# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 12:28:14 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [(2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(SCC(O)=O)nc2C(=O)NC(=Nc12)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
 8Y7  8Y7  '[(2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]acetic acid'  ligand  25  17  .  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_8Y7
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
 8Y7  C1   C  CR56   0  -0.084   1.3372   0.7188  -0.0246
 8Y7  C2   C  CR56   0   0.490   1.7201  -0.6082  -0.0403
 8Y7  C3   C  CR5    0   0.302  -0.4588  -0.3976  -0.0074
 8Y7  C4   C  CR6    0   0.487   2.3459   1.7200  -0.0257
 8Y7  C5   C  CR6    0   0.682   3.8939  -0.2001  -0.0670
 8Y7  C6   C  C      0   0.442  -4.4834   0.3717   0.0394
 8Y7  C8   C  CH2    0  -0.680  -2.9677   0.6400   0.0146
 8Y7  N9   N  N      0  -0.453  -0.0318   0.8310  -0.0043
 8Y7  N10  N  N      0  -0.510   2.9596  -1.1170  -0.0596
 8Y7  N11  N  NR5    0  -0.529   0.5616  -1.3205  -0.0290
 8Y7  N12  N  NR16   0  -0.723   3.6210   1.1364  -0.0484
 8Y7  N13  N  NH2    0  -0.833   5.1873  -0.5592  -0.1364
 8Y7  O14  O  OC    -1  -0.602  -5.2008   1.3846   0.0274
 8Y7  O15  O  O      0  -0.482   2.2235   2.9354  -0.0095
 8Y7  O16  O  O      0  -0.596  -4.8363  -0.8217   0.0701
 8Y7  S17  S  S2     0   0.021  -2.1118  -0.9540   0.0148
 8Y7  H1   H  HCH3   0   0.263  -0.0805  -3.1003   0.8679
 8Y7  H2   H  HCH3   0   0.263  -0.1281  -3.0916  -0.9073
 8Y7  H3   H  HCH3   0   0.275   1.4207  -3.1985  -0.0614
 8Y7  H4   H  HCH2   0   0.282  -2.6869   1.2091  -0.8726
 8Y7  H5   H  HCH2   0   0.282  -2.6617   1.2222   0.8848
 8Y7  H6   H  HNR6   0   0.423   4.3968   1.7860  -0.0571
 8Y7  H7   H  HNH2   0   0.412   5.9121   0.0955   0.1044
 8Y7  H8   H  HNH2   0   0.410   5.4015  -1.5293   0.0225
 8Y7  C7   C  CH3    0  -0.541   0.4283  -2.7583  -0.0323

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
 8Y7  C7   N11  single    1.444  0.020  1.444
 8Y7  N10  C5   double    1.309  0.020  1.309
 8Y7  N10  C2   single    1.340  0.020  1.340
 8Y7  N13  C5   single    1.344  0.020  1.344
 8Y7  N11  C2   aromatic  1.360  0.020  1.360
 8Y7  N11  C3   aromatic  1.376  0.020  1.376
 8Y7  C5   N12  single    1.364  0.020  1.364
 8Y7  C2   C1   aromatic  1.381  0.020  1.381
 8Y7  S17  C3   single    1.744  0.020  1.744
 8Y7  S17  C8   single    1.809  0.020  1.809
 8Y7  C3   N9   aromatic  1.301  0.020  1.301
 8Y7  N12  C4   single    1.403  0.020  1.403
 8Y7  C1   N9   aromatic  1.374  0.020  1.374
 8Y7  C1   C4   single    1.421  0.020  1.421
 8Y7  C4   O15  double    1.222  0.020  1.222
 8Y7  C8   C6   single    1.539  0.020  1.539
 8Y7  O16  C6   deloc     1.245  0.020  1.245
 8Y7  C6   O14  deloc     1.241  0.020  1.241
 8Y7  C7   H1   single    0.970  0.020  1.090
 8Y7  C7   H2   single    0.970  0.020  1.090
 8Y7  C7   H3   single    0.970  0.020  1.090
 8Y7  C8   H4   single    0.970  0.020  1.090
 8Y7  C8   H5   single    0.970  0.020  1.090
 8Y7  N12  H6   single    0.860  0.020  1.020
 8Y7  N13  H7   single    0.890  0.020  1.040
 8Y7  N13  H8   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
 8Y7  N9   C1   C4   130.52  3.000
