# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:16:38 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 1-{[1,3-dimethyl-7-(3-methylbutyl)-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl]methyl}piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCn1c(CN2CCC(CC2)C(N)=O)nc3N(C)C(=O)N(C)C(=O)c13
#
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
 3ST  3ST  1-{[1,3-dimethyl-7-(3-methylbutyl)-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl]methyl}piperidine-4-carboxamide  ligand  58  28  .  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_3ST
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
 3ST  C1   C  CR6   0   0.551  -3.2586   0.1996  -0.8036
 3ST  C2   C  CR56  0   0.118  -2.0840   0.3905  -0.0236
 3ST  C3   C  CR56  0   0.438  -1.9152   1.4594   0.8173
 3ST  C8   C  CR5   0   0.468  -0.1569   0.3039   0.9871
 3ST  N9   N  NR5   0  -0.501  -0.9244  -0.3437   0.0946
 3ST  C10  C  CH2   0  -0.326  -0.6312  -1.6298  -0.5200
 3ST  C11  C  CH2   0  -0.423  -1.2405  -2.7838   0.2634
 3ST  C15  C  CH2   0  -0.386   1.1860  -0.1817   1.4258
 3ST  C17  C  CH2   0  -0.282   2.5048   1.0286  -0.1856
 3ST  C18  C  CH2   0  -0.444   3.3422   0.8808  -1.4442
 3ST  C20  C  CH2   0  -0.431   4.1651  -1.2909  -0.5607
 3ST  C21  C  CH2   0  -0.288   3.2701  -1.0930   0.6531
 3ST  C22  C  C     0   0.535   5.6590   0.7511  -0.3770
 3ST  O28  O  O     0  -0.466  -3.4782  -0.7293  -1.5630
 3ST  N6   N  NR6   0  -0.606  -4.1863   1.2292  -0.6019
 3ST  C5   C  CR6   0   0.754  -4.0300   2.3307   0.2326
 3ST  O26  O  O     0  -0.497  -4.8985   3.1788   0.3176
 3ST  N4   N  NR6   0  -0.595  -2.8696   2.4262   0.9529
 3ST  C27  C  CH3   0  -0.534  -2.6812   3.5682   1.8309
 3ST  N7   N  N     0  -0.482  -0.7288   1.4116   1.4412
 3ST  C12  C  CH1   0  -0.239  -0.7888  -4.1576  -0.2340
 3ST  N16  N  NT    0  -0.417   2.1152  -0.2748   0.3209
 3ST  C19  C  CH1   0  -0.408   4.5929   0.0292  -1.1956
 3ST  N23  N  NH2   0  -0.804   6.0288   1.9519  -0.8540
 3ST  H1   H  HCH2  0   0.270  -1.0064  -1.6137  -1.5413
 3ST  H2   H  HCH2  0   0.281   0.4523  -1.7002  -0.5766
 3ST  H3   H  HCH2  0   0.224  -0.9763  -2.6835   1.3220
 3ST  H4   H  HCH2  0   0.240  -2.3303  -2.7147   0.2069
 3ST  H5   H  HCH3  0   0.228   1.3112  -3.6873  -0.6647
 3ST  H6   H  HCH3  0   0.216   1.0060  -4.2231   0.9877
 3ST  H7   H  HCH3  0   0.234   0.9996  -5.3813  -0.3400
 3ST  H8   H  HCH3  0   0.227  -2.6435  -5.1413   0.3374
 3ST  H9   H  HCH3  0   0.228  -1.2795  -6.2415   0.1441
 3ST  H10  H  HCH3  0   0.215  -1.3842  -5.2085   1.5690
 3ST  H11  H  HCH2  0   0.249   1.5332   0.4825   2.2311
 3ST  H12  H  HCH2  0   0.270   1.0790  -1.1755   1.8725
