# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 22:13:43 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: N-{3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]propyl}-N'-[2-(morpholin-4-yl)ethyl]thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2[nH]c(SCCCNC(=S)NCCN3CCOCC3)nc2C1=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
 XB1  XB1  N-{3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]propyl}-N'-[2-(morpholin-4-yl)ethyl]thiourea  ligand  56  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XB1
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
 XB1  C10  C  CH2   0  -0.350  35.0885  -36.5059   6.2327
 XB1  C15  C  CH2   0  -0.303  38.6441  -39.7800   5.8418
 XB1  C17  C  CH2   0  -0.348  40.2011  -37.9456   5.4787
 XB1  C20  C  CH2   0  -0.218  39.8177  -37.7963   2.9075
 XB1  C21  C  CH2   0  -0.280  38.9827  -38.8583   3.6244
 XB1  C26  C  CR6   0   0.746  34.4195  -29.7904   8.2753
 XB1  C28  C  CH3   0  -0.526  35.4709  -28.7423  10.1612
 XB1  C02  C  CR6   0   0.529  35.0011  -31.1515  10.2892
 XB1  C03  C  CR56  0  -0.060  34.4603  -32.2637   9.5687
 XB1  C04  C  CR56  0   0.660  33.9573  -32.0909   8.3056
 XB1  C06  C  CR5   0   0.220  33.7706  -34.1679   8.9490
 XB1  C08  C  CH2   0  -0.560  34.9788  -36.6277   8.7887
 XB1  C09  C  CH2   0  -0.451  35.7973  -36.2623   7.5651
 XB1  C12  C  C     0   0.403  35.0525  -38.9904   6.0230
 XB1  C14  C  CH2   0  -0.280  37.1853  -40.1708   5.6455
 XB1  C18  C  CH2   0  -0.147  40.2299  -36.5546   4.8496
 XB1  N05  N  NR15  0  -0.651  33.5228  -33.3004   7.9072
 XB1  N11  N  NH1   0  -0.597  34.4444  -37.7978   6.1272
 XB1  N13  N  NH1   0  -0.610  36.3712  -38.9943   5.8388
 XB1  N16  N  NT    0  -0.439  38.9853  -38.6110   5.0624
 XB1  N23  N  N     0  -0.393  34.3260  -33.5663   9.9568
 XB1  N24  N  NR6   0  -0.594  33.9193  -30.9113   7.6417
 XB1  N27  N  NR6   0  -0.606  34.9423  -29.9579   9.5511
 XB1  O01  O  O     0  -0.447  35.4638  -31.1931  11.4115
 XB1  O19  O  O2    0  -0.483  39.6890  -36.5481   3.5418
 XB1  O29  O  O     0  -0.471  34.4072  -28.7008   7.7427
 XB1  S07  S  S2    0   0.031  33.3259  -35.8528   8.8551
 XB1  S22  S  S1    0  -0.477  34.1436  -40.4135   6.1256
 XB1  H1   H  HCH2  0   0.268  35.7931  -36.3589   5.4099
 XB1  H2   H  HCH2  0   0.276  34.3064  -35.7632   6.0861
 XB1  H3   H  HCH2  0   0.221  39.2741  -40.6500   5.6031
 XB1  H4   H  HCH2  0   0.246  38.8035  -39.5439   6.8968
 XB1  H5   H  HCH2  0   0.214  41.1044  -38.5186   5.2192
 XB1  H6   H  HCH2  0   0.257  40.2046  -37.8382   6.5648
 XB1  H7   H  HCH2  0   0.249  39.4727  -37.6815   1.8793
