# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:00:31 2021
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-7-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C=C(Oc2c1scc2c3ccc4OCCOc4c3)N5CCNCC5
#
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
 UT4  UT4  3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-7-one  ligand  44  26  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UT4
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
 UT4  C01  C  CR6   0   0.482  -2.6749   8.6072  -2.9755
 UT4  C02  C  CR16  0  -0.629  -3.2411   8.5379  -1.6595
 UT4  C03  C  CR6   0   0.699  -3.8257   7.3955  -1.1621
 UT4  C04  C  CH2   0  -0.321  -5.3109   6.1841   0.3709
 UT4  C05  C  CH2   0  -0.326  -5.1742   5.7064   1.8099
 UT4  C06  C  CH2   0  -0.320  -4.2056   7.7768   2.4610
 UT4  C07  C  CH2   0  -0.314  -4.2909   8.3122   1.0352
 UT4  C08  C  CR56  0   0.365  -3.4513   6.2803  -3.1647
 UT4  C09  C  CR56  0  -0.433  -2.8226   7.3615  -3.7038
 UT4  C10  C  CR15  0  -0.561  -2.9927   5.4581  -5.2339
 UT4  C11  C  CR5   0   0.151  -3.5671   5.1563  -4.0300
 UT4  C12  C  CR6   0   0.088  -4.2291   3.8882  -3.6962
 UT4  C13  C  CR16  0  -0.314  -4.0161   3.2585  -2.4689
 UT4  C14  C  CR16  0  -0.349  -4.6495   2.0635  -2.1753
 UT4  C15  C  CR6   0   0.311  -5.4966   1.4646  -3.0984
 UT4  C16  C  CH2   0  -0.226  -7.1877  -0.0554  -3.6121
 UT4  C17  C  CH2   0  -0.229  -6.8201   0.1683  -5.0583
 UT4  C18  C  CR6   0   0.338  -5.6999   2.0789  -4.3392
 UT4  C19  C  CR16  0  -0.422  -5.0719   3.2823  -4.6239
 UT4  N01  N  NT    0  -0.515  -4.3141   7.2158   0.0782
 UT4  N02  N  NH1   0  -0.576  -5.1993   6.7752   2.7878
 UT4  O01  O  O     0  -0.480  -2.1384   9.6008  -3.4656
 UT4  O02  O  O     0  -0.465  -3.9453   6.2891  -1.9166
 UT4  O03  O  O2    0  -0.477  -6.1031   0.3028  -2.7675
 UT4  O04  O  O2    0  -0.480  -6.5073   1.5358  -5.2795
 UT4  S01  S  S2    0   0.272  -2.3398   7.0411  -5.3167
 UT4  H1   H  HCR6  0   0.280  -3.2123   9.4302  -1.0530
 UT4  H5   H  HCH2  0   0.270  -5.1957   5.3371  -0.2997
 UT4  H6   H  HCH2  0   0.252  -5.9793   5.0002   2.0180
 UT4  H7   H  HCH2  0   0.232  -4.2324   5.1590   1.9151
 UT4  H8   H  HCH2  0   0.232  -3.2133   7.3419   2.6131
 UT4  H9   H  HCH2  0   0.253  -4.2940   8.6176   3.1503
 UT4  H10  H  HCH2  0   0.267  -3.4210   8.9419   0.8589
 UT4  H11  H  HCH2  0   0.242  -5.1842   8.9368   0.9124
 UT4  H12  H  HCR5  0   0.308  -2.9078   4.7998  -6.0857
 UT4  H13  H  HCR6  0   0.254  -3.3446   3.6877  -1.7379
 UT4  H14  H  HCR6  0   0.271  -4.4864   1.5809  -1.2200
 UT4  H15  H  HCH2  0   0.245  -8.0760   0.5273  -3.3467
 UT4  H16  H  HCH2  0   0.263  -7.4012  -1.1080  -3.4324
 UT4  H17  H  HCH2  0   0.263  -7.6594  -0.0793  -5.7064
