# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 07:08:44 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-(2-methoxyethoxy)-6-(methylamino)-9-(phenylmethyl)-7H-purin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(OCCOC)nc2N(Cc3ccccc3)C(=O)Nc12
#
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
 RJE  RJE  2-(2-methoxyethoxy)-6-(methylamino)-9-(phenylmethyl)-7H-purin-8-one  ligand  43  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RJE
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
 RJE  C1    C  CH3   0  -0.508   2.6394  -3.8783  -1.4248
 RJE  N2    N  NH1   0  -0.658   1.3284  -3.5513  -0.9183
 RJE  C3    C  CR6   0   0.541   1.0022  -2.3365  -0.4597
 RJE  N4    N  N     0  -0.532   1.9290  -1.3680  -0.5089
 RJE  C5    C  CR6   0   0.571   1.6310  -0.1652  -0.0591
 RJE  O6    O  O2    0  -0.457   2.5644   0.7822  -0.1112
 RJE  C7    C  CH2   0  -0.194   3.8552   0.4403  -0.6043
 RJE  C8    C  CH2   0  -0.168   4.7236   1.6676  -0.5240
 RJE  O9    O  O2    0  -0.483   4.9045   2.0317   0.8187
 RJE  C10   C  CH3   0  -0.396   5.7119   3.1712   0.9660
 RJE  N11   N  N     0  -0.497   0.4841   0.2508   0.4625
 RJE  C12   C  CR56  0   0.493  -0.4219  -0.7121   0.5049
 RJE  N13   N  NR5   0  -0.560  -1.6922  -0.6143   1.0028
 RJE  C14   C  CH2   0  -0.422  -2.3129   0.5901   1.5143
 RJE  C15   C  CR6   0   0.131  -3.0075   1.3764   0.4323
 RJE  C16   C  CR16  0  -0.295  -4.3429   1.1314   0.1249
 RJE  C17   C  CR16  0  -0.244  -4.9732   1.8394  -0.8895
 RJE  C18   C  CR16  0  -0.263  -4.2731   2.7999  -1.6084
 RJE  C19   C  CR16  0  -0.243  -2.9410   3.0510  -1.3060
 RJE  C20   C  CR16  0  -0.294  -2.3126   2.3421  -0.2910
 RJE  C21   C  CR5   0   0.659  -2.3444  -1.8320   0.8727
 RJE  O22   O  O     0  -0.499  -3.4898  -2.0731   1.2085
 RJE  N23   N  NR15  0  -0.752  -1.4379  -2.6804   0.3066
 RJE  C25   C  CR56  0   0.141  -0.2465  -2.0100   0.0681
 RJE  H11C  H  HCH3  0   0.238   2.9064  -3.2625  -2.2837
 RJE  H12C  H  HCH3  0   0.236   3.4128  -3.7526  -0.6659
 RJE  H13C  H  HCH3  0   0.251   2.6287  -4.9183  -1.7381
 RJE  H2    H  HNH1  0   0.405   0.6508  -4.2904  -0.8561
 RJE  H71C  H  HCH2  0   0.233   4.2857  -0.3771  -0.0205
 RJE  H72C  H  HCH2  0   0.235   3.7990   0.1085  -1.6438
 RJE  H81C  H  HCH2  0   0.212   5.6820   1.4276  -1.0062
 RJE  H82C  H  HCH2  0   0.209   4.2762   2.4889  -1.1021
 RJE  H101  H  HCH3  0   0.205   5.2859   4.0464   0.4611
 RJE  H102  H  HCH3  0   0.234   5.7897   3.3932   2.0297
 RJE  H103  H  HCH3  0   0.204   6.7226   3.0150   0.5698
 RJE  H141  H  HCH2  0   0.287  -3.0141   0.3030   2.2966
 RJE  H142  H  HCH2  0   0.286  -1.5318   1.1873   1.9829
 RJE  H16   H  HCR6  0   0.252  -4.8937   0.3831   0.6811
 RJE  H20   H  HCR6  0   0.253  -1.2732   2.5387  -0.0580
 RJE  H17   H  HCR6  0   0.257  -6.0132   1.6431  -1.1166
