# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:05:16 2021
#   Inital geometry file: a 143 line input string
#   Ligand name: 1-({7-[(2R)-5-chloro-2-(piperazine-1-carbonyl)-2,3-dihydro-1-benzofuran-7-yl]thieno[3,2-b]pyridin-2-yl}methyl)pyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc2C[C@@H](Oc2c(c1)c3ccnc4cc(CN5C(=O)CCC5=O)sc34)C(=O)N6CCNCC6
#
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
 R44  R44  1-({7-[(2R)-5-chloro-2-(piperazine-1-carbonyl)-2,3-dihydro-1-benzofuran-7-yl]thieno[3,2-b]pyridin-2-yl}methyl)pyrrolidine-2,5-dione  ligand  58  35  .  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_R44
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
 R44  C2   C   CR6   0  -0.043  26.5023  -1.9607  27.4947
 R44  C3   C   CR16  0  -0.295  26.6793  -1.3526  26.2525
 R44  C4   C   CR56  0  -0.004  26.4303  -0.0010  26.1590
 R44  C5   C   CR56  0   0.415  25.9994   0.7057  27.2719
 R44  C6   C   CR6   0  -0.112  25.8411   0.1217  28.5148
 R44  C7   C   CR16  0  -0.253  26.1024  -1.2468  28.6123
 R44  C8   C   CR6   0   0.218  25.5145   0.9543  29.6883
 R44  C12  C   CR56  0   0.280  26.2054   2.0967  31.7147
 R44  C16  C   CR56  0  -0.257  26.4865   1.2294  30.6451
 R44  C19  C   CR5   0   0.558  31.1011   3.6011  32.2677
 R44  O20  O   O     0  -0.420  30.5733   4.2831  33.1093
 R44  C21  C   CH2   0  -0.604  32.2207   3.9799  31.3328
 R44  C23  C   CR5   0   0.560  31.4544   1.7351  30.9549
 R44  O25  O   O     0  -0.472  25.7996   2.0144  27.0160
 R44  C32  C   CH2   0  -0.306  29.2117   4.3375  27.5051
 R44  C33  C   CH2   0  -0.314  29.1077   4.2947  29.0222
 R44  C35  C   CH2   0  -0.297  26.7469   4.6945  28.8993
 R44  C36  C   CH2   0  -0.309  26.8347   4.7316  27.3819
 R44  CL1  CL  CL    0  -0.130  26.8090  -3.6619  27.6491
 R44  C9   C   CR16  0  -0.375  24.2871   1.5653  29.8744
 R44  C10  C   CR16  0  -0.086  24.0895   2.4032  30.9766
 R44  N11  N   N     0  -0.429  25.0141   2.6757  31.8785
 R44  C13  C   CR15  0  -0.215  27.3489   2.2851  32.5580
 R44  C14  C   CR5   0  -0.130  28.4273   1.5898  32.1327
 R44  S15  S   S2    0   0.223  28.1210   0.6722  30.6820
 R44  N18  N   NR5   0  -0.515  30.7693   2.2838  32.0172
 R44  C22  C   CH2   0  -0.591  32.3745   2.7881  30.3958
 R44  C26  C   CR15  0  -0.194  26.4788   2.3055  25.7782
 R44  C28  C   CH2   0  -0.479  26.5216   0.9723  25.0208
 R44  C29  C   C     0   0.569  27.8825   2.8181  26.1458
 R44  O30  O   O     0  -0.482  28.8755   2.2175  25.7611
 R44  N31  N   NT    0  -0.456  27.9478   3.9145  26.9222
 R44  N34  N   NH1   0  -0.596  28.0108   5.1338  29.4644
 R44  H1   H   HCR6  0   0.283  27.0099  -1.9251  25.3960
 R44  H2   H   HCR6  0   0.285  25.9927  -1.7456  29.5664
 R44  H5   H   HCH2  0   0.317  33.1186   4.1541  31.9282
 R44  H6   H   HCH2  0   0.266  30.0148   3.6936  27.1576
 R44  H7   H   HCH2  0   0.247  29.4305   5.3581  27.1781
 R44  H8   H   HCH2  0   0.203  28.9992   3.2423  29.3342
 R44  H9   H   HCH2  0   0.239  30.0395   4.6734  29.4470
 R44  H10  H   HCH2  0   0.240  25.9537   5.3699  29.2245