 UT4  H18  H  HCH2  0   0.246  -5.9692  -0.4615  -5.3389
 UT4  H19  H  HCR6  0   0.266  -5.2626   3.7510  -5.5822
 UT4  H21  H  HNH1  0   0.347  -6.1195   7.2009   2.8019
 UT4  H4   H  HCH2  0   0.242  -6.3146   6.5970   0.2088

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
 UT4  O04  C17  single    1.420  0.020  1.420
 UT4  O04  C18  single    1.353  0.020  1.353
 UT4  C10  S01  aromatic  1.714  0.020  1.714
 UT4  C10  C11  aromatic  1.368  0.020  1.368
 UT4  C17  C16  single    1.509  0.020  1.509
 UT4  S01  C09  aromatic  1.714  0.020  1.714
 UT4  C19  C18  aromatic  1.387  0.020  1.387
 UT4  C19  C12  aromatic  1.392  0.020  1.392
 UT4  C18  C15  aromatic  1.399  0.020  1.399
 UT4  C11  C12  single    1.469  0.020  1.469
 UT4  C11  C08  aromatic  1.423  0.020  1.423
 UT4  C12  C13  aromatic  1.396  0.020  1.396
 UT4  C16  O03  single    1.421  0.020  1.421
 UT4  C09  C08  aromatic  1.362  0.020  1.362
 UT4  C09  C01  single    1.450  0.020  1.450
 UT4  O01  C01  double    1.231  0.020  1.231
 UT4  C15  O03  single    1.352  0.020  1.352
 UT4  C15  C14  aromatic  1.389  0.020  1.389
 UT4  C08  O02  single    1.342  0.020  1.342
 UT4  C01  C02  single    1.434  0.020  1.434
 UT4  C13  C14  aromatic  1.384  0.020  1.384
 UT4  O02  C03  single    1.345  0.020  1.345
 UT4  C02  C03  double    1.376  0.020  1.376
 UT4  C03  N01  single    1.345  0.020  1.345
 UT4  N01  C04  single    1.464  0.020  1.464
 UT4  N01  C07  single    1.456  0.020  1.456
 UT4  C04  C05  single    1.522  0.020  1.522
 UT4  C07  C06  single    1.525  0.020  1.525
 UT4  C05  N02  single    1.449  0.020  1.449
 UT4  C06  N02  single    1.448  0.020  1.448
 UT4  C02  H1   single    0.930  0.020  1.080
 UT4  C04  H4   single    0.970  0.020  1.090
 UT4  C04  H5   single    0.970  0.020  1.090
 UT4  C05  H6   single    0.970  0.020  1.090
 UT4  C05  H7   single    0.970  0.020  1.090
 UT4  C06  H8   single    0.970  0.020  1.090
 UT4  C06  H9   single    0.970  0.020  1.090
 UT4  C07  H10  single    0.970  0.020  1.090
 UT4  C07  H11  single    0.970  0.020  1.090
 UT4  C10  H12  single    0.930  0.020  1.080
 UT4  C13  H13  single    0.930  0.020  1.080
 UT4  C14  H14  single    0.930  0.020  1.080
 UT4  C16  H15  single    0.970  0.020  1.090
 UT4  C16  H16  single    0.970  0.020  1.090
 UT4  C17  H17  single    0.970  0.020  1.090
 UT4  C17  H18  single    0.970  0.020  1.090
 UT4  C19  H19  single    0.930  0.020  1.080
 UT4  N02  H21  single    0.890  0.020  1.040

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
 UT4  O01  C01  C09  122.53  3.000
 UT4  O01  C01  C02  125.19  3.000
 UT4  C09  C01  C02  112.28  3.000
 UT4  H1   C02  C03  119.64  3.000
 UT4  H1   C02  C01  117.72  3.000
 UT4  C03  C02  C01  122.64  3.000
