# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:17:27 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-amino-8-{[2-(biphenyl-4-yl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(SCC(=O)c3ccc(cc3)c4ccccc4)nc2C(=O)N1
#
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
 X6L  X6L  2-amino-8-{[2-(biphenyl-4-yl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one  ligand  42  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X6L
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
 X6L  C22   C  CR16  0  -0.262   8.4642  -1.9352   0.1182
 X6L  C21   C  CR16  0  -0.240   7.4205  -2.5069  -0.5978
 X6L  C23   C  CR16  0  -0.240   8.2616  -0.7335   0.7845
 X6L  C20   C  CR16  0  -0.306   6.1831  -1.8827  -0.6465
 X6L  C24   C  CR16  0  -0.305   7.0257  -0.1066   0.7323
 X6L  C15   C  CR16  0  -0.296   4.5559   1.3845  -0.1100
 X6L  C17   C  CR16  0  -0.289   3.4748  -0.7547  -0.0197
 X6L  C14   C  CR16  0  -0.242   3.3243   2.0066  -0.1711
 X6L  C18   C  CR16  0  -0.273   2.2397  -0.1340  -0.0755
 X6L  C19   C  CR6   0   0.088   5.9689  -0.6731   0.0171
 X6L  C16   C  CR6   0   0.091   4.6537  -0.0080  -0.0374
 X6L  C13   C  CR6   0  -0.016   2.1478   1.2551  -0.1558
 X6L  C5    C  CR56  0  -0.083  -4.2308  -0.7254   0.1691
 X6L  C4    C  CR56  0   0.481  -5.1470   0.2773  -0.0852
 X6L  C7    C  CR5   0   0.299  -3.0871   1.0279  -0.1256
 X6L  C25   C  CR6   0   0.494  -4.7085  -2.0421   0.4168
 X6L  C2    C  CR6   0   0.689  -6.9289  -1.0190   0.0879
 X6L  C11   C  C     0   0.389   0.8449   1.9541  -0.2289
 X6L  C10   C  CH2   0  -0.702  -0.4068   1.1171  -0.1455
 X6L  N6    N  N     0  -0.442  -2.9467  -0.2346   0.1397
 X6L  N3    N  N     0  -0.504  -6.4824   0.1926  -0.1379
 X6L  N8    N  NR15  0  -0.689  -4.3989   1.3963  -0.2731
 X6L  N27   N  NR16  0  -0.723  -6.1083  -2.0762   0.3546
 X6L  N1    N  NH2   0  -0.832  -8.2445  -1.2704   0.0252
 X6L  O26   O  O     0  -0.477  -4.0731  -3.0560   0.6573
 X6L  O12   O  O     0  -0.385   0.7682   3.1582  -0.3466
 X6L  S9    S  S2    0   0.081  -1.8280   2.2257  -0.2823
 X6L  H22   H  HCR6  0   0.260   9.4298  -2.4223   0.1552
 X6L  H21   H  HCR6  0   0.261   7.5709  -3.4393  -1.1259
 X6L  H23   H  HCR6  0   0.261   9.0661  -0.2840   1.3518
 X6L  H20   H  HCR6  0   0.259   5.3856  -2.3306  -1.2262
 X6L  H24   H  HCR6  0   0.258   6.8775   0.8201   1.2724
 X6L  H15   H  HCR6  0   0.264   5.4531   1.9893  -0.1422
 X6L  H14   H  HCR6  0   0.268   3.2763   3.0853  -0.2363
 X6L  H17   H  HCR6  0   0.266   3.5185  -1.8331   0.0582
 X6L  H18   H  HCR6  0   0.273   1.3527  -0.7529  -0.0527
 X6L  H8    H  HNR5  0   0.426  -4.7530   2.3157  -0.4925
 X6L  H27   H  HNR6  0   0.425  -6.5309  -2.9816   0.5175
 X6L  H11N  H  HNH2  0   0.412  -8.8675  -0.4825  -0.0272
 X6L  H12N  H  HNH2  0   0.414  -8.6281  -2.1184   0.4062
 X6L  H101  H  HCH2  0   0.322  -0.4333   0.3745  -0.9450
