# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 06:05:44 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-[[2-[(~{R})-azanyl(phenyl)methyl]phenyl]methyl]-2-sulfanylidene-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](c1ccccc1)c2ccccc2CN3C(=S)NC(=O)c4[nH]ccc34
#
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
 UEB  UEB  "(S)-1-(2-(amino(phenyl)methyl)benzyl)-2-thioxo-1,2,3,5-tetrahydro-4H-pyrrolo[3,2-d]pyrimidin-4-one"
  ligand  44  26  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UEB
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
 UEB  C2   C  CH1   0  -0.249  -2.4942  21.6991  14.6818
 UEB  C7   C  CR16  0  -0.269  -5.3730  24.2043  12.6625
 UEB  C8   C  CR16  0  -0.235  -4.0565  24.6241  12.7811
 UEB  C9   C  CR16  0  -0.318  -3.1179  23.8225  13.4217
 UEB  C10  C  CR6   0   0.121  -2.7298  21.8070  16.1809
 UEB  C11  C  CR16  0  -0.275  -2.4590  23.0234  16.8028
 UEB  C12  C  CR16  0  -0.250  -2.6631  23.2007  18.1609
 UEB  C13  C  CR16  0  -0.252  -3.1475  22.1458  18.9199
 UEB  C14  C  CR16  0  -0.286  -3.4160  20.9287  18.3140
 UEB  C15  C  CR6   0   0.034  -3.2075  20.7397  16.9492
 UEB  C16  C  CH2   0  -0.401  -3.4808  19.3991  16.3004
 UEB  C21  C  C     0   0.536  -4.8115  16.4037  19.0939
 UEB  C27  C  CR15  0  -0.394  -1.6298  17.6535  17.9040
 UEB  N1   N  NH2   0  -0.783  -1.1223  22.0783  14.3838
 UEB  C4   C  CR6   0   0.136  -3.4836  22.5895  13.9505
 UEB  C5   C  CR16  0  -0.296  -4.8084  22.1737  13.8217
 UEB  C6   C  CR16  0  -0.239  -5.7467  22.9721  13.1866
 UEB  N17  N  NT    0  -0.543  -3.9601  18.3908  17.2267
 UEB  C18  C  C     0   0.372  -5.2834  18.2180  17.4487
 UEB  S19  S  S1    0  -0.354  -6.4777  19.1242  16.7093
 UEB  N20  N  NH1   0  -0.693  -5.6296  17.2435  18.3376
 UEB  C23  C  CR5   0   0.153  -3.4394  16.6685  18.8223
 UEB  N24  N  NR15  0  -0.639  -2.3200  16.1000  19.3473
 UEB  C26  C  CR15  0   0.001  -1.2346  16.6842  18.8045
 UEB  C28  C  CR5   0   0.303  -3.0368  17.6339  17.9205
 UEB  H1   H  HCH1  0   0.254  -2.7073  20.6728  14.3587
 UEB  H2   H  HCR6  0   0.252  -6.1029  24.8284  12.1633
 UEB  H3   H  HCR6  0   0.250  -3.7538  25.5805  12.3739
 UEB  H4   H  HCR6  0   0.249  -2.0939  24.1603  13.5094
 UEB  H5   H  HCR6  0   0.253  -2.0861  23.8481  16.2084
 UEB  H6   H  HCR6  0   0.252  -2.4477  24.1556  18.6226
 UEB  H7   H  HCR6  0   0.255  -3.3186  22.2660  19.9818
 UEB  H8   H  HCR6  0   0.254  -3.7881  20.1209  18.9302
 UEB  H9   H  HCH2  0   0.301  -4.2232  19.4919  15.5110
 UEB  H10  H  HCH2  0   0.295  -2.5754  19.0077  15.8343
 UEB  H11  H  HCR5  0   0.282  -0.9754  18.2867  17.3284
