# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:16:20 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-amino-8-{[2-(3-methylphenyl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)C(=O)CSc2[nH]c3N=C(N)NC(=O)c3n2
#
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
 YH3  YH3  2-amino-8-{[2-(3-methylphenyl)-2-oxoethyl]sulfanyl}-1,9-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_YH3
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
 YH3  O16  O  O     0  -0.384  -2.8224   2.1242  -0.0643
 YH3  C14  C  C     0   0.387  -2.6261   0.9284  -0.0601
 YH3  C15  C  CR6   0   0.019  -3.7380  -0.0525  -0.0376
 YH3  C17  C  CR16  0  -0.313  -5.0501   0.4223   0.0010
 YH3  C18  C  CR6   0   0.114  -6.1320  -0.4475   0.0239
 YH3  C22  C  CH3   0  -0.719  -7.5396   0.0722   0.0355
 YH3  C19  C  CR16  0  -0.286  -5.8746  -1.8188   0.0113
 YH3  C20  C  CR16  0  -0.223  -4.5761  -2.3048  -0.0267
 YH3  C21  C  CR16  0  -0.309  -3.5042  -1.4268  -0.0515
 YH3  C13  C  CH2   0  -0.701  -1.2157   0.3929  -0.0766
 YH3  S12  S  S2    0   0.083  -0.0893   1.8050  -0.0936
 YH3  C10  C  CR5   0   0.299   1.4159   0.9239  -0.0770
 YH3  N09  N  NR15  0  -0.689   2.6016   1.6108  -0.0623
 YH3  C04  C  CR56  0   0.481   3.5949   0.6835  -0.0476
 YH3  C05  C  CR56  0  -0.082   2.9451  -0.5358  -0.0553
 YH3  N11  N  N     0  -0.443   1.5806  -0.3634  -0.0737
 YH3  N03  N  N     0  -0.503   4.9114   0.9269  -0.0241
 YH3  C02  C  CR6   0   0.686   5.6348  -0.1655  -0.0124
 YH3  N08  N  NH2   0  -0.831   6.9747  -0.0812  -0.0290
 YH3  N01  N  NR16  0  -0.722   5.0918  -1.4172  -0.0216
 YH3  C06  C  CR6   0   0.493   3.7245  -1.7259  -0.0428
 YH3  O07  O  O     0  -0.477   3.3512  -2.8878  -0.0484
 YH3  H1   H  HCR6  0   0.258  -5.2258   1.4910   0.0173
 YH3  H2   H  HCH3  0   0.253  -7.9273   0.1628  -0.9812
 YH3  H3   H  HCH3  0   0.247  -8.2077  -0.5951   0.5788
 YH3  H4   H  HCH3  0   0.247  -7.5973   1.0585   0.4938
 YH3  H5   H  HCR6  0   0.261  -6.7025  -2.5171   0.0334
 YH3  H6   H  HCR6  0   0.266  -4.3995  -3.3720  -0.0344
 YH3  H7   H  HCR6  0   0.267  -2.4982  -1.8242  -0.0787
 YH3  H8   H  HCH2  0   0.322  -1.0315  -0.2280   0.8023
 YH3  H9   H  HCH2  0   0.322  -1.0528  -0.2339  -0.9555
 YH3  H10  H  HNR5  0   0.426   2.7265   2.6125  -0.0618
 YH3  H12  H  HNH2  0   0.411   7.3791   0.8220   0.1529
 YH3  H13  H  HNH2  0   0.413   7.5386  -0.8741   0.2272
 YH3  H14  H  HNR6  0   0.425   5.7194  -2.2114  -0.0219

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
 YH3  N08  C02  single    1.343  0.020  1.343
 YH3  C02  N03  double    1.310  0.020  1.310
 YH3  C02  N01  single    1.364  0.020  1.364
 YH3  N03  C04  single    1.339  0.020  1.339
 YH3  N01  C06  single    1.402  0.020  1.402
 YH3  C04  N09  aromatic  1.359  0.020  1.359
 YH3  C04  C05  aromatic  1.382  0.020  1.382
 YH3  N09  C10  aromatic  1.370  0.020  1.370
 YH3  C06  C05  single    1.423  0.020  1.423
 YH3  C06  O07  double    1.220  0.020  1.220
 YH3  C05  N11  aromatic  1.375  0.020  1.375