 X6L  H102  H  HCH2  0   0.324  -0.4401   0.5753   0.8017

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
 X6L  C22  C21   aromatic  1.389  0.020  1.389
 X6L  C22  C23   aromatic  1.389  0.020  1.389
 X6L  C21  C20   aromatic  1.387  0.020  1.387
 X6L  C23  C24   aromatic  1.387  0.020  1.387
 X6L  C20  C19   aromatic  1.396  0.020  1.396
 X6L  C24  C19   aromatic  1.396  0.020  1.396
 X6L  C15  C14   aromatic  1.381  0.020  1.381
 X6L  C15  C16   aromatic  1.398  0.020  1.398
 X6L  C17  C18   aromatic  1.383  0.020  1.383
 X6L  C17  C16   aromatic  1.396  0.020  1.396
 X6L  C14  C13   aromatic  1.396  0.020  1.396
 X6L  C18  C13   aromatic  1.394  0.020  1.394
 X6L  C19  C16   single    1.475  0.020  1.475
 X6L  C13  C11   single    1.480  0.020  1.480
 X6L  C5   C4    aromatic  1.382  0.020  1.382
 X6L  C5   C25   single    1.422  0.020  1.422
 X6L  C5   N6    aromatic  1.375  0.020  1.375
 X6L  C4   N3    single    1.339  0.020  1.339
 X6L  C4   N8    aromatic  1.359  0.020  1.359
 X6L  C7   N6    aromatic  1.298  0.020  1.298
 X6L  C7   N8    aromatic  1.371  0.020  1.371
 X6L  C7   S9    single    1.745  0.020  1.745
 X6L  C25  N27   single    1.402  0.020  1.402
 X6L  C25  O26   double    1.220  0.020  1.220
 X6L  C2   N3    double    1.311  0.020  1.311
 X6L  C2   N27   single    1.365  0.020  1.365
 X6L  C2   N1    single    1.341  0.020  1.341
 X6L  C11  C10   single    1.508  0.020  1.508
 X6L  C11  O12   double    1.212  0.020  1.212
 X6L  C10  S9    single    1.808  0.020  1.808
 X6L  C22  H22   single    0.930  0.020  1.080
 X6L  C21  H21   single    0.930  0.020  1.080
 X6L  C23  H23   single    0.930  0.020  1.080
 X6L  C20  H20   single    0.930  0.020  1.080
 X6L  C24  H24   single    0.930  0.020  1.080
 X6L  C15  H15   single    0.930  0.020  1.080
 X6L  C14  H14   single    0.930  0.020  1.080
 X6L  C17  H17   single    0.930  0.020  1.080
 X6L  C18  H18   single    0.930  0.020  1.080
 X6L  N8   H8    single    0.860  0.020  1.020
 X6L  N27  H27   single    0.860  0.020  1.020
 X6L  N1   H11N  single    0.890  0.020  1.040
 X6L  N1   H12N  single    0.890  0.020  1.040
 X6L  C10  H101  single    0.970  0.020  1.090
 X6L  C10  H102  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
 X6L  H22   C22  C23   120.21  3.000
 X6L  H22   C22  C21   120.20  3.000
 X6L  C23   C22  C21   119.60  3.000
 X6L  H21   C21  C20   119.65  3.000
 X6L  H21   C21  C22   120.12  3.000
 X6L  C20   C21  C22   120.22  3.000
 X6L  H23   C23  C24   119.64  3.000
 X6L  H23   C23  C22   120.16  3.000
 X6L  C24   C23  C22   120.20  3.000
 X6L  H20   C20  C19   119.99  3.000
 X6L  H20   C20  C21   119.33  3.000
 X6L  C19   C20  C21   120.67  3.000
 X6L  H24   C24  C19   119.95  3.000
 X6L  H24   C24  C23   119.34  3.000
 X6L  C19   C24  C23   120.70  3.000
 X6L  H15   C15  C16   120.01  3.000
 X6L  H15   C15  C14   119.09  3.000
 X6L  C16   C15  C14   120.89  3.000
