# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:13:50 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-methyl-1-(5-oxohexyl)-7-propyl-3,7-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCn1cnc2N(C)C(=O)N(CCCCC(C)=O)C(=O)c12
#
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
 POY  POY  3-methyl-1-(5-oxohexyl)-7-propyl-3,7-dihydro-1H-purine-2,6-dione  ligand  44  22  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_POY
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
 POY  N1    N  NR6   0  -0.615   0.0605   0.5372  -0.5746
 POY  C2    C  CR6   0   0.572   0.9204  -0.5079  -0.2196
 POY  C3    C  CR56  0   0.122   2.1824  -0.0274   0.2287
 POY  C4    C  CR56  0   0.432   2.4716   1.3086   0.3406
 POY  N5    N  NR6   0  -0.593   1.5642   2.2694  -0.0018
 POY  C6    C  CR6   0   0.756   0.3277   1.8996  -0.4625
 POY  N7    N  NR5   0  -0.476   3.3102  -0.6757   0.6790
 POY  C8    C  CR15  0   0.134   4.1784   0.2857   1.0091
 POY  N9    N  N     0  -0.475   3.7085   1.5078   0.8242
 POY  C10   C  CH2   0  -0.302  -1.2788   0.1734  -1.0410
 POY  C11   C  CH2   0  -0.431  -2.3051   0.1434   0.0823
 POY  C12   C  CH2   0  -0.426  -3.6713  -0.3000  -0.4252
 POY  C13   C  CH2   0  -0.561  -4.7129  -0.2810   0.6801
 POY  C14   C  C     0   0.395  -6.0950  -0.7168   0.2688
 POY  C15   C  CH3   0  -0.769  -7.1038  -0.8171   1.3809
 POY  O16   O  O     0  -0.409  -6.3759  -0.9810  -0.8794
 POY  O17   O  O     0  -0.468   0.5823  -1.6764  -0.3035
 POY  O18   O  O     0  -0.494  -0.5032   2.7358  -0.7632
 POY  C19   C  CH3   0  -0.532   1.8615   3.6845   0.1415
 POY  C20   C  CH2   0  -0.294   3.5714  -2.1057   0.6993
 POY  C21   C  CH2   0  -0.438   3.9090  -2.6563  -0.6785
 POY  C22   C  CH3   0  -0.670   4.1984  -4.1489  -0.6141
 POY  H8    H  HCR5  0   0.301   5.1617   0.0555   1.3911
 POY  H10   H  HCH2  0   0.261  -1.5769   0.8777  -1.8148
 POY  H10A  H  HCH2  0   0.261  -1.2081  -0.8043  -1.5121
 POY  H11   H  HCH2  0   0.231  -1.9661  -0.5369   0.8687
 POY  H11A  H  HCH2  0   0.232  -2.3824   1.1353   0.5350
 POY  H12   H  HCH2  0   0.229  -3.9885   0.3529  -1.2430
 POY  H12A  H  HCH2  0   0.229  -3.5954  -1.3065  -0.8459
 POY  H13   H  HCH2  0   0.264  -4.3996  -0.9065   1.5240
 POY  H13A  H  HCH2  0   0.269  -4.8045   0.7258   1.1049
 POY  H15   H  HCH3  0   0.257  -7.0239   0.0282   2.0644
 POY  H15A  H  HCH3  0   0.259  -8.1192  -0.8814   0.9949
 POY  H15B  H  HCH3  0   0.269  -6.8996  -1.7165   1.9672
 POY  H19   H  HCH3  0   0.259   1.7491   4.2005  -0.8093
 POY  H19A  H  HCH3  0   0.258   1.2053   4.1451   0.8775
 POY  H19B  H  HCH3  0   0.268   2.8882   3.7868   0.4761
 POY  H20   H  HCH2  0   0.267   4.4032  -2.2634   1.3859
 POY  H20A  H  HCH2  0   0.267   2.7027  -2.6113   1.1181
 POY  H21   H  HCH2  0   0.238   3.0764  -2.4722  -1.3602
 POY  H21A  H  HCH2  0   0.234   4.7741  -2.1196  -1.0750
 POY  H22   H  HCH3  0   0.225   5.0299  -4.3663   0.0584
 POY  H22A  H  HCH3  0   0.226   3.3299  -4.7056  -0.2584
 POY  H22B  H  HCH3  0   0.239   4.4585  -4.5376  -1.5981

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
 POY  N1   C2    single    1.399  0.020  1.399
 POY  N1   C6    single    1.393  0.020  1.393
 POY  N1   C10   single    1.464  0.020  1.464
 POY  C2   C3    single    1.423  0.020  1.423
 POY  C2   O17   double    1.219  0.020  1.219
 POY  C3   C4    aromatic  1.371  0.020  1.371
 POY  C3   N7    aromatic  1.377  0.020  1.377
 POY  C4   N5    single    1.365  0.020  1.365
 POY  C4   N9    aromatic  1.343  0.020  1.343