 YH3  C10  N11  aromatic  1.298  0.020  1.298
 YH3  C10  S12  single    1.744  0.020  1.744
 YH3  S12  C13  single    1.806  0.020  1.806
 YH3  C13  C14  single    1.509  0.020  1.509
 YH3  C21  C20  aromatic  1.386  0.020  1.386
 YH3  C21  C15  aromatic  1.394  0.020  1.394
 YH3  C20  C19  aromatic  1.387  0.020  1.387
 YH3  C14  C15  single    1.483  0.020  1.483
 YH3  C14  O16  double    1.212  0.020  1.212
 YH3  C15  C17  aromatic  1.396  0.020  1.396
 YH3  C19  C18  aromatic  1.395  0.020  1.395
 YH3  C17  C18  aromatic  1.388  0.020  1.388
 YH3  C18  C22  single    1.501  0.020  1.501
 YH3  C17  H1   single    0.930  0.020  1.080
 YH3  C22  H2   single    0.970  0.020  1.090
 YH3  C22  H3   single    0.970  0.020  1.090
 YH3  C22  H4   single    0.970  0.020  1.090
 YH3  C19  H5   single    0.930  0.020  1.080
 YH3  C20  H6   single    0.930  0.020  1.080
 YH3  C21  H7   single    0.930  0.020  1.080
 YH3  C13  H8   single    0.970  0.020  1.090
 YH3  C13  H9   single    0.970  0.020  1.090
 YH3  N09  H10  single    0.860  0.020  1.020
 YH3  N08  H12  single    0.890  0.020  1.040
 YH3  N08  H13  single    0.890  0.020  1.040
 YH3  N01  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
 YH3  C13  C14  C15  117.80  3.000
 YH3  C15  C14  O16  122.10  3.000
 YH3  C13  C14  O16  120.10  3.000
 YH3  C21  C15  C17  119.55  3.000
 YH3  C17  C15  C14  118.70  3.000
 YH3  C21  C15  C14  121.75  3.000
 YH3  H1   C17  C18  119.44  3.000
 YH3  H1   C17  C15  119.24  3.000
 YH3  C18  C17  C15  121.32  3.000
 YH3  C19  C18  C22  120.90  3.000
 YH3  C22  C18  C17  120.94  3.000
 YH3  C19  C18  C17  118.15  3.000
 YH3  H4   C22  H3   108.20  3.000
 YH3  H4   C22  H2   107.33  3.000
 YH3  H3   C22  H2   107.31  3.000
 YH3  H4   C22  C18  111.51  3.000
 YH3  H3   C22  C18  111.53  3.000
 YH3  H2   C22  C18  110.77  3.000
 YH3  H5   C19  C20  119.36  3.000
 YH3  H5   C19  C18  119.49  3.000
 YH3  C20  C19  C18  121.15  3.000
 YH3  H6   C20  C21  119.91  3.000
 YH3  H6   C20  C19  119.91  3.000
 YH3  C21  C20  C19  120.18  3.000
 YH3  H7   C21  C20  119.14  3.000
 YH3  H7   C21  C15  121.21  3.000
 YH3  C20  C21  C15  119.65  3.000
 YH3  H9   C13  H8   107.24  3.000
 YH3  H9   C13  S12  110.38  3.000
 YH3  H8   C13  S12  110.30  3.000
 YH3  H9   C13  C14  110.61  3.000
 YH3  H8   C13  C14  110.53  3.000
 YH3  S12  C13  C14  107.80  3.000
 YH3  C10  S12  C13   98.23  3.000
 YH3  N11  C10  N09  112.79  3.000
 YH3  N11  C10  S12  127.64  3.000
 YH3  N09  C10  S12  119.57  3.000
 YH3  H10  N09  C04  125.93  3.000
 YH3  H10  N09  C10  127.19  3.000
 YH3  C04  N09  C10  106.89  3.000
 YH3  N03  C04  C05  128.53  3.000
 YH3  C05  C04  N09  104.97  3.000
 YH3  N03  C04  N09  126.50  3.000
 YH3  C06  C05  N11  130.43  3.000
 YH3  N11  C05  C04  110.85  3.000
 YH3  C06  C05  C04  118.72  3.000
 YH3  C05  N11  C10  104.50  3.000
 YH3  C02  N03  C04  113.04  3.000
 YH3  N01  C02  N08  117.05  3.000
 YH3  N01  C02  N03  123.03  3.000
 YH3  N08  C02  N03  119.90  3.000