 3ST  H13  H  HCH2  0   0.199   3.0578   1.6077   0.5758
 3ST  H14  H  HCH2  0   0.250   1.6087   1.6062  -0.4238
 3ST  H15  H  HCH2  0   0.243   2.7380   0.3859  -2.2083
 3ST  H16  H  HCH2  0   0.239   3.5865   1.8685  -1.8382
 3ST  H17  H  HCH2  0   0.241   5.0298  -1.8921  -0.2785
 3ST  H18  H  HCH2  0   0.234   3.6120  -1.8618  -1.3116
 3ST  H19  H  HCH2  0   0.235   2.9112  -2.0680   0.9937
 3ST  H20  H  HCH2  0   0.208   3.8472  -0.6577   1.4828
 3ST  H21  H  HCH3  0   0.254  -6.2895   1.1715  -0.6439
 3ST  H22  H  HCH3  0   0.254  -5.5419   2.0384  -1.9953
 3ST  H23  H  HCH3  0   0.266  -5.4710   0.2749  -1.9260
 3ST  H24  H  HCH3  0   0.258  -2.6909   4.4975   1.2648
 3ST  H25  H  HCH3  0   0.258  -3.4594   3.6051   2.5903
 3ST  H26  H  HCH3  0   0.268  -1.7186   3.4675   2.3211
 3ST  H27  H  HCH1  0   0.221  -1.0217  -4.2292  -1.3032
 3ST  H29  H  HCH1  0   0.286   5.0563  -0.1834  -2.1662
 3ST  H30  H  HNH2  0   0.398   6.7801   2.4595  -0.4155
 3ST  H31  H  HNH2  0   0.404   5.6884   2.3066  -1.7305
 3ST  C25  C  CH3   0  -0.527  -5.4476   1.1805  -1.3325
 3ST  O24  O  O     0  -0.487   6.1638   0.2704   0.6282
 3ST  C13  C  CH3   0  -0.666   0.7134  -4.3677  -0.0559
 3ST  C14  C  CH3   0  -0.652  -1.5687  -5.2490   0.4925

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
 3ST  N23  C22  single    1.344  0.020  1.344
 3ST  C22  O24  double    1.223  0.020  1.223
 3ST  C22  C19  single    1.526  0.020  1.526
 3ST  C20  C19  single    1.526  0.020  1.526
 3ST  C20  C21  single    1.521  0.020  1.521
 3ST  C19  C18  single    1.533  0.020  1.533
 3ST  C18  C17  single    1.519  0.020  1.519
 3ST  C21  N16  single    1.454  0.020  1.454
 3ST  C27  N4   single    1.453  0.020  1.453
 3ST  N7   C8   aromatic  1.327  0.020  1.327
 3ST  N7   C3   aromatic  1.341  0.020  1.341
 3ST  C15  N16  single    1.447  0.020  1.447
 3ST  C15  C8   single    1.494  0.020  1.494
 3ST  N16  C17  single    1.452  0.020  1.452
 3ST  C8   N9   aromatic  1.344  0.020  1.344
 3ST  N4   C3   single    1.365  0.020  1.365
 3ST  N4   C5   single    1.369  0.020  1.369
 3ST  C3   C2   aromatic  1.370  0.020  1.370
 3ST  O26  C5   double    1.217  0.020  1.217
 3ST  C5   N6   single    1.391  0.020  1.391
 3ST  N9   C2   aromatic  1.378  0.020  1.378
 3ST  N9   C10  single    1.455  0.020  1.455
 3ST  C2   C1   single    1.423  0.020  1.423
 3ST  C10  C11  single    1.522  0.020  1.522
 3ST  C12  C11  single    1.529  0.020  1.529
 3ST  C12  C13  single    1.527  0.020  1.527
 3ST  C12  C14  single    1.525  0.020  1.525
 3ST  N6   C1   single    1.401  0.020  1.401
 3ST  N6   C25  single    1.458  0.020  1.458
