# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 20:46:38 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-[(2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]-N-phenylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(SCC(=O)Nc2ccccc2)nc3C(=O)NC(=Nc13)N
#
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
 8Y4  8Y4  2-[(2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]-N-phenylacetamide  ligand  37  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8Y4
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
 8Y4  C1   C  CR16  0  -0.274   7.6721   0.4185   0.0237
 8Y4  C2   C  CR16  0  -0.225   6.9799  -0.7083  -0.3920
 8Y4  C3   C  CR16  0  -0.264   6.9543   1.5406   0.4159
 8Y4  C4   C  CR16  0  -0.344   5.5912  -0.7341  -0.4186
 8Y4  C5   C  CR16  0  -0.251   5.5707   1.5334   0.3927
 8Y4  C6   C  CR6   0   0.388   4.8742   0.3947  -0.0206
 8Y4  C7   C  CR56  0   0.002  -3.0606   0.7563  -0.1413
 8Y4  C8   C  CR56  0   0.387  -3.6429  -0.4907  -0.0219
 8Y4  C9   C  CR5   0   0.320  -1.4734  -0.6309  -0.2175
 8Y4  C10  C  CR6   0   0.508  -3.8984   1.9064  -0.1225
 8Y4  C11  C  CR6   0   0.675  -5.7164   0.2577   0.1363
 8Y4  C12  C  C     0   0.584   2.5619  -0.4874  -0.2611
 8Y4  C14  C  CH2   0  -0.738   1.1325   0.0044  -0.1641
 8Y4  N15  N  N     0  -0.471  -1.6973   0.6470  -0.2634
 8Y4  N16  N  N     0  -0.512  -4.9396  -0.7948   0.1207
 8Y4  N17  N  NR5   0  -0.413  -2.6142  -1.3800  -0.0702
 8Y4  N18  N  NR16  0  -0.612  -5.2427   1.5322   0.0215
 8Y4  N19  N  NH2   0  -0.845  -7.0491   0.1077   0.2308
 8Y4  N20  N  NH1   0  -0.676   3.4752   0.4760  -0.0099
 8Y4  O21  O  O     0  -0.587  -3.5905   3.0838  -0.2066
 8Y4  O22  O  O     0  -0.361   2.8159  -1.6448  -0.5356
 8Y4  S23  S  S2    0   0.080   0.0657  -1.4423  -0.3413
 8Y4  H1   H  HCR6  0   0.263   8.7537   0.4246   0.0412
 8Y4  H2   H  HCR6  0   0.262   7.5216  -1.5918  -0.7046
 8Y4  H3   H  HCR6  0   0.228   7.4715   2.4330   0.7438
 8Y4  H4   H  HCR6  0   0.212   5.0874  -1.6264  -0.7493
 8Y4  H5   H  HCR6  0   0.205   5.0243   2.4158   0.7049
 8Y4  H6   H  HCH3  0   0.232  -2.4532  -3.2968  -0.9139
 8Y4  H7   H  HCH3  0   0.241  -2.0359  -3.1841   0.8101
 8Y4  H8   H  HCH3  0   0.323  -3.7235  -3.0822   0.2968
 8Y4  H9   H  HCH2  0   0.288   0.9452   0.4982   0.7910
 8Y4  H10  H  HCH2  0   0.305   0.9277   0.7282  -0.9553
 8Y4  H11  H  HNR6  0   0.413  -5.9083   2.2946   0.0325
 8Y4  H12  H  HNH2  0   0.414  -7.6339   0.8845   0.4890
 8Y4  H13  H  HNH2  0   0.415  -7.3902  -0.8051   0.4813
 8Y4  H14  H  HNH1  0   0.402   3.1075   1.3828   0.2399
 8Y4  C13  C  CH3   0  -0.577  -2.7040  -2.8182   0.0320

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
 8Y4  C13  N17  single    1.445  0.020  1.445
 8Y4  N19  C11  single    1.344  0.020  1.344
 8Y4  N16  C11  double    1.308  0.020  1.308
 8Y4  N16  C8   single    1.339  0.020  1.339
 8Y4  N17  C8   aromatic  1.361  0.020  1.361
 8Y4  N17  C9   aromatic  1.373  0.020  1.373
 8Y4  C11  N18  single    1.365  0.020  1.365
 8Y4  C8   C7   aromatic  1.381  0.020  1.381
 8Y4  S23  C9   single    1.744  0.020  1.744
 8Y4  S23  C14  single    1.806  0.020  1.806
 8Y4  C9   N15  aromatic  1.298  0.020  1.298
 8Y4  N18  C10  single    1.403  0.020  1.403
