# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 17:41:53 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  26  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  -0.081   1.3064   0.7187   0.0274
 8Y7  C2   C  CR56  0   0.496   1.7095  -0.6022   0.0148
 8Y7  C3   C  CR5   0   0.311  -0.4658  -0.4246   0.0495
 8Y7  C4   C  CR6   0   0.493   2.2994   1.7371   0.0165
 8Y7  C5   C  CR6   0   0.686   3.8756  -0.1602  -0.0221
 8Y7  C6   C  C     0   0.569  -4.4230   0.3538  -0.0293
 8Y7  C8   C  CH2   0  -0.671  -2.9394   0.6033  -0.0325
 8Y7  N9   N  N     0  -0.449  -0.0637   0.8096   0.0499
 8Y7  N10  N  N     0  -0.509   2.9552  -1.0920  -0.0127
 8Y7  N11  N  NR5   0  -0.531   0.5619  -1.3339   0.0283
 8Y7  N12  N  NR16  0  -0.724   3.5823   1.1724  -0.0078
 8Y7  N13  N  NH2   0  -0.832   5.1747  -0.4995  -0.0069
 8Y7  O14  O  OH1   0  -0.581  -5.0958   1.4854  -0.1342
 8Y7  O15  O  O     0  -0.477   2.1557   2.9491   0.0264
 8Y7  O16  O  O     0  -0.429  -4.9244  -0.7372   0.0582
 8Y7  S17  S  S2    0   0.065  -2.1129  -0.9991   0.0759
 8Y7  H1   H  HCH3  0   0.267  -0.0364  -3.1323   0.9216
 8Y7  H2   H  HCH3  0   0.267  -0.1180  -3.1060  -0.8542
 8Y7  H3   H  HCH3  0   0.280   1.4468  -3.1985  -0.0379
 8Y7  H4   H  HCH2  0   0.329  -2.6440   1.1231  -0.9451
 8Y7  H5   H  HCH2  0   0.330  -2.6623   1.2367   0.8116
 8Y7  H6   H  HNR6  0   0.425   4.3490   1.8331  -0.0043
 8Y7  H7   H  HNH2  0   0.413   5.8805   0.1691  -0.2649
 8Y7  H8   H  HNH2  0   0.411   5.3984  -1.4649  -0.1806
 8Y7  H9   H  HOH1  0   0.491  -6.0498   1.3133  -0.1269
 8Y7  C7   C  CH3   0  -0.546   0.4487  -2.7742   0.0147

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    1.445  0.020  1.445
 8Y7  N10  C5   double    1.310  0.020  1.310
 8Y7  N10  C2   single    1.339  0.020  1.339
 8Y7  N13  C5   single    1.343  0.020  1.343
 8Y7  N11  C2   aromatic  1.361  0.020  1.361
 8Y7  N11  C3   aromatic  1.372  0.020  1.372
 8Y7  C5   N12  single    1.365  0.020  1.365
 8Y7  C2   C1   aromatic  1.381  0.020  1.381
 8Y7  S17  C3   single    1.745  0.020  1.745
 8Y7  S17  C8   single    1.806  0.020  1.806
 8Y7  C3   N9   aromatic  1.298  0.020  1.298
 8Y7  N12  C4   single    1.402  0.020  1.402
 8Y7  C1   N9   aromatic  1.373  0.020  1.373
 8Y7  C1   C4   single    1.422  0.020  1.422
 8Y7  C4   O15  double    1.221  0.020  1.221
 8Y7  C8   C6   single    1.504  0.020  1.504
 8Y7  O16  C6   double    1.204  0.020  1.204
 8Y7  C6   O14  single    1.321  0.020  1.321
 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
 8Y7  O14  H9   single    0.850  0.020  0.980

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   130.48  3.000
 8Y7  C4   C1   C2   118.75  3.000
 8Y7  N9   C1   C2   110.77  3.000
 8Y7  N11  C2   N10  126.02  3.000
 8Y7  N11  C2   C1   105.54  3.000
 8Y7  N10  C2   C1   128.43  3.000
 8Y7  S17  C3   N11  119.28  3.000
 8Y7  S17  C3   N9   127.27  3.000
 8Y7  N11  C3   N9   113.46  3.000
 8Y7  O15  C4   N12  120.52  3.000
 8Y7  O15  C4   C1   128.96  3.000
 8Y7  N12  C4   C1   110.52  3.000
 8Y7  N13  C5   N12  117.04  3.000
 8Y7  N12  C5   N10  122.93  3.000
 8Y7  N13  C5   N10  120.00  3.000
 8Y7  O16  C6   O14  124.76  3.000
 8Y7  O14  C6   C8   111.11  3.000
 8Y7  O16  C6   C8   124.13  3.000
 8Y7  H5   C8   H4   107.56  3.000
 8Y7  H5   C8   S17  110.63  3.000
 8Y7  H4   C8   S17  110.42  3.000
 8Y7  H5   C8   C6   110.19  3.000
 8Y7  H4   C8   C6   110.36  3.000
 8Y7  S17  C8   C6   107.70  3.000
 8Y7  C3   N9   C1   104.25  3.000
 8Y7  C5   N10  C2   113.19  3.000
 8Y7  C7   N11  C3   127.01  3.000
 8Y7  C3   N11  C2   105.98  3.000
 8Y7  C7   N11  C2   127.00  3.000
 8Y7  H6   N12  C5   118.34  3.000
 8Y7  H6   N12  C4   115.48  3.000
 8Y7  C5   N12  C4   126.17  3.000
 8Y7  H8   N13  H7   115.95  3.000
 8Y7  H8   N13  C5   117.11  3.000
 8Y7  H7   N13  C5   120.53  3.000
 8Y7  H9   O14  C6   110.40  3.000
 8Y7  C8   S17  C3    97.99  3.000
 8Y7  H3   C7   H2   108.70  3.000
 8Y7  H3   C7   H1   108.74  3.000
 8Y7  H2   C7   H1   109.42  3.000
 8Y7  H3   C7   N11  108.54  3.000
 8Y7  H2   C7   N11  110.61  3.000
 8Y7  H1   C7   N11  110.78  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  CONST_20  H9   O14  C6   C8    180.00   0.0  0
 8Y7  Var_01    N11  C3   S17  C8   -175.88  30.0  2
 8Y7  Var_02    H1   C7   N11  C2    117.70  30.0  2
 8Y7  Var_03    C6   C8   S17  C3    179.87  30.0  3
 8Y7  Var_04    S17  C8   C6   O14  -178.72  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
 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
 8Y7  plan-2  H9   0.020

