# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 13:22:21 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: 1,5-anhydro-2,3-dideoxy-3-[(5S)-5H-imidazo[5,1-a]isoindol-5-yl]-D-threo-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1COCC[C@H]1[C@@H]2n3cncc3c4ccccc24
#
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
 QVY  QVY  1,5-anhydro-2,3-dideoxy-3-[(5S)-5H-imidazo[5,1-a]isoindol-5-yl]-D-threo-pentitol  ligand  35  19  .  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_QVY
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
 QVY  C4   C  CR56  0   0.099  44.4594  11.6371  -32.3806
 QVY  C14  C  CH1   0  -0.295  44.7817  13.1942  -30.4082
 QVY  C5   C  CR56  0   0.011  43.4287  10.6926  -32.4580
 QVY  C6   C  CR16  0  -0.364  43.6470   9.4492  -33.0315
 QVY  C7   C  CR55  0   0.385  42.2519  11.2947  -31.8695
 QVY  C8   C  CR15  0  -0.295  40.9214  11.1539  -31.5792
 QVY  C10  C  CR15  0   0.094  41.4816  13.1302  -30.9522
 QVY  C12  C  CR15  0  -0.104  43.9880  12.8972  -31.6878
 QVY  C3   C  CR16  0  -0.317  45.7164  11.3502  -32.8736
 QVY  C1   C  CR16  0  -0.254  44.9139   9.1640  -33.5278
 QVY  C2   C  CR16  0  -0.257  45.9381  10.1024  -33.4518
 QVY  N9   N  N     0  -0.451  40.4592  12.3066  -31.0086
 QVY  N11  N  N     0  -0.496  42.5881  12.5563  -31.4584
 QVY  C16  C  CH2   0  -0.454  44.7414  12.0638  -29.3828
 QVY  C17  C  CH2   0  -0.177  45.5785  12.4244  -28.1660
 QVY  O18  O  O2    0  -0.481  45.1739  13.6470  -27.5868
 QVY  C19  C  CH2   0  -0.200  45.2589  14.7148  -28.4978
 QVY  C20  C  CH1   0   0.043  44.3667  14.4901  -29.7205
 QVY  O22  O  OH1   0  -0.666  44.4873  15.5526  -30.6346
 QVY  H15  H  HCH1  0   0.255  45.8214  13.3220  -30.7391
 QVY  H1   H  HCR6  0   0.253  42.8531   8.7164  -33.0933
 QVY  H2   H  HCR5  0   0.257  40.2784  10.3057  -31.7557
 QVY  H3   H  HCR5  0   0.284  41.4551  14.1391  -30.5721
 QVY  H13  H  HCR5  0   0.308  44.0488  13.7577  -32.3578
 QVY  H4   H  HCR6  0   0.257  46.5183  12.0756  -32.8149
 QVY  H5   H  HCR6  0   0.261  45.1061   8.1996  -33.9795
 QVY  H6   H  HCR6  0   0.260  46.9170   9.8598  -33.8438
 QVY  H7   H  HCH2  0   0.238  43.7114  11.8653  -29.0716
 QVY  H8   H  HCH2  0   0.253  45.1304  11.1375  -29.8106
 QVY  H9   H  HCH2  0   0.242  45.4791  11.6594  -27.3950
 QVY  H10  H  HCH2  0   0.202  46.6393  12.4713  -28.4516
 QVY  H11  H  HCH2  0   0.202  46.2946  14.8684  -28.8385
 QVY  H12  H  HCH2  0   0.240  44.9461  15.6174  -27.9670
 QVY  H21  H  HCH1  0   0.210  43.3320  14.3918  -29.3609
 QVY  H14  H  HOH1  0   0.458  44.0634  16.3314  -30.2606

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
 QVY  C1   C2   aromatic  1.391  0.020  1.391
 QVY  C1   C6   aromatic  1.390  0.020  1.390
 QVY  C2   C3   aromatic  1.393  0.020  1.393
 QVY  C6   C5   aromatic  1.387  0.020  1.387
 QVY  C3   C4   aromatic  1.380  0.020  1.380
 QVY  C5   C4   aromatic  1.400  0.020  1.400
 QVY  C5   C7   aromatic  1.447  0.020  1.447
 QVY  C4   C12  single    1.513  0.020  1.513