 X6L  H17   C17  C16   120.00  3.000
 X6L  H17   C17  C18   119.09  3.000
 X6L  C16   C17  C18   120.90  3.000
 X6L  H14   C14  C13   120.01  3.000
 X6L  H14   C14  C15   119.43  3.000
 X6L  C13   C14  C15   120.56  3.000
 X6L  H18   C18  C13   121.13  3.000
 X6L  H18   C18  C17   118.32  3.000
 X6L  C13   C18  C17   120.54  3.000
 X6L  C16   C19  C24   120.73  3.000
 X6L  C16   C19  C20   120.66  3.000
 X6L  C24   C19  C20   118.61  3.000
 X6L  C19   C16  C17   120.77  3.000
 X6L  C19   C16  C15   120.90  3.000
 X6L  C17   C16  C15   118.33  3.000
 X6L  C11   C13  C18   122.09  3.000
 X6L  C11   C13  C14   119.14  3.000
 X6L  C18   C13  C14   118.77  3.000
 X6L  N6    C5   C25   130.37  3.000
 X6L  N6    C5   C4    110.87  3.000
 X6L  C25   C5   C4    118.76  3.000
 X6L  N8    C4   N3    126.55  3.000
 X6L  N8    C4   C5    104.95  3.000
 X6L  N3    C4   C5    128.50  3.000
 X6L  S9    C7   N8    119.77  3.000
 X6L  S9    C7   N6    127.45  3.000
 X6L  N8    C7   N6    112.78  3.000
 X6L  O26   C25  N27   120.57  3.000
 X6L  O26   C25  C5    128.94  3.000
 X6L  N27   C25  C5    110.50  3.000
 X6L  N1    C2   N27   116.99  3.000
 X6L  N1    C2   N3    119.97  3.000
 X6L  N27   C2   N3    123.02  3.000
 X6L  O12   C11  C10   120.27  3.000
 X6L  O12   C11  C13   121.97  3.000
 X6L  C10   C11  C13   117.75  3.000
 X6L  H102  C10  H101  107.28  3.000
 X6L  H102  C10  S9    110.24  3.000
 X6L  H101  C10  S9    110.04  3.000
 X6L  H102  C10  C11   110.41  3.000
 X6L  H101  C10  C11   110.93  3.000
 X6L  S9    C10  C11   107.94  3.000
 X6L  C7    N6   C5    104.51  3.000
 X6L  C2    N3   C4    113.04  3.000
 X6L  H8    N8   C7    127.16  3.000
 X6L  H8    N8   C4    125.94  3.000
 X6L  C7    N8   C4    106.89  3.000
 X6L  H27   N27  C2    118.25  3.000
 X6L  H27   N27  C25   115.57  3.000
 X6L  C2    N27  C25   126.18  3.000
 X6L  H12N  N1   H11N  116.36  3.000
 X6L  H12N  N1   C2    120.97  3.000
 X6L  H11N  N1   C2    117.60  3.000
 X6L  C10   S9   C7     98.02  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
 X6L  CONST_01  C19   C20  C21  C22     0.00   0.0  0
 X6L  CONST_02  C19   C24  C23  C22     0.00   0.0  0
 X6L  CONST_03  C24   C23  C22  C21     0.00   0.0  0
 X6L  CONST_04  C24   C19  C20  C21     0.00   0.0  0
 X6L  CONST_05  C16   C19  C20  C21   180.00   0.0  0
 X6L  CONST_06  C20   C21  C22  C23     0.00   0.0  0
 X6L  CONST_07  C20   C19  C24  C23     0.00   0.0  0
 X6L  CONST_08  C16   C19  C24  C23   180.00   0.0  0
 X6L  CONST_13  C18   C13  C14  C15     0.00   0.0  0
 X6L  CONST_14  C18   C17  C16  C15     0.00   0.0  0
 X6L  CONST_15  C14   C13  C18  C17     0.00   0.0  0
 X6L  CONST_16  C14   C15  C16  C17     0.00   0.0  0
 X6L  CONST_17  C19   C16  C15  C14   180.00   0.0  0
 X6L  CONST_18  C19   C16  C17  C18   180.00   0.0  0
 X6L  CONST_19  C13   C14  C15  C16     0.00   0.0  0
