# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 02:28:24 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (5S)-5-({4-[(6-methoxy-1-methyl-1H-benzimidazol-2-yl)methoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc(COc3ccc(C[C@@H]4SC(=O)NC4=O)cc3)n(C)c2c1
#
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
 7VA  7VA  (5S)-5-({4-[(6-methoxy-1-methyl-1H-benzimidazol-2-yl)methoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione  ligand  47  28  .  2021-08-05  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7VA
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
 7VA  C10  C  CR16  0  -0.284   2.5035  -0.1957  -1.3968
 7VA  C13  C  CR16  0  -0.359   1.1025  -1.8016   0.3767
 7VA  C17  C  CR5   0   0.439  -3.1152  -1.1031   0.3067
 7VA  C20  C  CR56  0   0.118  -5.2092  -1.1398  -0.0495
 7VA  C22  C  CR16  0  -0.430  -5.8157   1.2170   0.2603
 7VA  C24  C  CR16  0  -0.397  -7.4851  -0.4638  -0.3102
 7VA  C28  C  CH3   0  -0.435  -9.3829   1.6081  -0.2616
 7VA  N01  N  NR15  0  -0.659   7.3638   0.8509   0.6471
 7VA  C02  C  CR5   0   0.622   6.8334  -0.4077   0.5991
 7VA  C03  C  CR15  0  -0.552   5.3171  -0.3731   0.6189
 7VA  S04  S  S2    0   0.085   4.8367   1.3800   0.6641
 7VA  C05  C  CR5   0   0.404   6.5131   1.9296   0.6840
 7VA  O06  O  O     0  -0.401   6.8491   3.0813   0.7203
 7VA  C08  C  CH2   0  -0.497   4.7145  -1.1061  -0.5814
 7VA  C09  C  CR6   0   0.088   3.2126  -1.0572  -0.5619
 7VA  C11  C  CR16  0  -0.331   1.1220  -0.1303  -1.3546
 7VA  C12  C  CR6   0   0.382   0.4115  -0.9336  -0.4644
 7VA  C14  C  CR16  0  -0.281   2.4891  -1.8525   0.3182
 7VA  O15  O  O2    0  -0.474  -0.9340  -0.8105  -0.4924
 7VA  C16  C  CH2   0  -0.314  -1.6950  -1.5098   0.4749
 7VA  N18  N  NR5   0  -0.537  -3.5321   0.1864   0.4793
 7VA  C19  C  CR56  0   0.373  -4.8800   0.1933   0.2425
 7VA  N21  N  N     0  -0.470  -4.0787  -1.9213  -0.0051
 7VA  C23  C  CR6   0   0.382  -7.1330   0.8685  -0.0188
 7VA  C25  C  CR16  0  -0.319  -6.5313  -1.4673  -0.3276
 7VA  O27  O  O2    0  -0.477  -8.0242   1.8821   0.0095
 7VA  H1   H  HCR6  0   0.255   3.0378   0.4358  -2.0968
 7VA  H2   H  HCR6  0   0.286   0.5874  -2.4487   1.0740
 7VA  H3   H  HCR6  0   0.273  -5.5518   2.2444   0.4776
 7VA  H4   H  HCR6  0   0.277  -8.5113  -0.7259  -0.5261
 7VA  H5   H  HCH3  0   0.261  -2.3875   1.8556  -0.0906
 7VA  H6   H  HCH3  0   0.264  -3.3090   2.0285   1.4122
 7VA  H7   H  HCH3  0   0.268  -1.8576   1.0404   1.3885
 7VA  H8   H  HCH3  0   0.227  -9.5309   1.2145  -1.2707
 7VA  H9   H  HCH3  0   0.227  -9.8123   0.9049   0.4568
 7VA  H10  H  HCH3  0   0.258  -9.9101   2.5555  -0.1774
 7VA  H11  H  HNR5  0   0.440   8.3666   0.9980   0.6349
 7VA  H12  H  HCH2  0   0.279   5.0991  -0.6687  -1.5042
 7VA  H13  H  HCH2  0   0.283   5.0578  -2.1421  -0.5428
 7VA  H14  H  HCR6  0   0.265   0.5857   0.5436  -2.0111
 7VA  H15  H  HCR6  0   0.258   3.0108  -2.5373   0.9774
 7VA  H16  H  HCH2  0   0.257  -1.3427  -1.2786   1.4879
 7VA  H17  H  HCH2  0   0.274  -1.6297  -2.5924   0.3374
 7VA  H18  H  HCR6  0   0.260  -6.8170  -2.4863  -0.5545