 YH3  H13  N08  H12  115.85  3.000
 YH3  H13  N08  C02  120.44  3.000
 YH3  H12  N08  C02  117.09  3.000
 YH3  H14  N01  C06  115.59  3.000
 YH3  H14  N01  C02  118.23  3.000
 YH3  C06  N01  C02  126.18  3.000
 YH3  O07  C06  N01  120.54  3.000
 YH3  O07  C06  C05  128.96  3.000
 YH3  N01  C06  C05  110.50  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
 YH3  CONST_01  C19  C20  C21  C15     0.00   0.0  0
 YH3  CONST_02  C19  C18  C17  C15     0.00   0.0  0
 YH3  CONST_03  C20  C21  C15  C17     0.00   0.0  0
 YH3  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 YH3  CONST_05  C21  C20  C19  C18     0.00   0.0  0
 YH3  CONST_06  C21  C15  C17  C18     0.00   0.0  0
 YH3  CONST_07  C05  C04  N09  C10     0.00   0.0  0
 YH3  CONST_08  C04  C05  N11  C10     0.00   0.0  0
 YH3  CONST_09  N11  C05  C04  N09     0.00   0.0  0
 YH3  CONST_10  C05  N11  C10  N09     0.00   0.0  0
 YH3  CONST_11  N11  C10  N09  C04     0.00   0.0  0
 YH3  CONST_12  N01  C02  N03  C04     0.00   0.0  0
 YH3  CONST_13  C02  N01  C06  C05     0.00   0.0  0
 YH3  CONST_14  C06  N01  C02  N03     0.00   0.0  0
 YH3  CONST_15  C20  C21  C15  C14   180.00   0.0  0
 YH3  CONST_16  C18  C17  C15  C14   180.00   0.0  0
 YH3  CONST_17  C22  C18  C17  C15   180.00   0.0  0
 YH3  CONST_18  C20  C19  C18  C22   180.00   0.0  0
 YH3  CONST_19  C04  N09  C10  S12   180.00   0.0  0
 YH3  CONST_20  C05  N11  C10  S12   180.00   0.0  0
 YH3  CONST_21  N08  C02  N03  C04   180.00   0.0  0
 YH3  CONST_22  O07  C06  N01  C02   180.00   0.0  0
 YH3  CONST_23  C06  N01  C02  N08   180.00   0.0  0
 YH3  CONST_24  H6   C20  C21  C15   180.00   0.0  0
 YH3  CONST_25  H7   C21  C15  C17   180.00   0.0  0
 YH3  CONST_26  H5   C19  C18  C17   180.00   0.0  0
 YH3  CONST_27  H1   C17  C18  C19   180.00   0.0  0
 YH3  CONST_28  H10  N09  C04  C05   180.00   0.0  0
 YH3  CONST_29  H14  N01  C06  C05   180.00   0.0  0
 YH3  CONST_30  H12  N08  C02  N03     0.00   0.0  0
 YH3  Var_01    C21  C15  C14  O16   179.10  30.0  2
 YH3  Var_02    N09  C10  S12  C13  -178.98  30.0  1
 YH3  Var_03    H2   C22  C18  C17    91.93  30.0  2
 YH3  Var_04    S12  C13  C14  C15  -179.71  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
 YH3  plan-1  C14  0.020
 YH3  plan-1  C15  0.020
 YH3  plan-1  C17  0.020
 YH3  plan-1  C18  0.020
 YH3  plan-1  C22  0.020
 YH3  plan-1  C19  0.020
 YH3  plan-1  C20  0.020
 YH3  plan-1  C21  0.020
 YH3  plan-1  H1   0.020
 YH3  plan-1  H5   0.020
 YH3  plan-1  H6   0.020
 YH3  plan-1  H7   0.020
 YH3  plan-2  S12  0.020
 YH3  plan-2  C10  0.020
 YH3  plan-2  N09  0.020
 YH3  plan-2  C04  0.020
 YH3  plan-2  C05  0.020
 YH3  plan-2  N11  0.020
 YH3  plan-2  N03  0.020
 YH3  plan-2  C02  0.020
 YH3  plan-2  N08  0.020
 YH3  plan-2  N01  0.020
 YH3  plan-2  C06  0.020
 YH3  plan-2  O07  0.020
 YH3  plan-2  H10  0.020
 YH3  plan-2  H12  0.020
 YH3  plan-2  H13  0.020
 YH3  plan-2  H14  0.020
 YH3  plan-3  O16  0.020
 YH3  plan-3  C14  0.020
 YH3  plan-3  C15  0.020
 YH3  plan-3  C13  0.020

