# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 18:05:06 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(morpholin-4-yl)-7H-thieno[3,2-b]pyran-7-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C=C(Oc2c1scc2c3ccc4OCCOc4c3)N5CCOCC5
#
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
 82V  82V  3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(morpholin-4-yl)-7H-thieno[3,2-b]pyran-7-one  ligand  43  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_82V
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
 82V  C10  C  CH2   0  -0.329   1.9442   2.4830   0.5387
 82V  C13  C  CR56  0  -0.433   1.7698  -2.3948  -0.0744
 82V  C15  C  CR15  0  -0.560  -0.5693  -3.0933   0.1000
 82V  C17  C  CR6   0   0.088  -1.5991  -0.8005   0.3113
 82V  C20  C  CR6   0   0.311  -3.7692   0.9468   0.5712
 82V  C22  C  CH2   0  -0.227  -5.7754   1.7458  -0.3083
 82V  C26  C  CR16  0  -0.421  -2.7604  -0.9993  -0.4304
 82V  C02  C  CR6   0   0.484   3.2001  -2.1882  -0.1930
 82V  C03  C  CR16  0  -0.624   3.5520  -0.7968  -0.1550
 82V  C04  C  CR6   0   0.697   2.6127   0.2005  -0.0600
 82V  N05  N  NT    0  -0.525   2.8469   1.5269  -0.1018
 82V  C06  C  CH2   0  -0.325   4.2111   2.0084  -0.2492
 82V  C07  C  CH2   0  -0.187   4.2088   3.3970  -0.8641
 82V  O08  O  O2    0  -0.479   3.3958   4.2935  -0.1466
 82V  C09  C  CH2   0  -0.193   2.0640   3.8363  -0.1334
 82V  O11  O  O     0  -0.464   1.3029  -0.0766   0.0617
 82V  C12  C  CR56  0   0.364   0.8979  -1.3569   0.0642
 82V  S14  S  S2    0   0.274   0.9363  -3.8919  -0.0826
 82V  C16  C  CR5   0   0.151  -0.4712  -1.7311   0.1716
 82V  C18  C  CR16  0  -0.314  -1.5418   0.2752   1.1983
 82V  C19  C  CR16  0  -0.349  -2.6153   1.1404   1.3192
 82V  O21  O  O2    0  -0.477  -4.7886   1.8231   0.7106
 82V  C23  C  CH2   0  -0.229  -6.1094   0.3040  -0.6030
 82V  O24  O  O2    0  -0.480  -4.9495  -0.3866  -1.0444
 82V  C25  C  CR6   0   0.339  -3.8440  -0.1429  -0.3033
 82V  H1   H  HCH2  0   0.275   0.9110   2.1542   0.4615
 82V  H2   H  HCH2  0   0.250   2.1947   2.5689   1.6026
 82V  H3   H  HCR5  0   0.308  -1.4760  -3.6762   0.1634
 82V  H4   H  HCH2  0   0.263  -6.6552   2.2745   0.0554
 82V  H5   H  HCH2  0   0.246  -5.4202   2.2491  -1.2138
 82V  H6   H  HCR6  0   0.266  -2.8286  -1.8216  -1.1326
 82V  H7   H  HCR6  0   0.284   4.6007  -0.5439  -0.1941
 82V  H11  H  HCH2  0   0.250   4.7249   2.0153   0.7193
 82V  H12  H  HCH2  0   0.273   4.7650   1.3530  -0.9193
 82V  H13  H  HCH2  0   0.253   5.2259   3.7896  -0.8600
 82V  H14  H  HCH2  0   0.215   3.8756   3.3263  -1.9084
 82V  H15  H  HCH2  0   0.215   1.6675   3.7727  -1.1561
 82V  H16  H  HCH2  0   0.252   1.4663   4.5631   0.4172
 82V  H17  H  HCR6  0   0.254  -0.6661   0.4383   1.8120
 82V  H18  H  HCR6  0   0.272  -2.5681   1.9779   2.0039
 82V  H19  H  HCH2  0   0.246  -6.5202  -0.1841   0.2870
 82V  H20  H  HCH2  0   0.263  -6.8463   0.2395  -1.4019
 82V  O01  O  O     0  -0.476   3.9994  -3.1179  -0.2924

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
 82V  S14  C15  aromatic  1.714  0.020  1.714
 82V  S14  C13  aromatic  1.714  0.020  1.714
 82V  C15  C16  aromatic  1.368  0.020  1.368
 82V  O24  C23  single    1.420  0.020  1.420
 82V  O24  C25  single    1.353  0.020  1.353
 82V  C23  C22  single    1.509  0.020  1.509
 82V  C26  C25  aromatic  1.387  0.020  1.387
 82V  C26  C17  aromatic  1.392  0.020  1.392
 82V  C16  C17  single    1.469  0.020  1.469
 82V  C16  C12  aromatic  1.423  0.020  1.423
 82V  C25  C20  aromatic  1.399  0.020  1.399