 R44  H11  H   HCH2  0   0.218  26.4667   3.6789  29.2115
 R44  H12  H   HCH2  0   0.250  27.0167   5.7600  27.0542
 R44  H13  H   HCH2  0   0.272  25.8928   4.4233  26.9411
 R44  H14  H   HCR6  0   0.270  23.4794   1.4036  29.1735
 R44  H15  H   HCR6  0   0.268  23.1239   2.8760  31.1154
 R44  H16  H   HCR5  0   0.278  27.3485   2.9129  33.4383
 R44  H17  H   HCH2  0   0.312  33.3918   2.4016  30.3464
 R44  H18  H   HCR5  0   0.303  25.9048   3.0659  25.2471
 R44  H19  H   HCH2  0   0.286  25.6560   0.8796  24.3609
 R44  H20  H   HCH2  0   0.284  27.4183   0.8624  24.4158
 R44  H21  H   HNH1  0   0.353  27.9546   5.1211  30.4742
 R44  H22  H   HCH2  0   0.302  31.9887   4.9159  30.8259
 R44  H23  H   HCH2  0   0.299  32.0690   3.0130  29.3722
 R44  C17  C   CH2   0  -0.418  29.7760   1.5506  32.7747
 R44  O24  O   O     0  -0.428  31.2913   0.6042  30.5668
 R44  H3   H   HCH2  0   0.304  29.7117   1.9897  33.7683
 R44  H4   H   HCH2  0   0.307  30.1239   0.5245  32.8957

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
 R44  O30  C29  double    1.223  0.020  1.223
 R44  C28  C26  single    1.534  0.020  1.534
 R44  C28  C4   single    1.500  0.020  1.500
 R44  C29  C26  single    1.539  0.020  1.539
 R44  C29  N31  single    1.345  0.020  1.345
 R44  C26  O25  single    1.442  0.020  1.442
 R44  C32  N31  single    1.455  0.020  1.455
 R44  C32  C33  single    1.521  0.020  1.521
 R44  N31  C36  single    1.455  0.020  1.455
 R44  C4   C3   aromatic  1.378  0.020  1.378
 R44  C4   C5   aromatic  1.387  0.020  1.387
 R44  C3   C2   aromatic  1.394  0.020  1.394
 R44  C36  C35  single    1.520  0.020  1.520
 R44  O25  C5   single    1.348  0.020  1.348
 R44  C5   C6   aromatic  1.382  0.020  1.382
 R44  C33  N34  single    1.450  0.020  1.450
 R44  C2   CL1  single    1.735  0.020  1.735
 R44  C2   C7   aromatic  1.385  0.020  1.385
 R44  C35  N34  single    1.452  0.020  1.452
 R44  C6   C7   aromatic  1.397  0.020  1.397
 R44  C6   C8   single    1.475  0.020  1.475
 R44  C8   C9   aromatic  1.384  0.020  1.384
 R44  C8   C16  aromatic  1.391  0.020  1.391
 R44  C9   C10  aromatic  1.399  0.020  1.399
 R44  C16  S15  aromatic  1.727  0.020  1.727
 R44  C16  C12  aromatic  1.405  0.020  1.405
 R44  C10  N11  aromatic  1.320  0.020  1.320
 R44  S15  C14  aromatic  1.744  0.020  1.744
 R44  O24  C23  double    1.207  0.020  1.207
 R44  C22  C23  single    1.506  0.020  1.506
 R44  C22  C21  single    1.524  0.020  1.524
 R44  C12  N11  aromatic  1.335  0.020  1.335
 R44  C12  C13  aromatic  1.433  0.020  1.433
 R44  C23  N18  single    1.378  0.020  1.378
 R44  C14  C13  aromatic  1.352  0.020  1.352
 R44  C14  C17  single    1.494  0.020  1.494
 R44  C21  C19  single    1.507  0.020  1.507
 R44  N18  C17  single    1.448  0.020  1.448
 R44  N18  C19  single    1.381  0.020  1.381
 R44  C19  O20  double    1.205  0.020  1.205
 R44  C3   H1   single    0.930  0.020  1.080
 R44  C7   H2   single    0.930  0.020  1.080
 R44  C17  H3   single    0.970  0.020  1.090
 R44  C17  H4   single    0.970  0.020  1.090
 R44  C21  H5   single    0.970  0.020  1.090
