# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:58:04 2021
#   Inital geometry file: a 130 line input string
#   Ligand name: 1-{[7-(5-chloro-2-{[(3R,4S)-4-fluoropyrrolidin-3-yl]oxy}-3-methylphenyl)thieno[3,2-b]pyridin-2-yl]methyl}pyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Cl)cc(c1O[C@@H]2CNC[C@@H]2F)c3ccnc4cc(CN5C(=O)CCC5=O)sc34
#
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
 R3Y  R3Y  1-{[7-(5-chloro-2-{[(3R,4S)-4-fluoropyrrolidin-3-yl]oxy}-3-methylphenyl)thieno[3,2-b]pyridin-2-yl]methyl}pyrrolidine-2,5-dione  ligand  53  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R3Y
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
 R3Y  C1    C   CH3   0  -0.716  26.4955   0.9667  25.1093
 R3Y  C2    C   CR6   0   0.005  26.1813   0.2123  26.3661
 R3Y  C3    C   CR16  0  -0.260  26.1737  -1.1786  26.3723
 R3Y  C4    C   CR6   0  -0.027  25.8928  -1.8769  27.5351
 R3Y  C5    C   CR16  0  -0.260  25.5864  -1.2167  28.7105
 R3Y  C6    C   CR6   0  -0.057  25.5665   0.1734  28.7155
 R3Y  C7    C   CR6   0   0.302  25.8844   0.8805  27.5552
 R3Y  C11   C   CH2   0  -0.317  26.4730   4.1095  29.0354
 R3Y  C17   C   CR6   0   0.181  25.1969   0.8985  29.9507
 R3Y  C18   C   CR16  0  -0.362  23.9768   1.5360  30.0977
 R3Y  C19   C   CR16  0  -0.087  23.6892   2.2226  31.2808
 R3Y  C21   C   CR56  0   0.282  25.7112   1.7351  32.1695
 R3Y  C23   C   CR5   0  -0.136  27.8801   1.1252  32.7079
 R3Y  C30   C   CH2   0  -0.591  31.8510   2.4613  31.1809
 R3Y  C31   C   CH2   0  -0.596  31.4395   3.6811  31.9968
 R3Y  C32   C   C     0   0.559  30.3638   3.1865  32.9293
 R3Y  O8    O   O2    0  -0.485  25.8725   2.2408  27.5696
 R3Y  C9    C   CR15  0  -0.022  26.9303   2.8799  28.2581
 R3Y  N12   N   NR15  0  -0.607  27.6957   4.8713  29.2630
 R3Y  C13   C   CH2   0  -0.326  28.7018   4.4483  28.2747
 R3Y  C14   C   CR15  0   0.140  28.0090   3.4579  27.3541
 R3Y  F16   F   F     0  -0.380  27.3939   4.1320  26.3000
 R3Y  N20   N   N     0  -0.428  24.5264   2.3345  32.2962
 R3Y  C22   C   CR15  0  -0.211  26.7800   1.7886  33.1244
 R3Y  S24   S   S2    0   0.219  27.6795   0.3769  31.1446
 R3Y  C25   C   CR56  0  -0.260  26.0703   0.9969  31.0277
 R3Y  C26   C   CH2   0  -0.420  29.2011   1.0392  33.3998
 R3Y  N27   N   NT    0  -0.518  30.1955   1.8341  32.7071
 R3Y  C28   C   C     0   0.559  30.9895   1.3376  31.6946
 R3Y  CL34  CL  CL    0  -0.127  25.9097  -3.6095  27.5123
 R3Y  H1    H   HCH3  0   0.253  25.7231   1.6989  24.8762
 R3Y  H2    H   HCH3  0   0.255  27.4386   1.5078  25.1896
 R3Y  H3    H   HCH3  0   0.252  26.5806   0.2842  24.2659
 R3Y  H4    H   HCR6  0   0.280  26.4015  -1.7158  25.4606
 R3Y  H5    H   HCR6  0   0.287  25.3456  -1.7665  29.6108
 R3Y  H6    H   HCH2  0   0.234  25.7517   4.6799  28.4417
 R3Y  H7    H   HCH2  0   0.250  25.9888   3.8539  29.9775