 82V  C13  C02  single    1.450  0.020  1.450
 82V  C13  C12  aromatic  1.363  0.020  1.363
 82V  O01  C02  double    1.230  0.020  1.230
 82V  C17  C18  aromatic  1.395  0.020  1.395
 82V  C02  C03  single    1.436  0.020  1.436
 82V  C12  O11  single    1.343  0.020  1.343
 82V  C20  O21  single    1.351  0.020  1.351
 82V  C20  C19  aromatic  1.389  0.020  1.389
 82V  C22  O21  single    1.420  0.020  1.420
 82V  C18  C19  aromatic  1.384  0.020  1.384
 82V  O11  C04  single    1.344  0.020  1.344
 82V  C03  C04  double    1.373  0.020  1.373
 82V  C04  N05  single    1.348  0.020  1.348
 82V  N05  C06  single    1.454  0.020  1.454
 82V  N05  C10  single    1.463  0.020  1.463
 82V  C06  C07  single    1.519  0.020  1.519
 82V  C10  C09  single    1.516  0.020  1.516
 82V  C07  O08  single    1.407  0.020  1.407
 82V  C09  O08  single    1.408  0.020  1.408
 82V  C10  H1   single    0.970  0.020  1.090
 82V  C10  H2   single    0.970  0.020  1.090
 82V  C15  H3   single    0.930  0.020  1.080
 82V  C22  H4   single    0.970  0.020  1.090
 82V  C22  H5   single    0.970  0.020  1.090
 82V  C26  H6   single    0.930  0.020  1.080
 82V  C03  H7   single    0.930  0.020  1.080
 82V  C06  H11  single    0.970  0.020  1.090
 82V  C06  H12  single    0.970  0.020  1.090
 82V  C07  H13  single    0.970  0.020  1.090
 82V  C07  H14  single    0.970  0.020  1.090
 82V  C09  H15  single    0.970  0.020  1.090
 82V  C09  H16  single    0.970  0.020  1.090
 82V  C18  H17  single    0.930  0.020  1.080
 82V  C19  H18  single    0.930  0.020  1.080
 82V  C23  H19  single    0.970  0.020  1.090
 82V  C23  H20  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
 82V  H2   C10  H1   108.05  3.000
 82V  H2   C10  C09  110.01  3.000
 82V  H1   C10  C09  108.28  3.000
 82V  H2   C10  N05  109.58  3.000
 82V  H1   C10  N05  110.97  3.000
 82V  C09  C10  N05  109.91  3.000
 82V  S14  C13  C12  110.78  3.000
 82V  C12  C13  C02  122.07  3.000
 82V  S14  C13  C02  127.15  3.000
 82V  H3   C15  C16  126.50  3.000
 82V  H3   C15  S14  119.49  3.000
 82V  C16  C15  S14  114.00  3.000
 82V  C18  C17  C16  121.15  3.000
 82V  C18  C17  C26  118.88  3.000
 82V  C16  C17  C26  119.96  3.000
 82V  C25  C20  O21  121.94  3.000
 82V  O21  C20  C19  118.74  3.000
 82V  C25  C20  C19  119.32  3.000
 82V  H5   C22  H4   108.37  3.000
 82V  H5   C22  C23  110.45  3.000
 82V  H4   C22  C23  110.50  3.000
 82V  H5   C22  O21  110.04  3.000
 82V  H4   C22  O21  107.17  3.000
 82V  C23  C22  O21  110.23  3.000
 82V  H6   C26  C25  118.61  3.000
 82V  H6   C26  C17  120.41  3.000
 82V  C25  C26  C17  120.98  3.000
 82V  C03  C02  O01  125.12  3.000
 82V  C03  C02  C13  112.19  3.000
 82V  O01  C02  C13  122.68  3.000
 82V  H7   C03  C04  119.79  3.000
 82V  H7   C03  C02  117.66  3.000
 82V  C04  C03  C02  122.55  3.000
 82V  O11  C04  N05  112.02  3.000
 82V  N05  C04  C03  126.43  3.000
 82V  O11  C04  C03  121.53  3.000
 82V  C06  N05  C04  119.48  3.000
 82V  C06  N05  C10  114.01  3.000
 82V  C04  N05  C10  121.51  3.000
 82V  H12  C06  H11  108.00  3.000
 82V  H12  C06  C07  107.58  3.000
 82V  H11  C06  C07  110.65  3.000
 82V  H12  C06  N05  109.89  3.000
 82V  H11  C06  N05  110.62  3.000
 82V  C07  C06  N05  110.02  3.000
 82V  H14  C07  H13  108.04  3.000
 82V  H14  C07  O08  110.52  3.000
 82V  H13  C07  O08  107.92  3.000
 82V  H14  C07  C06  109.06  3.000
 82V  H13  C07  C06  109.04  3.000
 82V  O08  C07  C06  112.15  3.000
 82V  C09  O08  C07  110.14  3.000
