# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:07:55 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 8-(2,5-dimethoxybenzyl)-2-fluoro-7H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(Cc2[nH]c3c(N)nc(F)nc3n2)c1
#
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
 PU2  PU2  8-(2,5-dimethoxybenzyl)-2-fluoro-7H-purin-6-amine  ligand  36  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PU2
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
 PU2  C18   C  CH3   0  -0.433  -2.7057  -1.8198   1.5378
 PU2  N2    N  N     0  -0.467   0.5872   0.2091  -0.7659
 PU2  C12   C  CR56  0   0.298   0.3256  -0.1691  -2.0413
 PU2  N4    N  N     0  -0.486   1.0880  -0.9677  -2.8085
 PU2  C14   C  CR6   0   0.556   0.5713  -1.1418  -3.9866
 PU2  C9    C  CH2   0  -0.641  -0.5630   1.6651   0.8916
 PU2  N3    N  N     0  -0.501  -0.5342  -0.6808  -4.5270
 PU2  C11   C  CR56  0   0.153  -0.8693   0.3915  -2.4802
 PU2  C13   C  CR6   0   0.482  -1.3089   0.1173  -3.7824
 PU2  N5    N  NH2   0  -0.819  -2.4332   0.5953  -4.3157
 PU2  N1    N  NR15  0  -0.689  -1.3232   1.1280  -1.4158
 PU2  C10   C  CR5   0   0.508  -0.4219   0.9807  -0.4252
 PU2  C1    C  CR6   0   0.356  -0.9505  -0.4013   2.2696
 PU2  C6    C  CR6   0   0.070  -0.2052   0.7653   2.0411
 PU2  C5    C  CR16  0  -0.410   0.8471   1.0730   2.8798
 PU2  C2    C  CR16  0  -0.367  -0.6162  -1.2260   3.3304
 PU2  C3    C  CR16  0  -0.381   0.4495  -0.9063   4.1727
 PU2  C4    C  CR6   0   0.375   1.1875   0.2461   3.9544
 PU2  O1    O  O2    0  -0.478   2.2359   0.6470   4.7083
 PU2  O2    O  O2    0  -0.470  -1.9613  -0.6285   1.4035
 PU2  C7    C  CH3   0  -0.435   2.6237  -0.1698   5.7920
 PU2  H181  H  HCH3  0   0.257  -3.4289  -1.8266   0.7260
 PU2  H182  H  HCH3  0   0.226  -2.0740  -2.7082   1.4532
 PU2  H183  H  HCH3  0   0.226  -3.2438  -1.8618   2.4889
 PU2  H9C1  H  HCH2  0   0.288  -1.5815   2.0463   0.9966
 PU2  H9C2  H  HCH2  0   0.299   0.0960   2.5370   0.8975
 PU2  H5N1  H  HNH2  0   0.411  -2.6745   0.3649  -5.2645
 PU2  H5N2  H  HNH2  0   0.415  -3.0521   1.2035  -3.8102
 PU2  H1    H  HNR5  0   0.426  -2.1716   1.6697  -1.3588
 PU2  H5    H  HCR6  0   0.261   1.4229   1.9742   2.7025
 PU2  H2    H  HCR6  0   0.281  -1.1690  -2.1339   3.5318
 PU2  H3    H  HCR6  0   0.279   0.6750  -1.5813   4.9871
 PU2  H7C1  H  HCH3  0   0.257   3.4766   0.3166   6.2589
 PU2  H7C2  H  HCH3  0   0.225   1.8276  -0.2720   6.5350
 PU2  H7C3  H  HCH3  0   0.225   2.9252  -1.1690   5.4655
 PU2  F1    F  F     0  -0.295   1.2790  -1.9239  -4.8041

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
 PU2  C18  O2    single    1.411  0.020  1.411
 PU2  C18  H181  single    0.970  0.020  1.090
 PU2  C18  H182  single    0.970  0.020  1.090
 PU2  C18  H183  single    0.970  0.020  1.090
 PU2  N2   C12   aromatic  1.356  0.020  1.356
 PU2  N2   C10   aromatic  1.315  0.020  1.315
 PU2  C12  N4    aromatic  1.345  0.020  1.345
 PU2  C12  C11   aromatic  1.391  0.020  1.391
 PU2  N4   C14   aromatic  1.298  0.020  1.298
 PU2  C14  N3    aromatic  1.314  0.020  1.314
 PU2  C14  F1    single    1.335  0.020  1.335
 PU2  C9   C10   single    1.491  0.020  1.491
 PU2  C9   C6    single    1.503  0.020  1.503
 PU2  C9   H9C1  single    0.970  0.020  1.090
 PU2  C9   H9C2  single    0.970  0.020  1.090
 PU2  N3   C13   aromatic  1.338  0.020  1.338