 R3Y  H8    H   HCR6  0   0.273  23.2427   1.5064  29.3044
 R3Y  H9    H   HCR6  0   0.271  22.7280   2.7115  31.3896
 R3Y  H10   H   HCH2  0   0.312  32.9010   2.1972  31.3087
 R3Y  H11   H   HCH2  0   0.313  32.2582   4.0962  32.5850
 R3Y  H12   H   HCR5  0   0.238  27.4285   2.1845  28.9434
 R3Y  H13   H   HNR5  0   0.350  28.0345   4.7151  30.1999
 R3Y  H15   H   HCH2  0   0.233  29.5564   3.9602  28.7508
 R3Y  H16   H   HCH2  0   0.251  29.0996   5.2890  27.7014
 R3Y  H17   H   HCR5  0   0.246  28.6829   2.7159  26.9237
 R3Y  H18   H   HCR5  0   0.279  26.7189   2.3214  34.0631
 R3Y  H19   H   HCH2  0   0.307  29.1040   1.4106  34.4182
 R3Y  H20   H   HCH2  0   0.310  29.5586   0.0115  33.4588
 R3Y  H14   H   HCH2  0   0.303  31.6802   2.5821  30.1103
 R3Y  H21   H   HCH2  0   0.298  31.0446   4.4953  31.3881
 R3Y  O33   O   O     0  -0.420  29.7339   3.8202  33.7379
 R3Y  O29   O   O     0  -0.428  30.9518   0.1941  31.3124

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
 R3Y  C1   C2    single    1.499  0.020  1.499
 R3Y  F16  C14   single    1.394  0.020  1.394
 R3Y  C2   C3    aromatic  1.391  0.020  1.391
 R3Y  C2   C7    aromatic  1.396  0.020  1.396
 R3Y  C3   C4    aromatic  1.385  0.020  1.385
 R3Y  C14  C13   single    1.519  0.020  1.519
 R3Y  C14  C9    single    1.521  0.020  1.521
 R3Y  O8   C7    single    1.360  0.020  1.360
 R3Y  O8   C9    single    1.415  0.020  1.415
 R3Y  C7   C6    aromatic  1.395  0.020  1.395
 R3Y  C4   CL34  single    1.733  0.020  1.733
 R3Y  C4   C5    aromatic  1.383  0.020  1.383
 R3Y  C13  N12   single    1.472  0.020  1.472
 R3Y  C9   C11   single    1.525  0.020  1.525
 R3Y  C11  N12   single    1.458  0.020  1.458
 R3Y  C6   C5    aromatic  1.390  0.020  1.390
 R3Y  C6   C17   single    1.479  0.020  1.479
 R3Y  C17  C18   aromatic  1.384  0.020  1.384
 R3Y  C17  C25   aromatic  1.390  0.020  1.390
 R3Y  C18  C19   aromatic  1.398  0.020  1.398
 R3Y  C25  S24   aromatic  1.728  0.020  1.728
 R3Y  C25  C21   aromatic  1.406  0.020  1.406
 R3Y  S24  C23   aromatic  1.745  0.020  1.745
 R3Y  C19  N20   aromatic  1.321  0.020  1.321
 R3Y  O29  C28   double    1.206  0.020  1.206
 R3Y  C30  C28   single    1.506  0.020  1.506
 R3Y  C30  C31   single    1.524  0.020  1.524
 R3Y  C28  N27   single    1.379  0.020  1.379
 R3Y  C21  N20   aromatic  1.334  0.020  1.334
 R3Y  C21  C22   aromatic  1.434  0.020  1.434
 R3Y  C23  C22   aromatic  1.350  0.020  1.350
 R3Y  C23  C26   single    1.494  0.020  1.494
 R3Y  C31  C32   single    1.507  0.020  1.507
 R3Y  N27  C26   single    1.449  0.020  1.449
 R3Y  N27  C32   single    1.381  0.020  1.381
 R3Y  C32  O33   double    1.205  0.020  1.205
 R3Y  C1   H1    single    0.970  0.020  1.090
 R3Y  C1   H2    single    0.970  0.020  1.090
 R3Y  C1   H3    single    0.970  0.020  1.090
 R3Y  C3   H4    single    0.930  0.020  1.080
