# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 06:01:26 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-amino-8-{[2-(4-methylphenyl)-2-oxoethyl]sulfanyl}-1,7-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)C(=O)CSc2[nH]c3C(=O)NC(=Nc3n2)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
 YH6  YH6  2-amino-8-{[2-(4-methylphenyl)-2-oxoethyl]sulfanyl}-1,7-dihydro-6H-purin-6-one  ligand  35  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YH6
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
 YH6  O07  O  O     0  -0.480   5.7549  -1.4883   0.0035
 YH6  C06  C  CR6   0   0.509   4.9912  -0.5346  -0.0220
 YH6  N01  N  NR16  0  -0.720   5.4662   0.7768  -0.0811
 YH6  C02  C  CR6   0   0.670   4.6951   1.9066  -0.1149
 YH6  N08  N  NH2   0  -0.834   5.3515   3.0760  -0.2237
 YH6  N03  N  N     0  -0.506   3.3898   1.8873  -0.0867
 YH6  C04  C  CR56  0   0.317   2.8521   0.6514  -0.0334
 YH6  C05  C  CR56  0   0.067   3.5764  -0.5254  -0.0010
 YH6  N11  N  NR15  0  -0.673   2.6421  -1.5328   0.0477
 YH6  N09  N  N     0  -0.473   1.5192   0.3835  -0.0054
 YH6  C10  C  CR5   0   0.320   1.4396  -0.9300   0.0409
 YH6  S12  S  S2    0   0.090  -0.0177  -1.8801   0.0815
 YH6  C13  C  CH2   0  -0.701  -1.2281  -0.5367   0.0604
 YH6  C14  C  C     0   0.387  -2.5998  -1.1668   0.0410
 YH6  O16  O  O     0  -0.388  -2.7108  -2.3747   0.0463
 YH6  C15  C  CR6   0  -0.018  -3.7737  -0.2692   0.0121
 YH6  C17  C  CR16  0  -0.242  -5.0530  -0.8275  -0.0496
 YH6  C18  C  CR16  0  -0.281  -6.1708  -0.0166  -0.0811
 YH6  C19  C  CR6   0   0.103  -6.0519   1.3744  -0.0477
 YH6  C22  C  CH3   0  -0.722  -7.2694   2.2468  -0.0501
 YH6  C20  C  CR16  0  -0.280  -4.7741   1.9263   0.0118
 YH6  C21  C  CR16  0  -0.274  -3.6488   1.1196   0.0411
 YH6  H1   H  HNR6  0   0.426   6.4728   0.8783  -0.1069
 YH6  H2   H  HNH2  0   0.410   6.3335   3.1326  -0.0133
 YH6  H3   H  HNH2  0   0.408   4.8199   3.9161  -0.0694
 YH6  H4   H  HNR5  0   0.429   2.8257  -2.5242   0.0762
 YH6  H6   H  HCH2  0   0.324  -1.1064   0.0978   0.9399
 YH6  H7   H  HCH2  0   0.325  -1.0810   0.0919  -0.8193
 YH6  H8   H  HCR6  0   0.264  -5.1717  -1.9025  -0.0770
 YH6  H9   H  HCR6  0   0.258  -7.1542  -0.4678  -0.1352
 YH6  H10  H  HCH3  0   0.258  -7.6762   2.3377   0.9594
 YH6  H11  H  HCH3  0   0.250  -7.0434   3.2520  -0.4028
 YH6  H12  H  HCH3  0   0.251  -8.0578   1.8318  -0.6773
 YH6  H13  H  HCR6  0   0.260  -4.6561   3.0025   0.0330
 YH6  H14  H  HCR6  0   0.267  -2.6758   1.5918   0.0870

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
 YH6  N08  C02  single    1.345  0.020  1.345
 YH6  N03  C02  double    1.306  0.020  1.306
 YH6  N03  C04  single    1.349  0.020  1.349
 YH6  C02  N01  single    1.368  0.020  1.368
 YH6  C04  N09  aromatic  1.360  0.020  1.360
 YH6  C04  C05  aromatic  1.382  0.020  1.382
 YH6  N01  C06  single    1.396  0.020  1.396
 YH6  N09  C10  aromatic  1.317  0.020  1.317
 YH6  C05  C06  single    1.415  0.020  1.415
 YH6  C05  N11  aromatic  1.375  0.020  1.375