 8Y4  C7   N15  aromatic  1.373  0.020  1.373
 8Y4  C7   C10  single    1.423  0.020  1.423
 8Y4  C10  O21  double    1.220  0.020  1.220
 8Y4  C14  C12  single    1.515  0.020  1.515
 8Y4  C12  O22  double    1.216  0.020  1.216
 8Y4  C12  N20  single    1.351  0.020  1.351
 8Y4  N20  C6   single    1.401  0.020  1.401
 8Y4  C4   C6   aromatic  1.395  0.020  1.395
 8Y4  C4   C2   aromatic  1.389  0.020  1.389
 8Y4  C6   C5   aromatic  1.397  0.020  1.397
 8Y4  C2   C1   aromatic  1.386  0.020  1.386
 8Y4  C5   C3   aromatic  1.384  0.020  1.384
 8Y4  C1   C3   aromatic  1.389  0.020  1.389
 8Y4  C1   H1   single    0.930  0.020  1.080
 8Y4  C2   H2   single    0.930  0.020  1.080
 8Y4  C3   H3   single    0.930  0.020  1.080
 8Y4  C4   H4   single    0.930  0.020  1.080
 8Y4  C5   H5   single    0.930  0.020  1.080
 8Y4  C13  H6   single    0.970  0.020  1.090
 8Y4  C13  H7   single    0.970  0.020  1.090
 8Y4  C13  H8   single    0.970  0.020  1.090
 8Y4  C14  H9   single    0.970  0.020  1.090
 8Y4  C14  H10  single    0.970  0.020  1.090
 8Y4  N18  H11  single    0.860  0.020  1.020
 8Y4  N19  H12  single    0.890  0.020  1.040
 8Y4  N19  H13  single    0.890  0.020  1.040
 8Y4  N20  H14  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
 8Y4  H1   C1   C3   120.51  3.000
 8Y4  H1   C1   C2   120.58  3.000
 8Y4  C3   C1   C2   118.91  3.000
 8Y4  H2   C2   C4   118.66  3.000
 8Y4  H2   C2   C1   120.01  3.000
 8Y4  C4   C2   C1   121.34  3.000
 8Y4  H3   C3   C5   119.16  3.000
 8Y4  H3   C3   C1   120.32  3.000
 8Y4  C5   C3   C1   120.52  3.000
 8Y4  H4   C4   C6   121.17  3.000
 8Y4  H4   C4   C2   119.27  3.000
 8Y4  C6   C4   C2   119.55  3.000
 8Y4  H5   C5   C6   119.83  3.000
 8Y4  H5   C5   C3   119.67  3.000
 8Y4  C6   C5   C3   120.50  3.000
 8Y4  N20  C6   C5   116.61  3.000
 8Y4  C5   C6   C4   119.18  3.000
 8Y4  N20  C6   C4   124.20  3.000
 8Y4  N15  C7   C10  130.54  3.000
 8Y4  C10  C7   C8   118.70  3.000
 8Y4  N15  C7   C8   110.75  3.000
 8Y4  N17  C8   N16  125.96  3.000
 8Y4  N17  C8   C7   105.56  3.000
 8Y4  N16  C8   C7   128.48  3.000
 8Y4  S23  C9   N17  119.15  3.000
 8Y4  S23  C9   N15  127.41  3.000
 8Y4  N17  C9   N15  113.43  3.000
 8Y4  O21  C10  N18  120.42  3.000
 8Y4  O21  C10  C7   129.09  3.000
 8Y4  N18  C10  C7   110.49  3.000
 8Y4  N19  C11  N18  117.02  3.000
 8Y4  N18  C11  N16  122.98  3.000
 8Y4  N19  C11  N16  119.97  3.000
 8Y4  O22  C12  N20  125.41  3.000
 8Y4  N20  C12  C14  113.23  3.000
 8Y4  O22  C12  C14  121.36  3.000
 8Y4  H10  C14  H9   107.59  3.000
 8Y4  H10  C14  S23  110.43  3.000
 8Y4  H9   C14  S23  110.30  3.000
 8Y4  H10  C14  C12  110.23  3.000
 8Y4  H9   C14  C12  111.40  3.000
 8Y4  S23  C14  C12  106.92  3.000
 8Y4  C9   N15  C7   104.27  3.000
 8Y4  C11  N16  C8   113.16  3.000
 8Y4  C13  N17  C9   127.05  3.000
 8Y4  C9   N17  C8   105.99  3.000
 8Y4  C13  N17  C8   126.95  3.000
 8Y4  H11  N18  C11  118.32  3.000
 8Y4  H11  N18  C10  115.49  3.000
 8Y4  C11  N18  C10  126.18  3.000
 8Y4  H13  N19  H12  116.08  3.000
 8Y4  H13  N19  C11  117.05  3.000
 8Y4  H12  N19  C11  120.53  3.000
 8Y4  H14  N20  C12  116.12  3.000
 8Y4  H14  N20  C6   114.67  3.000
 8Y4  C12  N20  C6   129.20  3.000
 8Y4  C14  S23  C9    98.14  3.000