 RJE  H18   H  HCR6  0   0.257  -4.7658   3.3524  -2.3980
 RJE  H19   H  HCR6  0   0.256  -2.3901   3.8020  -1.8574
 RJE  H23   H  HNR5  0   0.420  -1.6542  -3.6381   0.0842

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
 RJE  C1   N2    single    1.443  0.020  1.443
 RJE  N2   C3    single    1.339  0.020  1.339
 RJE  C3   N4    aromatic  1.341  0.020  1.341
 RJE  C3   C25   aromatic  1.394  0.020  1.394
 RJE  N4   C5    aromatic  1.318  0.020  1.318
 RJE  C5   O6    single    1.331  0.020  1.331
 RJE  C5   N11   aromatic  1.327  0.020  1.327
 RJE  O6   C7    single    1.423  0.020  1.423
 RJE  C7   C8    single    1.506  0.020  1.506
 RJE  C8   O9    single    1.403  0.020  1.403
 RJE  O9   C10   single    1.404  0.020  1.404
 RJE  N11  C12   aromatic  1.323  0.020  1.323
 RJE  C12  N13   single    1.368  0.020  1.368
 RJE  C12  C25   aromatic  1.381  0.020  1.381
 RJE  N13  C14   single    1.448  0.020  1.448
 RJE  N13  C21   single    1.387  0.020  1.387
 RJE  C14  C15   single    1.507  0.020  1.507
 RJE  C15  C16   aromatic  1.392  0.020  1.392
 RJE  C15  C20   aromatic  1.392  0.020  1.392
 RJE  C16  C17   aromatic  1.388  0.020  1.388
 RJE  C17  C18   aromatic  1.389  0.020  1.389
 RJE  C18  C19   aromatic  1.389  0.020  1.389
 RJE  C19  C20   aromatic  1.388  0.020  1.388
 RJE  C21  O22   double    1.218  0.020  1.218
 RJE  C21  N23   single    1.365  0.020  1.365
 RJE  N23  C25   single    1.388  0.020  1.388
 RJE  C1   H11C  single    0.970  0.020  1.090
 RJE  C1   H12C  single    0.970  0.020  1.090
 RJE  C1   H13C  single    0.970  0.020  1.090
 RJE  N2   H2    single    0.860  0.020  1.020
 RJE  C7   H71C  single    0.970  0.020  1.090
 RJE  C7   H72C  single    0.970  0.020  1.090
 RJE  C8   H81C  single    0.970  0.020  1.090
 RJE  C8   H82C  single    0.970  0.020  1.090
 RJE  C10  H101  single    0.970  0.020  1.090
 RJE  C10  H102  single    0.970  0.020  1.090
 RJE  C10  H103  single    0.970  0.020  1.090
 RJE  C14  H141  single    0.970  0.020  1.090
 RJE  C14  H142  single    0.970  0.020  1.090
 RJE  C16  H16   single    0.930  0.020  1.080
 RJE  C20  H20   single    0.930  0.020  1.080
 RJE  C17  H17   single    0.930  0.020  1.080
 RJE  C18  H18   single    0.930  0.020  1.080
 RJE  C19  H19   single    0.930  0.020  1.080
 RJE  N23  H23   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
 RJE  H13C  C1   H12C  108.54  3.000
 RJE  H13C  C1   H11C  108.42  3.000
 RJE  H12C  C1   H11C  108.02  3.000
 RJE  H13C  C1   N2    108.02  3.000
 RJE  H12C  C1   N2    111.95  3.000
 RJE  H11C  C1   N2    111.78  3.000
 RJE  H2    N2   C3    118.82  3.000
 RJE  H2    N2   C1    117.89  3.000
 RJE  C3    N2   C1    123.18  3.000
 RJE  C25   C3   N4    117.62  3.000
 RJE  C25   C3   N2    124.08  3.000
 RJE  N4    C3   N2    118.31  3.000
