# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 21:54:25 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]amino}-3,7-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc(NCCN3CCOCC3)[nH]c2C1=O
#
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
 WDD  WDD  1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]amino}-3,7-dihydro-1H-purine-2,6-dione  ligand  42  22  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WDD
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
 WDD  C10   C  CH2   0  -0.301  31.0590   0.7421   4.4790
 WDD  C11   C  CH2   0  -0.279  31.9408   1.4584   3.4620
 WDD  C13   C  CH2   0  -0.306  32.0694   3.7647   4.2068
 WDD  C14   C  CH2   0  -0.184  33.0010   4.8098   4.7912
 WDD  C16   C  CH2   0  -0.186  34.8335   3.8044   3.7895
 WDD  C17   C  CH2   0  -0.304  33.9432   2.7422   3.1744
 WDD  C19   C  CR56  0   0.110  26.7516   2.2091   3.7026
 WDD  C20   C  CR6   0   0.522  25.4346   2.7024   3.6217
 WDD  C03   C  CR6   0   0.748  25.4135   1.6340   1.3698
 WDD  C06   C  CR56  0   0.460  27.3547   1.4827   2.7115
 WDD  C08   C  CR5   0   0.750  28.7898   1.6219   4.2561
 WDD  N02   N  NR6   0  -0.605  24.8324   2.3650   2.3935
 WDD  N04   N  NR6   0  -0.592  26.7032   1.1944   1.5491
 WDD  N07   N  N     0  -0.529  28.6053   1.1167   3.0342
 WDD  N09   N  NH1   0  -0.694  29.9123   1.4761   4.9683
 WDD  N12   N  NT    0  -0.425  32.7774   2.5100   4.0115
 WDD  N18   N  NR15  0  -0.723  27.7095   2.2911   4.7027
 WDD  O15   O  O2    0  -0.479  34.1377   5.0141   3.9847
 WDD  O22   O  O     0  -0.495  24.8039   1.3879   0.3451
 WDD  H101  H  HCH2  0   0.246  30.7134  -0.1907   4.0293
 WDD  H102  H  HCH2  0   0.256  31.6607   0.4718   5.3462
 WDD  H112  H  HCH2  0   0.207  31.3310   1.8153   2.6173
 WDD  H111  H  HCH2  0   0.239  32.6034   0.6906   3.0539
 WDD  H132  H  HCH2  0   0.241  31.2399   3.6288   4.8999
 WDD  H131  H  HCH2  0   0.195  31.6410   4.1358   3.2590
 WDD  H142  H  HCH2  0   0.197  33.2996   4.5012   5.8035
 WDD  H141  H  HCH2  0   0.233  32.4816   5.7660   4.8729
 WDD  H162  H  HCH2  0   0.234  35.6764   4.0137   3.1289
 WDD  H161  H  HCH2  0   0.197  35.2367   3.4344   4.7434
 WDD  H172  H  HCH2  0   0.195  33.6599   3.0498   2.1529
 WDD  H171  H  HCH2  0   0.240  34.5143   1.8149   3.0846
 WDD  H013  H  HCH3  0   0.263  23.1339   3.3930   2.9938
 WDD  H011  H  HCH3  0   0.250  23.4134   3.4176   1.2502
 WDD  H012  H  HCH3  0   0.249  22.7989   1.9517   2.0302
 WDD  H051  H  HCH3  0   0.266  28.3409   0.1747   0.8037
 WDD  H052  H  HCH3  0   0.255  26.7852  -0.4722   0.2693
 WDD  H053  H  HCH3  0   0.256  27.4058   1.0354  -0.4252
 WDD  H091  H  HNH1  0   0.408  29.9554   1.8934   5.8824
 WDD  H181  H  HNR5  0   0.421  27.6057   2.7423   5.5981
 WDD  O21   O  O     0  -0.480  24.8433   3.3431   4.4786
 WDD  C01   C  CH3   0  -0.525  23.4657   2.8041   2.1473
 WDD  C05   C  CH3   0  -0.532  27.3389   0.4398   0.4831

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
 WDD  O22  C03   double    1.217  0.020  1.217
 WDD  C05  N04   single    1.453  0.020  1.453
 WDD  C03  N04   single    1.374  0.020  1.374
 WDD  C03  N02   single    1.386  0.020  1.386
 WDD  C01  N02   single    1.456  0.020  1.456
 WDD  N04  C06   single    1.363  0.020  1.363
 WDD  C16  O15   single    1.409  0.020  1.409
 WDD  C16  C17   single    1.516  0.020  1.516
 WDD  N02  C20   single    1.409  0.020  1.409
 WDD  O15  C14   single    1.409  0.020  1.409