 YH6  C06  O07  double    1.222  0.020  1.222
 YH6  C10  N11  aromatic  1.345  0.020  1.345
 YH6  C10  S12  single    1.740  0.020  1.740
 YH6  S12  C13  single    1.808  0.020  1.808
 YH6  C20  C21  aromatic  1.385  0.020  1.385
 YH6  C20  C19  aromatic  1.393  0.020  1.393
 YH6  C22  C19  single    1.498  0.020  1.498
 YH6  C21  C15  aromatic  1.395  0.020  1.395
 YH6  C19  C18  aromatic  1.396  0.020  1.396
 YH6  C15  C14  single    1.478  0.020  1.478
 YH6  C15  C17  aromatic  1.397  0.020  1.397
 YH6  C18  C17  aromatic  1.381  0.020  1.381
 YH6  C14  C13  single    1.510  0.020  1.510
 YH6  C14  O16  double    1.213  0.020  1.213
 YH6  N01  H1   single    0.860  0.020  1.020
 YH6  N08  H2   single    0.890  0.020  1.040
 YH6  N08  H3   single    0.890  0.020  1.040
 YH6  N11  H4   single    0.860  0.020  1.020
 YH6  C13  H6   single    0.970  0.020  1.090
 YH6  C13  H7   single    0.970  0.020  1.090
 YH6  C17  H8   single    0.930  0.020  1.080
 YH6  C18  H9   single    0.930  0.020  1.080
 YH6  C22  H10  single    0.970  0.020  1.090
 YH6  C22  H11  single    0.970  0.020  1.090
 YH6  C22  H12  single    0.970  0.020  1.090
 YH6  C20  H13  single    0.930  0.020  1.080
 YH6  C21  H14  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
 YH6  C05  C06  N01  109.56  3.000
 YH6  C05  C06  O07  129.02  3.000
 YH6  N01  C06  O07  121.42  3.000
 YH6  H1   N01  C02  118.49  3.000
 YH6  H1   N01  C06  115.71  3.000
 YH6  C02  N01  C06  125.80  3.000
 YH6  N03  C02  N08  120.15  3.000
 YH6  N03  C02  N01  123.41  3.000
 YH6  N08  C02  N01  116.41  3.000
 YH6  H3   N08  H2   115.90  3.000
 YH6  H3   N08  C02  117.10  3.000
 YH6  H2   N08  C02  120.55  3.000
 YH6  C04  N03  C02  114.38  3.000
 YH6  N09  C04  C05  110.20  3.000
 YH6  C05  C04  N03  124.90  3.000
 YH6  N09  C04  N03  124.89  3.000
 YH6  N11  C05  C04  105.58  3.000
 YH6  N11  C05  C06  132.47  3.000
 YH6  C04  C05  C06  121.94  3.000
 YH6  H4   N11  C10  127.11  3.000
 YH6  H4   N11  C05  126.69  3.000
 YH6  C10  N11  C05  106.19  3.000
 YH6  C10  N09  C04  104.87  3.000
 YH6  S12  C10  N09  126.59  3.000
 YH6  S12  C10  N11  120.25  3.000
 YH6  N09  C10  N11  113.15  3.000
 YH6  C13  S12  C10   98.90  3.000
 YH6  H7   C13  H6   107.44  3.000
 YH6  H7   C13  C14  110.64  3.000
 YH6  H6   C13  C14  110.76  3.000
 YH6  H7   C13  S12  110.31  3.000
 YH6  H6   C13  S12  110.36  3.000
 YH6  C14  C13  S12  107.35  3.000
 YH6  C15  C14  O16  122.15  3.000
 YH6  O16  C14  C13  119.91  3.000
 YH6  C15  C14  C13  117.93  3.000
 YH6  C21  C15  C17  118.74  3.000
 YH6  C17  C15  C14  119.04  3.000
 YH6  C21  C15  C14  122.22  3.000
 YH6  H8   C17  C18  119.60  3.000
 YH6  H8   C17  C15  119.92  3.000
 YH6  C18  C17  C15  120.49  3.000
 YH6  H9   C18  C19  119.56  3.000
 YH6  H9   C18  C17  119.42  3.000
 YH6  C19  C18  C17  121.02  3.000
 YH6  C20  C19  C22  120.99  3.000
 YH6  C22  C19  C18  120.72  3.000
 YH6  C20  C19  C18  118.28  3.000
 YH6  H12  C22  H11  108.37  3.000
 YH6  H12  C22  H10  107.12  3.000
