# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 19:30:14 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-hydroxy-4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccc(cc1)c2csc3C(=O)C=C(Oc23)N4CCOCC4
#
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
 82Y  82Y  N-hydroxy-4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzamide  ligand  42  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_82Y
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
 82Y  C10  C  CR16  0  -0.260   2.8226  -0.2601   0.7620
 82Y  C15  C  CR56  0   0.370  -1.3225   1.3094   0.0600
 82Y  C17  C  CR6   0   0.699  -2.5970  -0.6282   0.0161
 82Y  C22  C  CH2   0  -0.325  -3.7042  -2.7789  -0.0665
 82Y  C26  C  CH2   0  -0.329  -1.2968  -2.6777   0.3662
 82Y  O01  O  OH1   0  -0.539   6.8822  -1.3889   1.0063
 82Y  N02  N  NH1   0  -0.384   5.5876  -0.9676   0.9397
 82Y  C03  C  C     0   0.501   5.1828  -0.3017  -0.1652
 82Y  O04  O  O     0  -0.457   5.8606  -0.1911  -1.1700
 82Y  C05  C  CR6   0  -0.072   3.8090   0.2737  -0.0642
 82Y  C06  C  CR16  0  -0.247   3.4988   1.3722  -0.8613
 82Y  C07  C  CR16  0  -0.290   2.2363   1.9359  -0.8206
 82Y  C08  C  CR6   0   0.100   1.2466   1.4088   0.0099
 82Y  C09  C  CR16  0  -0.297   1.5574   0.3021   0.7999
 82Y  C11  C  CR5   0   0.151  -0.0884   2.0181   0.0480
 82Y  C12  C  CR15  0  -0.554  -0.3408   3.3624   0.0567
 82Y  S13  S  S2    0   0.284  -2.0064   3.7551   0.0883
 82Y  C14  C  CR56  0  -0.434  -2.4348   2.0957   0.0806
 82Y  O16  O  O     0  -0.466  -1.3924  -0.0303   0.0160
 82Y  C18  C  CR16  0  -0.625  -3.7599   0.1001   0.0828
 82Y  C19  C  CR6   0   0.486  -3.7730   1.5354   0.0974
 82Y  O20  O  O     0  -0.475  -4.7836   2.2346   0.1397
 82Y  N21  N  NT    0  -0.525  -2.4959  -1.9682  -0.0794
 82Y  C23  C  CH2   0  -0.188  -3.4491  -4.1087  -0.7526
 82Y  O24  O  O2    0  -0.478  -2.3412  -4.7826  -0.2074
 82Y  C25  C  CH2   0  -0.193  -1.1791  -4.0029  -0.3593
 82Y  H1   H  HCR6  0   0.270   3.0181  -1.1306   1.3749
 82Y  H3   H  HCH2  0   0.251  -4.0505  -2.9326   0.9622
 82Y  H4   H  HCH2  0   0.273  -4.4959  -2.2729  -0.6163
 82Y  H5   H  HCH2  0   0.274  -0.4023  -2.0961   0.1591
 82Y  H6   H  HCH2  0   0.250  -1.3483  -2.8444   1.4486
 82Y  H7   H  HOH1  0   0.480   6.8584  -2.3416   0.8511
 82Y  H8   H  HNH1  0   0.418   5.1744  -0.7798   1.8424
 82Y  H9   H  HCR6  0   0.268   4.2465   1.7916  -1.5208
 82Y  H10  H  HCR6  0   0.264   2.0141   2.7831  -1.4568
 82Y  H11  H  HCR6  0   0.263   0.8192  -0.1227   1.4668
 82Y  H12  H  HCR5  0   0.313   0.3940   4.1533   0.0664
 82Y  H13  H  HCR6  0   0.284  -4.7086  -0.4124   0.1361