 RJE  C5    N4   C3    119.34  3.000
 RJE  N11   C5   O6    113.47  3.000
 RJE  N11   C5   N4    128.00  3.000
 RJE  O6    C5   N4    118.52  3.000
 RJE  C7    O6   C5    118.59  3.000
 RJE  H72C  C7   H71C  107.55  3.000
 RJE  H72C  C7   C8    109.15  3.000
 RJE  H71C  C7   C8    110.73  3.000
 RJE  H72C  C7   O6    110.85  3.000
 RJE  H71C  C7   O6    110.60  3.000
 RJE  C8    C7   O6    107.98  3.000
 RJE  H82C  C8   H81C  106.68  3.000
 RJE  H82C  C8   O9    111.21  3.000
 RJE  H81C  C8   O9    111.35  3.000
 RJE  H82C  C8   C7    110.25  3.000
 RJE  H81C  C8   C7    107.55  3.000
 RJE  O9    C8   C7    109.70  3.000
 RJE  C10   O9   C8    112.66  3.000
 RJE  H103  C10  H102  108.42  3.000
 RJE  H103  C10  H101  107.78  3.000
 RJE  H102  C10  H101  108.34  3.000
 RJE  H103  C10  O9    112.11  3.000
 RJE  H102  C10  O9    107.99  3.000
 RJE  H101  C10  O9    112.08  3.000
 RJE  C12   N11  C5    112.11  3.000
 RJE  C25   C12  N13   107.48  3.000
 RJE  C25   C12  N11   125.95  3.000
 RJE  N13   C12  N11   126.56  3.000
 RJE  C21   N13  C14   124.16  3.000
 RJE  C21   N13  C12   109.86  3.000
 RJE  C14   N13  C12   125.88  3.000
 RJE  H142  C14  H141  107.29  3.000
 RJE  H142  C14  C15   110.69  3.000
 RJE  H141  C14  C15   110.89  3.000
 RJE  H142  C14  N13   107.49  3.000
 RJE  H141  C14  N13   108.09  3.000
 RJE  C15   C14  N13   112.20  3.000
 RJE  C20   C15  C16   119.08  3.000
 RJE  C20   C15  C14   120.32  3.000
 RJE  C16   C15  C14   120.59  3.000
 RJE  H16   C16  C17   119.78  3.000
 RJE  H16   C16  C15   119.74  3.000
 RJE  C17   C16  C15   120.48  3.000
 RJE  H17   C17  C18   120.07  3.000
 RJE  H17   C17  C16   119.80  3.000
 RJE  C18   C17  C16   120.13  3.000
 RJE  H18   C18  C19   120.20  3.000
 RJE  H18   C18  C17   120.07  3.000
 RJE  C19   C18  C17   119.72  3.000
 RJE  H19   C19  C20   119.76  3.000
 RJE  H19   C19  C18   120.18  3.000
 RJE  C20   C19  C18   120.06  3.000
 RJE  H20   C20  C19   119.92  3.000
 RJE  H20   C20  C15   119.54  3.000
 RJE  C19   C20  C15   120.54  3.000
 RJE  N23   C21  O22   128.04  3.000
 RJE  N23   C21  N13   105.80  3.000
 RJE  O22   C21  N13   126.16  3.000
 RJE  H23   N23  C25   127.31  3.000
 RJE  H23   N23  C21   122.71  3.000
 RJE  C25   N23  C21   109.96  3.000
 RJE  N23   C25  C12   106.90  3.000
 RJE  N23   C25  C3    136.12  3.000
 RJE  C12   C25  C3    116.98  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
 RJE  CONST_01  N11   C5   N4   C3      0.00   0.0  0
 RJE  CONST_02  N11   C12  C25  C3      0.00   0.0  0
 RJE  CONST_03  C12   C25  C3   N4      0.00   0.0  0
 RJE  CONST_04  C12   N11  C5   N4      0.00   0.0  0
 RJE  CONST_05  C25   C3   N4   C5      0.00   0.0  0
 RJE  CONST_06  C25   C12  N11  C5      0.00   0.0  0
 RJE  CONST_07  C18   C17  C16  C15     0.00   0.0  0
