# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 21:41:03 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON1C(=O)Nc2sc(Cc3ccccc3)cc2C1=O
#
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
 ZW2  ZW2  6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione  ligand  29  19  .  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_ZW2
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
 ZW2  C1   C  CR6   0   0.564   2.6721  -0.9331  -0.8654
 ZW2  C10  C  CR16  0  -0.240  -4.3698  -1.3289   1.3038
 ZW2  C11  C  CR16  0  -0.268  -5.1855  -0.2419   1.5998
 ZW2  C12  C  CR16  0  -0.239  -5.0722   0.9239   0.8568
 ZW2  C13  C  CR16  0  -0.314  -4.1471   1.0035  -0.1784
 ZW2  C2   C  CR56  0  -0.069   1.3561  -0.3637  -0.7186
 ZW2  C3   C  CR56  0   0.113   1.1414   0.6182   0.2092
 ZW2  C4   C  CR6   0   0.692   3.4057   0.6187   0.9689
 ZW2  C5   C  CR15  0  -0.239   0.1710  -0.6948  -1.4423
 ZW2  C6   C  CR5   0  -0.127  -0.9000   0.0349  -1.0569
 ZW2  C7   C  CH2   0  -0.579  -2.3000   0.0125  -1.5799
 ZW2  C8   C  CR6   0   0.105  -3.3271  -0.0778  -0.4795
 ZW2  C9   C  CR16  0  -0.279  -3.4460  -1.2447   0.2736
 ZW2  N1   N  NR6   0  -0.318   3.6026  -0.3802   0.0221
 ZW2  N2   N  NR16  0  -0.732   2.1228   1.0923   1.0217
 ZW2  O1   O  OH1   0  -0.514   4.8830  -0.7972  -0.1106
 ZW2  O2   O  O     0  -0.428   2.9900  -1.8003  -1.6485
 ZW2  O3   O  O     0  -0.454   4.2899   1.0261   1.6838
 ZW2  S    S  S2    0   0.277  -0.4859   1.1511   0.2245
 ZW2  H2   H  HCR6  0   0.257  -5.9054  -0.3057   2.4053
 ZW2  H3   H  HCR6  0   0.257  -5.7040   1.7740   1.0801
 ZW2  H4   H  HCR6  0   0.253  -4.0667   1.9160  -0.7576
 ZW2  H5   H  HCR5  0   0.277   0.1288  -1.4472  -2.2166
 ZW2  H6   H  HCH2  0   0.283  -2.4831   0.9048  -2.1849
 ZW2  H7   H  HCH2  0   0.284  -2.3869  -0.8428  -2.2537
 ZW2  H8   H  HCR6  0   0.251  -2.8089  -2.0928   0.0498
 ZW2  H9   H  HNR6  0   0.443   1.9359   1.8110   1.7071
 ZW2  H10  H  HOH1  0   0.489   4.9907  -1.5595   0.4768
 ZW2  H1   H  HCR6  0   0.256  -4.4548  -2.2429   1.8776

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
 ZW2  C12  C13  aromatic  1.391  0.020  1.391
 ZW2  C12  C11  aromatic  1.387  0.020  1.387
 ZW2  C13  C8   aromatic  1.390  0.020  1.390
 ZW2  C11  C10  aromatic  1.391  0.020  1.391
 ZW2  C8   C7   single    1.508  0.020  1.508
 ZW2  C8   C9   aromatic  1.394  0.020  1.394
 ZW2  C10  C9   aromatic  1.386  0.020  1.386
 ZW2  C7   C6   single    1.495  0.020  1.495
 ZW2  C6   S    aromatic  1.749  0.020  1.749
 ZW2  C6   C5   aromatic  1.352  0.020  1.352
 ZW2  S    C3   aromatic  1.712  0.020  1.712