 WDD  C17  N12   single    1.454  0.020  1.454
 WDD  C06  C19   aromatic  1.369  0.020  1.369
 WDD  C06  N07   aromatic  1.342  0.020  1.342
 WDD  C20  C19   single    1.409  0.020  1.409
 WDD  C20  O21   double    1.222  0.020  1.222
 WDD  C14  C13   single    1.517  0.020  1.517
 WDD  C19  N18   aromatic  1.387  0.020  1.387
 WDD  N07  C08   aromatic  1.335  0.020  1.335
 WDD  N12  C13   single    1.454  0.020  1.454
 WDD  N12  C11   single    1.452  0.020  1.452
 WDD  C11  C10   single    1.525  0.020  1.525
 WDD  N18  C08   aromatic  1.347  0.020  1.347
 WDD  C08  N09   single    1.337  0.020  1.337
 WDD  C10  N09   single    1.447  0.020  1.447
 WDD  C10  H101  single    0.970  0.020  1.090
 WDD  C10  H102  single    0.970  0.020  1.090
 WDD  C11  H112  single    0.970  0.020  1.090
 WDD  C11  H111  single    0.970  0.020  1.090
 WDD  C13  H132  single    0.970  0.020  1.090
 WDD  C13  H131  single    0.970  0.020  1.090
 WDD  C14  H142  single    0.970  0.020  1.090
 WDD  C14  H141  single    0.970  0.020  1.090
 WDD  C16  H162  single    0.970  0.020  1.090
 WDD  C16  H161  single    0.970  0.020  1.090
 WDD  C17  H172  single    0.970  0.020  1.090
 WDD  C17  H171  single    0.970  0.020  1.090
 WDD  C01  H013  single    0.970  0.020  1.090
 WDD  C01  H011  single    0.970  0.020  1.090
 WDD  C01  H012  single    0.970  0.020  1.090
 WDD  C05  H051  single    0.970  0.020  1.090
 WDD  C05  H052  single    0.970  0.020  1.090
 WDD  C05  H053  single    0.970  0.020  1.090
 WDD  N09  H091  single    0.860  0.020  1.020
 WDD  N18  H181  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
 WDD  H102  C10  H101  106.90  3.000
 WDD  H102  C10  N09   107.12  3.000
 WDD  H101  C10  N09   108.78  3.000
 WDD  H102  C10  C11   109.15  3.000
 WDD  H101  C10  C11   108.04  3.000
 WDD  N09   C10  C11   116.46  3.000
 WDD  H111  C11  H112  106.07  3.000
 WDD  H111  C11  N12   107.50  3.000
 WDD  H112  C11  N12   112.00  3.000
 WDD  H111  C11  C10   105.64  3.000
 WDD  H112  C11  C10   110.10  3.000
 WDD  N12   C11  C10   114.90  3.000
 WDD  H131  C13  H132  107.01  3.000
 WDD  H131  C13  N12   111.33  3.000
 WDD  H132  C13  N12   110.40  3.000
 WDD  H131  C13  C14   109.71  3.000
 WDD  H132  C13  C14   107.96  3.000
 WDD  N12   C13  C14   110.32  3.000
 WDD  H141  C14  H142  107.84  3.000
 WDD  H141  C14  O15   107.45  3.000
 WDD  H142  C14  O15   110.40  3.000
 WDD  H141  C14  C13   109.89  3.000
 WDD  H142  C14  C13   109.15  3.000
 WDD  O15   C14  C13   112.01  3.000
 WDD  H161  C16  H162  107.84  3.000
 WDD  H161  C16  O15   110.47  3.000
 WDD  H162  C16  O15   107.49  3.000
 WDD  H161  C16  C17   109.35  3.000
 WDD  H162  C16  C17   110.02  3.000
 WDD  O15   C16  C17   111.57  3.000
 WDD  H171  C17  H172  107.14  3.000
 WDD  H171  C17  N12   109.32  3.000
 WDD  H172  C17  N12   111.81  3.000
 WDD  H171  C17  C16   108.72  3.000
 WDD  H172  C17  C16   109.32  3.000
 WDD  N12   C17  C16   110.43  3.000
 WDD  N18   C19  C06   104.42  3.000
 WDD  N18   C19  C20   131.78  3.000
 WDD  C06   C19  C20   123.79  3.000
 WDD  O21   C20  N02   122.00  3.000
 WDD  O21   C20  C19   126.54  3.000
 WDD  N02   C20  C19   111.46  3.000
 WDD  O22   C03  N04   121.00  3.000
 WDD  N04   C03  N02   117.77  3.000
 WDD  O22   C03  N02   121.23  3.000
 WDD  N07   C06  N04   126.34  3.000
 WDD  N07   C06  C19   112.40  3.000
 WDD  N04   C06  C19   121.26  3.000
 WDD  N18   C08  N09   123.42  3.000
 WDD  N09   C08  N07   124.20  3.000