 UEB  H12  H  HNH2  0   0.357  -0.4922  21.4713  14.8937
 UEB  H13  H  HNH2  0   0.354  -0.9363  21.9156  13.4010
 UEB  H15  H  HCR6  0   0.248  -5.1134  21.2154  14.2275
 UEB  H16  H  HCR6  0   0.252  -6.7705  22.6314  13.0981
 UEB  H17  H  HNH1  0   0.430  -6.6264  17.1328  18.4776
 UEB  H18  H  HNR5  0   0.427  -2.3070  15.3626  20.0350
 UEB  H19  H  HCR5  0   0.299  -0.2399  16.3809  19.0870
 UEB  O22  O  O     0  -0.444  -5.2776  15.5859  19.8625

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
 UEB  C7   C8   aromatic  1.387  0.020  1.387
 UEB  C7   C6   aromatic  1.390  0.020  1.390
 UEB  C8   C9   aromatic  1.391  0.020  1.391
 UEB  C6   C5   aromatic  1.386  0.020  1.386
 UEB  C9   C4   aromatic  1.390  0.020  1.390
 UEB  C5   C4   aromatic  1.394  0.020  1.394
 UEB  C4   C2   single    1.519  0.020  1.519
 UEB  N1   C2   single    1.454  0.020  1.454
 UEB  C2   C10  single    1.521  0.020  1.521
 UEB  C10  C11  aromatic  1.393  0.020  1.393
 UEB  C10  C15  aromatic  1.399  0.020  1.399
 UEB  C16  C15  single    1.514  0.020  1.514
 UEB  C16  N17  single    1.451  0.020  1.451
 UEB  C11  C12  aromatic  1.385  0.020  1.385
 UEB  C15  C14  aromatic  1.394  0.020  1.394
 UEB  S19  C18  double    1.672  0.020  1.672
 UEB  N17  C18  single    1.353  0.020  1.353
 UEB  N17  C28  single    1.381  0.020  1.381
 UEB  C18  N20  single    1.364  0.020  1.364
 UEB  C27  C28  aromatic  1.407  0.020  1.407
 UEB  C27  C26  aromatic  1.381  0.020  1.381
 UEB  C28  C23  aromatic  1.381  0.020  1.381
 UEB  C12  C13  aromatic  1.387  0.020  1.387
 UEB  C14  C13  aromatic  1.386  0.020  1.386
 UEB  N20  C21  single    1.395  0.020  1.395
 UEB  C26  N24  aromatic  1.347  0.020  1.347
 UEB  C23  C21  single    1.424  0.020  1.424
 UEB  C23  N24  aromatic  1.361  0.020  1.361
 UEB  C21  O22  double    1.215  0.020  1.215
 UEB  C2   H1   single    0.970  0.020  1.090
 UEB  C7   H2   single    0.930  0.020  1.080
 UEB  C8   H3   single    0.930  0.020  1.080
 UEB  C9   H4   single    0.930  0.020  1.080
 UEB  C11  H5   single    0.930  0.020  1.080
 UEB  C12  H6   single    0.930  0.020  1.080
 UEB  C13  H7   single    0.930  0.020  1.080
 UEB  C14  H8   single    0.930  0.020  1.080
 UEB  C16  H9   single    0.970  0.020  1.090
 UEB  C16  H10  single    0.970  0.020  1.090
 UEB  C27  H11  single    0.930  0.020  1.080
 UEB  N1   H12  single    0.890  0.020  1.040
 UEB  N1   H13  single    0.890  0.020  1.040
 UEB  C5   H15  single    0.930  0.020  1.080
 UEB  C6   H16  single    0.930  0.020  1.080
 UEB  N20  H17  single    0.860  0.020  1.020
 UEB  N24  H18  single    0.860  0.020  1.020