 ZW2  C5   C2   aromatic  1.428  0.020  1.428
 ZW2  C3   C2   aromatic  1.368  0.020  1.368
 ZW2  C3   N2   single    1.360  0.020  1.360
 ZW2  C2   C1   single    1.441  0.020  1.441
 ZW2  N2   C4   single    1.368  0.020  1.368
 ZW2  C1   O2   double    1.211  0.020  1.211
 ZW2  C1   N1   single    1.400  0.020  1.400
 ZW2  C4   N1   single    1.390  0.020  1.390
 ZW2  C4   O3   double    1.208  0.020  1.208
 ZW2  N1   O1   single    1.353  0.020  1.353
 ZW2  C10  H1   single    0.930  0.020  1.080
 ZW2  C11  H2   single    0.930  0.020  1.080
 ZW2  C12  H3   single    0.930  0.020  1.080
 ZW2  C13  H4   single    0.930  0.020  1.080
 ZW2  C5   H5   single    0.930  0.020  1.080
 ZW2  C7   H6   single    0.970  0.020  1.090
 ZW2  C7   H7   single    0.970  0.020  1.090
 ZW2  C9   H8   single    0.930  0.020  1.080
 ZW2  N2   H9   single    0.860  0.020  1.020
 ZW2  O1   H10  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
 ZW2  O2   C1   N1   121.23  3.000
 ZW2  N1   C1   C2   112.73  3.000
 ZW2  O2   C1   C2   126.04  3.000
 ZW2  H1   C10  C9   119.83  3.000
 ZW2  H1   C10  C11  120.07  3.000
 ZW2  C9   C10  C11  120.10  3.000
 ZW2  H2   C11  C12  120.18  3.000
 ZW2  H2   C11  C10  120.16  3.000
 ZW2  C12  C11  C10  119.67  3.000
 ZW2  H3   C12  C13  119.79  3.000
 ZW2  H3   C12  C11  120.12  3.000
 ZW2  C13  C12  C11  120.08  3.000
 ZW2  H4   C13  C8   119.69  3.000
 ZW2  H4   C13  C12  119.70  3.000
 ZW2  C8   C13  C12  120.61  3.000
 ZW2  C5   C2   C3   112.34  3.000
 ZW2  C3   C2   C1   119.74  3.000
 ZW2  C5   C2   C1   127.93  3.000
 ZW2  S    C3   N2   124.90  3.000
 ZW2  N2   C3   C2   122.85  3.000
 ZW2  S    C3   C2   112.25  3.000
 ZW2  O3   C4   N2   123.14  3.000
 ZW2  O3   C4   N1   122.80  3.000
 ZW2  N2   C4   N1   114.06  3.000
 ZW2  H5   C5   C6   123.31  3.000
 ZW2  H5   C5   C2   123.87  3.000
 ZW2  C6   C5   C2   112.82  3.000
 ZW2  S    C6   C7   119.19  3.000
 ZW2  S    C6   C5   111.45  3.000
 ZW2  C7   C6   C5   129.35  3.000
 ZW2  H7   C7   H6   106.52  3.000
 ZW2  H7   C7   C8   110.43  3.000
 ZW2  H6   C7   C8   109.79  3.000
 ZW2  H7   C7   C6   107.58  3.000
 ZW2  H6   C7   C6   109.77  3.000
 ZW2  C8   C7   C6   112.55  3.000
 ZW2  C9   C8   C7   120.17  3.000
 ZW2  C9   C8   C13  118.93  3.000
 ZW2  C7   C8   C13  120.88  3.000
 ZW2  H8   C9   C8   119.55  3.000
 ZW2  H8   C9   C10  119.84  3.000
 ZW2  C8   C9   C10  120.61  3.000
 ZW2  O1   N1   C4   114.97  3.000
 ZW2  O1   N1   C1   116.44  3.000
 ZW2  C4   N1   C1   128.42  3.000
 ZW2  H9   N2   C4   116.47  3.000
 ZW2  H9   N2   C3   121.32  3.000
 ZW2  C4   N2   C3   122.21  3.000