 UT4  O02  C03  N01  112.04  3.000
 UT4  N01  C03  C02  126.75  3.000
 UT4  O02  C03  C02  121.20  3.000
 UT4  H5   C04  H4   107.40  3.000
 UT4  H5   C04  N01  110.72  3.000
 UT4  H4   C04  N01  109.15  3.000
 UT4  H5   C04  C05  109.22  3.000
 UT4  H4   C04  C05  109.87  3.000
 UT4  N01  C04  C05  110.42  3.000
 UT4  H7   C05  H6   107.03  3.000
 UT4  H7   C05  N02  108.60  3.000
 UT4  H6   C05  N02  109.63  3.000
 UT4  H7   C05  C04  108.97  3.000
 UT4  H6   C05  C04  108.49  3.000
 UT4  N02  C05  C04  113.89  3.000
 UT4  H9   C06  H8   106.99  3.000
 UT4  H9   C06  N02  109.57  3.000
 UT4  H8   C06  N02  108.42  3.000
 UT4  H9   C06  C07  108.40  3.000
 UT4  H8   C06  C07  108.68  3.000
 UT4  N02  C06  C07  114.54  3.000
 UT4  H11  C07  H10  107.66  3.000
 UT4  H11  C07  N01  110.02  3.000
 UT4  H10  C07  N01  110.01  3.000
 UT4  H11  C07  C06  110.49  3.000
 UT4  H10  C07  C06  108.05  3.000
 UT4  N01  C07  C06  110.55  3.000
 UT4  O02  C08  C11  122.72  3.000
 UT4  O02  C08  C09  122.19  3.000
 UT4  C11  C08  C09  115.08  3.000
 UT4  S01  C09  C08  110.74  3.000
 UT4  C08  C09  C01  122.00  3.000
 UT4  S01  C09  C01  127.19  3.000
 UT4  H12  C10  S01  119.66  3.000
 UT4  H12  C10  C11  126.36  3.000
 UT4  S01  C10  C11  113.97  3.000
 UT4  C12  C11  C10  125.44  3.000
 UT4  C12  C11  C08  125.47  3.000
 UT4  C10  C11  C08  109.07  3.000
 UT4  C19  C12  C13  118.81  3.000
 UT4  C13  C12  C11  121.37  3.000
 UT4  C19  C12  C11  119.81  3.000
 UT4  H13  C13  C14  118.91  3.000
 UT4  H13  C13  C12  120.67  3.000
 UT4  C14  C13  C12  120.42  3.000
 UT4  H14  C14  C15  119.09  3.000
 UT4  H14  C14  C13  120.21  3.000
 UT4  C15  C14  C13  120.70  3.000
 UT4  O03  C15  C18  121.95  3.000
 UT4  O03  C15  C14  118.79  3.000
 UT4  C18  C15  C14  119.25  3.000
 UT4  H16  C16  H15  108.38  3.000
 UT4  H16  C16  O03  107.18  3.000
 UT4  H15  C16  O03  109.95  3.000
 UT4  H16  C16  C17  110.44  3.000
 UT4  H15  C16  C17  110.55  3.000
 UT4  O03  C16  C17  110.27  3.000
 UT4  H18  C17  H17  108.39  3.000
 UT4  H18  C17  O04  110.04  3.000
 UT4  H17  C17  O04  107.22  3.000
 UT4  H18  C17  C16  110.46  3.000
 UT4  H17  C17  C16  110.43  3.000
 UT4  O04  C17  C16  110.23  3.000
 UT4  O04  C18  C19  118.41  3.000
 UT4  C19  C18  C15  119.81  3.000
 UT4  O04  C18  C15  121.78  3.000
 UT4  H19  C19  C18  118.50  3.000
 UT4  H19  C19  C12  120.50  3.000
 UT4  C18  C19  C12  120.99  3.000
 UT4  C07  N01  C04  114.22  3.000
 UT4  C07  N01  C03  119.99  3.000
 UT4  C04  N01  C03  121.72  3.000
 UT4  H21  N02  C06  109.60  3.000
 UT4  H21  N02  C05  109.57  3.000
 UT4  C06  N02  C05  110.24  3.000
 UT4  C08  O02  C03  119.63  3.000
 UT4  C16  O03  C15  114.44  3.000
 UT4  C18  O04  C17  114.19  3.000