 XB1  H8   H  HCH2  0   0.210  40.8695  -38.1067   2.8561
 XB1  H9   H  HCH2  0   0.234  37.9530  -38.8424   3.2576
 XB1  H10  H  HCH2  0   0.208  39.3962  -39.8486   3.3777
 XB1  H11  H  HCH3  0   0.267  35.8869  -28.9935  11.1288
 XB1  H12  H  HCH3  0   0.255  36.2552  -28.3137   9.5415
 XB1  H13  H  HCH3  0   0.254  34.6834  -28.0039  10.2978
 XB1  H14  H  HCH2  0   0.297  35.5123  -36.3738   9.7035
 XB1  H15  H  HCH2  0   0.291  34.7672  -37.6979   8.8232
 XB1  H16  H  HCH2  0   0.258  36.7283  -36.8326   7.6174
 XB1  H17  H  HCH2  0   0.258  36.0882  -35.2099   7.6047
 XB1  H19  H  HCH2  0   0.240  37.0169  -40.6010   4.6538
 XB1  H20  H  HCH2  0   0.258  36.9147  -40.9364   6.3722
 XB1  H21  H  HCH2  0   0.202  41.2597  -36.1750   4.8498
 XB1  H22  H  HCH2  0   0.218  39.6222  -35.8684   5.4441
 XB1  H23  H  HCH3  0   0.286  33.4529  -29.8243   5.9301
 XB1  H24  H  HCH3  0   0.268  33.8905  -31.5092   5.6341
 XB1  H25  H  HCH3  0   0.269  32.3002  -31.1058   6.3217
 XB1  H26  H  HNR5  0   0.445  33.1027  -33.5495   7.0222
 XB1  H27  H  HNH1  0   0.401  33.4557  -37.8390   6.3118
 XB1  H29  H  HNH1  0   0.411  36.8713  -38.1294   5.6678
 XB1  C25  C  CH3   0  -0.558  33.3557  -30.8364   6.3034

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
 XB1  C20  O19  single    1.406  0.020  1.406
 XB1  C20  C21  single    1.529  0.020  1.529
 XB1  O19  C18  single    1.415  0.020  1.415
 XB1  C21  N16  single    1.459  0.020  1.459
 XB1  C18  C17  single    1.527  0.020  1.527
 XB1  N16  C17  single    1.447  0.020  1.447
 XB1  N16  C15  single    1.446  0.020  1.446
 XB1  C15  C14  single    1.523  0.020  1.523
 XB1  C14  N13  single    1.444  0.020  1.444
 XB1  N13  C12  single    1.332  0.020  1.332
 XB1  C25  N24  single    1.454  0.020  1.454
 XB1  S22  C12  double    1.692  0.020  1.692
 XB1  N11  C12  single    1.343  0.020  1.343
 XB1  N11  C10  single    1.447  0.020  1.447
 XB1  N24  C04  single    1.354  0.020  1.354
 XB1  N24  C26  single    1.381  0.020  1.381
 XB1  N05  C04  aromatic  1.345  0.020  1.345
 XB1  N05  C06  aromatic  1.378  0.020  1.378
 XB1  C10  C09  single    1.529  0.020  1.529
 XB1  O29  C26  double    1.213  0.020  1.213
 XB1  C04  C03  aromatic  1.371  0.020  1.371
 XB1  C26  N27  single    1.389  0.020  1.389
 XB1  S07  C06  single    1.745  0.020  1.745
 XB1  S07  C08  single    1.827  0.020  1.827
 XB1  C06  N23  aromatic  1.299  0.020  1.299
 XB1  C09  C08  single    1.517  0.020  1.517
 XB1  C03  N23  aromatic  1.366  0.020  1.366
 XB1  C03  C02  single    1.431  0.020  1.431
 XB1  N27  C02  single    1.405  0.020  1.405
 XB1  N27  C28  single    1.459  0.020  1.459