 R44  C32  H6   single    0.970  0.020  1.090
 R44  C32  H7   single    0.970  0.020  1.090
 R44  C33  H8   single    0.970  0.020  1.090
 R44  C33  H9   single    0.970  0.020  1.090
 R44  C35  H10  single    0.970  0.020  1.090
 R44  C35  H11  single    0.970  0.020  1.090
 R44  C36  H12  single    0.970  0.020  1.090
 R44  C36  H13  single    0.970  0.020  1.090
 R44  C9   H14  single    0.930  0.020  1.080
 R44  C10  H15  single    0.930  0.020  1.080
 R44  C13  H16  single    0.930  0.020  1.080
 R44  C22  H17  single    0.970  0.020  1.090
 R44  C26  H18  single    0.970  0.020  1.090
 R44  C28  H19  single    0.970  0.020  1.090
 R44  C28  H20  single    0.970  0.020  1.090
 R44  N34  H21  single    0.890  0.020  1.040
 R44  C21  H22  single    0.970  0.020  1.090
 R44  C22  H23  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
 R44  CL1  C2   C7   118.97  3.000
 R44  C7   C2   C3   122.06  3.000
 R44  CL1  C2   C3   118.97  3.000
 R44  H1   C3   C4   121.37  3.000
 R44  H1   C3   C2   120.89  3.000
 R44  C4   C3   C2   117.74  3.000
 R44  C28  C4   C5   107.28  3.000
 R44  C5   C4   C3   120.11  3.000
 R44  C28  C4   C3   132.61  3.000
 R44  O25  C5   C6   124.31  3.000
 R44  C6   C5   C4   122.81  3.000
 R44  O25  C5   C4   112.85  3.000
 R44  C8   C6   C7   122.60  3.000
 R44  C8   C6   C5   120.14  3.000
 R44  C7   C6   C5   117.08  3.000
 R44  H2   C7   C6   119.62  3.000
 R44  H2   C7   C2   120.21  3.000
 R44  C6   C7   C2   120.18  3.000
 R44  C9   C8   C16  116.10  3.000
 R44  C16  C8   C6   120.26  3.000
 R44  C9   C8   C6   123.54  3.000
 R44  C13  C12  N11  125.65  3.000
 R44  C13  C12  C16  111.67  3.000
 R44  N11  C12  C16  122.66  3.000
 R44  S15  C16  C12  111.85  3.000
 R44  C12  C16  C8   120.37  3.000
 R44  S15  C16  C8   127.73  3.000
 R44  N18  C19  C21  107.80  3.000
 R44  N18  C19  O20  124.14  3.000
 R44  C21  C19  O20  128.06  3.000
 R44  H22  C21  H5   106.98  3.000
 R44  H22  C21  C22  114.04  3.000
 R44  H5   C21  C22  112.16  3.000
 R44  H22  C21  C19  110.27  3.000
 R44  H5   C21  C19  108.23  3.000
 R44  C22  C21  C19  105.06  3.000
 R44  O24  C23  C22  128.20  3.000
 R44  C22  C23  N18  108.16  3.000
 R44  O24  C23  N18  123.63  3.000
 R44  C26  O25  C5   106.81  3.000
 R44  H7   C32  H6   108.03  3.000
 R44  H7   C32  N31  108.98  3.000
 R44  H6   C32  N31  109.98  3.000
 R44  H7   C32  C33  109.76  3.000
 R44  H6   C32  C33  110.67  3.000
 R44  N31  C32  C33  109.39  3.000
 R44  H9   C33  H8   107.75  3.000
 R44  H9   C33  N34  109.04  3.000
 R44  H8   C33  N34  113.04  3.000
 R44  H9   C33  C32  108.66  3.000
 R44  H8   C33  C32  108.40  3.000
 R44  N34  C33  C32  109.85  3.000
 R44  H11  C35  H10  107.58  3.000
 R44  H11  C35  N34  113.01  3.000
 R44  H10  C35  N34  109.23  3.000
 R44  H11  C35  C36  108.72  3.000
 R44  H10  C35  C36  108.92  3.000
 R44  N34  C35  C36  109.31  3.000
 R44  H13  C36  H12  106.84  3.000
 R44  H13  C36  N31  112.10  3.000
 R44  H12  C36  N31  107.80  3.000
 R44  H13  C36  C35  110.39  3.000
 R44  H12  C36  C35  109.35  3.000