 YH6  H11  C22  H10  107.45  3.000
 YH6  H12  C22  C19  111.54  3.000
 YH6  H11  C22  C19  111.68  3.000
 YH6  H10  C22  C19  110.47  3.000
 YH6  H13  C20  C21  119.34  3.000
 YH6  H13  C20  C19  119.64  3.000
 YH6  C21  C20  C19  121.02  3.000
 YH6  H14  C21  C20  118.50  3.000
 YH6  H14  C21  C15  121.05  3.000
 YH6  C20  C21  C15  120.45  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
 YH6  CONST_01  N11  C10  N09  C04     0.00   0.0  0
 YH6  CONST_02  C10  N11  C05  C04     0.00   0.0  0
 YH6  CONST_03  C10  N09  C04  C05     0.00   0.0  0
 YH6  CONST_04  N09  C10  N11  C05     0.00   0.0  0
 YH6  CONST_05  N09  C04  C05  N11     0.00   0.0  0
 YH6  CONST_06  C19  C20  C21  C15     0.00   0.0  0
 YH6  CONST_07  C19  C18  C17  C15     0.00   0.0  0
 YH6  CONST_08  C20  C21  C15  C17     0.00   0.0  0
 YH6  CONST_09  C20  C19  C18  C17     0.00   0.0  0
 YH6  CONST_10  C21  C20  C19  C18     0.00   0.0  0
 YH6  CONST_11  C21  C15  C17  C18     0.00   0.0  0
 YH6  CONST_12  N03  C02  N01  C06     0.00   0.0  0
 YH6  CONST_13  C04  N03  C02  N01     0.00   0.0  0
 YH6  CONST_14  C05  C06  N01  C02     0.00   0.0  0
 YH6  CONST_15  S12  C10  N09  C04   180.00   0.0  0
 YH6  CONST_16  S12  C10  N11  C05   180.00   0.0  0
 YH6  CONST_17  C20  C21  C15  C14   180.00   0.0  0
 YH6  CONST_18  C18  C17  C15  C14   180.00   0.0  0
 YH6  CONST_19  C22  C19  C18  C17   180.00   0.0  0
 YH6  CONST_20  C21  C20  C19  C22   180.00   0.0  0
 YH6  CONST_21  C02  N01  C06  O07   180.00   0.0  0
 YH6  CONST_22  N08  C02  N01  C06   180.00   0.0  0
 YH6  CONST_23  C04  N03  C02  N08   180.00   0.0  0
 YH6  CONST_24  H4   N11  C05  C06     0.00   0.0  0
 YH6  CONST_25  H13  C20  C21  C15   180.00   0.0  0
 YH6  CONST_26  H9   C18  C17  C15   180.00   0.0  0
 YH6  CONST_27  H14  C21  C15  C17   180.00   0.0  0
 YH6  CONST_28  H8   C17  C18  C19   180.00   0.0  0
 YH6  CONST_29  H1   N01  C02  N03   180.00   0.0  0
 YH6  CONST_31  H3   N08  C02  N01   180.00   0.0  0
 YH6  Var_01    C21  C15  C14  C13    -1.87  30.0  2
 YH6  Var_02    H10  C22  C19  C18    82.48  30.0  2
 YH6  Var_03    C14  C13  S12  C10   177.98  30.0  3
 YH6  Var_04    C15  C14  C13  S12  -179.59  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
 YH6  plan-1  C14  0.020
 YH6  plan-1  C15  0.020
 YH6  plan-1  C17  0.020
 YH6  plan-1  C18  0.020
 YH6  plan-1  C19  0.020
 YH6  plan-1  C22  0.020
 YH6  plan-1  C20  0.020
 YH6  plan-1  C21  0.020
 YH6  plan-1  H8   0.020
 YH6  plan-1  H9   0.020
 YH6  plan-1  H13  0.020
 YH6  plan-1  H14  0.020
 YH6  plan-2  O07  0.020
 YH6  plan-2  C06  0.020
 YH6  plan-2  N01  0.020
 YH6  plan-2  C02  0.020
 YH6  plan-2  N08  0.020
 YH6  plan-2  N03  0.020
 YH6  plan-2  C04  0.020
 YH6  plan-2  C05  0.020
 YH6  plan-2  N11  0.020
 YH6  plan-2  N09  0.020
 YH6  plan-2  C10  0.020
 YH6  plan-2  S12  0.020
 YH6  plan-2  H1   0.020
 YH6  plan-2  H2   0.020
 YH6  plan-2  H3   0.020
 YH6  plan-2  H4   0.020
 YH6  plan-3  C13  0.020
 YH6  plan-3  C14  0.020
 YH6  plan-3  O16  0.020
 YH6  plan-3  C15  0.020