 7VA  H19  H  HCR5  0   0.354   4.9838  -0.8436   1.5473
 7VA  C26  C  CH3   0  -0.533  -2.7252   1.3390   0.8069
 7VA  O07  O  O     0  -0.410   7.4811  -1.4216   0.5389

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
 7VA  O27  C28  single    1.412  0.020  1.412
 7VA  O27  C23  single    1.350  0.020  1.350
 7VA  C23  C22  aromatic  1.391  0.020  1.391
 7VA  C23  C24  aromatic  1.408  0.020  1.408
 7VA  C22  C19  aromatic  1.387  0.020  1.387
 7VA  C24  C25  aromatic  1.385  0.020  1.385
 7VA  C26  N18  single    1.445  0.020  1.445
 7VA  C19  N18  aromatic  1.369  0.020  1.369
 7VA  C19  C20  aromatic  1.404  0.020  1.404
 7VA  N18  C17  aromatic  1.366  0.020  1.366
 7VA  C25  C20  aromatic  1.390  0.020  1.390
 7VA  C20  N21  aromatic  1.375  0.020  1.375
 7VA  C17  N21  aromatic  1.302  0.020  1.302
 7VA  C17  C16  single    1.487  0.020  1.487
 7VA  C16  O15  single    1.416  0.020  1.416
 7VA  O15  C12  single    1.351  0.020  1.351
 7VA  C12  C11  aromatic  1.394  0.020  1.394
 7VA  C12  C13  aromatic  1.392  0.020  1.392
 7VA  C11  C10  aromatic  1.384  0.020  1.384
 7VA  C13  C14  aromatic  1.389  0.020  1.389
 7VA  C10  C09  aromatic  1.394  0.020  1.394
 7VA  C14  C09  aromatic  1.389  0.020  1.389
 7VA  C09  C08  single    1.503  0.020  1.503
 7VA  S04  C03  single    1.818  0.020  1.818
 7VA  S04  C05  single    1.764  0.020  1.764
 7VA  C08  C03  single    1.530  0.020  1.530
 7VA  C03  C02  single    1.517  0.020  1.517
 7VA  O06  C05  double    1.200  0.020  1.200
 7VA  C05  N01  single    1.374  0.020  1.374
 7VA  C02  N01  single    1.367  0.020  1.367
 7VA  C02  O07  double    1.205  0.020  1.205
 7VA  C10  H1   single    0.930  0.020  1.080
 7VA  C13  H2   single    0.930  0.020  1.080
 7VA  C22  H3   single    0.930  0.020  1.080
 7VA  C24  H4   single    0.930  0.020  1.080
 7VA  C26  H5   single    0.970  0.020  1.090
 7VA  C26  H6   single    0.970  0.020  1.090
 7VA  C26  H7   single    0.970  0.020  1.090
 7VA  C28  H8   single    0.970  0.020  1.090
 7VA  C28  H9   single    0.970  0.020  1.090
 7VA  C28  H10  single    0.970  0.020  1.090
 7VA  N01  H11  single    0.860  0.020  1.020
 7VA  C08  H12  single    0.970  0.020  1.090
 7VA  C08  H13  single    0.970  0.020  1.090
 7VA  C11  H14  single    0.930  0.020  1.080
 7VA  C14  H15  single    0.930  0.020  1.080
 7VA  C16  H16  single    0.970  0.020  1.090
 7VA  C16  H17  single    0.970  0.020  1.090
 7VA  C25  H18  single    0.930  0.020  1.080
 7VA  C03  H19  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
 7VA  H1   C10  C11  118.98  3.000
 7VA  H1   C10  C09  119.76  3.000
 7VA  C11  C10  C09  121.26  3.000
 7VA  H2   C13  C14  118.72  3.000
 7VA  H2   C13  C12  121.74  3.000
 7VA  C14  C13  C12  119.54  3.000
 7VA  N21  C17  N18  113.43  3.000
 7VA  N21  C17  C16  124.20  3.000
 7VA  N18  C17  C16  122.37  3.000
 7VA  C25  C20  N21  130.88  3.000
 7VA  N21  C20  C19  109.88  3.000
 7VA  C25  C20  C19  119.24  3.000
 7VA  H3   C22  C23  120.59  3.000
 7VA  H3   C22  C19  122.58  3.000