 R44  N31  C36  C35  110.23  3.000
 R44  H14  C9   C10  119.66  3.000
 R44  H14  C9   C8   120.61  3.000
 R44  C10  C9   C8   119.73  3.000
 R44  H15  C10  N11  116.51  3.000
 R44  H15  C10  C9   119.21  3.000
 R44  N11  C10  C9   124.28  3.000
 R44  C10  N11  C12  116.85  3.000
 R44  H16  C13  C14  123.72  3.000
 R44  H16  C13  C12  123.72  3.000
 R44  C14  C13  C12  112.57  3.000
 R44  S15  C14  C13  113.10  3.000
 R44  C13  C14  C17  126.75  3.000
 R44  S15  C14  C17  120.15  3.000
 R44  C14  S15  C16   90.82  3.000
 R44  C23  N18  C19  113.58  3.000
 R44  C19  N18  C17  123.55  3.000
 R44  C23  N18  C17  122.86  3.000
 R44  H23  C22  H17  106.97  3.000
 R44  H23  C22  C23  108.74  3.000
 R44  H17  C22  C23  109.83  3.000
 R44  H23  C22  C21  112.78  3.000
 R44  H17  C22  C21  113.55  3.000
 R44  C23  C22  C21  104.89  3.000
 R44  H18  C26  C29  111.35  3.000
 R44  H18  C26  C28  112.34  3.000
 R44  C29  C26  C28  112.45  3.000
 R44  H18  C26  O25  108.12  3.000
 R44  C29  C26  O25  106.97  3.000
 R44  C28  C26  O25  105.16  3.000
 R44  H20  C28  H19  107.99  3.000
 R44  H20  C28  C26  112.68  3.000
 R44  H19  C28  C26  110.48  3.000
 R44  H20  C28  C4   114.00  3.000
 R44  H19  C28  C4   110.79  3.000
 R44  C26  C28  C4   100.81  3.000
 R44  N31  C29  O30  122.86  3.000
 R44  N31  C29  C26  116.98  3.000
 R44  O30  C29  C26  120.14  3.000
 R44  C29  N31  C36  127.07  3.000
 R44  C36  N31  C32  112.01  3.000
 R44  C29  N31  C32  120.70  3.000
 R44  H21  N34  C35  109.65  3.000
 R44  H21  N34  C33  109.83  3.000
 R44  C35  N34  C33  111.38  3.000
 R44  H4   C17  H3   107.30  3.000
 R44  H4   C17  N18  108.40  3.000
 R44  H3   C17  N18  108.28  3.000
 R44  H4   C17  C14  111.13  3.000
 R44  H3   C17  C14  109.17  3.000
 R44  N18  C17  C14  112.40  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
 R44  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 R44  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 R44  CONST_03  C8   C6   C7   C2    180.00   0.0  0
 R44  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 R44  CONST_05  C6   C7   C2   C3      0.00   0.0  0
 R44  CONST_06  C7   C2   C3   C4      0.00   0.0  0
 R44  CONST_07  C7   C6   C5   C4      0.00   0.0  0
 R44  CONST_08  C8   C6   C5   C4    180.00   0.0  0
 R44  CONST_11  C10  C9   C8   C6    180.00   0.0  0
 R44  CONST_12  S15  C16  C8   C6      0.00   0.0  0
 R44  CONST_13  C12  C16  C8   C6    180.00   0.0  0
 R44  CONST_16  N11  C10  C9   C8      0.00   0.0  0
 R44  CONST_17  C14  S15  C16  C8    180.00   0.0  0
 R44  CONST_18  N11  C12  C16  C8      0.00   0.0  0
 R44  CONST_19  C13  C12  C16  C8    180.00   0.0  0
 R44  CONST_20  C9   C8   C16  C12     0.00   0.0  0
 R44  CONST_21  C14  S15  C16  C12     0.00   0.0  0
 R44  CONST_22  C9   C10  N11  C12     0.00   0.0  0
 R44  CONST_23  S15  C14  C13  C12     0.00   0.0  0
 R44  CONST_24  C10  C9   C8   C16     0.00   0.0  0
 R44  CONST_25  C13  C14  S15  C16     0.00   0.0  0
 R44  CONST_26  C10  N11  C12  C16     0.00   0.0  0
 R44  CONST_27  C14  C13  C12  C16     0.00   0.0  0