 POY  N5   C6    single    1.370  0.020  1.370
 POY  N5   C19   single    1.453  0.020  1.453
 POY  C6   O18   double    1.217  0.020  1.217
 POY  N7   C8    aromatic  1.337  0.020  1.337
 POY  N7   C20   single    1.454  0.020  1.454
 POY  C8   N9    aromatic  1.322  0.020  1.322
 POY  C10  C11   single    1.522  0.020  1.522
 POY  C11  C12   single    1.523  0.020  1.523
 POY  C12  C13   single    1.519  0.020  1.519
 POY  C13  C14   single    1.506  0.020  1.506
 POY  C14  C15   single    1.505  0.020  1.505
 POY  C14  O16   double    1.211  0.020  1.211
 POY  C20  C21   single    1.522  0.020  1.522
 POY  C21  C22   single    1.522  0.020  1.522
 POY  C8   H8    single    0.930  0.020  1.080
 POY  C10  H10   single    0.970  0.020  1.090
 POY  C10  H10A  single    0.970  0.020  1.090
 POY  C11  H11   single    0.970  0.020  1.090
 POY  C11  H11A  single    0.970  0.020  1.090
 POY  C12  H12   single    0.970  0.020  1.090
 POY  C12  H12A  single    0.970  0.020  1.090
 POY  C13  H13   single    0.970  0.020  1.090
 POY  C13  H13A  single    0.970  0.020  1.090
 POY  C15  H15   single    0.970  0.020  1.090
 POY  C15  H15A  single    0.970  0.020  1.090
 POY  C15  H15B  single    0.970  0.020  1.090
 POY  C19  H19   single    0.970  0.020  1.090
 POY  C19  H19A  single    0.970  0.020  1.090
 POY  C19  H19B  single    0.970  0.020  1.090
 POY  C20  H20   single    0.970  0.020  1.090
 POY  C20  H20A  single    0.970  0.020  1.090
 POY  C21  H21   single    0.970  0.020  1.090
 POY  C21  H21A  single    0.970  0.020  1.090
 POY  C22  H22   single    0.970  0.020  1.090
 POY  C22  H22A  single    0.970  0.020  1.090
 POY  C22  H22B  single    0.970  0.020  1.090

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
 POY  C10   N1   C6    116.37  3.000
 POY  C10   N1   C2    117.22  3.000
 POY  C6    N1   C2    126.32  3.000
 POY  O17   C2   C3    126.25  3.000
 POY  O17   C2   N1    121.87  3.000
 POY  C3    C2   N1    111.89  3.000
 POY  N7    C3   C4    105.03  3.000
 POY  N7    C3   C2    132.12  3.000
 POY  C4    C3   C2    122.80  3.000
 POY  N9    C4   N5    126.73  3.000
 POY  N9    C4   C3    111.60  3.000
 POY  N5    C4   C3    121.67  3.000
 POY  C19   N5   C6    118.72  3.000
 POY  C19   N5   C4    121.65  3.000
 POY  C6    N5   C4    119.61  3.000
 POY  O18   C6   N5    120.93  3.000
 POY  O18   C6   N1    121.42  3.000
 POY  N5    C6   N1    117.65  3.000
 POY  C20   N7   C8    125.96  3.000
 POY  C20   N7   C3    127.95  3.000
 POY  C8    N7   C3    105.91  3.000
 POY  H8    C8   N9    124.76  3.000
 POY  H8    C8   N7    121.70  3.000
 POY  N9    C8   N7    113.54  3.000
 POY  C8    N9   C4    103.92  3.000
 POY  H10A  C10  H10   106.96  3.000
 POY  H10A  C10  C11   110.23  3.000
 POY  H10   C10  C11   110.67  3.000
 POY  H10A  C10  N1    107.57  3.000
 POY  H10   C10  N1    108.44  3.000
 POY  C11   C10  N1    112.75  3.000
 POY  H11A  C11  H11   106.78  3.000
 POY  H11A  C11  C12   109.80  3.000
 POY  H11   C11  C12   109.66  3.000
 POY  H11A  C11  C10   109.60  3.000
 POY  H11   C11  C10   109.51  3.000
 POY  C12   C11  C10   111.38  3.000
 POY  H12A  C12  H12   106.38  3.000
 POY  H12A  C12  C13   109.82  3.000
 POY  H12   C12  C13   109.75  3.000
 POY  H12A  C12  C11   109.50  3.000
 POY  H12   C12  C11   109.60  3.000
 POY  C13   C12  C11   111.65  3.000
 POY  H13A  C13  H13   104.45  3.000
 POY  H13A  C13  C14   107.14  3.000
 POY  H13   C13  C14   107.90  3.000
 POY  H13A  C13  C12   110.53  3.000