 7VA  C23  C22  C19  116.83  3.000
 7VA  H4   C24  C25  118.41  3.000
 7VA  H4   C24  C23  120.53  3.000
 7VA  C25  C24  C23  121.06  3.000
 7VA  H10  C28  H9   108.61  3.000
 7VA  H10  C28  H8   108.63  3.000
 7VA  H9   C28  H8   108.78  3.000
 7VA  H10  C28  O27  106.41  3.000
 7VA  H9   C28  O27  112.12  3.000
 7VA  H8   C28  O27  112.17  3.000
 7VA  H11  N01  C05  119.92  3.000
 7VA  H11  N01  C02  121.14  3.000
 7VA  C05  N01  C02  118.92  3.000
 7VA  O07  C02  C03  123.87  3.000
 7VA  O07  C02  N01  124.63  3.000
 7VA  C03  C02  N01  111.50  3.000
 7VA  H19  C03  C08  109.88  3.000
 7VA  H19  C03  S04  108.26  3.000
 7VA  C08  C03  S04  112.17  3.000
 7VA  H19  C03  C02  107.83  3.000
 7VA  C08  C03  C02  111.87  3.000
 7VA  S04  C03  C02  106.65  3.000
 7VA  C05  S04  C03   92.84  3.000
 7VA  O06  C05  S04  124.42  3.000
 7VA  O06  C05  N01  125.50  3.000
 7VA  S04  C05  N01  110.08  3.000
 7VA  H13  C08  H12  107.42  3.000
 7VA  H13  C08  C09  110.15  3.000
 7VA  H12  C08  C09  110.50  3.000
 7VA  H13  C08  C03  107.63  3.000
 7VA  H12  C08  C03  109.43  3.000
 7VA  C09  C08  C03  111.58  3.000
 7VA  C14  C09  C08  120.66  3.000
 7VA  C08  C09  C10  121.39  3.000
 7VA  C14  C09  C10  117.93  3.000
 7VA  H14  C11  C12  119.57  3.000
 7VA  H14  C11  C10  120.35  3.000
 7VA  C12  C11  C10  120.08  3.000
 7VA  O15  C12  C11  116.22  3.000
 7VA  C11  C12  C13  119.48  3.000
 7VA  O15  C12  C13  124.30  3.000
 7VA  H15  C14  C09  119.74  3.000
 7VA  H15  C14  C13  118.55  3.000
 7VA  C09  C14  C13  121.71  3.000
 7VA  C16  O15  C12  118.43  3.000
 7VA  H17  C16  H16  107.79  3.000
 7VA  H17  C16  O15  111.78  3.000
 7VA  H16  C16  O15  110.75  3.000
 7VA  H17  C16  C17  108.28  3.000
 7VA  H16  C16  C17  110.71  3.000
 7VA  O15  C16  C17  107.52  3.000
 7VA  C19  N18  C26  125.83  3.000
 7VA  C19  N18  C17  106.47  3.000
 7VA  C26  N18  C17  127.68  3.000
 7VA  N18  C19  C22  131.76  3.000
 7VA  N18  C19  C20  105.20  3.000
 7VA  C22  C19  C20  123.04  3.000
 7VA  C20  N21  C17  105.01  3.000
 7VA  O27  C23  C24  123.33  3.000
 7VA  C24  C23  C22  121.02  3.000
 7VA  O27  C23  C22  115.65  3.000
 7VA  H18  C25  C24  120.21  3.000
 7VA  H18  C25  C20  120.98  3.000
 7VA  C24  C25  C20  118.81  3.000
 7VA  C23  O27  C28  119.04  3.000
 7VA  H7   C26  H6   107.76  3.000
 7VA  H7   C26  H5   108.91  3.000
 7VA  H6   C26  H5   108.93  3.000
 7VA  H7   C26  N18  110.37  3.000
 7VA  H6   C26  N18  109.40  3.000
 7VA  H5   C26  N18  111.40  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
 7VA  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 7VA  CONST_02  C13  C14  C09  C10    0.00   0.0  0
 7VA  CONST_03  C22  C19  N18  C17  180.00   0.0  0
 7VA  CONST_04  C20  C19  N18  C17    0.00   0.0  0
 7VA  CONST_05  C19  C20  N21  C17    0.00   0.0  0
 7VA  CONST_06  C25  C20  N21  C17  180.00   0.0  0
 7VA  CONST_07  C23  C22  C19  C20    0.00   0.0  0
 7VA  CONST_08  C23  C24  C25  C20    0.00   0.0  0
 7VA  CONST_09  N18  C17  N21  C20    0.00   0.0  0
 7VA  CONST_10  C25  C24  C23  C22    0.00   0.0  0
 7VA  CONST_11  C25  C20  C19  C22    0.00   0.0  0