 QVY  C7   C8   aromatic  1.369  0.020  1.369
 QVY  C7   N11  aromatic  1.369  0.020  1.369
 QVY  C8   N9   aromatic  1.367  0.020  1.367
 QVY  C12  N11  single    1.459  0.020  1.459
 QVY  C12  C14  single    1.535  0.020  1.535
 QVY  N11  C10  aromatic  1.345  0.020  1.345
 QVY  N9   C10  aromatic  1.314  0.020  1.314
 QVY  O22  C20  single    1.407  0.020  1.407
 QVY  C14  C20  single    1.525  0.020  1.525
 QVY  C14  C16  single    1.527  0.020  1.527
 QVY  C20  C19  single    1.530  0.020  1.530
 QVY  C16  C17  single    1.520  0.020  1.520
 QVY  C19  O18  single    1.406  0.020  1.406
 QVY  C17  O18  single    1.412  0.020  1.412
 QVY  C14  H15  single    0.970  0.020  1.090
 QVY  C6   H1   single    0.930  0.020  1.080
 QVY  C8   H2   single    0.930  0.020  1.080
 QVY  C10  H3   single    0.930  0.020  1.080
 QVY  C12  H13  single    0.970  0.020  1.090
 QVY  C3   H4   single    0.930  0.020  1.080
 QVY  C1   H5   single    0.930  0.020  1.080
 QVY  C2   H6   single    0.930  0.020  1.080
 QVY  C16  H7   single    0.970  0.020  1.090
 QVY  C16  H8   single    0.970  0.020  1.090
 QVY  C17  H9   single    0.970  0.020  1.090
 QVY  C17  H10  single    0.970  0.020  1.090
 QVY  C19  H11  single    0.970  0.020  1.090
 QVY  C19  H12  single    0.970  0.020  1.090
 QVY  C20  H21  single    0.970  0.020  1.090
 QVY  O22  H14  single    0.850  0.020  0.980

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
 QVY  C3   C4   C12  128.33  3.000
 QVY  C12  C4   C5   110.96  3.000
 QVY  C3   C4   C5   120.69  3.000
 QVY  H15  C14  C20  107.14  3.000
 QVY  H15  C14  C16  108.26  3.000
 QVY  C20  C14  C16  108.61  3.000
 QVY  H15  C14  C12  105.12  3.000
 QVY  C16  C14  C12  113.77  3.000
 QVY  C20  C14  C12  113.57  3.000
 QVY  C7   C5   C6   132.02  3.000
 QVY  C7   C5   C4   107.19  3.000
 QVY  C6   C5   C4   120.79  3.000
 QVY  H1   C6   C1   120.62  3.000
 QVY  H1   C6   C5   121.02  3.000
 QVY  C1   C6   C5   118.36  3.000
 QVY  N11  C7   C8   105.65  3.000
 QVY  N11  C7   C5   107.81  3.000
 QVY  C8   C7   C5   146.49  3.000
 QVY  H2   C8   N9   121.99  3.000
 QVY  H2   C8   C7   128.71  3.000
 QVY  N9   C8   C7   109.30  3.000
 QVY  H3   C10  N11  123.49  3.000
 QVY  H3   C10  N9   125.62  3.000
 QVY  N11  C10  N9   110.88  3.000
 QVY  H13  C12  N11  109.50  3.000
 QVY  H13  C12  C14  109.28  3.000
 QVY  N11  C12  C14  114.23  3.000
 QVY  H13  C12  C4   110.97  3.000
 QVY  C14  C12  C4   112.45  3.000
 QVY  N11  C12  C4   100.15  3.000
 QVY  H4   C3   C2   120.31  3.000
 QVY  H4   C3   C4   121.04  3.000
 QVY  C2   C3   C4   118.64  3.000
 QVY  H5   C1   C2   119.55  3.000
 QVY  H5   C1   C6   119.58  3.000
 QVY  C2   C1   C6   120.87  3.000
 QVY  H6   C2   C1   119.68  3.000
 QVY  H6   C2   C3   119.68  3.000
 QVY  C1   C2   C3   120.64  3.000
 QVY  C10  N9   C8   106.46  3.000
 QVY  C12  N11  C10  138.48  3.000
 QVY  C10  N11  C7   107.71  3.000
 QVY  C12  N11  C7   113.82  3.000
 QVY  H8   C16  H7   107.03  3.000
 QVY  H8   C16  C17  108.58  3.000