 PU2  C11  C13   aromatic  1.401  0.020  1.401
 PU2  C11  N1    aromatic  1.372  0.020  1.372
 PU2  C13  N5    single    1.333  0.020  1.333
 PU2  N5   H5N1  single    0.860  0.020  1.020
 PU2  N5   H5N2  single    0.860  0.020  1.020
 PU2  N1   C10   aromatic  1.347  0.020  1.347
 PU2  N1   H1    single    0.860  0.020  1.020
 PU2  C1   C6    aromatic  1.403  0.020  1.403
 PU2  C1   C2    aromatic  1.385  0.020  1.385
 PU2  C1   O2    single    1.350  0.020  1.350
 PU2  C6   C5    aromatic  1.380  0.020  1.380
 PU2  C5   C4    aromatic  1.398  0.020  1.398
 PU2  C5   H5    single    0.930  0.020  1.080
 PU2  C2   C3    aromatic  1.396  0.020  1.396
 PU2  C2   H2    single    0.930  0.020  1.080
 PU2  C3   C4    aromatic  1.386  0.020  1.386
 PU2  C3   H3    single    0.930  0.020  1.080
 PU2  C4   O1    single    1.352  0.020  1.352
 PU2  O1   C7    single    1.411  0.020  1.411
 PU2  C7   H7C1  single    0.970  0.020  1.090
 PU2  C7   H7C2  single    0.970  0.020  1.090
 PU2  C7   H7C3  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
 PU2  H183  C18  H182  108.68  3.000
 PU2  H183  C18  H181  108.78  3.000
 PU2  H182  C18  H181  108.75  3.000
 PU2  H183  C18  O2    112.01  3.000
 PU2  H182  C18  O2    111.95  3.000
 PU2  H181  C18  O2    106.57  3.000
 PU2  C10   N2   C12   105.03  3.000
 PU2  C11   C12  N4    123.13  3.000
 PU2  C11   C12  N2    110.50  3.000
 PU2  N4    C12  N2    126.38  3.000
 PU2  C14   N4   C12   111.83  3.000
 PU2  F1    C14  N3    113.57  3.000
 PU2  F1    C14  N4    115.05  3.000
 PU2  N3    C14  N4    131.38  3.000
 PU2  H9C2  C9   H9C1  106.46  3.000
 PU2  H9C2  C9   C6    109.26  3.000
 PU2  H9C1  C9   C6    110.94  3.000
 PU2  H9C2  C9   C10   108.29  3.000
 PU2  H9C1  C9   C10   109.47  3.000
 PU2  C6    C9   C10   112.22  3.000
 PU2  C13   N3   C14   117.86  3.000
 PU2  N1    C11  C13   136.24  3.000
 PU2  N1    C11  C12   104.83  3.000
 PU2  C13   C11  C12   118.93  3.000
 PU2  N5    C13  C11   124.48  3.000
 PU2  N5    C13  N3    118.64  3.000
 PU2  C11   C13  N3    116.88  3.000
 PU2  H5N2  N5   H5N1  117.76  3.000
 PU2  H5N2  N5   C13   122.39  3.000
 PU2  H5N1  N5   C13   119.84  3.000
 PU2  H1    N1   C10   125.46  3.000
 PU2  H1    N1   C11   127.65  3.000
 PU2  C10   N1   C11   106.88  3.000
 PU2  N1    C10  C9    122.40  3.000
 PU2  N1    C10  N2    112.77  3.000
 PU2  C9    C10  N2    124.81  3.000
 PU2  O2    C1   C2    124.88  3.000
 PU2  O2    C1   C6    115.66  3.000
 PU2  C2    C1   C6    119.46  3.000
 PU2  C5    C6   C1    119.43  3.000
 PU2  C5    C6   C9    120.84  3.000
 PU2  C1    C6   C9    119.73  3.000
 PU2  H5    C5   C4    119.21  3.000
 PU2  H5    C5   C6    119.40  3.000
 PU2  C4    C5   C6    121.39  3.000
 PU2  H2    C2   C3    118.04  3.000
 PU2  H2    C2   C1    121.27  3.000
 PU2  C3    C2   C1    120.69  3.000
 PU2  H3    C3   C4    121.78  3.000
 PU2  H3    C3   C2    118.08  3.000
 PU2  C4    C3   C2    120.14  3.000
 PU2  O1    C4   C3    124.86  3.000
 PU2  O1    C4   C5    116.23  3.000
 PU2  C3    C4   C5    118.90  3.000
 PU2  C7    O1   C4    118.01  3.000
 PU2  C1    O2   C18   118.42  3.000
 PU2  H7C3  C7   H7C2  108.55  3.000
 PU2  H7C3  C7   H7C1  108.70  3.000
 PU2  H7C2  C7   H7C1  108.73  3.000
 PU2  H7C3  C7   O1    112.04  3.000
 PU2  H7C2  C7   O1    112.07  3.000
 PU2  H7C1  C7   O1    106.64  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