 3ST  C1   O28  double    1.220  0.020  1.220
 3ST  C10  H1   single    0.970  0.020  1.090
 3ST  C10  H2   single    0.970  0.020  1.090
 3ST  C11  H3   single    0.970  0.020  1.090
 3ST  C11  H4   single    0.970  0.020  1.090
 3ST  C13  H5   single    0.970  0.020  1.090
 3ST  C13  H6   single    0.970  0.020  1.090
 3ST  C13  H7   single    0.970  0.020  1.090
 3ST  C14  H8   single    0.970  0.020  1.090
 3ST  C14  H9   single    0.970  0.020  1.090
 3ST  C14  H10  single    0.970  0.020  1.090
 3ST  C15  H11  single    0.970  0.020  1.090
 3ST  C15  H12  single    0.970  0.020  1.090
 3ST  C17  H13  single    0.970  0.020  1.090
 3ST  C17  H14  single    0.970  0.020  1.090
 3ST  C18  H15  single    0.970  0.020  1.090
 3ST  C18  H16  single    0.970  0.020  1.090
 3ST  C20  H17  single    0.970  0.020  1.090
 3ST  C20  H18  single    0.970  0.020  1.090
 3ST  C21  H19  single    0.970  0.020  1.090
 3ST  C21  H20  single    0.970  0.020  1.090
 3ST  C25  H21  single    0.970  0.020  1.090
 3ST  C25  H22  single    0.970  0.020  1.090
 3ST  C25  H23  single    0.970  0.020  1.090
 3ST  C27  H24  single    0.970  0.020  1.090
 3ST  C27  H25  single    0.970  0.020  1.090
 3ST  C27  H26  single    0.970  0.020  1.090
 3ST  C12  H27  single    0.970  0.020  1.090
 3ST  C19  H29  single    0.970  0.020  1.090
 3ST  N23  H30  single    0.860  0.020  1.020
 3ST  N23  H31  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
 3ST  N6   C1   O28  122.02  3.000
 3ST  O28  C1   C2   126.31  3.000
 3ST  N6   C1   C2   111.67  3.000
 3ST  N9   C2   C3   105.03  3.000
 3ST  N9   C2   C1   132.10  3.000
 3ST  C3   C2   C1   122.87  3.000
 3ST  N7   C3   N4   126.68  3.000
 3ST  N4   C3   C2   121.81  3.000
 3ST  N7   C3   C2   111.51  3.000
 3ST  N7   C8   C15  123.94  3.000
 3ST  C15  C8   N9   123.50  3.000
 3ST  N7   C8   N9   112.56  3.000
 3ST  C10  N9   C8   126.26  3.000
 3ST  C10  N9   C2   127.19  3.000
 3ST  C8   N9   C2   106.32  3.000
 3ST  H2   C10  H1   107.20  3.000
 3ST  H2   C10  C11  112.13  3.000
 3ST  H1   C10  C11  110.87  3.000
 3ST  H2   C10  N9   106.26  3.000
 3ST  H1   C10  N9   108.29  3.000
 3ST  C11  C10  N9   111.84  3.000
 3ST  H4   C11  H3   106.53  3.000
 3ST  H4   C11  C12  109.53  3.000
 3ST  H3   C11  C12  108.98  3.000
 3ST  H4   C11  C10  108.93  3.000
 3ST  H3   C11  C10  109.35  3.000
 3ST  C12  C11  C10  113.29  3.000
 3ST  H12  C15  H11  106.28  3.000
 3ST  H12  C15  N16  108.42  3.000
 3ST  H11  C15  N16  113.28  3.000
 3ST  H12  C15  C8   109.09  3.000
 3ST  H11  C15  C8   107.60  3.000
 3ST  N16  C15  C8   111.96  3.000
 3ST  H14  C17  H13  106.48  3.000
 3ST  H14  C17  N16  109.31  3.000
