# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:39:48 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CNC(=O)C2=Nc3sccc3C(=O)N2)c1
#
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
 WLL  WLL  N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide  ligand  35  22  .  2022-07-22  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_WLL
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
 WLL  C19  C  CR16  0  -0.226   3.9174  -0.0365   1.7674
 WLL  C20  C  CR16  0  -0.318   2.9255   0.6682   1.1111
 WLL  C18  C  CR16  0  -0.395   4.9680  -0.6261   1.0693
 WLL  C10  C  CR15  0  -0.177  -5.2301  -1.0793   0.2747
 WLL  C16  C  CR16  0  -0.404   4.0102   0.2022  -0.9815
 WLL  C9   C  CR15  0  -0.462  -5.0464  -2.1787  -0.4985
 WLL  C6   C  CR56  0  -0.062  -4.0672  -0.2644   0.3157
 WLL  C15  C  CR6   0   0.140   2.9722   0.7882  -0.2789
 WLL  C17  C  CR6   0   0.399   5.0174  -0.5033  -0.3152
 WLL  C7   C  CR56  0  -0.023  -3.0251  -0.7773  -0.4353
 WLL  C4   C  CR6   0   0.545  -3.8683   0.9795   1.0181
 WLL  C2   C  CR6   0   0.414  -1.6434   0.8974   0.0522
 WLL  C11  C  C     0   0.526  -0.3314   1.6384  -0.0247
 WLL  C22  C  CH3   0  -0.436   7.0560  -1.7062  -0.4713
 WLL  C14  C  CH2   0  -0.386   1.9106   1.5662  -1.0165
 WLL  N1   N  N     0  -0.451  -1.8059  -0.2149  -0.5806
 WLL  N3   N  NR16  0  -0.696  -2.5903   1.4847   0.8124
 WLL  N13  N  NH1   0  -0.622   0.5814   1.0453  -0.7884
 WLL  O12  O  O     0  -0.475  -0.1967   2.6879   0.5853
 WLL  O21  O  O2    0  -0.472   5.9842  -1.0257  -1.0929
 WLL  S8   S  S2    0   0.259  -3.4689  -2.2569  -1.1919
 WLL  H1   H  HCR6  0   0.259   3.8867  -0.1321   2.8452
 WLL  H2   H  HCR6  0   0.249   2.1254   1.1311   1.6749
 WLL  H3   H  HCR6  0   0.279   5.7269  -1.1668   1.6178
 WLL  H4   H  HCR5  0   0.283  -6.1507  -0.8561   0.7931
 WLL  H5   H  HCR6  0   0.260   4.0541   0.2874  -2.0616
 WLL  H6   H  HCR5  0   0.311  -5.7583  -2.9621  -0.7077
 WLL  H7   H  HCH3  0   0.259   7.7317  -2.0103  -1.2669
 WLL  H8   H  HCH3  0   0.229   7.5988  -1.0618   0.2253
 WLL  H9   H  HCH3  0   0.228   6.7207  -2.5985   0.0640
 WLL  H10  H  HCH2  0   0.276   1.9261   2.6115  -0.7086
 WLL  H11  H  HCH2  0   0.281   2.1085   1.5460  -2.0887
 WLL  H12  H  HNR6  0   0.434  -2.3497   2.3639   1.2590
 WLL  H13  H  HNH1  0   0.420   0.3364   0.1618  -1.2123
 WLL  O5   O  O     0  -0.447  -4.6780   1.5603   1.7148

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
 WLL  C22  O21  single    1.414  0.020  1.414
 WLL  O21  C17  single    1.346  0.020  1.346
 WLL  C17  C18  aromatic  1.391  0.020  1.391
 WLL  C17  C16  aromatic  1.399  0.020  1.399
 WLL  C18  C19  aromatic  1.392  0.020  1.392
 WLL  C16  C15  aromatic  1.384  0.020  1.384
 WLL  C19  C20  aromatic  1.382  0.020  1.382
 WLL  C15  C20  aromatic  1.396  0.020  1.396
 WLL  C15  C14  single    1.509  0.020  1.509
 WLL  C14  N13  single    1.446  0.020  1.446
 WLL  O12  C11  double    1.221  0.020  1.221
 WLL  N13  C11  single    1.330  0.020  1.330