 POY  H13   C13  C12   110.92  3.000
 POY  C14   C13  C12   115.27  3.000
 POY  O16   C14  C15   122.04  3.000
 POY  O16   C14  C13   122.33  3.000
 POY  C15   C14  C13   115.63  3.000
 POY  H15B  C15  H15A  108.42  3.000
 POY  H15B  C15  H15   106.75  3.000
 POY  H15A  C15  H15   109.68  3.000
 POY  H15B  C15  C14   109.03  3.000
 POY  H15A  C15  C14   111.55  3.000
 POY  H15   C15  C14   111.26  3.000
 POY  H19B  C19  H19A  108.80  3.000
 POY  H19B  C19  H19   108.82  3.000
 POY  H19A  C19  H19   109.15  3.000
 POY  H19B  C19  N5    108.42  3.000
 POY  H19A  C19  N5    110.82  3.000
 POY  H19   C19  N5    110.77  3.000
 POY  H20A  C20  H20   107.42  3.000
 POY  H20A  C20  C21   110.93  3.000
 POY  H20   C20  C21   110.40  3.000
 POY  H20A  C20  N7    108.59  3.000
 POY  H20   C20  N7    106.75  3.000
 POY  C21   C20  N7    112.53  3.000
 POY  H21A  C21  H21   107.12  3.000
 POY  H21A  C21  C22   110.28  3.000
 POY  H21   C21  C22   109.68  3.000
 POY  H21A  C21  C20   109.06  3.000
 POY  H21   C21  C20   109.58  3.000
 POY  C22   C21  C20   111.03  3.000
 POY  H22B  C22  H22A  107.60  3.000
 POY  H22B  C22  H22   107.68  3.000
 POY  H22A  C22  H22   107.69  3.000
 POY  H22B  C22  C21   110.93  3.000
 POY  H22A  C22  C21   111.28  3.000
 POY  H22   C22  C21   111.49  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
 POY  CONST_01  C8   N9   C4   C3      0.00   0.0  0
 POY  CONST_02  N9   C8   N7   C3      0.00   0.0  0
 POY  CONST_03  C8   N7   C3   C4      0.00   0.0  0
 POY  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 POY  CONST_05  N9   C4   C3   N7      0.00   0.0  0
 POY  CONST_06  C4   N5   C6   N1      0.00   0.0  0
 POY  CONST_07  N5   C6   N1   C2      0.00   0.0  0
 POY  CONST_08  C6   N1   C2   C3      0.00   0.0  0
 POY  CONST_09  C20  N7   C3   C2      0.00   0.0  0
 POY  CONST_10  C20  N7   C3   C4    180.00   0.0  0
 POY  CONST_11  C20  N7   C8   N9    180.00   0.0  0
 POY  CONST_12  C19  N5   C6   N1    180.00   0.0  0
 POY  CONST_13  O18  C6   N1   C2    180.00   0.0  0
 POY  CONST_14  C10  N1   C2   C3    180.00   0.0  0
 POY  CONST_15  O18  C6   N5   C4    180.00   0.0  0
 POY  CONST_16  C10  N1   C6   N5    180.00   0.0  0
 POY  CONST_17  O17  C2   N1   C6    180.00   0.0  0
 POY  CONST_18  H8   C8   N7   C3    180.00   0.0  0
 POY  CONST_19  O17  C2   N1   C10     0.00   0.0  0
 POY  CONST_20  O18  C6   N1   C10     0.00   0.0  0
 POY  CONST_21  C19  N5   C6   O18     0.00   0.0  0
 POY  Var_01    C11  C10  N1   C2     92.49  30.0  3
 POY  Var_02    C21  C20  N7   C3     75.72  30.0  2
 POY  Var_03    H19  C19  N5   C4    123.20  30.0  3
 POY  Var_04    C12  C11  C10  N1   -177.39  30.0  3
 POY  Var_05    C22  C21  C20  N7    179.06  30.0  3
 POY  Var_06    C13  C12  C11  C10  -177.82  30.0  3
 POY  Var_07    C14  C13  C12  C11  -179.53  30.0  3
 POY  Var_08    C15  C14  C13  C12   174.85  30.0  3
 POY  Var_09    H15  C15  C14  C13    42.49  30.0  3
 POY  Var_10    H22  C22  C21  C20   -58.92  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
 POY  plan-1  N1   0.020
 POY  plan-1  C2   0.020
 POY  plan-1  C3   0.020
 POY  plan-1  C4   0.020
 POY  plan-1  N5   0.020
 POY  plan-1  C6   0.020
 POY  plan-1  N7   0.020
 POY  plan-1  C8   0.020
 POY  plan-1  N9   0.020
 POY  plan-1  C10  0.020
 POY  plan-1  O17  0.020
 POY  plan-1  O18  0.020
 POY  plan-1  C19  0.020
 POY  plan-1  C20  0.020
 POY  plan-1  H8   0.020
 POY  plan-2  C13  0.020
 POY  plan-2  C14  0.020
 POY  plan-2  C15  0.020
 POY  plan-2  O16  0.020

