST_22  C20   C14  C16  C17     0.00   0.0  0
 054  CONST_23  C20   C19  N18  C17     0.00   0.0  0
 054  CONST_24  C30   C29  C28  C27     0.00   0.0  0
 054  CONST_25  C29   C30  S31  C27     0.00   0.0  0
 054  CONST_26  C30   S31  C27  C28     0.00   0.0  0
 054  CONST_27  S31   C30  C29  C28     0.00   0.0  0
 054  CONST_28  S31   C27  C28  C29     0.00   0.0  0
 054  CONST_29  N21   C9   C5   C4      0.00   0.0  0
 054  CONST_30  N21   C9   C5   C6    180.00   0.0  0
 054  CONST_31  N21   C9   C8   N7    180.00   0.0  0
 054  CONST_32  N23   C22  N21  C9    180.00   0.0  0
 054  CONST_33  C29   N23  C22  N21     0.00   0.0  0
 054  CONST_34  C24   N21  C22  N23     0.00   0.0  0
 054  CONST_35  C15   C1   C2   C3    180.00   0.0  0
 054  CONST_36  C13   N7   C6   C3      0.00   0.0  0
 054  CONST_37  C15   C1   C4   C5    180.00   0.0  0
 054  CONST_38  C13   N7   C6   C5    180.00   0.0  0
 054  CONST_39  C10   C8   C9   C5    180.00   0.0  0
 054  CONST_40  C10   C8   N7   C6    180.00   0.0  0
 054  CONST_41  C13   N7   C8   C9    180.00   0.0  0
 054  CONST_42  N21   C9   C8   C10     0.00   0.0  0
 054  CONST_43  C19   C20  C14  C13   180.00   0.0  0
 054  CONST_44  C17   C16  C14  C13   180.00   0.0  0
 054  CONST_45  N35   C19  C20  C14   180.00   0.0  0
 054  CONST_46  N35   C19  N18  C17   180.00   0.0  0
 054  CONST_47  O26   C22  N21  C9      0.00   0.0  0
 054  CONST_48  O26   C22  N21  C24   180.00   0.0  0
 054  CONST_49  C29   N23  C22  O26   180.00   0.0  0
 054  CONST_50  H3    C3   C2   C1    180.00   0.0  0
 054  CONST_51  H4    C4   C1   C2    180.00   0.0  0
 054  CONST_52  H2    C2   C1   C4    180.00   0.0  0
 054  CONST_53  H17   C17  C16  C14   180.00   0.0  0
 054  CONST_54  H20   C20  C14  C16   180.00   0.0  0
 054  CONST_55  H16   C16  C17  N18   180.00   0.0  0
 054  CONST_56  H30   C30  C29  N23     0.00   0.0  0
 054  CONST_57  H27   C27  C28  C24     0.00   0.0  0
 054  CONST_58  HN23  N23  C22  N21   180.00   0.0  0
 054  CONST_61  HO12  O12  C10  C8    180.00   0.0  0
 054  Var_01    C24   N21  C9   C5    -93.06  30.0  2
 054  Var_02    C14   C13  N7   C6     93.45  30.0  2
 054  Var_03    C20   C14  C13  N7     -5.52  30.0  2
 054  Var_04    F32   C15  C1   C2     60.04  30.0  2
 054  Var_05    O11   C10  C8   N7   -170.27  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
 054  plan-1  C13   0.020
 054  plan-1  C14   0.020
 054  plan-1  C16   0.020
 054  plan-1  C17   0.020
 054  plan-1  N18   0.020
 054  plan-1  C19   0.020
 054  plan-1  C20   0.020
 054  plan-1  N35   0.020
 054  plan-1  H16   0.020
 054  plan-1  H17   0.020
 054  plan-1  H20   0.020
 054  plan-2  C8    0.020
 054  plan-2  C10   0.020
 054  plan-2  O11   0.020
 054  plan-2  O12   0.020
 054  plan-2  HO12  0.020
 054  plan-3  C1    0.020
 054  plan-3  C2    0.020
 054  plan-3  C3    0.020
 054  plan-3  C4    0.020
 054  plan-3  C5    0.020
 054  plan-3  C6    0.020
 054  plan-3  N7    0.020
 054  plan-3  C8    0.020
 054  plan-3  C9    0.020
 054  plan-3  C10   0.020
 054  plan-3  C13   0.020
 054  plan-3  C15   0.020
 054  plan-3  N21   0.020
 054  plan-3  H2    0.020
 054  plan-3  H3    0.020
 054  plan-3  H4    0.020
 054  plan-4  C9    0.020
 054  plan-4  N21   0.020
 054  plan-4  C22   0.020
 054  plan-4  N23   0.020
 054  plan-4  C24   0.020
 054  plan-4  O25   0.020
 054  plan-4  O26   0.020
 054  plan-4  C27   0.020
 054  plan-4  C28   0.020
 054  plan-4  C29   0.020
 054  plan-4  C30   0.020
 054  plan-4  S31   0.020
 054  plan-4  HN23  0.020
 054  plan-4  H27   0.020
 054  plan-4  H30   0.020
 054  plan-5  C19   0.020
 054  plan-5  N35   0.020
 054  plan-5  HN35  0.020
 054  plan-5  HN3A  0.020