 8Y7  C4   C1   C2   118.69  3.000
 8Y7  N9   C1   C2   110.79  3.000
 8Y7  N11  C2   N10  126.09  3.000
 8Y7  N11  C2   C1   105.49  3.000
 8Y7  N10  C2   C1   128.42  3.000
 8Y7  S17  C3   N11  119.27  3.000
 8Y7  S17  C3   N9   127.76  3.000
 8Y7  N11  C3   N9   112.97  3.000
 8Y7  O15  C4   N12  120.35  3.000
 8Y7  O15  C4   C1   129.03  3.000
 8Y7  N12  C4   C1   110.61  3.000
 8Y7  N13  C5   N12  117.06  3.000
 8Y7  N12  C5   N10  122.91  3.000
 8Y7  N13  C5   N10  120.00  3.000
 8Y7  O16  C6   O14  128.22  3.000
 8Y7  O14  C6   C8   115.26  3.000
 8Y7  O16  C6   C8   116.52  3.000
 8Y7  H5   C8   H4   107.34  3.000
 8Y7  H5   C8   S17  109.72  3.000
 8Y7  H4   C8   S17  109.76  3.000
 8Y7  H5   C8   C6   110.88  3.000
 8Y7  H4   C8   C6   110.95  3.000
 8Y7  S17  C8   C6   108.20  3.000
 8Y7  C3   N9   C1   104.47  3.000
 8Y7  C5   N10  C2   113.22  3.000
 8Y7  C7   N11  C3   126.83  3.000
 8Y7  C3   N11  C2   106.29  3.000
 8Y7  C7   N11  C2   126.88  3.000
 8Y7  H6   N12  C5   118.39  3.000
 8Y7  H6   N12  C4   115.47  3.000
 8Y7  C5   N12  C4   126.14  3.000
 8Y7  H8   N13  H7   115.87  3.000
 8Y7  H8   N13  C5   117.02  3.000
 8Y7  H7   N13  C5   120.47  3.000
 8Y7  C8   S17  C3    99.63  3.000
 8Y7  H3   C7   H2   108.74  3.000
 8Y7  H3   C7   H1   108.77  3.000
 8Y7  H2   C7   H1   109.22  3.000
 8Y7  H3   C7   N11  108.62  3.000
 8Y7  H2   C7   N11  110.72  3.000
 8Y7  H1   C7   N11  110.72  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
 8Y7  CONST_01  C3   N11  C2   C1      0.00   0.0  0
 8Y7  CONST_02  N11  C3   N9   C1      0.00   0.0  0
 8Y7  CONST_03  N9   C3   N11  C2      0.00   0.0  0
 8Y7  CONST_04  C3   N9   C1   C2      0.00   0.0  0
 8Y7  CONST_05  N11  C2   C1   N9      0.00   0.0  0
 8Y7  CONST_06  C5   N12  C4   C1      0.00   0.0  0
 8Y7  CONST_07  N12  C5   N10  C2      0.00   0.0  0
 8Y7  CONST_08  N10  C5   N12  C4      0.00   0.0  0
 8Y7  CONST_09  C7   N11  C2   C1    180.00   0.0  0
 8Y7  CONST_10  S17  C3   N9   C1    180.00   0.0  0
 8Y7  CONST_11  S17  C3   N11  C2    180.00   0.0  0
 8Y7  CONST_12  N10  C2   N11  C7      0.00   0.0  0
 8Y7  CONST_13  N9   C3   N11  C7    180.00   0.0  0
 8Y7  CONST_14  N13  C5   N10  C2    180.00   0.0  0
 8Y7  CONST_15  N13  C5   N12  C4    180.00   0.0  0
 8Y7  CONST_16  O15  C4   N12  C5    180.00   0.0  0
 8Y7  CONST_17  H6   N12  C4   C1    180.00   0.0  0
 8Y7  CONST_19  H8   N13  C5   N10     0.00   0.0  0
 8Y7  Var_01    N11  C3   S17  C8   -179.25  30.0  2
 8Y7  Var_02    H1   C7   N11  C2    118.50  30.0  2
 8Y7  Var_03    C6   C8   S17  C3   -179.76  30.0  3
 8Y7  Var_04    S17  C8   C6   O14  -179.26  30.0  3

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
 8Y7  plan-1  C1   0.020
 8Y7  plan-1  C2   0.020
 8Y7  plan-1  C3   0.020
 8Y7  plan-1  C4   0.020
 8Y7  plan-1  C5   0.020
 8Y7  plan-1  N9   0.020
 8Y7  plan-1  N10  0.020
 8Y7  plan-1  N11  0.020
 8Y7  plan-1  N12  0.020
 8Y7  plan-1  N13  0.020
 8Y7  plan-1  O15  0.020
 8Y7  plan-1  S17  0.020
 8Y7  plan-1  H6   0.020
 8Y7  plan-1  H7   0.020
 8Y7  plan-1  H8   0.020
 8Y7  plan-1  C7   0.020
 8Y7  plan-2  C6   0.020
 8Y7  plan-2  C8   0.020
 8Y7  plan-2  O14  0.020
 8Y7  plan-2  O16  0.020