 82Y  H16  H  HCH2  0   0.253  -4.3244  -4.7468  -0.6284
 82Y  H17  H  HCH2  0   0.215  -3.3047  -3.9385  -1.8284
 82Y  H18  H  HCH2  0   0.216  -0.9721  -3.8217  -1.4229
 82Y  H19  H  HCH2  0   0.252  -0.3422  -4.5640   0.0574

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
 82Y  O01  N02  single    1.363  0.020  1.363
 82Y  C25  O24  single    1.408  0.020  1.408
 82Y  C25  C26  single    1.515  0.020  1.515
 82Y  O04  C03  double    1.217  0.020  1.217
 82Y  N02  C03  single    1.352  0.020  1.352
 82Y  O24  C23  single    1.407  0.020  1.407
 82Y  C03  C05  single    1.493  0.020  1.493
 82Y  C23  C22  single    1.518  0.020  1.518
 82Y  C26  N21  single    1.463  0.020  1.463
 82Y  C05  C06  aromatic  1.392  0.020  1.392
 82Y  C05  C10  aromatic  1.393  0.020  1.393
 82Y  C06  C07  aromatic  1.383  0.020  1.383
 82Y  C10  C09  aromatic  1.385  0.020  1.385
 82Y  N21  C22  single    1.455  0.020  1.455
 82Y  N21  C17  single    1.347  0.020  1.347
 82Y  O16  C17  single    1.345  0.020  1.345
 82Y  O16  C15  single    1.342  0.020  1.342
 82Y  C17  C18  double    1.374  0.020  1.374
 82Y  C07  C08  aromatic  1.395  0.020  1.395
 82Y  C09  C08  aromatic  1.395  0.020  1.395
 82Y  C08  C11  single    1.468  0.020  1.468
 82Y  C18  C19  single    1.435  0.020  1.435
 82Y  C15  C11  aromatic  1.423  0.020  1.423
 82Y  C15  C14  aromatic  1.362  0.020  1.362
 82Y  C11  C12  aromatic  1.368  0.020  1.368
 82Y  C19  C14  single    1.451  0.020  1.451
 82Y  C19  O20  double    1.230  0.020  1.230
 82Y  C14  S13  aromatic  1.714  0.020  1.714
 82Y  C12  S13  aromatic  1.712  0.020  1.712
 82Y  C10  H1   single    0.930  0.020  1.080
 82Y  C22  H3   single    0.970  0.020  1.090
 82Y  C22  H4   single    0.970  0.020  1.090
 82Y  C26  H5   single    0.970  0.020  1.090
 82Y  C26  H6   single    0.970  0.020  1.090
 82Y  O01  H7   single    0.850  0.020  0.980
 82Y  N02  H8   single    0.890  0.020  1.040
 82Y  C06  H9   single    0.930  0.020  1.080
 82Y  C07  H10  single    0.930  0.020  1.080
 82Y  C09  H11  single    0.930  0.020  1.080
 82Y  C12  H12  single    0.930  0.020  1.080
 82Y  C18  H13  single    0.930  0.020  1.080
 82Y  C23  H16  single    0.970  0.020  1.090
 82Y  C23  H17  single    0.970  0.020  1.090
 82Y  C25  H18  single    0.970  0.020  1.090
 82Y  C25  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
 82Y  H1   C10  C09  118.42  3.000
 82Y  H1   C10  C05  121.07  3.000
 82Y  C09  C10  C05  120.50  3.000
 82Y  O16  C15  C14  122.28  3.000
 82Y  C14  C15  C11  114.88  3.000
 82Y  O16  C15  C11  122.81  3.000
 82Y  N21  C17  C18  126.46  3.000
 82Y  C18  C17  O16  121.50  3.000