 X6L  CONST_20  C13   C18  C17  C16     0.00   0.0  0
 X6L  CONST_21  C7    N8   C4   C5      0.00   0.0  0
 X6L  CONST_22  N8    C7   N6   C5      0.00   0.0  0
 X6L  CONST_23  C7    N6   C5   C4      0.00   0.0  0
 X6L  CONST_24  N6    C7   N8   C4      0.00   0.0  0
 X6L  CONST_25  N8    C4   C5   N6      0.00   0.0  0
 X6L  CONST_26  C2    N27  C25  C5      0.00   0.0  0
 X6L  CONST_27  N27   C2   N3   C4      0.00   0.0  0
 X6L  CONST_28  N3    C2   N27  C25     0.00   0.0  0
 X6L  CONST_29  C11   C13  C14  C15   180.00   0.0  0
 X6L  CONST_30  C11   C13  C18  C17   180.00   0.0  0
 X6L  CONST_31  S9    C7   N6   C5    180.00   0.0  0
 X6L  CONST_32  S9    C7   N8   C4    180.00   0.0  0
 X6L  CONST_33  N1    C2   N3   C4    180.00   0.0  0
 X6L  CONST_34  N1    C2   N27  C25   180.00   0.0  0
 X6L  CONST_35  O26   C25  N27  C2    180.00   0.0  0
 X6L  CONST_36  H20   C20  C21  C22   180.00   0.0  0
 X6L  CONST_37  H24   C24  C23  C22   180.00   0.0  0
 X6L  CONST_38  H23   C23  C22  C21   180.00   0.0  0
 X6L  CONST_39  H21   C21  C22  C23   180.00   0.0  0
 X6L  CONST_40  H22   C22  C21  C20   180.00   0.0  0
 X6L  CONST_41  H17   C17  C16  C15   180.00   0.0  0
 X6L  CONST_42  H15   C15  C16  C17   180.00   0.0  0
 X6L  CONST_43  H18   C18  C13  C14   180.00   0.0  0
 X6L  CONST_44  H14   C14  C13  C18   180.00   0.0  0
 X6L  CONST_45  H8    N8   C4   C5    180.00   0.0  0
 X6L  CONST_46  H27   N27  C25  C5    180.00   0.0  0
 X6L  CONST_47  H11N  N1   C2   N3      0.00   0.0  0
 X6L  Var_01    C10   C11  C13  C14  -177.22  30.0  2
 X6L  Var_02    N6    C7   S9   C10     5.79  30.0  1
 X6L  Var_03    S9    C10  C11  C13  -179.28  30.0  3
 X6L  Var_04    C11   C10  S9   C7   -178.92  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
 X6L  plan-1  C22   0.020
 X6L  plan-1  C21   0.020
 X6L  plan-1  C23   0.020
 X6L  plan-1  C20   0.020
 X6L  plan-1  C24   0.020
 X6L  plan-1  C19   0.020
 X6L  plan-1  C16   0.020
 X6L  plan-1  H22   0.020
 X6L  plan-1  H21   0.020
 X6L  plan-1  H23   0.020
 X6L  plan-1  H20   0.020
 X6L  plan-1  H24   0.020
 X6L  plan-2  C15   0.020
 X6L  plan-2  C17   0.020
 X6L  plan-2  C14   0.020
 X6L  plan-2  C18   0.020
 X6L  plan-2  C19   0.020
 X6L  plan-2  C16   0.020
 X6L  plan-2  C13   0.020
 X6L  plan-2  C11   0.020
 X6L  plan-2  H15   0.020
 X6L  plan-2  H14   0.020
 X6L  plan-2  H17   0.020
 X6L  plan-2  H18   0.020
 X6L  plan-3  C5    0.020
 X6L  plan-3  C4    0.020
 X6L  plan-3  C7    0.020
 X6L  plan-3  C25   0.020
 X6L  plan-3  C2    0.020
 X6L  plan-3  N6    0.020
 X6L  plan-3  N3    0.020
 X6L  plan-3  N8    0.020
 X6L  plan-3  N27   0.020
 X6L  plan-3  N1    0.020
 X6L  plan-3  O26   0.020
 X6L  plan-3  S9    0.020
 X6L  plan-3  H8    0.020
 X6L  plan-3  H27   0.020
 X6L  plan-3  H11N  0.020
 X6L  plan-3  H12N  0.020
 X6L  plan-4  C13   0.020
 X6L  plan-4  C11   0.020
 X6L  plan-4  C10   0.020
 X6L  plan-4  O12   0.020