 XB1  C02  O01  double    1.215  0.020  1.215
 XB1  C10  H1   single    0.970  0.020  1.090
 XB1  C10  H2   single    0.970  0.020  1.090
 XB1  C15  H3   single    0.970  0.020  1.090
 XB1  C15  H4   single    0.970  0.020  1.090
 XB1  C17  H5   single    0.970  0.020  1.090
 XB1  C17  H6   single    0.970  0.020  1.090
 XB1  C20  H7   single    0.970  0.020  1.090
 XB1  C20  H8   single    0.970  0.020  1.090
 XB1  C21  H9   single    0.970  0.020  1.090
 XB1  C21  H10  single    0.970  0.020  1.090
 XB1  C28  H11  single    0.970  0.020  1.090
 XB1  C28  H12  single    0.970  0.020  1.090
 XB1  C28  H13  single    0.970  0.020  1.090
 XB1  C08  H14  single    0.970  0.020  1.090
 XB1  C08  H15  single    0.970  0.020  1.090
 XB1  C09  H16  single    0.970  0.020  1.090
 XB1  C09  H17  single    0.970  0.020  1.090
 XB1  C14  H19  single    0.970  0.020  1.090
 XB1  C14  H20  single    0.970  0.020  1.090
 XB1  C18  H21  single    0.970  0.020  1.090
 XB1  C18  H22  single    0.970  0.020  1.090
 XB1  C25  H23  single    0.970  0.020  1.090
 XB1  C25  H24  single    0.970  0.020  1.090
 XB1  C25  H25  single    0.970  0.020  1.090
 XB1  N05  H26  single    0.860  0.020  1.020
 XB1  N11  H27  single    0.860  0.020  1.020
 XB1  N13  H29  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
 XB1  H2   C10  H1   105.67  3.000
 XB1  H2   C10  N11  106.23  3.000
 XB1  H1   C10  N11  110.61  3.000
 XB1  H2   C10  C09  109.99  3.000
 XB1  H1   C10  C09  109.61  3.000
 XB1  N11  C10  C09  114.33  3.000
 XB1  H4   C15  H3   107.26  3.000
 XB1  H4   C15  N16  108.14  3.000
 XB1  H3   C15  N16  112.78  3.000
 XB1  H4   C15  C14  108.64  3.000
 XB1  H3   C15  C14  108.52  3.000
 XB1  N16  C15  C14  111.35  3.000
 XB1  H6   C17  H5   106.45  3.000
 XB1  H6   C17  N16  109.53  3.000
 XB1  H5   C17  N16  112.48  3.000
 XB1  H6   C17  C18  108.68  3.000
 XB1  H5   C17  C18  111.20  3.000
 XB1  N16  C17  C18  108.43  3.000
 XB1  H8   C20  H7   106.78  3.000
 XB1  H8   C20  O19  111.09  3.000
 XB1  H7   C20  O19  107.63  3.000
 XB1  H8   C20  C21  110.40  3.000
 XB1  H7   C20  C21  110.01  3.000
 XB1  O19  C20  C21  110.80  3.000
 XB1  H10  C21  H9   106.95  3.000
 XB1  H10  C21  N16  111.88  3.000
 XB1  H9   C21  N16  109.26  3.000
 XB1  H10  C21  C20  108.34  3.000
 XB1  H9   C21  C20  110.29  3.000
 XB1  N16  C21  C20  110.07  3.000
 XB1  O29  C26  N27  121.03  3.000
 XB1  N27  C26  N24  117.38  3.000
 XB1  O29  C26  N24  121.59  3.000
 XB1  H13  C28  H12  109.03  3.000
 XB1  H13  C28  H11  108.86  3.000
 XB1  H12  C28  H11  108.88  3.000
 XB1  H13  C28  N27  110.83  3.000