 3ST  H13  C17  N16  111.38  3.000
 3ST  H14  C17  C18  108.85  3.000
 3ST  H13  C17  C18  110.25  3.000
 3ST  N16  C17  C18  110.47  3.000
 3ST  H16  C18  H15  106.33  3.000
 3ST  H16  C18  C19  112.26  3.000
 3ST  H15  C18  C19  108.24  3.000
 3ST  H16  C18  C17  109.54  3.000
 3ST  H15  C18  C17  108.58  3.000
 3ST  C19  C18  C17  111.68  3.000
 3ST  H18  C20  H17  106.92  3.000
 3ST  H18  C20  C19  107.93  3.000
 3ST  H17  C20  C19  111.25  3.000
 3ST  H18  C20  C21  108.56  3.000
 3ST  H17  C20  C21  109.38  3.000
 3ST  C19  C20  C21  112.60  3.000
 3ST  H20  C21  H19  106.86  3.000
 3ST  H20  C21  N16  111.48  3.000
 3ST  H19  C21  N16  108.20  3.000
 3ST  H20  C21  C20  110.16  3.000
 3ST  H19  C21  C20  109.01  3.000
 3ST  N16  C21  C20  111.00  3.000
 3ST  N23  C22  O24  121.96  3.000
 3ST  O24  C22  C19  122.91  3.000
 3ST  N23  C22  C19  115.12  3.000
 3ST  C5   N6   C25  115.10  3.000
 3ST  C25  N6   C1   118.44  3.000
 3ST  C5   N6   C1   126.46  3.000
 3ST  N4   C5   O26  121.30  3.000
 3ST  O26  C5   N6   120.91  3.000
 3ST  N4   C5   N6   117.78  3.000
 3ST  C27  N4   C5   118.86  3.000
 3ST  C5   N4   C3   119.40  3.000
 3ST  C27  N4   C3   121.73  3.000
 3ST  H26  C27  H25  108.81  3.000
 3ST  H26  C27  H24  108.80  3.000
 3ST  H25  C27  H24  109.14  3.000
 3ST  H26  C27  N4   108.37  3.000
 3ST  H25  C27  N4   110.84  3.000
 3ST  H24  C27  N4   110.84  3.000
 3ST  C8   N7   C3   104.58  3.000
 3ST  H27  C12  C14  108.00  3.000
 3ST  H27  C12  C13  108.27  3.000
 3ST  C14  C12  C13  110.42  3.000
 3ST  H27  C12  C11  108.25  3.000
 3ST  C14  C12  C11  109.68  3.000
 3ST  C13  C12  C11  112.10  3.000
 3ST  C21  N16  C17  111.83  3.000
 3ST  C17  N16  C15  112.40  3.000
 3ST  C21  N16  C15  111.83  3.000
 3ST  H29  C19  C22  105.75  3.000
 3ST  H29  C19  C20  108.60  3.000
 3ST  C22  C19  C20  112.46  3.000
 3ST  H29  C19  C18  107.99  3.000
 3ST  C20  C19  C18  108.62  3.000
 3ST  C22  C19  C18  113.22  3.000
 3ST  H31  N23  H30  117.04  3.000
 3ST  H31  N23  C22  122.12  3.000
 3ST  H30  N23  C22  120.06  3.000
 3ST  H23  C25  H22  108.88  3.000
 3ST  H23  C25  H21  108.87  3.000
 3ST  H22  C25  H21  108.97  3.000
 3ST  H23  C25  N6   108.73  3.000
 3ST  H22  C25  N6   110.72  3.000
 3ST  H21  C25  N6   110.64  3.000
 3ST  H7   C13  H6   107.53  3.000
 3ST  H7   C13  H5   106.88  3.000
 3ST  H6   C13  H5   107.67  3.000
 3ST  H7   C13  C12  110.82  3.000
 3ST  H6   C13  C12  110.87  3.000
 3ST  H5   C13  C12  112.83  3.000
 3ST  H10  C14  H9   107.67  3.000
 3ST  H10  C14  H8   107.61  3.000
 3ST  H9   C14  H8   107.78  3.000
 3ST  H10  C14  C12  110.87  3.000
 3ST  H9   C14  C12  111.30  3.000