 R3Y  C5   H5    single    0.930  0.020  1.080
 R3Y  C11  H6    single    0.970  0.020  1.090
 R3Y  C11  H7    single    0.970  0.020  1.090
 R3Y  C18  H8    single    0.930  0.020  1.080
 R3Y  C19  H9    single    0.930  0.020  1.080
 R3Y  C30  H10   single    0.970  0.020  1.090
 R3Y  C31  H11   single    0.970  0.020  1.090
 R3Y  C9   H12   single    0.970  0.020  1.090
 R3Y  N12  H13   single    0.890  0.020  1.040
 R3Y  C13  H15   single    0.970  0.020  1.090
 R3Y  C13  H16   single    0.970  0.020  1.090
 R3Y  C14  H17   single    0.970  0.020  1.090
 R3Y  C22  H18   single    0.930  0.020  1.080
 R3Y  C26  H19   single    0.970  0.020  1.090
 R3Y  C26  H20   single    0.970  0.020  1.090
 R3Y  C30  H14   single    0.970  0.020  1.090
 R3Y  C31  H21   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
 R3Y  H3    C1   H2   107.50  3.000
 R3Y  H3    C1   H1   108.12  3.000
 R3Y  H2    C1   H1   107.19  3.000
 R3Y  H3    C1   C2   110.52  3.000
 R3Y  H2    C1   C2   111.67  3.000
 R3Y  H1    C1   C2   111.65  3.000
 R3Y  C7    C2   C3   118.28  3.000
 R3Y  C7    C2   C1   121.19  3.000
 R3Y  C3    C2   C1   120.53  3.000
 R3Y  H4    C3   C4   119.97  3.000
 R3Y  H4    C3   C2   119.44  3.000
 R3Y  C4    C3   C2   120.59  3.000
 R3Y  CL34  C4   C5   119.39  3.000
 R3Y  C5    C4   C3   121.19  3.000
 R3Y  CL34  C4   C3   119.41  3.000
 R3Y  H5    C5   C6   120.13  3.000
 R3Y  H5    C5   C4   120.93  3.000
 R3Y  C6    C5   C4   118.93  3.000
 R3Y  C17   C6   C7   120.19  3.000
 R3Y  C17   C6   C5   119.78  3.000
 R3Y  C7    C6   C5   120.03  3.000
 R3Y  O8    C7   C6   119.73  3.000
 R3Y  C6    C7   C2   120.94  3.000
 R3Y  O8    C7   C2   119.31  3.000
 R3Y  H7    C11  H6   107.36  3.000
 R3Y  H7    C11  N12  111.11  3.000
 R3Y  H6    C11  N12  111.40  3.000
 R3Y  H7    C11  C9   112.63  3.000
 R3Y  H6    C11  C9   109.96  3.000
 R3Y  N12   C11  C9   104.44  3.000
 R3Y  C25   C17  C18  116.03  3.000
 R3Y  C25   C17  C6   121.65  3.000
 R3Y  C18   C17  C6   122.32  3.000
 R3Y  H8    C18  C19  119.65  3.000
 R3Y  H8    C18  C17  120.52  3.000
 R3Y  C19   C18  C17  119.83  3.000
 R3Y  H9    C19  N20  116.53  3.000
 R3Y  H9    C19  C18  119.28  3.000
 R3Y  N20   C19  C18  124.19  3.000
 R3Y  C25   C21  C22  111.70  3.000
 R3Y  C22   C21  N20  125.59  3.000
 R3Y  C25   C21  N20  122.67  3.000
 R3Y  C26   C23  S24  119.47  3.000
 R3Y  C26   C23  C22  127.29  3.000
 R3Y  S24   C23  C22  113.16  3.000
 R3Y  H14   C30  H10  107.03  3.000
 R3Y  H14   C30  C28  109.13  3.000
 R3Y  H10   C30  C28  109.28  3.000
 R3Y  H14   C30  C31  113.23  3.000
 R3Y  H10   C30  C31  113.03  3.000
 R3Y  C28   C30  C31  105.07  3.000
 R3Y  H21   C31  H11  106.78  3.000
 R3Y  H21   C31  C32  109.38  3.000
 R3Y  H11   C31  C32  109.09  3.000
 R3Y  H21   C31  C30  113.36  3.000
 R3Y  H11   C31  C30  113.00  3.000
 R3Y  C32   C31  C30  105.15  3.000
 R3Y  O33   C32  N27  124.01  3.000