 8Y4  H8   C13  H7   108.67  3.000
 8Y4  H8   C13  H6   108.72  3.000
 8Y4  H7   C13  H6   109.37  3.000
 8Y4  H8   C13  N17  108.52  3.000
 8Y4  H7   C13  N17  110.30  3.000
 8Y4  H6   C13  N17  111.20  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
 8Y4  CONST_01  C6   C4   C2   C1      0.00   0.0  0
 8Y4  CONST_02  C6   C5   C3   C1      0.00   0.0  0
 8Y4  CONST_03  C5   C6   C4   C2      0.00   0.0  0
 8Y4  CONST_04  C5   C3   C1   C2      0.00   0.0  0
 8Y4  CONST_05  C4   C6   C5   C3      0.00   0.0  0
 8Y4  CONST_06  C4   C2   C1   C3      0.00   0.0  0
 8Y4  CONST_07  C9   N17  C8   C7      0.00   0.0  0
 8Y4  CONST_08  N17  C9   N15  C7      0.00   0.0  0
 8Y4  CONST_09  N15  C9   N17  C8      0.00   0.0  0
 8Y4  CONST_10  C9   N15  C7   C8      0.00   0.0  0
 8Y4  CONST_11  N17  C8   C7   N15     0.00   0.0  0
 8Y4  CONST_12  C11  N18  C10  C7      0.00   0.0  0
 8Y4  CONST_13  N18  C11  N16  C8      0.00   0.0  0
 8Y4  CONST_14  N16  C11  N18  C10     0.00   0.0  0
 8Y4  CONST_15  N20  C6   C4   C2    180.00   0.0  0
 8Y4  CONST_16  N20  C6   C5   C3    180.00   0.0  0
 8Y4  CONST_17  C13  N17  C8   C7    180.00   0.0  0
 8Y4  CONST_18  S23  C9   N15  C7    180.00   0.0  0
 8Y4  CONST_19  S23  C9   N17  C8    180.00   0.0  0
 8Y4  CONST_20  N16  C8   N17  C13     0.00   0.0  0
 8Y4  CONST_21  N15  C9   N17  C13   180.00   0.0  0
 8Y4  CONST_22  N19  C11  N16  C8    180.00   0.0  0
 8Y4  CONST_23  N19  C11  N18  C10   180.00   0.0  0
 8Y4  CONST_24  O21  C10  N18  C11   180.00   0.0  0
 8Y4  CONST_25  H4   C4   C2   C1    180.00   0.0  0
 8Y4  CONST_26  H5   C5   C3   C1    180.00   0.0  0
 8Y4  CONST_27  H3   C3   C1   C2    180.00   0.0  0
 8Y4  CONST_28  H2   C2   C1   C3    180.00   0.0  0
 8Y4  CONST_29  H1   C1   C2   C4    180.00   0.0  0
 8Y4  CONST_30  H11  N18  C10  C7    180.00   0.0  0
 8Y4  CONST_31  C12  N20  C6   C4      0.00   0.0  0
 8Y4  CONST_32  C12  N20  C6   C5    180.00   0.0  0
 8Y4  CONST_33  H14  N20  C6   C4    180.00   0.0  0
 8Y4  CONST_35  H13  N19  C11  N16     0.00   0.0  0
 8Y4  CONST_36  C14  C12  N20  C6    180.00   0.0  0
 8Y4  CONST_37  O22  C12  N20  C6      0.00   0.0  0
 8Y4  Var_01    N17  C9   S23  C14  -168.92  30.0  2
 8Y4  Var_02    H6   C13  N17  C8    111.63  30.0  2
 8Y4  Var_03    C12  C14  S23  C9   -179.36  30.0  3
 8Y4  Var_04    S23  C14  C12  N20  -173.71  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
 8Y4  plan-1  C1   0.020
 8Y4  plan-1  C2   0.020
 8Y4  plan-1  C3   0.020
 8Y4  plan-1  C4   0.020
 8Y4  plan-1  C5   0.020
 8Y4  plan-1  C6   0.020
 8Y4  plan-1  N20  0.020
 8Y4  plan-1  H1   0.020
 8Y4  plan-1  H2   0.020
 8Y4  plan-1  H3   0.020
 8Y4  plan-1  H4   0.020
 8Y4  plan-1  H5   0.020
 8Y4  plan-2  C7   0.020
 8Y4  plan-2  C8   0.020
 8Y4  plan-2  C9   0.020
 8Y4  plan-2  C10  0.020
 8Y4  plan-2  C11  0.020
 8Y4  plan-2  N15  0.020
 8Y4  plan-2  N16  0.020
 8Y4  plan-2  N17  0.020
 8Y4  plan-2  N18  0.020
 8Y4  plan-2  N19  0.020
 8Y4  plan-2  O21  0.020
 8Y4  plan-2  S23  0.020
 8Y4  plan-2  H11  0.020
 8Y4  plan-2  H12  0.020
 8Y4  plan-2  H13  0.020
 8Y4  plan-2  C13  0.020
 8Y4  plan-3  C6   0.020
 8Y4  plan-3  C12  0.020
 8Y4  plan-3  C14  0.020
 8Y4  plan-3  N20  0.020
 8Y4  plan-3  O22  0.020
 8Y4  plan-3  H14  0.020