 UEB  C26  H19  single    0.930  0.020  1.080

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
 UEB  H1   C2   C4   106.27  3.000
 UEB  H1   C2   N1   111.52  3.000
 UEB  C4   C2   N1   111.29  3.000
 UEB  H1   C2   C10  109.06  3.000
 UEB  N1   C2   C10  109.24  3.000
 UEB  C4   C2   C10  109.40  3.000
 UEB  H2   C7   C6   120.25  3.000
 UEB  H2   C7   C8   120.33  3.000
 UEB  C6   C7   C8   119.42  3.000
 UEB  H3   C8   C9   119.59  3.000
 UEB  H3   C8   C7   120.04  3.000
 UEB  C9   C8   C7   120.37  3.000
 UEB  H4   C9   C4   119.67  3.000
 UEB  H4   C9   C8   119.75  3.000
 UEB  C4   C9   C8   120.58  3.000
 UEB  C15  C10  C11  119.17  3.000
 UEB  C15  C10  C2   122.67  3.000
 UEB  C11  C10  C2   118.16  3.000
 UEB  H5   C11  C12  119.45  3.000
 UEB  H5   C11  C10  119.14  3.000
 UEB  C12  C11  C10  121.41  3.000
 UEB  H6   C12  C13  120.47  3.000
 UEB  H6   C12  C11  120.13  3.000
 UEB  C13  C12  C11  119.39  3.000
 UEB  H7   C13  C14  119.73  3.000
 UEB  H7   C13  C12  120.51  3.000
 UEB  C14  C13  C12  119.76  3.000
 UEB  H8   C14  C15  120.53  3.000
 UEB  H8   C14  C13  118.25  3.000
 UEB  C15  C14  C13  121.22  3.000
 UEB  C16  C15  C14  120.84  3.000
 UEB  C14  C15  C10  119.04  3.000
 UEB  C16  C15  C10  120.11  3.000
 UEB  H10  C16  H9   106.68  3.000
 UEB  H10  C16  N17  107.32  3.000
 UEB  H9   C16  N17  107.29  3.000
 UEB  H10  C16  C15  110.54  3.000
 UEB  H9   C16  C15  111.01  3.000
 UEB  N17  C16  C15  113.67  3.000
 UEB  C23  C21  O22  127.99  3.000
 UEB  O22  C21  N20  121.53  3.000
 UEB  C23  C21  N20  110.47  3.000
 UEB  H11  C27  C28  128.45  3.000
 UEB  H11  C27  C26  125.96  3.000
 UEB  C28  C27  C26  105.59  3.000
 UEB  H13  N1   H12  106.13  3.000
 UEB  H13  N1   C2   109.27  3.000
 UEB  H12  N1   C2   109.12  3.000
 UEB  C5   C4   C9   118.63  3.000
 UEB  C5   C4   C2   119.24  3.000
 UEB  C9   C4   C2   122.12  3.000
 UEB  H15  C5   C6   119.34  3.000
 UEB  H15  C5   C4   119.75  3.000
 UEB  C6   C5   C4   120.91  3.000
 UEB  H16  C6   C5   119.76  3.000
 UEB  H16  C6   C7   120.15  3.000
 UEB  C5   C6   C7   120.08  3.000
 UEB  C28  N17  C18  120.11  3.000
 UEB  C28  N17  C16  118.74  3.000
 UEB  C18  N17  C16  121.12  3.000
 UEB  N20  C18  S19  119.62  3.000
 UEB  N20  C18  N17  116.52  3.000
 UEB  S19  C18  N17  123.85  3.000
 UEB  H17  N20  C18  114.72  3.000
 UEB  H17  N20  C21  115.88  3.000
 UEB  C18  N20  C21  129.39  3.000
 UEB  C28  C23  N24  107.70  3.000
 UEB  N24  C23  C21  129.90  3.000
 UEB  C28  C23  C21  122.39  3.000
 UEB  H18  N24  C26  125.56  3.000
 UEB  H18  N24  C23  125.40  3.000
 UEB  C26  N24  C23  109.04  3.000
 UEB  H19  C26  N24  121.07  3.000