 RJE  CONST_08  C18   C19  C20  C15     0.00   0.0  0
 RJE  CONST_09  C19   C20  C15  C16     0.00   0.0  0
 RJE  CONST_10  C19   C18  C17  C16     0.00   0.0  0
 RJE  CONST_11  C20   C15  C16  C17     0.00   0.0  0
 RJE  CONST_12  C20   C19  C18  C17     0.00   0.0  0
 RJE  CONST_13  N23   C21  N13  C12     0.00   0.0  0
 RJE  CONST_14  C21   N23  C25  C12     0.00   0.0  0
 RJE  CONST_15  N23   C25  C12  N13     0.00   0.0  0
 RJE  CONST_16  C25   N23  C21  N13     0.00   0.0  0
 RJE  CONST_17  C25   C12  N13  C21     0.00   0.0  0
 RJE  CONST_18  C5    N4   C3   N2    180.00   0.0  0
 RJE  CONST_19  C12   C25  C3   N2    180.00   0.0  0
 RJE  CONST_20  N23   C25  C3   N2      0.00   0.0  0
 RJE  CONST_21  O6    C5   N4   C3    180.00   0.0  0
 RJE  CONST_22  C12   N11  C5   O6    180.00   0.0  0
 RJE  CONST_23  C17   C16  C15  C14   180.00   0.0  0
 RJE  CONST_24  C19   C20  C15  C14   180.00   0.0  0
 RJE  CONST_25  O22   C21  N13  C12   180.00   0.0  0
 RJE  CONST_26  C25   C12  N13  C14   180.00   0.0  0
 RJE  CONST_27  N23   C21  N13  C14   180.00   0.0  0
 RJE  CONST_28  C25   N23  C21  O22   180.00   0.0  0
 RJE  CONST_29  H17   C17  C16  C15   180.00   0.0  0
 RJE  CONST_30  H19   C19  C20  C15   180.00   0.0  0
 RJE  CONST_31  H20   C20  C15  C16   180.00   0.0  0
 RJE  CONST_32  H18   C18  C17  C16   180.00   0.0  0
 RJE  CONST_33  H16   C16  C17  C18   180.00   0.0  0
 RJE  CONST_34  H23   N23  C25  C12   180.00   0.0  0
 RJE  CONST_35  N4    C3   N2   C1      0.00   0.0  0
 RJE  CONST_36  C25   C3   N2   C1    180.00   0.0  0
 RJE  CONST_37  O22   C21  N13  C14     0.00   0.0  0
 RJE  CONST_38  H2    N2   C3   N4    180.00   0.0  0
 RJE  Var_01    C15   C14  N13  C12    88.67  30.0  3
 RJE  Var_02    C16   C15  C14  N13    89.61  30.0  2
 RJE  Var_03    N11   C5   O6   C7    177.60  30.0  2
 RJE  Var_04    C8    C7   O6   C5   -178.49  30.0  3
 RJE  Var_05    H11C  C1   N2   C3    -60.22  30.0  3
 RJE  Var_06    O9    C8   C7   O6     64.82  30.0  3
 RJE  Var_07    H101  C10  O9   C8     59.93  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
 RJE  plan-1  C14  0.020
 RJE  plan-1  C15  0.020
 RJE  plan-1  C16  0.020
 RJE  plan-1  C17  0.020
 RJE  plan-1  C18  0.020
 RJE  plan-1  C19  0.020
 RJE  plan-1  C20  0.020
 RJE  plan-1  H16  0.020
 RJE  plan-1  H20  0.020
 RJE  plan-1  H17  0.020
 RJE  plan-1  H18  0.020
 RJE  plan-1  H19  0.020
 RJE  plan-2  N2   0.020
 RJE  plan-2  C3   0.020
 RJE  plan-2  N4   0.020
 RJE  plan-2  C5   0.020
 RJE  plan-2  O6   0.020
 RJE  plan-2  N11  0.020
 RJE  plan-2  C12  0.020
 RJE  plan-2  N13  0.020
 RJE  plan-2  C14  0.020
 RJE  plan-2  C21  0.020
 RJE  plan-2  O22  0.020
 RJE  plan-2  N23  0.020
 RJE  plan-2  C25  0.020
 RJE  plan-2  H23  0.020
 RJE  plan-3  C1   0.020
 RJE  plan-3  N2   0.020
 RJE  plan-3  C3   0.020
 RJE  plan-3  H2   0.020

