# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:22:26 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 3-[[5-chloranyl-1-(3-methylsulfonylpropyl)indol-2-yl]methyl]-1-[2,2,2-tris(fluoranyl)ethyl]imidazo[4,5-c]pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)CCCn1c(CN2C(=O)N(CC(F)(F)F)c3ccncc23)cc4cc(Cl)ccc14
#
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
 6YA  6YA  3-[[5-chloranyl-1-(3-methylsulfonylpropyl)indol-2-yl]methyl]-1-[2,2,2-tris(fluoranyl)ethyl]imidazo[4,5-c]pyridin-2-one  ligand  53  33  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6YA
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
 6YA  C10  C   CR16  0  -0.312   3.0045  -2.7096  -0.6944
 6YA  C13  C   CH2   0  -0.619   4.4516   1.8609  -1.1022
 6YA  C17  C   CH3   0  -0.787   6.5718   3.6662  -0.7272
 6YA  C20  C   CR5   0   0.702  -2.1566   1.7435   0.3131
 6YA  C24  C   CR56  0   0.240  -2.6452   0.6085  -1.5733
 6YA  C28  C   CR16  0  -0.373  -5.0442   0.5446  -1.5214
 6YA  C01  C   CR15  0  -0.442  -0.3119  -1.3853  -0.1666
 6YA  C02  C   CR5   0   0.360   0.3178  -0.3245  -0.7518
 6YA  N03  N   NR5   0  -0.583   1.6168  -0.6553  -1.0496
 6YA  C04  C   CR56  0   0.370   1.8468  -1.9401  -0.6325
 6YA  C05  C   CR56  0   0.075   0.6482  -2.4365  -0.0795
 6YA  C06  C   CR16  0  -0.315   0.6046  -3.7444   0.4118
 6YA  C07  C   CR6   0  -0.051   1.7567  -4.4972   0.3382
 6YA  CL8  CL  CL    0  -0.144   1.7427  -6.1290   0.9432
 6YA  C09  C   CR16  0  -0.241   2.9491  -3.9997  -0.2033
 6YA  C11  C   CH2   0  -0.335   2.6248   0.2322  -1.5825
 6YA  C12  C   CH2   0  -0.451   3.4149   0.9357  -0.4825
 6YA  S14  S   S     0   1.195   5.4270   2.6501   0.1758
 6YA  O15  O   OS    0  -0.687   4.5489   3.5151   0.9650
 6YA  O16  O   OS    0  -0.687   6.1758   1.6129   0.8868
 6YA  C18  C   CH2   0  -0.407  -0.2239   1.0313  -1.0749
 6YA  N19  N   NR5   0  -0.605  -1.6298   1.1204  -0.7919
 6YA  N22  N   NR5   0  -0.618  -3.5336   1.6137   0.2015
 6YA  C23  C   CR56  0   0.435  -3.8499   0.9238  -0.9453
 6YA  C25  C   CR16  0  -0.101  -2.6499  -0.0926  -2.7598
 6YA  N26  N   N     0  -0.413  -3.7989  -0.4602  -3.3231
 6YA  C27  C   CR16  0  -0.084  -4.9428  -0.1473  -2.7251
 6YA  C29  C   CH2   0  -0.518  -4.4535   2.1666   1.1520
 6YA  C30  C   CT    0   0.988  -4.8399   1.1473   2.2031
 6YA  F31  F   F     0  -0.299  -3.7763   0.6875   2.8697
 6YA  F32  F   F     0  -0.299  -5.6802   1.6800   3.0938
 6YA  F33  F   F     0  -0.302  -5.4454   0.0827   1.6611
 6YA  H1   H   HCR6  0   0.274   3.9295  -2.3261  -1.1050
 6YA  H2   H   HCH2  0   0.305   5.1489   1.3167  -1.7425
 6YA  H3   H   HCH2  0   0.306   3.9864   2.6535  -1.6909
 6YA  H4   H   HCH3  0   0.313   7.1836   4.1911   0.0050
 6YA  H5   H   HCH3  0   0.296   7.1990   3.0361  -1.3533