 UEB  H19  C26  C27  129.25  3.000
 UEB  N24  C26  C27  109.67  3.000
 UEB  C23  C28  N17  121.08  3.000
 UEB  C23  C28  C27  107.99  3.000
 UEB  N17  C28  C27  130.92  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
 UEB  CONST_01  C4   C9   C8   C7      0.00   0.0  0
 UEB  CONST_02  C4   C5   C6   C7      0.00   0.0  0
 UEB  CONST_03  C5   C6   C7   C8      0.00   0.0  0
 UEB  CONST_04  C5   C4   C9   C8      0.00   0.0  0
 UEB  CONST_05  C6   C7   C8   C9      0.00   0.0  0
 UEB  CONST_06  C6   C5   C4   C9      0.00   0.0  0
 UEB  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 UEB  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 UEB  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 UEB  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 UEB  CONST_11  C15  C10  C11  C12     0.00   0.0  0
 UEB  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 UEB  CONST_13  N24  C23  C28  C27     0.00   0.0  0
 UEB  CONST_14  C23  N24  C26  C27     0.00   0.0  0
 UEB  CONST_15  C26  C27  C28  C23     0.00   0.0  0
 UEB  CONST_16  C28  C27  C26  N24     0.00   0.0  0
 UEB  CONST_17  C28  C23  N24  C26     0.00   0.0  0
 UEB  CONST_18  N17  C18  N20  C21     0.00   0.0  0
 UEB  CONST_19  C23  C21  N20  C18     0.00   0.0  0
 UEB  CONST_20  C28  N17  C18  N20     0.00   0.0  0
 UEB  CONST_21  C8   C9   C4   C2    180.00   0.0  0
 UEB  CONST_22  C6   C5   C4   C2    180.00   0.0  0
 UEB  CONST_23  C12  C11  C10  C2    180.00   0.0  0
 UEB  CONST_24  C14  C15  C10  C2    180.00   0.0  0
 UEB  CONST_25  C16  C15  C10  C11   180.00   0.0  0
 UEB  CONST_26  C16  C15  C14  C13   180.00   0.0  0
 UEB  CONST_27  N20  C18  N17  C16   180.00   0.0  0
 UEB  CONST_28  S19  C18  N20  C21   180.00   0.0  0
 UEB  CONST_29  O22  C21  N20  C18   180.00   0.0  0
 UEB  CONST_30  C28  N17  C18  S19   180.00   0.0  0
 UEB  CONST_31  H4   C9   C8   C7    180.00   0.0  0
 UEB  CONST_32  H15  C5   C6   C7    180.00   0.0  0
 UEB  CONST_33  H16  C6   C7   C8    180.00   0.0  0
 UEB  CONST_34  H2   C7   C8   C9    180.00   0.0  0
 UEB  CONST_35  H15  C5   C4   C9    180.00   0.0  0
 UEB  CONST_36  H6   C12  C11  C10   180.00   0.0  0
 UEB  CONST_37  H8   C14  C15  C10   180.00   0.0  0
 UEB  CONST_38  H7   C13  C12  C11   180.00   0.0  0
 UEB  CONST_39  H8   C14  C13  C12   180.00   0.0  0
 UEB  CONST_40  H5   C11  C12  C13   180.00   0.0  0
 UEB  CONST_41  H6   C12  C13  C14   180.00   0.0  0
 UEB  CONST_42  H5   C11  C10  C15   180.00   0.0  0
 UEB  CONST_43  H7   C13  C14  C15   180.00   0.0  0
 UEB  CONST_44  H18  N24  C23  C21     0.00   0.0  0
 UEB  CONST_45  H18  N24  C26  C27   180.00   0.0  0