 WLL  C11  C2   single    1.509  0.020  1.509
 WLL  C2   N3   single    1.349  0.020  1.349
 WLL  C2   N1   double    1.290  0.020  1.290
 WLL  N3   C4   single    1.389  0.020  1.389
 WLL  N1   C7   single    1.350  0.020  1.350
 WLL  C4   O5   double    1.216  0.020  1.216
 WLL  C4   C6   single    1.442  0.020  1.442
 WLL  C7   C6   aromatic  1.383  0.020  1.383
 WLL  C7   S8   aromatic  1.720  0.020  1.720
 WLL  C6   C10  aromatic  1.421  0.020  1.421
 WLL  C10  C9   aromatic  1.357  0.020  1.357
 WLL  S8   C9   aromatic  1.725  0.020  1.725
 WLL  C19  H1   single    0.930  0.020  1.080
 WLL  C20  H2   single    0.930  0.020  1.080
 WLL  C18  H3   single    0.930  0.020  1.080
 WLL  C10  H4   single    0.930  0.020  1.080
 WLL  C16  H5   single    0.930  0.020  1.080
 WLL  C9   H6   single    0.930  0.020  1.080
 WLL  C22  H7   single    0.970  0.020  1.090
 WLL  C22  H8   single    0.970  0.020  1.090
 WLL  C22  H9   single    0.970  0.020  1.090
 WLL  C14  H10  single    0.970  0.020  1.090
 WLL  C14  H11  single    0.970  0.020  1.090
 WLL  N3   H12  single    0.860  0.020  1.020
 WLL  N13  H13  single    0.860  0.020  1.020

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
 WLL  H1   C19  C18  118.89  3.000
 WLL  H1   C19  C20  119.83  3.000
 WLL  C18  C19  C20  121.28  3.000
 WLL  H2   C20  C15  120.43  3.000
 WLL  H2   C20  C19  120.06  3.000
 WLL  C15  C20  C19  119.51  3.000
 WLL  H3   C18  C17  121.61  3.000
 WLL  H3   C18  C19  119.15  3.000
 WLL  C17  C18  C19  119.25  3.000
 WLL  H4   C10  C6   124.43  3.000
 WLL  H4   C10  C9   123.81  3.000
 WLL  C6   C10  C9   111.75  3.000
 WLL  H5   C16  C17  119.01  3.000
 WLL  H5   C16  C15  120.19  3.000
 WLL  C17  C16  C15  120.80  3.000
 WLL  H6   C9   S8   119.51  3.000
 WLL  H6   C9   C10  127.56  3.000
 WLL  S8   C9   C10  112.93  3.000
 WLL  C4   C6   C7   118.70  3.000
 WLL  C7   C6   C10  112.85  3.000
 WLL  C4   C6   C10  128.44  3.000
 WLL  C14  C15  C16  119.87  3.000
 WLL  C14  C15  C20  120.50  3.000
 WLL  C16  C15  C20  119.62  3.000
 WLL  O21  C17  C16  115.96  3.000
 WLL  C16  C17  C18  119.55  3.000
 WLL  O21  C17  C18  124.49  3.000
 WLL  S8   C7   N1   122.95  3.000
 WLL  S8   C7   C6   111.31  3.000
 WLL  N1   C7   C6   125.74  3.000
 WLL  O5   C4   N3   121.58  3.000
 WLL  O5   C4   C6   126.81  3.000
 WLL  N3   C4   C6   111.61  3.000
 WLL  N3   C2   N1   124.30  3.000
 WLL  N1   C2   C11  120.53  3.000
 WLL  N3   C2   C11  115.17  3.000
 WLL  O12  C11  N13  126.47  3.000
 WLL  N13  C11  C2   114.03  3.000
 WLL  O12  C11  C2   119.50  3.000
 WLL  H9   C22  H8   108.75  3.000
 WLL  H9   C22  H7   108.70  3.000
 WLL  H8   C22  H7   108.82  3.000
 WLL  H9   C22  O21  112.06  3.000
 WLL  H8   C22  O21  111.90  3.000
 WLL  H7   C22  O21  106.51  3.000
 WLL  H11  C14  H10  107.04  3.000
 WLL  H11  C14  N13  108.38  3.000
 WLL  H10  C14  N13  108.31  3.000
 WLL  H11  C14  C15  110.08  3.000
 WLL  H10  C14  C15  110.27  3.000
 WLL  N13  C14  C15  112.58  3.000
 WLL  C2   N1   C7   114.84  3.000