 6YA  H6   H   HCH3  0   0.295   6.0227   4.3827  -1.3340
 6YA  H7   H   HCR6  0   0.289  -6.0096   0.7605  -1.0867
 6YA  H8   H   HCR5  0   0.254  -1.3389  -1.4220   0.1601
 6YA  H9   H   HCR6  0   0.271  -0.3037  -4.1499   0.8377
 6YA  H10  H   HCR6  0   0.275   3.8303  -4.6254  -0.2335
 6YA  H11  H   HCH2  0   0.284   3.2945  -0.3459  -2.2211
 6YA  H12  H   HCH2  0   0.285   2.1423   0.9623  -2.2328
 6YA  H13  H   HCH2  0   0.268   3.9057   0.1907   0.1467
 6YA  H14  H   HCH2  0   0.265   2.7341   1.5060   0.1525
 6YA  H15  H   HCH2  0   0.303   0.2853   1.8082  -0.5004
 6YA  H16  H   HCH2  0   0.301  -0.0640   1.2769  -2.1283
 6YA  H17  H   HCR6  0   0.278  -1.7311  -0.3643  -3.2672
 6YA  H18  H   HCR6  0   0.270  -5.8496  -0.4653  -3.2259
 6YA  H19  H   HCH2  0   0.326  -3.9982   3.0295   1.6379
 6YA  H20  H   HCH2  0   0.325  -5.3514   2.5149   0.6397
 6YA  O21  O   O     0  -0.471  -1.5548   2.3073   1.1995

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
 6YA  F32  C30  single    1.335  0.020  1.335
 6YA  F33  C30  single    1.339  0.020  1.339
 6YA  C30  C29  single    1.514  0.020  1.514
 6YA  C30  F31  single    1.337  0.020  1.337
 6YA  C29  N22  single    1.434  0.020  1.434
 6YA  C28  C27  aromatic  1.392  0.020  1.392
 6YA  C28  C23  aromatic  1.379  0.020  1.379
 6YA  O16  S14  double    1.464  0.020  1.464
 6YA  C27  N26  aromatic  1.328  0.020  1.328
 6YA  N22  C23  single    1.375  0.020  1.375
 6YA  N22  C20  single    1.388  0.020  1.388
 6YA  C23  C24  aromatic  1.395  0.020  1.395
 6YA  C17  S14  single    1.777  0.020  1.777
 6YA  S14  O15  double    1.464  0.020  1.464
 6YA  S14  C13  single    1.791  0.020  1.791
 6YA  N26  C25  aromatic  1.331  0.020  1.331
 6YA  C20  O21  double    1.211  0.020  1.211
 6YA  C20  N19  single    1.374  0.020  1.374
 6YA  C24  C25  aromatic  1.378  0.020  1.378
 6YA  C24  N19  single    1.380  0.020  1.380
 6YA  N19  C18  single    1.437  0.020  1.437
 6YA  C13  C12  single    1.521  0.020  1.521
 6YA  C12  C11  single    1.526  0.020  1.526
 6YA  C11  N03  single    1.445  0.020  1.445
 6YA  C18  C02  single    1.495  0.020  1.495
 6YA  N03  C02  aromatic  1.373  0.020  1.373
 6YA  N03  C04  aromatic  1.370  0.020  1.370
 6YA  C02  C01  aromatic  1.365  0.020  1.365
 6YA  C04  C10  aromatic  1.392  0.020  1.392
 6YA  C04  C05  aromatic  1.410  0.020  1.410
 6YA  C01  C05  aromatic  1.426  0.020  1.426
 6YA  C10  C09  aromatic  1.381  0.020  1.381
 6YA  C05  C06  aromatic  1.398  0.020  1.398
 6YA  C09  C07  aromatic  1.401  0.020  1.401
 6YA  C06  C07  aromatic  1.378  0.020  1.378
 6YA  C07  CL8  single    1.740  0.020  1.740
 6YA  C10  H1   single    0.930  0.020  1.080
 6YA  C13  H2   single    0.970  0.020  1.090
 6YA  C13  H3   single    0.970  0.020  1.090
