# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:44:15 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-amino-8-{[2-(2-methylphenyl)-2-oxoethyl]sulfanyl}-1,7-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1C(=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
 YH4  YH4  2-amino-8-{[2-(2-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_YH4
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
 YH4  O16  O  O     0  -0.385   2.9571  -1.9650   0.0802
 YH4  C14  C  C     0   0.375   2.7705  -0.7673   0.0539
 YH4  C15  C  CR6   0  -0.032   3.8659   0.2307   0.0402
 YH4  C21  C  CR6   0   0.119   5.2249  -0.1502   0.0425
 YH4  C22  C  CH3   0  -0.718   5.7127  -1.5700   0.0557
 YH4  C20  C  CR16  0  -0.299   6.1821   0.8624   0.0303
 YH4  C19  C  CR16  0  -0.229   5.8377   2.2051   0.0172
 YH4  C18  C  CR16  0  -0.256   4.5018   2.5755   0.0142
 YH4  C17  C  CR16  0  -0.288   3.5325   1.5900   0.0257
 YH4  C13  C  CH2   0  -0.703   1.3461  -0.2525   0.0343
 YH4  S12  S  S2    0   0.091   0.2563  -1.6963   0.0633
 YH4  C10  C  CR5   0   0.320  -1.2743  -0.8686   0.0264
 YH4  N11  N  NR15  0  -0.674  -2.4246  -1.5664   0.0362
 YH4  C05  C  CR56  0   0.067  -3.4376  -0.6375   0.0004
 YH4  C06  C  CR6   0   0.509  -4.8474  -0.7597  -0.0077
 YH4  O07  O  O     0  -0.480  -5.5320  -1.7717   0.0188
 YH4  N01  N  NR16  0  -0.719  -5.4259   0.5099  -0.0518
 YH4  C02  C  CR6   0   0.669  -4.7485   1.6982  -0.0812
 YH4  N08  N  NH2   0  -0.834  -5.4988   2.8121  -0.1707
 YH4  N03  N  N     0  -0.505  -3.4458   1.7834  -0.0662
 YH4  C04  C  CR56  0   0.317  -2.8105   0.5940  -0.0288
 YH4  N09  N  N     0  -0.472  -1.4604   0.4343  -0.0122
 YH4  H1   H  HCH3  0   0.249   5.3631  -2.1319  -0.8095
 YH4  H2   H  HCH3  0   0.242   6.8020  -1.5856   0.0456
 YH4  H3   H  HCH3  0   0.249   5.3789  -2.1095   0.9412
 YH4  H4   H  HCR6  0   0.260   7.2296   0.5879   0.0317
 YH4  H5   H  HCR6  0   0.269   6.6139   2.9589   0.0083
 YH4  H6   H  HCR6  0   0.267   4.2168   3.6188   0.0044
 YH4  H7   H  HCR6  0   0.273   2.4953   1.8963   0.0232
 YH4  H8   H  HCH2  0   0.324   1.1480   0.3831   0.8985
 YH4  H9   H  HCH2  0   0.324   1.1578   0.3408  -0.8620
 YH4  H10  H  HNR5  0   0.429  -2.5278  -2.5693   0.0644
 YH4  H11  H  HNR6  0   0.426  -6.4374   0.5305  -0.0706
 YH4  H12  H  HNH2  0   0.410  -6.4766   2.7867   0.0635
 YH4  H13  H  HNH2  0   0.408  -5.0334   3.6898  -0.0112

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
 YH4  N08  C02  single    1.346  0.020  1.346
 YH4  N03  C02  double    1.306  0.020  1.306
 YH4  N03  C04  single    1.349  0.020  1.349
 YH4  C02  N01  single    1.368  0.020  1.368
 YH4  N01  C06  single    1.396  0.020  1.396
 YH4  C04  N09  aromatic  1.360  0.020  1.360
 YH4  C04  C05  aromatic  1.382  0.020  1.382
 YH4  N09  C10  aromatic  1.317  0.020  1.317
 YH4  C06  C05  single    1.415  0.020  1.415
 YH4  C06  O07  double    1.222  0.020  1.222
 YH4  C05  N11  aromatic  1.375  0.020  1.375
 YH4  C10  N11  aromatic  1.345  0.020  1.345