 PU2  CONST_01  C14   N4   C12  N2    180.00   0.0  0
 PU2  CONST_02  C13   C11  C12  N2    180.00   0.0  0
 PU2  CONST_03  N1    C11  C12  N2      0.00   0.0  0
 PU2  CONST_04  C11   N1   C10  N2      0.00   0.0  0
 PU2  CONST_05  N1    C10  N2   C12     0.00   0.0  0
 PU2  CONST_06  N3    C14  N4   C12     0.00   0.0  0
 PU2  CONST_07  N3    C13  C11  C12     0.00   0.0  0
 PU2  CONST_08  C10   N1   C11  C12     0.00   0.0  0
 PU2  CONST_09  C10   N2   C12  N4    180.00   0.0  0
 PU2  CONST_10  C13   C11  C12  N4      0.00   0.0  0
 PU2  CONST_11  N1    C11  C12  N4    180.00   0.0  0
 PU2  CONST_12  C13   N3   C14  N4      0.00   0.0  0
 PU2  CONST_13  C11   C12  N4   C14     0.00   0.0  0
 PU2  CONST_14  C11   C13  N3   C14     0.00   0.0  0
 PU2  CONST_15  N1    C11  C13  N3    180.00   0.0  0
 PU2  CONST_16  C10   N2   C12  C11     0.00   0.0  0
 PU2  CONST_17  C10   N1   C11  C13   180.00   0.0  0
 PU2  CONST_18  C4    C5   C6   C1      0.00   0.0  0
 PU2  CONST_19  C4    C3   C2   C1      0.00   0.0  0
 PU2  CONST_20  C3    C2   C1   C6      0.00   0.0  0
 PU2  CONST_21  C3    C4   C5   C6      0.00   0.0  0
 PU2  CONST_22  C2    C1   C6   C5      0.00   0.0  0
 PU2  CONST_23  C2    C3   C4   C5      0.00   0.0  0
 PU2  CONST_24  C9    C10  N2   C12   180.00   0.0  0
 PU2  CONST_25  F1    C14  N4   C12   180.00   0.0  0
 PU2  CONST_26  N5    C13  C11  C12   180.00   0.0  0
 PU2  CONST_27  N5    C13  N3   C14   180.00   0.0  0
 PU2  CONST_28  C11   N1   C10  C9    180.00   0.0  0
 PU2  CONST_29  C2    C1   C6   C9    180.00   0.0  0
 PU2  CONST_30  C4    C5   C6   C9    180.00   0.0  0
 PU2  CONST_31  F1    C14  N3   C13   180.00   0.0  0
 PU2  CONST_32  N1    C11  C13  N5      0.00   0.0  0
 PU2  CONST_33  O1    C4   C5   C6    180.00   0.0  0
 PU2  CONST_34  O2    C1   C6   C5    180.00   0.0  0
 PU2  CONST_35  O1    C4   C3   C2    180.00   0.0  0
 PU2  CONST_36  O2    C1   C2   C3    180.00   0.0  0
 PU2  CONST_37  H1    N1   C10  N2    180.00   0.0  0
 PU2  CONST_38  H5    C5   C6   C1    180.00   0.0  0
 PU2  CONST_39  H3    C3   C2   C1    180.00   0.0  0
 PU2  CONST_40  H2    C2   C1   C6    180.00   0.0  0
 PU2  CONST_41  H5N1  N5   C13  N3      0.00   0.0  0
 PU2  CONST_42  H5N2  N5   C13  N3    180.00   0.0  0
 PU2  Var_01    C6    C9   C10  N2    -43.47  30.0  1
 PU2  Var_02    C1    C6   C9   C10   -62.19  30.0  2
 PU2  Var_03    C6    C1   O2   C18   176.81  30.0  1
 PU2  Var_04    H181  C18  O2   C1   -177.46  30.0  3
 PU2  Var_05    H7C1  C7   O1   C4    179.57  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
 PU2  plan-1  C9    0.020
 PU2  plan-1  C1    0.020
 PU2  plan-1  C6    0.020
 PU2  plan-1  C5    0.020
 PU2  plan-1  C2    0.020
 PU2  plan-1  C3    0.020
 PU2  plan-1  C4    0.020
 PU2  plan-1  O1    0.020
 PU2  plan-1  O2    0.020
 PU2  plan-1  H5    0.020
 PU2  plan-1  H2    0.020
 PU2  plan-1  H3    0.020
 PU2  plan-2  N2    0.020
 PU2  plan-2  C12   0.020
 PU2  plan-2  N4    0.020
 PU2  plan-2  C14   0.020
 PU2  plan-2  C9    0.020
 PU2  plan-2  N3    0.020
 PU2  plan-2  C11   0.020
 PU2  plan-2  C13   0.020
 PU2  plan-2  N5    0.020
 PU2  plan-2  N1    0.020
 PU2  plan-2  C10   0.020
 PU2  plan-2  H1    0.020
 PU2  plan-2  F1    0.020
 PU2  plan-3  C13   0.020
 PU2  plan-3  N5    0.020
 PU2  plan-3  H5N1  0.020
 PU2  plan-3  H5N2  0.020