 82Y  N21  C17  O16  112.03  3.000
 82Y  H4   C22  H3   108.02  3.000
 82Y  H4   C22  C23  107.53  3.000
 82Y  H3   C22  C23  110.76  3.000
 82Y  H4   C22  N21  109.90  3.000
 82Y  H3   C22  N21  110.41  3.000
 82Y  C23  C22  N21  110.16  3.000
 82Y  H6   C26  H5   107.95  3.000
 82Y  H6   C26  C25  110.08  3.000
 82Y  H5   C26  C25  108.23  3.000
 82Y  H6   C26  N21  109.63  3.000
 82Y  H5   C26  N21  110.92  3.000
 82Y  C25  C26  N21  110.00  3.000
 82Y  H7   O01  N02  105.88  3.000
 82Y  H8   N02  C03  121.07  3.000
 82Y  H8   N02  O01  113.71  3.000
 82Y  C03  N02  O01  118.46  3.000
 82Y  C05  C03  O04  122.24  3.000
 82Y  C05  C03  N02  114.21  3.000
 82Y  O04  C03  N02  123.55  3.000
 82Y  C06  C05  C03  118.06  3.000
 82Y  C06  C05  C10  118.96  3.000
 82Y  C03  C05  C10  122.96  3.000
 82Y  H9   C06  C07  119.40  3.000
 82Y  H9   C06  C05  120.06  3.000
 82Y  C07  C06  C05  120.53  3.000
 82Y  H10  C07  C08  119.99  3.000
 82Y  H10  C07  C06  119.27  3.000
 82Y  C08  C07  C06  120.73  3.000
 82Y  C11  C08  C09  121.15  3.000
 82Y  C11  C08  C07  120.25  3.000
 82Y  C09  C08  C07  118.60  3.000
 82Y  H11  C09  C08  120.58  3.000
 82Y  H11  C09  C10  118.74  3.000
 82Y  C08  C09  C10  120.67  3.000
 82Y  C12  C11  C08  125.16  3.000
 82Y  C12  C11  C15  109.23  3.000
 82Y  C08  C11  C15  125.60  3.000
 82Y  H12  C12  S13  119.62  3.000
 82Y  H12  C12  C11  126.47  3.000
 82Y  S13  C12  C11  113.90  3.000
 82Y  C14  S13  C12   91.20  3.000
 82Y  C19  C14  S13  127.19  3.000
 82Y  S13  C14  C15  110.78  3.000
 82Y  C19  C14  C15  122.03  3.000
 82Y  C17  O16  C15  119.37  3.000
 82Y  H13  C18  C19  117.78  3.000
 82Y  H13  C18  C17  119.65  3.000
 82Y  C19  C18  C17  122.57  3.000
 82Y  O20  C19  C18  125.20  3.000
 82Y  O20  C19  C14  122.61  3.000
 82Y  C18  C19  C14  112.19  3.000
 82Y  C26  N21  C22  114.06  3.000
 82Y  C22  N21  C17  119.43  3.000
 82Y  C26  N21  C17  121.49  3.000
 82Y  H17  C23  H16  107.92  3.000
 82Y  H17  C23  O24  110.50  3.000
 82Y  H16  C23  O24  107.93  3.000
 82Y  H17  C23  C22  109.20  3.000
 82Y  H16  C23  C22  109.04  3.000
 82Y  O24  C23  C22  112.14  3.000
 82Y  C25  O24  C23  110.06  3.000
 82Y  H19  C25  H18  108.07  3.000
 82Y  H19  C25  O24  107.90  3.000
 82Y  H18  C25  O24  110.58  3.000
 82Y  H19  C25  C26  109.06  3.000
 82Y  H18  C25  C26  109.51  3.000
 82Y  O24  C25  C26  111.63  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
 82Y  CONST_01  C07  C06  C05  C10     0.00   0.0  0
 82Y  CONST_02  C07  C08  C09  C10     0.00   0.0  0
 82Y  CONST_03  C11  C08  C09  C10   180.00   0.0  0
 82Y  CONST_06  S13  C12  C11  C15     0.00   0.0  0