 R3Y  O33   C32  C31  128.00  3.000
 R3Y  N27   C32  C31  107.99  3.000
 R3Y  C9    O8   C7   116.76  3.000
 R3Y  H12   C9   C14  106.87  3.000
 R3Y  H12   C9   O8   110.94  3.000
 R3Y  C14   C9   O8   114.37  3.000
 R3Y  H12   C9   C11  109.22  3.000
 R3Y  O8    C9   C11  112.84  3.000
 R3Y  C14   C9   C11  102.07  3.000
 R3Y  H13   N12  C13  110.46  3.000
 R3Y  H13   N12  C11  110.22  3.000
 R3Y  C13   N12  C11  108.54  3.000
 R3Y  H16   C13  H15  106.70  3.000
 R3Y  H16   C13  C14  110.47  3.000
 R3Y  H15   C13  C14  109.23  3.000
 R3Y  H16   C13  N12  112.33  3.000
 R3Y  H15   C13  N12  111.72  3.000
 R3Y  C14   C13  N12  106.40  3.000
 R3Y  H17   C14  F16  107.64  3.000
 R3Y  H17   C14  C13  113.62  3.000
 R3Y  F16   C14  C13  110.13  3.000
 R3Y  H17   C14  C9   114.46  3.000
 R3Y  C13   C14  C9   102.18  3.000
 R3Y  F16   C14  C9   108.67  3.000
 R3Y  C21   N20  C19  116.87  3.000
 R3Y  H18   C22  C23  123.77  3.000
 R3Y  H18   C22  C21  123.67  3.000
 R3Y  C23   C22  C21  112.55  3.000
 R3Y  C25   S24  C23   90.79  3.000
 R3Y  S24   C25  C21  111.79  3.000
 R3Y  C21   C25  C17  120.38  3.000
 R3Y  S24   C25  C17  127.73  3.000
 R3Y  H20   C26  H19  107.49  3.000
 R3Y  H20   C26  N27  108.54  3.000
 R3Y  H19   C26  N27  108.74  3.000
 R3Y  H20   C26  C23  111.68  3.000
 R3Y  H19   C26  C23  109.57  3.000
 R3Y  N27   C26  C23  110.72  3.000
 R3Y  C28   N27  C26  123.26  3.000
 R3Y  C26   N27  C32  122.95  3.000
 R3Y  C28   N27  C32  113.61  3.000
 R3Y  N27   C28  C30  108.13  3.000
 R3Y  N27   C28  O29  123.77  3.000
 R3Y  C30   C28  O29  128.10  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
 R3Y  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 R3Y  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 R3Y  CONST_03  C17   C6   C7   C2    180.00   0.0  0
 R3Y  CONST_04  C6    C7   C2   C3      0.00   0.0  0
 R3Y  CONST_05  C6    C5   C4   C3      0.00   0.0  0
 R3Y  CONST_06  C7    C2   C3   C4      0.00   0.0  0
 R3Y  CONST_07  C7    C6   C5   C4      0.00   0.0  0
 R3Y  CONST_08  C17   C6   C5   C4    180.00   0.0  0
 R3Y  CONST_11  C19   C18  C17  C6    180.00   0.0  0
 R3Y  CONST_12  S24   C25  C17  C6      0.00   0.0  0
 R3Y  CONST_13  C21   C25  C17  C6    180.00   0.0  0
 R3Y  CONST_16  N20   C19  C18  C17     0.00   0.0  0
 R3Y  CONST_17  C23   S24  C25  C17   180.00   0.0  0
 R3Y  CONST_18  N20   C21  C25  C17     0.00   0.0  0
 R3Y  CONST_19  C22   C21  C25  C17   180.00   0.0  0
 R3Y  CONST_20  S24   C25  C17  C18   180.00   0.0  0
 R3Y  CONST_21  C21   C25  C17  C18     0.00   0.0  0
 R3Y  CONST_22  C21   N20  C19  C18     0.00   0.0  0
 R3Y  CONST_23  C25   C17  C18  C19     0.00   0.0  0
 R3Y  CONST_24  C25   C21  N20  C19     0.00   0.0  0
 R3Y  CONST_25  C22   C21  N20  C19   180.00   0.0  0
 R3Y  CONST_26  C23   S24  C25  C21     0.00   0.0  0
 R3Y  CONST_27  S24   C23  C22  C21     0.00   0.0  0