 7VA  CONST_12  N21  C20  C19  C22  180.00   0.0  0
 7VA  CONST_13  C19  C22  C23  C24    0.00   0.0  0
 7VA  CONST_14  C19  C20  C25  C24    0.00   0.0  0
 7VA  CONST_15  N21  C20  C25  C24  180.00   0.0  0
 7VA  CONST_16  C12  C11  C10  C09    0.00   0.0  0
 7VA  CONST_17  C12  C13  C14  C09    0.00   0.0  0
 7VA  CONST_18  C14  C13  C12  C11    0.00   0.0  0
 7VA  CONST_19  C14  C09  C10  C11    0.00   0.0  0
 7VA  CONST_20  C23  C22  C19  N18  180.00   0.0  0
 7VA  CONST_21  C25  C20  C19  N18  180.00   0.0  0
 7VA  CONST_22  N21  C20  C19  N18    0.00   0.0  0
 7VA  CONST_23  N21  C17  N18  C19    0.00   0.0  0
 7VA  CONST_24  C05  N01  C02  C03    0.00   0.0  0
 7VA  CONST_25  O15  C12  C11  C10  180.00   0.0  0
 7VA  CONST_26  C08  C09  C14  C13  180.00   0.0  0
 7VA  CONST_27  C26  N18  C19  C20  180.00   0.0  0
 7VA  CONST_28  C16  C17  N21  C20  180.00   0.0  0
 7VA  CONST_29  C26  N18  C19  C22    0.00   0.0  0
 7VA  CONST_30  N21  C17  N18  C26  180.00   0.0  0
 7VA  CONST_31  C11  C10  C09  C08  180.00   0.0  0
 7VA  CONST_32  O15  C12  C13  C14  180.00   0.0  0
 7VA  CONST_33  C19  N18  C17  C16  180.00   0.0  0
 7VA  CONST_34  O27  C23  C22  C19  180.00   0.0  0
 7VA  CONST_35  O27  C23  C24  C25  180.00   0.0  0
 7VA  CONST_36  O07  C02  N01  C05  180.00   0.0  0
 7VA  CONST_37  H15  C14  C09  C10  180.00   0.0  0
 7VA  CONST_38  H14  C11  C12  C13  180.00   0.0  0
 7VA  CONST_39  H3   C22  C19  C20  180.00   0.0  0
 7VA  CONST_40  H4   C24  C25  C20  180.00   0.0  0
 7VA  CONST_41  H2   C13  C14  C09  180.00   0.0  0
 7VA  CONST_42  H1   C10  C11  C12  180.00   0.0  0
 7VA  CONST_43  H18  C25  C20  C19  180.00   0.0  0
 7VA  CONST_44  H11  N01  C02  C03  180.00   0.0  0
 7VA  Var_01    S04  C05  N01  C02    0.20  30.0  1
 7VA  Var_02    C03  C08  C09  C10  103.30  30.0  2
 7VA  Var_03    N18  C17  C16  O15  -62.09  30.0  2
 7VA  Var_04    H5   C26  N18  C17   92.02  30.0  2
 7VA  Var_05    H8   C28  O27  C23  -61.73  30.0  3

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
 7VA  chir_01  C03  S04  C08  C02  negativ

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
 7VA  plan-1  C10  0.020
 7VA  plan-1  C13  0.020
 7VA  plan-1  C08  0.020
 7VA  plan-1  C09  0.020
 7VA  plan-1  C11  0.020
 7VA  plan-1  C12  0.020
 7VA  plan-1  C14  0.020
 7VA  plan-1  O15  0.020
 7VA  plan-1  H1   0.020
 7VA  plan-1  H2   0.020
 7VA  plan-1  H14  0.020
 7VA  plan-1  H15  0.020
 7VA  plan-2  C17  0.020
 7VA  plan-2  C20  0.020
 7VA  plan-2  C22  0.020
 7VA  plan-2  C24  0.020
 7VA  plan-2  C16  0.020
 7VA  plan-2  N18  0.020
 7VA  plan-2  C19  0.020
 7VA  plan-2  N21  0.020
 7VA  plan-2  C23  0.020
 7VA  plan-2  C25  0.020
 7VA  plan-2  O27  0.020
 7VA  plan-2  H3   0.020
 7VA  plan-2  H4   0.020
 7VA  plan-2  H18  0.020
 7VA  plan-2  C26  0.020
 7VA  plan-3  N01  0.020
 7VA  plan-3  S04  0.020
 7VA  plan-3  C05  0.020
 7VA  plan-3  O06  0.020
 7VA  plan-4  N01  0.020
 7VA  plan-4  C02  0.020
 7VA  plan-4  C03  0.020
 7VA  plan-4  C05  0.020
 7VA  plan-4  H11  0.020
 7VA  plan-4  O07  0.020