 R44  CONST_28  S15  C16  C8   C9    180.00   0.0  0
 R44  CONST_29  C13  C12  N11  C10   180.00   0.0  0
 R44  CONST_30  S15  C16  C12  N11   180.00   0.0  0
 R44  CONST_31  C14  C13  C12  N11   180.00   0.0  0
 R44  CONST_32  S15  C16  C12  C13     0.00   0.0  0
 R44  CONST_33  O25  C5   C6   C8      0.00   0.0  0
 R44  CONST_34  C23  N18  C19  C21     0.00   0.0  0
 R44  CONST_35  CL1  C2   C3   C4    180.00   0.0  0
 R44  CONST_36  CL1  C2   C7   C6    180.00   0.0  0
 R44  CONST_37  C17  C14  C13  C12   180.00   0.0  0
 R44  CONST_38  C17  C14  S15  C16   180.00   0.0  0
 R44  CONST_39  C26  C29  N31  C32   180.00   0.0  0
 R44  CONST_40  C26  C29  N31  C36     0.00   0.0  0
 R44  CONST_41  C21  C19  N18  C17   180.00   0.0  0
 R44  CONST_42  C23  N18  C19  O20   180.00   0.0  0
 R44  CONST_43  H2   C7   C2   C3    180.00   0.0  0
 R44  CONST_44  H1   C3   C4   C5    180.00   0.0  0
 R44  CONST_45  H14  C9   C8   C6      0.00   0.0  0
 R44  CONST_46  H15  C10  C9   C8    180.00   0.0  0
 R44  CONST_47  H16  C13  C12  C16   180.00   0.0  0
 R44  CONST_48  O30  C29  N31  C32     0.00   0.0  0
 R44  CONST_49  O30  C29  N31  C36   180.00   0.0  0
 R44  CONST_50  O20  C19  N18  C17     0.00   0.0  0
 R44  Var_01    C26  C28  C4   C3   -164.71  30.0  1
 R44  Var_02    C23  C22  C21  C19    -6.76  30.0  1
 R44  Var_03    C22  C23  N18  C19     0.07  30.0  1
 R44  Var_04    N18  C23  C22  C21     4.37  30.0  1
 R44  Var_05    C35  C36  N31  C32   -57.13  30.0  1
 R44  Var_06    C35  N34  C33  C32    59.56  30.0  1
 R44  Var_07    C36  N31  C32  C33    57.03  30.0  1
 R44  Var_08    C36  C35  N34  C33   -58.86  30.0  1
 R44  Var_09    C22  C21  C19  N18     7.01  30.0  1
 R44  Var_10    N34  C33  C32  N31   -57.28  30.0  1
 R44  Var_11    N34  C35  C36  N31    56.63  30.0  1
 R44  Var_12    C14  C17  N18  C19    94.40  30.0  3
 R44  Var_13    N18  C17  C14  C13  -107.54  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
 R44  chir_01  C26  C28  C29  O25  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
 R44  plan-1  C2   0.020
 R44  plan-1  C3   0.020
 R44  plan-1  C4   0.020
 R44  plan-1  C5   0.020
 R44  plan-1  C6   0.020
 R44  plan-1  C7   0.020
 R44  plan-1  C8   0.020
 R44  plan-1  O25  0.020
 R44  plan-1  CL1  0.020
 R44  plan-1  C28  0.020
 R44  plan-1  H1   0.020
 R44  plan-1  H2   0.020
 R44  plan-2  C6   0.020
 R44  plan-2  C8   0.020
 R44  plan-2  C12  0.020
 R44  plan-2  C16  0.020
 R44  plan-2  C9   0.020
 R44  plan-2  C10  0.020
 R44  plan-2  N11  0.020
 R44  plan-2  C13  0.020
 R44  plan-2  C14  0.020
 R44  plan-2  S15  0.020
 R44  plan-2  H14  0.020
 R44  plan-2  H15  0.020
 R44  plan-2  H16  0.020
 R44  plan-2  C17  0.020
 R44  plan-3  C23  0.020
 R44  plan-3  N18  0.020
 R44  plan-3  C22  0.020
 R44  plan-3  O24  0.020
 R44  plan-4  C32  0.020
 R44  plan-4  C36  0.020
 R44  plan-4  C26  0.020
 R44  plan-4  C29  0.020
 R44  plan-4  O30  0.020
 R44  plan-4  N31  0.020
 R44  plan-5  C19  0.020
 R44  plan-5  O20  0.020
 R44  plan-5  C21  0.020
 R44  plan-5  C23  0.020
 R44  plan-5  N18  0.020
 R44  plan-5  C17  0.020