 XB1  H12  C28  N27  110.57  3.000
 XB1  H11  C28  N27  108.63  3.000
 XB1  O01  C02  N27  122.04  3.000
 XB1  O01  C02  C03  125.63  3.000
 XB1  N27  C02  C03  112.33  3.000
 XB1  N23  C03  C04  110.25  3.000
 XB1  N23  C03  C02  129.43  3.000
 XB1  C04  C03  C02  120.31  3.000
 XB1  N24  C04  N05  128.97  3.000
 XB1  N05  C04  C03  106.14  3.000
 XB1  N24  C04  C03  124.89  3.000
 XB1  S07  C06  N23  126.73  3.000
 XB1  N23  C06  N05  111.83  3.000
 XB1  S07  C06  N05  121.42  3.000
 XB1  H15  C08  H14  107.28  3.000
 XB1  H15  C08  S07  103.85  3.000
 XB1  H14  C08  S07  108.29  3.000
 XB1  H15  C08  C09  111.49  3.000
 XB1  H14  C08  C09  110.93  3.000
 XB1  S07  C08  C09  114.54  3.000
 XB1  H17  C09  H16  105.90  3.000
 XB1  H17  C09  C08  110.27  3.000
 XB1  H16  C09  C08  107.18  3.000
 XB1  H17  C09  C10  107.97  3.000
 XB1  H16  C09  C10  110.70  3.000
 XB1  C08  C09  C10  114.49  3.000
 XB1  S22  C12  N13  122.55  3.000
 XB1  S22  C12  N11  119.94  3.000
 XB1  N13  C12  N11  117.51  3.000
 XB1  H20  C14  H19  106.86  3.000
 XB1  H20  C14  N13  110.07  3.000
 XB1  H19  C14  N13  110.79  3.000
 XB1  H20  C14  C15  109.41  3.000
 XB1  H19  C14  C15  111.42  3.000
 XB1  N13  C14  C15  108.28  3.000
 XB1  H22  C18  H21  107.73  3.000
 XB1  H22  C18  O19  106.70  3.000
 XB1  H21  C18  O19  110.93  3.000
 XB1  H22  C18  C17  109.73  3.000
 XB1  H21  C18  C17  109.44  3.000
 XB1  O19  C18  C17  112.19  3.000
 XB1  H26  N05  C06  125.55  3.000
 XB1  H26  N05  C04  127.95  3.000
 XB1  C06  N05  C04  106.50  3.000
 XB1  H27  N11  C12  115.01  3.000
 XB1  H27  N11  C10  117.40  3.000
 XB1  C12  N11  C10  126.64  3.000
 XB1  H29  N13  C14  113.24  3.000
 XB1  H29  N13  C12  120.62  3.000
 XB1  C14  N13  C12  125.41  3.000
 XB1  C21  N16  C17  111.28  3.000
 XB1  C17  N16  C15  114.51  3.000
 XB1  C21  N16  C15  113.19  3.000
 XB1  C06  N23  C03  105.27  3.000
 XB1  C25  N24  C04  120.46  3.000
 XB1  C04  N24  C26  118.15  3.000
 XB1  C25  N24  C26  121.38  3.000
 XB1  C02  N27  C28  118.24  3.000
 XB1  C28  N27  C26  114.83  3.000
 XB1  C02  N27  C26  126.93  3.000
 XB1  C18  O19  C20  112.19  3.000
 XB1  C08  S07  C06  100.42  3.000
 XB1  H25  C25  H24  109.47  3.000
 XB1  H25  C25  H23  108.90  3.000
 XB1  H24  C25  H23  108.74  3.000
 XB1  H25  C25  N24  110.32  3.000
 XB1  H24  C25  N24  110.08  3.000
 XB1  H23  C25  N24  109.30  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
 XB1  CONST_01  C06  N05  C04  C03     0.00   0.0  0
 XB1  CONST_02  N05  C06  N23  C03     0.00   0.0  0
 XB1  CONST_03  N23  C06  N05  C04     0.00   0.0  0
 XB1  CONST_04  C06  N23  C03  C04     0.00   0.0  0
