# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 11:20:41 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 2-[(6-amino-7H-purin-8-yl)sulfanyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CSc1[nH]c2c(N)ncnc2n1
#
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
 3D3  3D3  2-[(6-amino-7H-purin-8-yl)sulfanyl]acetamide  ligand  23  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3D3
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
 3D3  N1    N  N     0  -0.467  -0.1796   0.9277   0.0044
 3D3  C3    C  CR56  0   0.307  -1.5437   0.9126  -0.0070
 3D3  N7    N  N     0  -0.449  -2.3468   1.9819   0.0047
 3D3  C9    C  CR16  0   0.026  -3.6263   1.6669  -0.0156
 3D3  N8    N  N     0  -0.466  -4.1808   0.4560  -0.0423
 3D3  C6    C  CR6   0   0.461  -3.3929  -0.6212  -0.0541
 3D3  N13   N  NH2   0  -0.825  -3.9570  -1.8385  -0.1144
 3D3  C2    C  CR56  0   0.157  -2.0121  -0.3964  -0.0370
 3D3  N4    N  NR15  0  -0.690  -0.8861  -1.1838  -0.0458
 3D3  C5    C  CR5   0   0.316   0.1683  -0.3358  -0.0201
 3D3  S10   S  S2    0   0.084   1.7890  -0.9642  -0.0237
 3D3  C14   C  CH2   0  -0.678   2.6921   0.6018   0.0077
 3D3  C11   C  C     0   0.540   4.1673   0.2544  -0.0100
 3D3  O12   O  O     0  -0.479   4.5431  -0.9074  -0.0317
 3D3  N15   N  NH2   0  -0.795   4.9836   1.3107   0.0004
 3D3  H9    H  HCR6  0   0.249  -4.3273   2.4951  -0.0079
 3D3  H131  H  HNH2  0   0.406  -3.4234  -2.6677   0.0797
 3D3  H132  H  HNH2  0   0.402  -4.9523  -1.9082   0.0165
 3D3  H4    H  HNR5  0   0.430  -0.8403  -2.1909  -0.0705
 3D3  H141  H  HCH2  0   0.323   2.4386   1.1687   0.9041
 3D3  H142  H  HCH2  0   0.323   2.4274   1.2105  -0.8576
 3D3  H151  H  HNH2  0   0.410   5.9824   1.1823  -0.0114
 3D3  H152  H  HNH2  0   0.417   4.6364   2.2547   0.0137

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
 3D3  N1   C3    aromatic  1.364  0.020  1.364
 3D3  N1   C5    aromatic  1.311  0.020  1.311
 3D3  C3   N7    aromatic  1.337  0.020  1.337
 3D3  C3   C2    aromatic  1.391  0.020  1.391
 3D3  N7   C9    aromatic  1.318  0.020  1.318
 3D3  C9   N8    aromatic  1.332  0.020  1.332
 3D3  C9   H9    single    0.930  0.020  1.080
 3D3  N8   C6    aromatic  1.335  0.020  1.335
 3D3  C6   N13   single    1.343  0.020  1.343
 3D3  C6   C2    aromatic  1.399  0.020  1.399
 3D3  N13  H131  single    0.890  0.020  1.040
 3D3  N13  H132  single    0.890  0.020  1.040
 3D3  C2   N4    aromatic  1.374  0.020  1.374
 3D3  N4   C5    aromatic  1.353  0.020  1.353
 3D3  N4   H4    single    0.860  0.020  1.020
 3D3  C5   S10   single    1.738  0.020  1.738
 3D3  S10  C14   single    1.808  0.020  1.808
 3D3  C14  C11   single    1.516  0.020  1.516
 3D3  C14  H141  single    0.970  0.020  1.090
 3D3  C14  H142  single    0.970  0.020  1.090
 3D3  C11  O12   double    1.221  0.020  1.221
 3D3  C11  N15   single    1.335  0.020  1.335
 3D3  N15  H151  single    0.860  0.020  1.020
 3D3  N15  H152  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
 3D3  C5    N1   C3    104.75  3.000
 3D3  C2    C3   N7    123.40  3.000
 3D3  C2    C3   N1    110.33  3.000
 3D3  N7    C3   N1    126.27  3.000
 3D3  C9    N7   C3    113.07  3.000
 3D3  H9    C9   N8    115.16  3.000
 3D3  H9    C9   N7    116.40  3.000
 3D3  N8    C9   N7    128.44  3.000
 3D3  C6    N8   C9    119.22  3.000