 UEB  CONST_46  H3   C8   C9   C4    180.00   0.0  0
 UEB  CONST_47  H16  C6   C5   C4    180.00   0.0  0
 UEB  CONST_48  H2   C7   C6   C5    180.00   0.0  0
 UEB  CONST_49  H4   C9   C4   C5    180.00   0.0  0
 UEB  CONST_50  H3   C8   C7   C6    180.00   0.0  0
 UEB  CONST_51  H11  C27  C28  N17     0.00   0.0  0
 UEB  CONST_52  H11  C27  C28  C23   180.00   0.0  0
 UEB  CONST_53  H19  C26  N24  C23   180.00   0.0  0
 UEB  CONST_54  H11  C27  C26  N24   180.00   0.0  0
 UEB  CONST_55  H19  C26  C27  C28   180.00   0.0  0
 UEB  CONST_56  H18  N24  C23  C28   180.00   0.0  0
 UEB  CONST_57  H17  N20  C18  N17   180.00   0.0  0
 UEB  CONST_58  H17  N20  C21  C23   180.00   0.0  0
 UEB  CONST_59  S19  C18  N17  C16     0.00   0.0  0
 UEB  CONST_60  H17  N20  C18  S19     0.00   0.0  0
 UEB  CONST_61  H17  N20  C21  O22     0.00   0.0  0
 UEB  Var_01    N17  C16  C15  C10   179.49  30.0  1
 UEB  Var_02    N17  C16  C15  C14    -0.02  30.0  1
 UEB  Var_03    C18  N17  C16  C15    90.86  30.0  3
 UEB  Var_04    C28  N17  C16  C15   -86.88  30.0  3
 UEB  Var_05    H9   C16  C15  C10   -59.44  30.0  1
 UEB  Var_06    H10  C16  C15  C10    58.74  30.0  1
 UEB  Var_07    H9   C16  C15  C14   121.05  30.0  1
 UEB  Var_08    H10  C16  C15  C14  -120.77  30.0  1
 UEB  Var_09    H9   C16  N17  C18   -32.27  30.0  2
 UEB  Var_10    H10  C16  N17  C18  -146.59  30.0  2
 UEB  Var_11    H9   C16  N17  C28   149.99  30.0  2
 UEB  Var_12    H10  C16  N17  C28    35.67  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 UEB  chir_01  C2  C4  N1  C10  negativ

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
 UEB  plan-1  C2   0.020
 UEB  plan-1  C7   0.020
 UEB  plan-1  C8   0.020
 UEB  plan-1  C9   0.020
 UEB  plan-1  C4   0.020
 UEB  plan-1  C5   0.020
 UEB  plan-1  C6   0.020
 UEB  plan-1  H2   0.020
 UEB  plan-1  H3   0.020
 UEB  plan-1  H4   0.020
 UEB  plan-1  H15  0.020
 UEB  plan-1  H16  0.020
 UEB  plan-2  C2   0.020
 UEB  plan-2  C10  0.020
 UEB  plan-2  C11  0.020
 UEB  plan-2  C12  0.020
 UEB  plan-2  C13  0.020
 UEB  plan-2  C14  0.020
 UEB  plan-2  C15  0.020
 UEB  plan-2  C16  0.020
 UEB  plan-2  H5   0.020
 UEB  plan-2  H6   0.020
 UEB  plan-2  H7   0.020
 UEB  plan-2  H8   0.020
 UEB  plan-3  C16  0.020
 UEB  plan-3  C21  0.020
 UEB  plan-3  C27  0.020
 UEB  plan-3  N17  0.020
 UEB  plan-3  C18  0.020
 UEB  plan-3  S19  0.020
 UEB  plan-3  N20  0.020
 UEB  plan-3  C23  0.020
 UEB  plan-3  N24  0.020
 UEB  plan-3  C26  0.020
 UEB  plan-3  C28  0.020
 UEB  plan-3  H11  0.020
 UEB  plan-3  H17  0.020
 UEB  plan-3  H18  0.020
 UEB  plan-3  H19  0.020
 UEB  plan-3  O22  0.020