 R3Y  CONST_28  C25   C21  C22  C23     0.00   0.0  0
 R3Y  CONST_29  N20   C21  C22  C23   180.00   0.0  0
 R3Y  CONST_30  S24   C25  C21  N20   180.00   0.0  0
 R3Y  CONST_31  S24   C25  C21  C22     0.00   0.0  0
 R3Y  CONST_32  C25   S24  C23  C22     0.00   0.0  0
 R3Y  CONST_33  C28   N27  C32  C31     0.00   0.0  0
 R3Y  CONST_34  C4    C3   C2   C1    180.00   0.0  0
 R3Y  CONST_35  C6    C7   C2   C1    180.00   0.0  0
 R3Y  CONST_36  CL34  C4   C3   C2    180.00   0.0  0
 R3Y  CONST_37  O8    C7   C2   C3    180.00   0.0  0
 R3Y  CONST_38  O8    C7   C6   C5    180.00   0.0  0
 R3Y  CONST_39  CL34  C4   C5   C6    180.00   0.0  0
 R3Y  CONST_40  O8    C7   C6   C17     0.00   0.0  0
 R3Y  CONST_41  C26   C23  C22  C21   180.00   0.0  0
 R3Y  CONST_42  C26   C23  S24  C25   180.00   0.0  0
 R3Y  CONST_43  C26   N27  C32  C31   180.00   0.0  0
 R3Y  CONST_44  O33   C32  N27  C28   180.00   0.0  0
 R3Y  CONST_45  H5    C5   C4   C3    180.00   0.0  0
 R3Y  CONST_46  H4    C3   C4   C5    180.00   0.0  0
 R3Y  CONST_47  H8    C18  C17  C6      0.00   0.0  0
 R3Y  CONST_48  H9    C19  C18  C17   180.00   0.0  0
 R3Y  CONST_49  H18   C22  C21  N20     0.00   0.0  0
 R3Y  CONST_50  O33   C32  N27  C26     0.00   0.0  0
 R3Y  Var_01    C14   C13  N12  C11     4.12  30.0  1
 R3Y  Var_02    C32   N27  C28  C30     2.30  30.0  1
 R3Y  Var_03    N27   C32  C31  C30     1.42  30.0  1
 R3Y  Var_04    N27   C28  C30  C31    -1.23  30.0  1
 R3Y  Var_05    C28   C30  C31  C32    -0.11  30.0  1
 R3Y  Var_06    C13   N12  C11  C9     20.84  30.0  1
 R3Y  Var_07    C28   N27  C26  C23   -89.69  30.0  1
 R3Y  Var_08    N27   C26  C23  C22  -107.41  30.0  2
 R3Y  Var_09    H1    C1   C2   C3    126.98  30.0  2

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
 R3Y  chir_01  C9   C14  O8  C11  positiv
 R3Y  chir_02  C14  F16  C9  C13  positiv

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
 R3Y  plan-1  C1    0.020
 R3Y  plan-1  C2    0.020
 R3Y  plan-1  C3    0.020
 R3Y  plan-1  C4    0.020
 R3Y  plan-1  C5    0.020
 R3Y  plan-1  C6    0.020
 R3Y  plan-1  C7    0.020
 R3Y  plan-1  C17   0.020
 R3Y  plan-1  O8    0.020
 R3Y  plan-1  CL34  0.020
 R3Y  plan-1  H4    0.020
 R3Y  plan-1  H5    0.020
 R3Y  plan-2  C6    0.020
 R3Y  plan-2  C17   0.020
 R3Y  plan-2  C18   0.020
 R3Y  plan-2  C19   0.020
 R3Y  plan-2  C21   0.020
 R3Y  plan-2  C23   0.020
 R3Y  plan-2  N20   0.020
 R3Y  plan-2  C22   0.020
 R3Y  plan-2  S24   0.020
 R3Y  plan-2  C25   0.020
 R3Y  plan-2  C26   0.020
 R3Y  plan-2  H8    0.020
 R3Y  plan-2  H9    0.020
 R3Y  plan-2  H18   0.020
 R3Y  plan-3  C31   0.020
 R3Y  plan-3  C32   0.020
 R3Y  plan-3  C26   0.020
 R3Y  plan-3  N27   0.020
 R3Y  plan-3  C28   0.020
 R3Y  plan-3  O33   0.020
 R3Y  plan-4  C30   0.020
 R3Y  plan-4  N27   0.020
 R3Y  plan-4  C28   0.020
 R3Y  plan-4  O29   0.020