 6YA  C17  H4   single    0.970  0.020  1.090
 6YA  C17  H5   single    0.970  0.020  1.090
 6YA  C17  H6   single    0.970  0.020  1.090
 6YA  C28  H7   single    0.930  0.020  1.080
 6YA  C01  H8   single    0.930  0.020  1.080
 6YA  C06  H9   single    0.930  0.020  1.080
 6YA  C09  H10  single    0.930  0.020  1.080
 6YA  C11  H11  single    0.970  0.020  1.090
 6YA  C11  H12  single    0.970  0.020  1.090
 6YA  C12  H13  single    0.970  0.020  1.090
 6YA  C12  H14  single    0.970  0.020  1.090
 6YA  C18  H15  single    0.970  0.020  1.090
 6YA  C18  H16  single    0.970  0.020  1.090
 6YA  C25  H17  single    0.930  0.020  1.080
 6YA  C27  H18  single    0.930  0.020  1.080
 6YA  C29  H19  single    0.970  0.020  1.090
 6YA  C29  H20  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
 6YA  H1   C10  C09  120.01  3.000
 6YA  H1   C10  C04  122.14  3.000
 6YA  C09  C10  C04  117.86  3.000
 6YA  H3   C13  H2   108.53  3.000
 6YA  H3   C13  S14  107.28  3.000
 6YA  H2   C13  S14  106.88  3.000
 6YA  H3   C13  C12  111.77  3.000
 6YA  H2   C13  C12  111.77  3.000
 6YA  S14  C13  C12  110.39  3.000
 6YA  H6   C17  H5   110.59  3.000
 6YA  H6   C17  H4   109.95  3.000
 6YA  H5   C17  H4   110.02  3.000
 6YA  H6   C17  S14  109.57  3.000
 6YA  H5   C17  S14  109.44  3.000
 6YA  H4   C17  S14  107.21  3.000
 6YA  N22  C20  O21  126.56  3.000
 6YA  O21  C20  N19  127.56  3.000
 6YA  N22  C20  N19  105.87  3.000
 6YA  C25  C24  C23  119.98  3.000
 6YA  C25  C24  N19  132.76  3.000
 6YA  C23  C24  N19  107.27  3.000
 6YA  H7   C28  C27  120.82  3.000
 6YA  H7   C28  C23  123.41  3.000
 6YA  C27  C28  C23  115.77  3.000
 6YA  H8   C01  C05  126.69  3.000
 6YA  H8   C01  C02  126.55  3.000
 6YA  C05  C01  C02  106.76  3.000
 6YA  C18  C02  N03  120.95  3.000
 6YA  N03  C02  C01  110.00  3.000
 6YA  C18  C02  C01  129.05  3.000
 6YA  C11  N03  C04  124.83  3.000
 6YA  C04  N03  C02  108.58  3.000
 6YA  C11  N03  C02  126.29  3.000
 6YA  C05  C04  N03  107.86  3.000
 6YA  C05  C04  C10  122.00  3.000
 6YA  N03  C04  C10  130.14  3.000
 6YA  C06  C05  C04  119.59  3.000
 6YA  C06  C05  C01  133.63  3.000
 6YA  C04  C05  C01  106.78  3.000
 6YA  H9   C06  C07  121.20  3.000
 6YA  H9   C06  C05  121.01  3.000
 6YA  C07  C06  C05  117.79  3.000
 6YA  C09  C07  CL8  118.31  3.000
 6YA  CL8  C07  C06  119.13  3.000
 6YA  C09  C07  C06  122.56  3.000
 6YA  H10  C09  C07  119.93  3.000
 6YA  H10  C09  C10  119.86  3.000
 6YA  C07  C09  C10  120.21  3.000
 6YA  H12  C11  H11  106.10  3.000
 6YA  H12  C11  C12  110.51  3.000
 6YA  H11  C11  C12  110.38  3.000
 6YA  H12  C11  N03  108.82  3.000
 6YA  H11  C11  N03  108.58  3.000
 6YA  C12  C11  N03  112.24  3.000
 6YA  H14  C12  H13  107.55  3.000
 6YA  H14  C12  C11  109.70  3.000