 82Y  CONST_07  C12  S13  C14  C15     0.00   0.0  0
 82Y  CONST_08  C08  C07  C06  C05     0.00   0.0  0
 82Y  CONST_09  C08  C09  C10  C05     0.00   0.0  0
 82Y  CONST_10  C09  C10  C05  C06     0.00   0.0  0
 82Y  CONST_11  C09  C08  C07  C06     0.00   0.0  0
 82Y  CONST_12  C11  C08  C07  C06   180.00   0.0  0
 82Y  CONST_14  C14  C15  C11  C08   180.00   0.0  0
 82Y  CONST_15  S13  C12  C11  C08   180.00   0.0  0
 82Y  CONST_17  S13  C14  C15  C11     0.00   0.0  0
 82Y  CONST_18  C14  S13  C12  C11     0.00   0.0  0
 82Y  CONST_19  C14  C15  C11  C12     0.00   0.0  0
 82Y  CONST_20  O16  C15  C11  C08     0.00   0.0  0
 82Y  CONST_21  C07  C06  C05  C03   180.00   0.0  0
 82Y  CONST_22  C09  C10  C05  C03   180.00   0.0  0
 82Y  CONST_23  H9   C06  C05  C10   180.00   0.0  0
 82Y  CONST_24  H12  C12  C11  C15   180.00   0.0  0
 82Y  CONST_25  H10  C07  C06  C05   180.00   0.0  0
 82Y  CONST_26  H11  C09  C10  C05   180.00   0.0  0
 82Y  CONST_27  H1   C10  C05  C06   180.00   0.0  0
 82Y  CONST_28  C05  C03  N02  O01   180.00   0.0  0
 82Y  CONST_30  O04  C03  N02  O01     0.00   0.0  0
 82Y  Var_01    N21  C17  O16  C15   177.77  30.0  1
 82Y  Var_02    C18  C19  C14  C15    -0.30  30.0  1
 82Y  Var_03    C25  C26  N21  C17  -155.81  30.0  1
 82Y  Var_04    C23  C22  N21  C17   155.96  30.0  1
 82Y  Var_05    C11  C15  O16  C17  -179.27  30.0  1
 82Y  Var_06    C14  C19  C18  C17    -1.97  30.0  1
 82Y  Var_07    O16  C17  N21  C22   178.77  30.0  2
 82Y  Var_08    C19  C18  C17  O16     2.79  30.0  1
 82Y  Var_09    O24  C25  C26  N21   -54.99  30.0  1
 82Y  Var_10    O24  C23  C22  N21    53.81  30.0  1
 82Y  Var_11    O04  C03  C05  C10   152.34  30.0  2

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
 82Y  plan-1  C10  0.020
 82Y  plan-1  C03  0.020
 82Y  plan-1  C05  0.020
 82Y  plan-1  C06  0.020
 82Y  plan-1  C07  0.020
 82Y  plan-1  C08  0.020
 82Y  plan-1  C09  0.020
 82Y  plan-1  C11  0.020
 82Y  plan-1  H1   0.020
 82Y  plan-1  H9   0.020
 82Y  plan-1  H10  0.020
 82Y  plan-1  H11  0.020
 82Y  plan-2  C15  0.020
 82Y  plan-2  C08  0.020
 82Y  plan-2  C11  0.020
 82Y  plan-2  C12  0.020
 82Y  plan-2  S13  0.020
 82Y  plan-2  C14  0.020
 82Y  plan-2  O16  0.020
 82Y  plan-2  C19  0.020
 82Y  plan-2  H12  0.020
 82Y  plan-3  O01  0.020
 82Y  plan-3  N02  0.020
 82Y  plan-3  C03  0.020
 82Y  plan-3  O04  0.020
 82Y  plan-3  C05  0.020
 82Y  plan-3  H8   0.020
 82Y  plan-4  C14  0.020
 82Y  plan-4  C18  0.020
 82Y  plan-4  C19  0.020
 82Y  plan-4  O20  0.020
 82Y  plan-5  C17  0.020
 82Y  plan-5  C22  0.020
 82Y  plan-5  C26  0.020
 82Y  plan-5  N21  0.020