 QVY  H7   C16  C17  109.50  3.000
 QVY  H8   C16  C14  110.83  3.000
 QVY  H7   C16  C14  110.50  3.000
 QVY  C17  C16  C14  110.33  3.000
 QVY  H10  C17  H9   107.55  3.000
 QVY  H10  C17  O18  110.24  3.000
 QVY  H9   C17  O18  106.93  3.000
 QVY  H10  C17  C16  109.48  3.000
 QVY  H9   C17  C16  110.44  3.000
 QVY  O18  C17  C16  112.08  3.000
 QVY  C19  O18  C17  111.99  3.000
 QVY  H12  C19  H11  107.72  3.000
 QVY  H12  C19  C20  110.03  3.000
 QVY  H11  C19  C20  108.77  3.000
 QVY  H12  C19  O18  107.17  3.000
 QVY  H11  C19  O18  111.30  3.000
 QVY  C20  C19  O18  111.77  3.000
 QVY  H21  C20  O22  111.14  3.000
 QVY  H21  C20  C19  107.48  3.000
 QVY  O22  C20  C19  111.00  3.000
 QVY  H21  C20  C14  109.12  3.000
 QVY  C19  C20  C14  109.06  3.000
 QVY  O22  C20  C14  109.00  3.000
 QVY  H14  O22  C20  108.72  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
 QVY  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 QVY  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 QVY  CONST_03  C8   C7   C5   C4   180.00   0.0  0
 QVY  CONST_04  N11  C7   C5   C4     0.00   0.0  0
 QVY  CONST_05  C2   C1   C6   C5     0.00   0.0  0
 QVY  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 QVY  CONST_07  N9   C8   C7   C5   180.00   0.0  0
 QVY  CONST_08  C10  N11  C7   C5   180.00   0.0  0
 QVY  CONST_09  C3   C2   C1   C6     0.00   0.0  0
 QVY  CONST_10  C3   C4   C5   C6     0.00   0.0  0
 QVY  CONST_11  C8   C7   C5   C6     0.00   0.0  0
 QVY  CONST_12  N11  C7   C5   C6   180.00   0.0  0
 QVY  CONST_13  C1   C6   C5   C7   180.00   0.0  0
 QVY  CONST_14  C3   C4   C5   C7   180.00   0.0  0
 QVY  CONST_15  C10  N9   C8   C7     0.00   0.0  0
 QVY  CONST_16  N9   C10  N11  C7     0.00   0.0  0
 QVY  CONST_17  C10  N11  C7   C8     0.00   0.0  0
 QVY  CONST_18  N11  C10  N9   C8     0.00   0.0  0
 QVY  CONST_19  N11  C7   C8   N9     0.00   0.0  0
 QVY  CONST_20  H6   C2   C3   C4   180.00   0.0  0
 QVY  CONST_21  H1   C6   C5   C4   180.00   0.0  0
 QVY  CONST_22  H5   C1   C6   C5   180.00   0.0  0
 QVY  CONST_23  H4   C3   C4   C5   180.00   0.0  0
 QVY  CONST_24  H2   C8   C7   C5     0.00   0.0  0
 QVY  CONST_25  H3   C10  N11  C7   180.00   0.0  0
 QVY  Var_01    O18  C17  C16  C14   55.78  30.0  1
 QVY  Var_02    C20  C19  O18  C17   60.30  30.0  1

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
 QVY  chir_01  C14  C12  C20  C16  negativ
 QVY  chir_02  C12  N11  C14  C4   negativ
 QVY  chir_03  C20  O22  C14  C19  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
 QVY  plan-1  C4   0.020
 QVY  plan-1  C5   0.020
 QVY  plan-1  C6   0.020
 QVY  plan-1  C7   0.020
 QVY  plan-1  C8   0.020
 QVY  plan-1  C10  0.020
 QVY  plan-1  C12  0.020
 QVY  plan-1  C3   0.020
 QVY  plan-1  C1   0.020
 QVY  plan-1  C2   0.020
 QVY  plan-1  N9   0.020
 QVY  plan-1  N11  0.020
 QVY  plan-1  H1   0.020
 QVY  plan-1  H2   0.020
 QVY  plan-1  H3   0.020
 QVY  plan-1  H4   0.020
 QVY  plan-1  H5   0.020
 QVY  plan-1  H6   0.020