 6YA  H13  C12  C11  109.49  3.000
 6YA  H14  C12  C13  110.13  3.000
 6YA  H13  C12  C13  110.08  3.000
 6YA  C11  C12  C13  109.85  3.000
 6YA  O16  S14  O15  117.63  3.000
 6YA  O15  S14  C17  108.81  3.000
 6YA  O16  S14  C17  108.81  3.000
 6YA  O15  S14  C13  108.57  3.000
 6YA  C17  S14  C13  103.90  3.000
 6YA  O16  S14  C13  108.24  3.000
 6YA  H16  C18  H15  106.19  3.000
 6YA  H16  C18  N19  108.59  3.000
 6YA  H15  C18  N19  107.97  3.000
 6YA  H16  C18  C02  111.02  3.000
 6YA  H15  C18  C02  111.25  3.000
 6YA  N19  C18  C02  111.60  3.000
 6YA  C18  N19  C24  125.84  3.000
 6YA  C18  N19  C20  124.18  3.000
 6YA  C24  N19  C20  109.98  3.000
 6YA  C29  N22  C23  126.78  3.000
 6YA  C23  N22  C20  110.02  3.000
 6YA  C29  N22  C20  123.19  3.000
 6YA  N22  C23  C28  133.27  3.000
 6YA  N22  C23  C24  106.87  3.000
 6YA  C28  C23  C24  119.85  3.000
 6YA  H17  C25  N26  117.65  3.000
 6YA  H17  C25  C24  121.83  3.000
 6YA  N26  C25  C24  120.51  3.000
 6YA  C27  N26  C25  119.19  3.000
 6YA  H18  C27  N26  116.33  3.000
 6YA  H18  C27  C28  118.98  3.000
 6YA  N26  C27  C28  124.69  3.000
 6YA  H20  C29  H19  107.48  3.000
 6YA  H20  C29  C30  109.33  3.000
 6YA  H19  C29  C30  109.27  3.000
 6YA  H20  C29  N22  109.87  3.000
 6YA  H19  C29  N22  109.44  3.000
 6YA  C30  C29  N22  111.36  3.000
 6YA  F33  C30  F32  107.61  3.000
 6YA  F33  C30  F31  106.75  3.000
 6YA  F32  C30  F31  107.78  3.000
 6YA  F31  C30  C29  112.00  3.000
 6YA  F33  C30  C29  111.69  3.000
 6YA  F32  C30  C29  110.79  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
 6YA  CONST_01  C02  N03  C04  C10   180.00   0.0  0
 6YA  CONST_02  C01  C05  C04  C10   180.00   0.0  0
 6YA  CONST_03  C06  C05  C04  C10     0.00   0.0  0
 6YA  CONST_04  C06  C07  C09  C10     0.00   0.0  0
 6YA  CONST_05  C27  C28  C23  C24     0.00   0.0  0
 6YA  CONST_06  C27  N26  C25  C24     0.00   0.0  0
 6YA  CONST_07  C25  N26  C27  C28     0.00   0.0  0
 6YA  CONST_08  C25  C24  C23  C28     0.00   0.0  0
 6YA  CONST_09  C04  N03  C02  C01     0.00   0.0  0
 6YA  CONST_10  N03  C04  C05  C01     0.00   0.0  0
 6YA  CONST_11  C07  C06  C05  C01   180.00   0.0  0
 6YA  CONST_12  C05  C04  N03  C02     0.00   0.0  0
 6YA  CONST_13  C04  C05  C01  C02     0.00   0.0  0
 6YA  CONST_14  C06  C05  C01  C02   180.00   0.0  0
 6YA  CONST_15  C05  C01  C02  N03     0.00   0.0  0
 6YA  CONST_16  C09  C10  C04  N03   180.00   0.0  0
 6YA  CONST_17  C06  C05  C04  N03   180.00   0.0  0
 6YA  CONST_18  C07  C09  C10  C04     0.00   0.0  0
 6YA  CONST_19  C07  C06  C05  C04     0.00   0.0  0
 6YA  CONST_20  C09  C10  C04  C05     0.00   0.0  0
 6YA  CONST_21  C09  C07  C06  C05     0.00   0.0  0
 6YA  CONST_22  N26  C27  C28  C23     0.00   0.0  0