 YH4  C10  S12  single    1.741  0.020  1.741
 YH4  C13  S12  single    1.809  0.020  1.809
 YH4  C13  C14  single    1.515  0.020  1.515
 YH4  C18  C17  aromatic  1.382  0.020  1.382
 YH4  C18  C19  aromatic  1.386  0.020  1.386
 YH4  C17  C15  aromatic  1.400  0.020  1.400
 YH4  C19  C20  aromatic  1.386  0.020  1.386
 YH4  C15  C14  single    1.482  0.020  1.482
 YH4  C15  C21  aromatic  1.411  0.020  1.411
 YH4  C20  C21  aromatic  1.393  0.020  1.393
 YH4  C14  O16  double    1.212  0.020  1.212
 YH4  C21  C22  single    1.501  0.020  1.501
 YH4  C22  H1   single    0.970  0.020  1.090
 YH4  C22  H2   single    0.970  0.020  1.090
 YH4  C22  H3   single    0.970  0.020  1.090
 YH4  C20  H4   single    0.930  0.020  1.080
 YH4  C19  H5   single    0.930  0.020  1.080
 YH4  C18  H6   single    0.930  0.020  1.080
 YH4  C17  H7   single    0.930  0.020  1.080
 YH4  C13  H8   single    0.970  0.020  1.090
 YH4  C13  H9   single    0.970  0.020  1.090
 YH4  N11  H10  single    0.860  0.020  1.020
 YH4  N01  H11  single    0.860  0.020  1.020
 YH4  N08  H12  single    0.890  0.020  1.040
 YH4  N08  H13  single    0.890  0.020  1.040

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
 YH4  C13  C14  C15  117.78  3.000
 YH4  C15  C14  O16  123.48  3.000
 YH4  C13  C14  O16  118.73  3.000
 YH4  C17  C15  C21  119.44  3.000
 YH4  C21  C15  C14  122.00  3.000
 YH4  C17  C15  C14  118.56  3.000
 YH4  C20  C21  C22  117.65  3.000
 YH4  C22  C21  C15  124.62  3.000
 YH4  C20  C21  C15  117.73  3.000
 YH4  H3   C22  H2   107.87  3.000
 YH4  H3   C22  H1   106.96  3.000
 YH4  H2   C22  H1   107.83  3.000
 YH4  H3   C22  C21  112.08  3.000
 YH4  H2   C22  C21  109.78  3.000
 YH4  H1   C22  C21  112.12  3.000
 YH4  H4   C20  C19  119.07  3.000
 YH4  H4   C20  C21  118.70  3.000
 YH4  C19  C20  C21  122.23  3.000
 YH4  H5   C19  C18  120.34  3.000
 YH4  H5   C19  C20  119.78  3.000
 YH4  C18  C19  C20  119.89  3.000
 YH4  H6   C18  C17  120.20  3.000
 YH4  H6   C18  C19  120.77  3.000
 YH4  C17  C18  C19  119.02  3.000
 YH4  H7   C17  C18  118.07  3.000
 YH4  H7   C17  C15  120.24  3.000
 YH4  C18  C17  C15  121.70  3.000
 YH4  H9   C13  H8   107.61  3.000
 YH4  H9   C13  S12  110.07  3.000
 YH4  H8   C13  S12  110.06  3.000
 YH4  H9   C13  C14  110.96  3.000
 YH4  H8   C13  C14  111.00  3.000
 YH4  S12  C13  C14  107.16  3.000
 YH4  C10  S12  C13   98.62  3.000
 YH4  N09  C10  N11  113.12  3.000
 YH4  N11  C10  S12  120.34  3.000
 YH4  N09  C10  S12  126.54  3.000
 YH4  H10  N11  C05  126.67  3.000
 YH4  H10  N11  C10  127.11  3.000
 YH4  C05  N11  C10  106.22  3.000
 YH4  C04  C05  C06  121.92  3.000
 YH4  C06  C05  N11  132.52  3.000
 YH4  C04  C05  N11  105.56  3.000
 YH4  N01  C06  O07  121.45  3.000
 YH4  O07  C06  C05  129.01  3.000
 YH4  N01  C06  C05  109.54  3.000
 YH4  H11  N01  C02  118.48  3.000
 YH4  H11  N01  C06  115.68  3.000
 YH4  C02  N01  C06  125.84  3.000
 YH4  N03  C02  N08  120.20  3.000
 YH4  N03  C02  N01  123.40  3.000