 UT4  C10  S01  C09   91.14  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
 UT4  CONST_01  S01  C10  C11  C08     0.00   0.0  0
 UT4  CONST_04  C10  S01  C09  C08     0.00   0.0  0
 UT4  CONST_05  C11  C10  S01  C09     0.00   0.0  0
 UT4  CONST_06  C10  C11  C08  C09     0.00   0.0  0
 UT4  CONST_07  C12  C11  C08  C09   180.00   0.0  0
 UT4  CONST_10  C18  C19  C12  C11   180.00   0.0  0
 UT4  CONST_11  C14  C13  C12  C11   180.00   0.0  0
 UT4  CONST_12  S01  C09  C08  C11     0.00   0.0  0
 UT4  CONST_13  C15  C18  C19  C12     0.00   0.0  0
 UT4  CONST_14  S01  C10  C11  C12   180.00   0.0  0
 UT4  CONST_15  C15  C14  C13  C12     0.00   0.0  0
 UT4  CONST_16  C18  C19  C12  C13     0.00   0.0  0
 UT4  CONST_17  C18  C15  C14  C13     0.00   0.0  0
 UT4  CONST_18  C19  C18  C15  C14     0.00   0.0  0
 UT4  CONST_19  C19  C12  C13  C14     0.00   0.0  0
 UT4  CONST_20  O02  C08  C11  C12     0.00   0.0  0
 UT4  CONST_21  H12  C10  C11  C08   180.00   0.0  0
 UT4  CONST_22  H19  C19  C12  C11     0.00   0.0  0
 UT4  CONST_23  H13  C13  C12  C11     0.00   0.0  0
 UT4  CONST_24  H14  C14  C13  C12   180.00   0.0  0
 UT4  Var_01    O02  C03  C02  C01    -2.81  30.0  1
 UT4  Var_02    S01  C09  C01  C02   177.58  30.0  1
 UT4  Var_03    C04  N01  C03  C02   157.95  30.0  2
 UT4  Var_04    C11  C08  O02  C03  -178.59  30.0  1
 UT4  Var_05    C09  C01  C02  C03     1.31  30.0  1
 UT4  Var_06    C05  C04  N01  C03   151.03  30.0  1
 UT4  Var_07    C06  C07  N01  C03  -151.54  30.0  1
 UT4  Var_08    C06  N02  C05  C04   -53.62  30.0  1
 UT4  Var_09    C07  C06  N02  C05    52.91  30.0  1
 UT4  Var_10    C17  C16  O03  C15    43.96  30.0  1
 UT4  Var_11    C18  C15  O03  C16   -14.94  30.0  1
 UT4  Var_12    C19  C18  O04  C17   164.26  30.0  1
 UT4  Var_13    N02  C05  C04  N01    53.11  30.0  1
 UT4  Var_14    N02  C06  C07  N01   -51.57  30.0  1
 UT4  Var_15    O04  C17  C16  O03   -60.15  30.0  1
 UT4  Var_16    H17  C17  O04  C18   165.47  30.0  1

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
 UT4  plan-1  C01  0.020
 UT4  plan-1  C08  0.020
 UT4  plan-1  C09  0.020
 UT4  plan-1  C10  0.020
 UT4  plan-1  C11  0.020
 UT4  plan-1  C12  0.020
 UT4  plan-1  O02  0.020
 UT4  plan-1  S01  0.020
 UT4  plan-1  H12  0.020
 UT4  plan-2  C11  0.020
 UT4  plan-2  C12  0.020
 UT4  plan-2  C13  0.020
 UT4  plan-2  C14  0.020
 UT4  plan-2  C15  0.020
 UT4  plan-2  C18  0.020
 UT4  plan-2  C19  0.020
 UT4  plan-2  O03  0.020
 UT4  plan-2  O04  0.020
 UT4  plan-2  H13  0.020
 UT4  plan-2  H14  0.020
 UT4  plan-2  H19  0.020
 UT4  plan-3  C01  0.020
 UT4  plan-3  C02  0.020
 UT4  plan-3  C09  0.020
 UT4  plan-3  O01  0.020
 UT4  plan-4  C03  0.020
 UT4  plan-4  C04  0.020
 UT4  plan-4  C07  0.020
 UT4  plan-4  N01  0.020