 6YA  CONST_23  N26  C25  C24  C23     0.00   0.0  0
 6YA  CONST_24  C24  C23  N22  C20     0.00   0.0  0
 6YA  CONST_25  C23  C24  N19  C20     0.00   0.0  0
 6YA  CONST_26  N22  C20  N19  C24     0.00   0.0  0
 6YA  CONST_27  C23  N22  C20  N19     0.00   0.0  0
 6YA  CONST_28  N22  C23  C24  N19     0.00   0.0  0
 6YA  CONST_29  C11  N03  C04  C10     0.00   0.0  0
 6YA  CONST_30  CL8  C07  C09  C10   180.00   0.0  0
 6YA  CONST_31  C11  N03  C02  C01   180.00   0.0  0
 6YA  CONST_32  C18  C02  N03  C04   180.00   0.0  0
 6YA  CONST_33  C11  N03  C04  C05   180.00   0.0  0
 6YA  CONST_34  C18  C02  C01  C05   180.00   0.0  0
 6YA  CONST_35  CL8  C07  C06  C05   180.00   0.0  0
 6YA  CONST_36  C29  N22  C23  C24   180.00   0.0  0
 6YA  CONST_37  O21  C20  N19  C24   180.00   0.0  0
 6YA  CONST_38  N22  C20  N19  C18   180.00   0.0  0
 6YA  CONST_39  C23  C24  N19  C18   180.00   0.0  0
 6YA  CONST_40  C29  N22  C20  N19   180.00   0.0  0
 6YA  CONST_41  C23  N22  C20  O21   180.00   0.0  0
 6YA  CONST_42  H7   C28  C23  C24   180.00   0.0  0
 6YA  CONST_43  H9   C06  C05  C01     0.00   0.0  0
 6YA  CONST_44  H8   C01  C02  N03   180.00   0.0  0
 6YA  CONST_45  H1   C10  C04  N03     0.00   0.0  0
 6YA  CONST_46  H10  C09  C10  C04   180.00   0.0  0
 6YA  CONST_47  H17  C25  C24  N19     0.00   0.0  0
 6YA  CONST_48  H18  C27  C28  C23   180.00   0.0  0
 6YA  CONST_49  O21  C20  N19  C18     0.00   0.0  0
 6YA  CONST_50  C29  N22  C20  O21     0.00   0.0  0
 6YA  Var_01    C02  C18  N19  C20   102.74  30.0  3
 6YA  Var_02    N19  C18  C02  C01    -4.96  30.0  2
 6YA  Var_03    C30  C29  N22  C20   -94.49  30.0  2
 6YA  Var_04    C12  C11  N03  C02    89.87  30.0  1
 6YA  Var_05    N03  C11  C12  C13  -179.62  30.0  3
 6YA  Var_06    F32  C30  C29  N22   179.04  30.0  3
 6YA  Var_07    C12  C13  S14  C17   179.62  30.0  3
 6YA  Var_08    S14  C13  C12  C11  -177.98  30.0  1
 6YA  Var_09    H4   C17  S14  C13   178.86  30.0  3

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
 6YA  plan-1  C10  0.020
 6YA  plan-1  C01  0.020
 6YA  plan-1  C02  0.020
 6YA  plan-1  N03  0.020
 6YA  plan-1  C04  0.020
 6YA  plan-1  C05  0.020
 6YA  plan-1  C06  0.020
 6YA  plan-1  C07  0.020
 6YA  plan-1  CL8  0.020
 6YA  plan-1  C09  0.020
 6YA  plan-1  C11  0.020
 6YA  plan-1  C18  0.020
 6YA  plan-1  H1   0.020
 6YA  plan-1  H8   0.020
 6YA  plan-1  H9   0.020
 6YA  plan-1  H10  0.020
 6YA  plan-2  C20  0.020
 6YA  plan-2  C24  0.020
 6YA  plan-2  C28  0.020
 6YA  plan-2  C18  0.020
 6YA  plan-2  N19  0.020
 6YA  plan-2  N22  0.020
 6YA  plan-2  C23  0.020
 6YA  plan-2  C25  0.020
 6YA  plan-2  N26  0.020
 6YA  plan-2  C27  0.020
 6YA  plan-2  C29  0.020
 6YA  plan-2  H7   0.020
 6YA  plan-2  H17  0.020
 6YA  plan-2  H18  0.020
 6YA  plan-2  O21  0.020