 3ST  H8   C14  C12  111.42  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
 3ST  CONST_01  C8   N7   C3   C2      0.00   0.0  0
 3ST  CONST_02  N7   C8   N9   C2      0.00   0.0  0
 3ST  CONST_03  N9   C8   N7   C3      0.00   0.0  0
 3ST  CONST_04  C8   N9   C2   C3      0.00   0.0  0
 3ST  CONST_05  N7   C3   C2   N9      0.00   0.0  0
 3ST  CONST_06  N4   C5   N6   C1      0.00   0.0  0
 3ST  CONST_07  C5   N6   C1   C2      0.00   0.0  0
 3ST  CONST_08  N6   C5   N4   C3      0.00   0.0  0
 3ST  CONST_09  C10  N9   C2   C1      0.00   0.0  0
 3ST  CONST_10  C15  C8   N9   C2    180.00   0.0  0
 3ST  CONST_11  C15  C8   N7   C3    180.00   0.0  0
 3ST  CONST_12  C10  N9   C2   C3    180.00   0.0  0
 3ST  CONST_13  N7   C8   N9   C10   180.00   0.0  0
 3ST  CONST_14  O26  C5   N6   C1    180.00   0.0  0
 3ST  CONST_15  C25  N6   C1   C2    180.00   0.0  0
 3ST  CONST_16  O26  C5   N4   C3    180.00   0.0  0
 3ST  CONST_17  N4   C5   N6   C25   180.00   0.0  0
 3ST  CONST_18  C5   N6   C1   O28   180.00   0.0  0
 3ST  CONST_19  C27  N4   C5   N6    180.00   0.0  0
 3ST  CONST_20  O26  C5   N6   C25     0.00   0.0  0
 3ST  CONST_21  O28  C1   N6   C25     0.00   0.0  0
 3ST  CONST_22  C27  N4   C5   O26     0.00   0.0  0
 3ST  CONST_23  H30  N23  C22  C19   180.00   0.0  0
 3ST  CONST_24  H31  N23  C22  C19     0.00   0.0  0
 3ST  Var_01    C20  C21  N16  C17   -58.50  30.0  1
 3ST  Var_02    C21  N16  C17  C18    60.11  30.0  1
 3ST  Var_03    C19  C20  C21  N16    54.79  30.0  1
 3ST  Var_04    C19  C18  C17  N16   -57.68  30.0  1
 3ST  Var_05    N16  C15  C8   N9     60.75  30.0  1
 3ST  Var_06    C11  C10  N9   C2    -81.17  30.0  2
 3ST  Var_07    H21  C25  N6   C1    121.50  30.0  3
 3ST  Var_08    H24  C27  N4   C3    117.92  30.0  3
 3ST  Var_09    C12  C11  C10  N9   -171.72  30.0  3
 3ST  Var_10    C13  C12  C11  C10    63.62  30.0  1
 3ST  Var_11    H5   C13  C12  C11   -64.86  30.0  3
 3ST  Var_12    H8   C14  C12  C11    58.63  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 3ST  chir_01  C19  C22  C20  C18  negativ

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
 3ST  plan-1  C1   0.020
 3ST  plan-1  C2   0.020
 3ST  plan-1  C3   0.020
 3ST  plan-1  C8   0.020
 3ST  plan-1  N9   0.020
 3ST  plan-1  C10  0.020
 3ST  plan-1  C15  0.020
 3ST  plan-1  O28  0.020
 3ST  plan-1  N6   0.020
 3ST  plan-1  C5   0.020
 3ST  plan-1  O26  0.020
 3ST  plan-1  N4   0.020
 3ST  plan-1  C27  0.020
 3ST  plan-1  N7   0.020
 3ST  plan-1  C25  0.020
 3ST  plan-2  C22  0.020
 3ST  plan-2  C19  0.020
 3ST  plan-2  N23  0.020
 3ST  plan-2  H30  0.020
 3ST  plan-2  H31  0.020
 3ST  plan-2  O24  0.020