 YH4  N08  C02  N01  116.37  3.000
 YH4  H13  N08  H12  115.78  3.000
 YH4  H13  N08  C02  116.96  3.000
 YH4  H12  N08  C02  120.37  3.000
 YH4  C04  N03  C02  114.37  3.000
 YH4  N09  C04  N03  124.86  3.000
 YH4  N09  C04  C05  110.22  3.000
 YH4  N03  C04  C05  124.92  3.000
 YH4  C04  N09  C10  104.89  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
 YH4  CONST_01  C19  C18  C17  C15     0.00   0.0  0
 YH4  CONST_02  C19  C20  C21  C15     0.00   0.0  0
 YH4  CONST_03  C18  C17  C15  C21     0.00   0.0  0
 YH4  CONST_04  C18  C19  C20  C21     0.00   0.0  0
 YH4  CONST_05  C17  C18  C19  C20     0.00   0.0  0
 YH4  CONST_06  C17  C15  C21  C20     0.00   0.0  0
 YH4  CONST_07  C05  C04  N09  C10     0.00   0.0  0
 YH4  CONST_08  C04  C05  N11  C10     0.00   0.0  0
 YH4  CONST_09  N09  C04  C05  N11     0.00   0.0  0
 YH4  CONST_10  C04  N09  C10  N11     0.00   0.0  0
 YH4  CONST_11  N09  C10  N11  C05     0.00   0.0  0
 YH4  CONST_12  C02  N01  C06  C05     0.00   0.0  0
 YH4  CONST_13  N03  C02  N01  C06     0.00   0.0  0
 YH4  CONST_14  C04  N03  C02  N01     0.00   0.0  0
 YH4  CONST_15  C18  C17  C15  C14   180.00   0.0  0
 YH4  CONST_16  C20  C21  C15  C14   180.00   0.0  0
 YH4  CONST_17  C17  C15  C21  C22   180.00   0.0  0
 YH4  CONST_18  C19  C20  C21  C22   180.00   0.0  0
 YH4  CONST_19  C04  N09  C10  S12   180.00   0.0  0
 YH4  CONST_20  C05  N11  C10  S12   180.00   0.0  0
 YH4  CONST_21  N08  C02  N01  C06   180.00   0.0  0
 YH4  CONST_22  C02  N01  C06  O07   180.00   0.0  0
 YH4  CONST_23  C04  N03  C02  N08   180.00   0.0  0
 YH4  CONST_24  H6   C18  C17  C15   180.00   0.0  0
 YH4  CONST_25  H4   C20  C21  C15   180.00   0.0  0
 YH4  CONST_26  H7   C17  C15  C21   180.00   0.0  0
 YH4  CONST_27  H5   C19  C20  C21   180.00   0.0  0
 YH4  CONST_28  H10  N11  C05  C06     0.00   0.0  0
 YH4  CONST_29  H11  N01  C06  C05   180.00   0.0  0
 YH4  CONST_31  H13  N08  C02  N01   180.00   0.0  0
 YH4  Var_01    C17  C15  C14  O16  -179.25  30.0  2
 YH4  Var_02    N09  C10  S12  C13     0.08  30.0  3
 YH4  Var_03    H1   C22  C21  C15    59.66  30.0  2
 YH4  Var_04    S12  C13  C14  C15  -179.80  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
 YH4  plan-1  C14  0.020
 YH4  plan-1  C15  0.020
 YH4  plan-1  C21  0.020
 YH4  plan-1  C22  0.020
 YH4  plan-1  C20  0.020
 YH4  plan-1  C19  0.020
 YH4  plan-1  C18  0.020
 YH4  plan-1  C17  0.020
 YH4  plan-1  H4   0.020
 YH4  plan-1  H5   0.020
 YH4  plan-1  H6   0.020
 YH4  plan-1  H7   0.020
 YH4  plan-2  S12  0.020
 YH4  plan-2  C10  0.020
 YH4  plan-2  N11  0.020
 YH4  plan-2  C05  0.020
 YH4  plan-2  C06  0.020
 YH4  plan-2  O07  0.020
 YH4  plan-2  N01  0.020
 YH4  plan-2  C02  0.020
 YH4  plan-2  N08  0.020
 YH4  plan-2  N03  0.020
 YH4  plan-2  C04  0.020
 YH4  plan-2  N09  0.020
 YH4  plan-2  H10  0.020
 YH4  plan-2  H11  0.020
 YH4  plan-2  H12  0.020
 YH4  plan-2  H13  0.020
 YH4  plan-3  O16  0.020
 YH4  plan-3  C14  0.020
 YH4  plan-3  C15  0.020
 YH4  plan-3  C13  0.020