 ZW2  H10  O1   N1   106.76  3.000
 ZW2  C6   S    C3    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
 ZW2  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 ZW2  CONST_02  C13  C8   C9   C10    0.00   0.0  0
 ZW2  CONST_03  C8   C13  C12  C11    0.00   0.0  0
 ZW2  CONST_04  C8   C9   C10  C11    0.00   0.0  0
 ZW2  CONST_05  C9   C8   C13  C12    0.00   0.0  0
 ZW2  CONST_06  C9   C10  C11  C12    0.00   0.0  0
 ZW2  CONST_07  S    C6   C5   C2     0.00   0.0  0
 ZW2  CONST_08  C6   S    C3   C2     0.00   0.0  0
 ZW2  CONST_09  C5   C6   S    C3     0.00   0.0  0
 ZW2  CONST_10  C6   C5   C2   C3     0.00   0.0  0
 ZW2  CONST_11  S    C3   C2   C5     0.00   0.0  0
 ZW2  CONST_12  N2   C4   N1   C1     0.00   0.0  0
 ZW2  CONST_13  C4   N1   C1   C2     0.00   0.0  0
 ZW2  CONST_14  N1   C4   N2   C3     0.00   0.0  0
 ZW2  CONST_15  C7   C8   C9   C10  180.00   0.0  0
 ZW2  CONST_16  C7   C8   C13  C12  180.00   0.0  0
 ZW2  CONST_17  C7   C6   C5   C2   180.00   0.0  0
 ZW2  CONST_18  C7   C6   S    C3   180.00   0.0  0
 ZW2  CONST_19  O3   C4   N1   C1   180.00   0.0  0
 ZW2  CONST_20  O1   N1   C1   C2   180.00   0.0  0
 ZW2  CONST_21  O3   C4   N2   C3   180.00   0.0  0
 ZW2  CONST_22  O2   C1   N1   C4   180.00   0.0  0
 ZW2  CONST_23  O1   N1   C4   N2   180.00   0.0  0
 ZW2  CONST_24  H5   C5   C2   C1     0.00   0.0  0
 ZW2  CONST_25  H3   C12  C11  C10  180.00   0.0  0
 ZW2  CONST_26  H4   C13  C12  C11  180.00   0.0  0
 ZW2  CONST_27  H8   C9   C10  C11  180.00   0.0  0
 ZW2  CONST_28  H1   C10  C11  C12  180.00   0.0  0
 ZW2  CONST_29  H2   C11  C12  C13  180.00   0.0  0
 ZW2  CONST_30  H9   N2   C4   N1   180.00   0.0  0
 ZW2  CONST_31  O2   C1   N1   O1     0.00   0.0  0
 ZW2  CONST_32  O3   C4   N1   O1     0.00   0.0  0
 ZW2  Var_01    C6   C7   C8   C13  109.78  30.0  2
 ZW2  Var_02    C8   C7   C6   C5   131.37  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
 ZW2  plan-1  C10  0.020
 ZW2  plan-1  C11  0.020
 ZW2  plan-1  C12  0.020
 ZW2  plan-1  C13  0.020
 ZW2  plan-1  C7   0.020
 ZW2  plan-1  C8   0.020
 ZW2  plan-1  C9   0.020
 ZW2  plan-1  H2   0.020
 ZW2  plan-1  H3   0.020
 ZW2  plan-1  H4   0.020
 ZW2  plan-1  H8   0.020
 ZW2  plan-1  H1   0.020
 ZW2  plan-2  C1   0.020
 ZW2  plan-2  C2   0.020
 ZW2  plan-2  C3   0.020
 ZW2  plan-2  C4   0.020
 ZW2  plan-2  C5   0.020
 ZW2  plan-2  C6   0.020
 ZW2  plan-2  C7   0.020
 ZW2  plan-2  N1   0.020
 ZW2  plan-2  N2   0.020
 ZW2  plan-2  O1   0.020
 ZW2  plan-2  O2   0.020
 ZW2  plan-2  O3   0.020
 ZW2  plan-2  S    0.020
 ZW2  plan-2  H5   0.020
 ZW2  plan-2  H9   0.020