 82V  H16  C09  H15  108.10  3.000
 82V  H16  C09  O08  107.87  3.000
 82V  H15  C09  O08  110.57  3.000
 82V  H16  C09  C10  109.14  3.000
 82V  H15  C09  C10  109.42  3.000
 82V  O08  C09  C10  111.64  3.000
 82V  C12  O11  C04  119.38  3.000
 82V  C16  C12  O11  122.74  3.000
 82V  O11  C12  C13  122.21  3.000
 82V  C16  C12  C13  115.02  3.000
 82V  C15  S14  C13   91.13  3.000
 82V  C12  C16  C17  125.39  3.000
 82V  C12  C16  C15  109.08  3.000
 82V  C17  C16  C15  125.52  3.000
 82V  H17  C18  C19  118.96  3.000
 82V  H17  C18  C17  120.67  3.000
 82V  C19  C18  C17  120.37  3.000
 82V  H18  C19  C18  120.32  3.000
 82V  H18  C19  C20  118.99  3.000
 82V  C18  C19  C20  120.68  3.000
 82V  C22  O21  C20  114.51  3.000
 82V  H20  C23  H19  108.43  3.000
 82V  H20  C23  O24  107.21  3.000
 82V  H19  C23  O24  110.01  3.000
 82V  H20  C23  C22  110.47  3.000
 82V  H19  C23  C22  110.50  3.000
 82V  O24  C23  C22  110.15  3.000
 82V  C25  O24  C23  114.17  3.000
 82V  O24  C25  C26  118.49  3.000
 82V  C26  C25  C20  119.76  3.000
 82V  O24  C25  C20  121.75  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
 82V  CONST_01  C16  C15  S14  C13     0.00   0.0  0
 82V  CONST_02  C15  C16  C12  C13     0.00   0.0  0
 82V  CONST_03  C17  C16  C12  C13   180.00   0.0  0
 82V  CONST_04  C12  C13  S14  C15     0.00   0.0  0
 82V  CONST_07  C20  C25  C26  C17     0.00   0.0  0
 82V  CONST_08  S14  C15  C16  C17   180.00   0.0  0
 82V  CONST_09  C20  C19  C18  C17     0.00   0.0  0
 82V  CONST_10  C19  C20  C25  C26     0.00   0.0  0
 82V  CONST_12  C19  C18  C17  C26     0.00   0.0  0
 82V  CONST_13  S14  C15  C16  C12     0.00   0.0  0
 82V  CONST_15  C16  C12  C13  S14     0.00   0.0  0
 82V  CONST_16  C25  C26  C17  C16   180.00   0.0  0
 82V  CONST_17  C19  C18  C17  C16   180.00   0.0  0
 82V  CONST_18  C25  C26  C17  C18     0.00   0.0  0
 82V  CONST_19  C25  C20  C19  C18     0.00   0.0  0
 82V  CONST_20  O11  C12  C16  C17     0.00   0.0  0
 82V  CONST_21  H3   C15  S14  C13   180.00   0.0  0
 82V  CONST_22  H18  C19  C18  C17   180.00   0.0  0
 82V  CONST_23  H6   C26  C25  C20   180.00   0.0  0
 82V  CONST_24  H17  C18  C19  C20   180.00   0.0  0
 82V  Var_01    O11  C04  N05  C10    27.32  30.0  2
 82V  Var_02    C07  C06  N05  C10   -49.22  30.0  1
 82V  Var_03    C04  C03  C02  C13    -1.95  30.0  1
 82V  Var_04    C23  C22  O21  C20    43.81  30.0  1
 82V  Var_05    C25  C20  O21  C22   -14.59  30.0  1
 82V  Var_06    S14  C13  C02  C03   179.65  30.0  1
 82V  Var_07    C16  C12  O11  C04  -179.17  30.0  1
 82V  Var_08    C09  C10  N05  C04  -155.30  30.0  1
 82V  Var_09    O08  C07  C06  N05    53.98  30.0  1
 82V  Var_10    O08  C09  C10  N05   -55.01  30.0  1
 82V  Var_11    O24  C23  C22  O21   -60.25  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
 82V  plan-1  C13  0.020
 82V  plan-1  C15  0.020
 82V  plan-1  C17  0.020
 82V  plan-1  C02  0.020
 82V  plan-1  O11  0.020
 82V  plan-1  C12  0.020
 82V  plan-1  S14  0.020
 82V  plan-1  C16  0.020
 82V  plan-1  H3   0.020
 82V  plan-2  C17  0.020
 82V  plan-2  C20  0.020
 82V  plan-2  C26  0.020
 82V  plan-2  C16  0.020
 82V  plan-2  C18  0.020
 82V  plan-2  C19  0.020
 82V  plan-2  O21  0.020
 82V  plan-2  O24  0.020
 82V  plan-2  C25  0.020
 82V  plan-2  H6   0.020
 82V  plan-2  H17  0.020
 82V  plan-2  H18  0.020
 82V  plan-3  C13  0.020
 82V  plan-3  C02  0.020
 82V  plan-3  C03  0.020
 82V  plan-3  O01  0.020
 82V  plan-4  C10  0.020
 82V  plan-4  C04  0.020
 82V  plan-4  N05  0.020
 82V  plan-4  C06  0.020