 WDD  N18   C08  N07   112.37  3.000
 WDD  C03   N02  C01   115.32  3.000
 WDD  C01   N02  C20   118.44  3.000
 WDD  C03   N02  C20   126.23  3.000
 WDD  C06   N04  C05   121.76  3.000
 WDD  C06   N04  C03   119.48  3.000
 WDD  C05   N04  C03   118.76  3.000
 WDD  C08   N07  C06   104.22  3.000
 WDD  H091  N09  C08   118.34  3.000
 WDD  H091  N09  C10   118.94  3.000
 WDD  C08   N09  C10   122.72  3.000
 WDD  C17   N12  C13   109.27  3.000
 WDD  C13   N12  C11   113.29  3.000
 WDD  C17   N12  C11   111.09  3.000
 WDD  H181  N18  C08   126.83  3.000
 WDD  H181  N18  C19   126.57  3.000
 WDD  C08   N18  C19   106.58  3.000
 WDD  C16   O15  C14   110.69  3.000
 WDD  H012  C01  H011  108.87  3.000
 WDD  H012  C01  H013  108.79  3.000
 WDD  H011  C01  H013  108.85  3.000
 WDD  H012  C01  N02   110.91  3.000
 WDD  H011  C01  N02   110.76  3.000
 WDD  H013  C01  N02   108.62  3.000
 WDD  H053  C05  H052  109.03  3.000
 WDD  H053  C05  H051  108.89  3.000
 WDD  H052  C05  H051  108.86  3.000
 WDD  H053  C05  N04   110.80  3.000
 WDD  H052  C05  N04   110.91  3.000
 WDD  H051  C05  N04   108.31  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
 WDD  CONST_01  C08   N07  C06  C19     0.00   0.0  0
 WDD  CONST_02  N07   C08  N18  C19     0.00   0.0  0
 WDD  CONST_03  C08   N18  C19  C06     0.00   0.0  0
 WDD  CONST_04  N18   C08  N07  C06     0.00   0.0  0
 WDD  CONST_05  N18   C19  C06  N07     0.00   0.0  0
 WDD  CONST_06  C03   N02  C20  C19     0.00   0.0  0
 WDD  CONST_07  N04   C03  N02  C20     0.00   0.0  0
 WDD  CONST_08  N02   C03  N04  C06     0.00   0.0  0
 WDD  CONST_09  N09   C08  N18  C19   180.00   0.0  0
 WDD  CONST_10  N09   C08  N07  C06   180.00   0.0  0
 WDD  CONST_11  C01   N02  C20  C19   180.00   0.0  0
 WDD  CONST_12  O22   C03  N02  C20   180.00   0.0  0
 WDD  CONST_13  N04   C03  N02  C01   180.00   0.0  0
 WDD  CONST_14  O21   C20  N02  C03   180.00   0.0  0
 WDD  CONST_15  N02   C03  N04  C05   180.00   0.0  0
 WDD  CONST_16  O22   C03  N04  C06   180.00   0.0  0
 WDD  CONST_17  H181  N18  C19  C20     0.00   0.0  0
 WDD  CONST_18  N07   C08  N09  C10     0.00   0.0  0
 WDD  CONST_19  N18   C08  N09  C10   180.00   0.0  0
 WDD  CONST_20  O22   C03  N02  C01     0.00   0.0  0
 WDD  CONST_21  O21   C20  N02  C01     0.00   0.0  0
 WDD  CONST_22  O22   C03  N04  C05     0.00   0.0  0
 WDD  CONST_23  H091  N09  C08  N07   180.00   0.0  0
 WDD  Var_01    C16   C17  N12  C13    56.49  30.0  1
 WDD  Var_02    C17   C16  O15  C14    57.07  30.0  1
 WDD  Var_03    C17   N12  C13  C14   -55.99  30.0  1
 WDD  Var_04    O15   C16  C17  N12   -57.60  30.0  1
 WDD  Var_05    O15   C14  C13  N12    56.89  30.0  1
 WDD  Var_06    H142  C14  O15  C16    64.99  30.0  1
 WDD  Var_07    H013  C01  N02  C20     2.49  30.0  3
 WDD  Var_08    H051  C05  N04  C03  -179.62  30.0  3
 WDD  Var_09    C08   N09  C10  C11    77.59  30.0  3
 WDD  Var_10    N12   C11  C10  N09    73.81  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
 WDD  plan-1  C19   0.020
 WDD  plan-1  C20   0.020
 WDD  plan-1  C03   0.020
 WDD  plan-1  C06   0.020
 WDD  plan-1  C08   0.020
 WDD  plan-1  N02   0.020
 WDD  plan-1  N04   0.020
 WDD  plan-1  N07   0.020
 WDD  plan-1  N09   0.020
 WDD  plan-1  N18   0.020
 WDD  plan-1  O22   0.020
 WDD  plan-1  H181  0.020
 WDD  plan-1  O21   0.020
 WDD  plan-1  C01   0.020
 WDD  plan-1  C05   0.020
 WDD  plan-2  C10   0.020
 WDD  plan-2  C08   0.020
 WDD  plan-2  N09   0.020
 WDD  plan-2  H091  0.020