 WLL  H12  N3   C2   117.30  3.000
 WLL  H12  N3   C4   117.90  3.000
 WLL  C2   N3   C4   124.80  3.000
 WLL  H13  N13  C14  118.16  3.000
 WLL  H13  N13  C11  117.69  3.000
 WLL  C14  N13  C11  124.13  3.000
 WLL  C22  O21  C17  118.51  3.000
 WLL  C7   S8   C9    91.16  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
 WLL  CONST_01  C16  C17  C18  C19     0.00   0.0  0
 WLL  CONST_02  C16  C15  C20  C19     0.00   0.0  0
 WLL  CONST_03  C17  C18  C19  C20     0.00   0.0  0
 WLL  CONST_04  C17  C16  C15  C20     0.00   0.0  0
 WLL  CONST_05  C15  C16  C17  C18     0.00   0.0  0
 WLL  CONST_06  C15  C20  C19  C18     0.00   0.0  0
 WLL  CONST_07  S8   C7   C6   C10     0.00   0.0  0
 WLL  CONST_08  C7   S8   C9   C10     0.00   0.0  0
 WLL  CONST_09  C7   C6   C10  C9      0.00   0.0  0
 WLL  CONST_10  C6   C7   S8   C9      0.00   0.0  0
 WLL  CONST_11  S8   C9   C10  C6      0.00   0.0  0
 WLL  CONST_12  C2   N3   C4   C6      0.00   0.0  0
 WLL  CONST_13  N3   C2   N1   C7      0.00   0.0  0
 WLL  CONST_14  N1   C2   N3   C4      0.00   0.0  0
 WLL  CONST_15  O21  C17  C18  C19   180.00   0.0  0
 WLL  CONST_16  C14  C15  C20  C19   180.00   0.0  0
 WLL  CONST_17  O21  C17  C16  C15   180.00   0.0  0
 WLL  CONST_18  C14  C15  C16  C17   180.00   0.0  0
 WLL  CONST_19  C11  C2   N1   C7    180.00   0.0  0
 WLL  CONST_20  C11  C2   N3   C4    180.00   0.0  0
 WLL  CONST_21  O5   C4   N3   C2    180.00   0.0  0
 WLL  CONST_22  H3   C18  C19  C20   180.00   0.0  0
 WLL  CONST_23  H5   C16  C15  C20   180.00   0.0  0
 WLL  CONST_24  H2   C20  C19  C18   180.00   0.0  0
 WLL  CONST_25  H6   C9   C10  C6    180.00   0.0  0
 WLL  CONST_26  H1   C19  C20  C15   180.00   0.0  0
 WLL  CONST_27  H4   C10  C6   C7    180.00   0.0  0
 WLL  CONST_28  H12  N3   C4   C6    180.00   0.0  0
 WLL  CONST_29  C14  N13  C11  C2    180.00   0.0  0
 WLL  CONST_30  H13  N13  C11  C2      0.00   0.0  0
 WLL  CONST_31  O12  C11  N13  C14     0.00   0.0  0
 WLL  Var_01    N13  C14  C15  C20   -58.66  30.0  2
 WLL  Var_02    O12  C11  C2   N1   -179.77  30.0  2
 WLL  Var_03    C11  N13  C14  C15   106.48  30.0  3
 WLL  Var_04    H7   C22  O21  C17  -177.94  30.0  3

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
 WLL  plan-1  C19  0.020
 WLL  plan-1  C20  0.020
 WLL  plan-1  C18  0.020
 WLL  plan-1  C16  0.020
 WLL  plan-1  C15  0.020
 WLL  plan-1  C17  0.020
 WLL  plan-1  C14  0.020
 WLL  plan-1  O21  0.020
 WLL  plan-1  H1   0.020
 WLL  plan-1  H2   0.020
 WLL  plan-1  H3   0.020
 WLL  plan-1  H5   0.020
 WLL  plan-2  C10  0.020
 WLL  plan-2  C9   0.020
 WLL  plan-2  C6   0.020
 WLL  plan-2  C7   0.020
 WLL  plan-2  C4   0.020
 WLL  plan-2  C2   0.020
 WLL  plan-2  C11  0.020
 WLL  plan-2  N1   0.020
 WLL  plan-2  N3   0.020
 WLL  plan-2  S8   0.020
 WLL  plan-2  H4   0.020
 WLL  plan-2  H6   0.020
 WLL  plan-2  H12  0.020
 WLL  plan-2  O5   0.020
 WLL  plan-3  C2   0.020
 WLL  plan-3  C11  0.020
 WLL  plan-3  C14  0.020
 WLL  plan-3  N13  0.020
 WLL  plan-3  O12  0.020
 WLL  plan-3  H13  0.020