 3D3  C2    C6   N13   124.10  3.000
 3D3  C2    C6   N8    116.92  3.000
 3D3  N13   C6   N8    118.95  3.000
 3D3  H132  N13  H131  116.29  3.000
 3D3  H132  N13  C6    118.19  3.000
 3D3  H131  N13  C6    121.08  3.000
 3D3  N4    C2   C6    135.78  3.000
 3D3  N4    C2   C3    105.28  3.000
 3D3  C6    C2   C3    118.94  3.000
 3D3  H4    N4   C5    126.22  3.000
 3D3  H4    N4   C2    127.57  3.000
 3D3  C5    N4   C2    106.22  3.000
 3D3  S10   C5   N4    119.99  3.000
 3D3  S10   C5   N1    126.58  3.000
 3D3  N4    C5   N1    113.43  3.000
 3D3  C14   S10  C5     98.77  3.000
 3D3  H142  C14  H141  107.80  3.000
 3D3  H142  C14  C11   110.79  3.000
 3D3  H141  C14  C11   110.79  3.000
 3D3  H142  C14  S10   110.40  3.000
 3D3  H141  C14  S10   110.39  3.000
 3D3  C11   C14  S10   106.70  3.000
 3D3  N15   C11  O12   124.38  3.000
 3D3  N15   C11  C14   114.44  3.000
 3D3  O12   C11  C14   121.18  3.000
 3D3  H152  N15  H151  117.53  3.000
 3D3  H152  N15  C11   122.11  3.000
 3D3  H151  N15  C11   120.36  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
 3D3  CONST_01  C9    N7   C3   N1    180.00   0.0  0
 3D3  CONST_02  C6    C2   C3   N1    180.00   0.0  0
 3D3  CONST_03  N4    C2   C3   N1      0.00   0.0  0
 3D3  CONST_04  C2    N4   C5   N1      0.00   0.0  0
 3D3  CONST_05  N4    C5   N1   C3      0.00   0.0  0
 3D3  CONST_06  N8    C9   N7   C3      0.00   0.0  0
 3D3  CONST_07  N8    C6   C2   C3      0.00   0.0  0
 3D3  CONST_08  C5    N4   C2   C3      0.00   0.0  0
 3D3  CONST_09  C5    N1   C3   N7    180.00   0.0  0
 3D3  CONST_10  C6    C2   C3   N7      0.00   0.0  0
 3D3  CONST_11  N4    C2   C3   N7    180.00   0.0  0
 3D3  CONST_12  C6    N8   C9   N7      0.00   0.0  0
 3D3  CONST_13  C2    C3   N7   C9      0.00   0.0  0
 3D3  CONST_14  C2    C6   N8   C9      0.00   0.0  0
 3D3  CONST_15  N4    C2   C6   N8    180.00   0.0  0
 3D3  CONST_16  C5    N4   C2   C6    180.00   0.0  0
 3D3  CONST_17  C5    N1   C3   C2      0.00   0.0  0
 3D3  CONST_18  S10   C5   N1   C3    180.00   0.0  0
 3D3  CONST_19  N13   C6   C2   C3    180.00   0.0  0
 3D3  CONST_20  N13   C6   N8   C9    180.00   0.0  0
 3D3  CONST_21  N4    C2   C6   N13     0.00   0.0  0
 3D3  CONST_22  S10   C5   N4   C2    180.00   0.0  0
 3D3  CONST_23  H4    N4   C5   N1    180.00   0.0  0
 3D3  CONST_24  H9    C9   N7   C3    180.00   0.0  0
 3D3  CONST_25  H131  N13  C6   N8    180.00   0.0  0
 3D3  CONST_26  H132  N13  C6   N8      0.00   0.0  0
 3D3  CONST_27  H151  N15  C11  C14   180.00   0.0  0
 3D3  CONST_28  H152  N15  C11  C14     0.00   0.0  0
 3D3  Var_01    C11   C14  S10  C5   -179.28  30.0  3
 3D3  Var_02    O12   C11  C14  S10    -0.45  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
 3D3  plan-1  N1    0.020
 3D3  plan-1  C3    0.020
 3D3  plan-1  N7    0.020
 3D3  plan-1  C9    0.020
 3D3  plan-1  N8    0.020
 3D3  plan-1  C6    0.020
 3D3  plan-1  N13   0.020
 3D3  plan-1  C2    0.020
 3D3  plan-1  N4    0.020
 3D3  plan-1  C5    0.020
 3D3  plan-1  S10   0.020
 3D3  plan-1  H9    0.020
 3D3  plan-1  H4    0.020
 3D3  plan-2  C14   0.020
 3D3  plan-2  C11   0.020
 3D3  plan-2  O12   0.020
 3D3  plan-2  N15   0.020
 3D3  plan-2  H151  0.020
 3D3  plan-2  H152  0.020
 3D3  plan-3  C6    0.020
 3D3  plan-3  N13   0.020
 3D3  plan-3  H131  0.020
 3D3  plan-3  H132  0.020