 XB1  CONST_05  N23  C03  C04  N05     0.00   0.0  0
 XB1  CONST_06  C03  C02  N27  C26     0.00   0.0  0
 XB1  CONST_07  N24  C26  N27  C02     0.00   0.0  0
 XB1  CONST_08  N27  C26  N24  C04     0.00   0.0  0
 XB1  CONST_09  S07  C06  N23  C03   180.00   0.0  0
 XB1  CONST_10  S07  C06  N05  C04   180.00   0.0  0
 XB1  CONST_11  O01  C02  N27  C26   180.00   0.0  0
 XB1  CONST_12  N24  C26  N27  C28   180.00   0.0  0
 XB1  CONST_13  C03  C02  N27  C28   180.00   0.0  0
 XB1  CONST_14  O29  C26  N27  C02   180.00   0.0  0
 XB1  CONST_15  O29  C26  N24  C04   180.00   0.0  0
 XB1  CONST_16  N27  C26  N24  C25   180.00   0.0  0
 XB1  CONST_17  H26  N05  C04  C03   180.00   0.0  0
 XB1  CONST_18  O29  C26  N27  C28     0.00   0.0  0
 XB1  CONST_19  O01  C02  N27  C28     0.00   0.0  0
 XB1  CONST_20  O29  C26  N24  C25     0.00   0.0  0
 XB1  CONST_21  N13  C12  N11  C10     0.00   0.0  0
 XB1  CONST_22  S22  C12  N11  C10   180.00   0.0  0
 XB1  CONST_23  S22  C12  N13  C14     0.00   0.0  0
 XB1  CONST_24  N11  C12  N13  C14   180.00   0.0  0
 XB1  CONST_25  H29  N13  C12  N11     0.00   0.0  0
 XB1  CONST_26  H27  N11  C12  N13   180.00   0.0  0
 XB1  Var_01    C20  C21  N16  C17   -28.70  30.0  1
 XB1  Var_02    C18  C17  N16  C21    65.52  30.0  1
 XB1  Var_03    O19  C20  C21  N16   -35.28  30.0  1
 XB1  Var_04    O19  C18  C17  N16   -36.70  30.0  1
 XB1  Var_05    H21  C18  O19  C20    95.73  30.0  1
 XB1  Var_06    H7   C20  O19  C18  -174.38  30.0  1
 XB1  Var_07    C14  C15  N16  C17   162.63  30.0  3
 XB1  Var_08    N05  C06  S07  C08   111.53  30.0  2
 XB1  Var_09    H23  C25  N24  C26     2.76  30.0  3
 XB1  Var_10    H11  C28  N27  C26  -177.69  30.0  3
 XB1  Var_11    C09  C08  S07  C06   -63.31  30.0  3
 XB1  Var_12    N16  C15  C14  N13   -50.05  30.0  1
 XB1  Var_13    S07  C08  C09  C10   -53.49  30.0  3
 XB1  Var_14    C12  N13  C14  C15  -165.22  30.0  3
 XB1  Var_15    N11  C10  C09  C08   -46.84  30.0  2
 XB1  Var_16    C12  N11  C10  C09   -70.27  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
 XB1  plan-1  C26  0.020
 XB1  plan-1  C28  0.020
 XB1  plan-1  C02  0.020
 XB1  plan-1  C03  0.020
 XB1  plan-1  C04  0.020
 XB1  plan-1  C06  0.020
 XB1  plan-1  N05  0.020
 XB1  plan-1  N23  0.020
 XB1  plan-1  N24  0.020
 XB1  plan-1  N27  0.020
 XB1  plan-1  O01  0.020
 XB1  plan-1  O29  0.020
 XB1  plan-1  S07  0.020
 XB1  plan-1  H26  0.020
 XB1  plan-1  C25  0.020
 XB1  plan-2  C10  0.020
 XB1  plan-2  C12  0.020
 XB1  plan-2  C14  0.020
 XB1  plan-2  N11  0.020
 XB1  plan-2  N13  0.020
 XB1  plan-2  S22  0.020
 XB1  plan-2  H27  0.020
 XB1  plan-2  H29  0.020

