# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 18:00:04 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 9-butyl-8-(4-methoxybenzyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCn1c(Cc2ccc(OC)cc2)nc3c(N)ncnc13
#
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
 PU4  PU4  9-butyl-8-(4-methoxybenzyl)-9H-purin-6-amine  ligand  44  23  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PU4
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
 PU4  C18   C  CH3   0  -0.662   5.2750   0.2142   1.9200
 PU4  C17   C  CH2   0  -0.427   4.0960  -0.4133   1.1909
 PU4  C16   C  CH2   0  -0.428   2.7596   0.1669   1.6354
 PU4  C15   C  CH2   0  -0.320   1.5948  -0.4830   0.9019
 PU4  N2    N  NR5   0  -0.528   0.3148   0.0993   1.2535
 PU4  C12   C  CR56  0   0.478  -0.4524  -0.2577   2.3211
 PU4  N4    N  N     0  -0.459  -0.2337  -1.2304   3.2038
 PU4  C14   C  CR16  0   0.034  -1.1984  -1.2989   4.1045
 PU4  N3    N  N     0  -0.473  -2.2895  -0.5439   4.2077
 PU4  C11   C  CR56  0  -0.003  -1.5338   0.6095   2.3031
 PU4  C13   C  CR6   0   0.436  -2.4923   0.4318   3.3150
 PU4  N5    N  NH2   0  -0.818  -3.5773   1.2065   3.4293
 PU4  N1    N  N     0  -0.466  -1.4315   1.4869   1.2564
 PU4  C10   C  CR5   0   0.468  -0.3193   1.1591   0.6558
 PU4  C9    C  CH2   0  -0.620   0.2006   1.8141  -0.5773
 PU4  C1    C  CR6   0   0.086   0.0018   0.9724  -1.8172
 PU4  C6    C  CR16  0  -0.254  -1.2592   0.4765  -2.1509
 PU4  C5    C  CR16  0  -0.326  -1.4525  -0.2757  -3.2930
 PU4  C2    C  CR16  0  -0.310   1.0587   0.6857  -2.6676
 PU4  C3    C  CR16  0  -0.372   0.8844  -0.0698  -3.8233
 PU4  C4    C  CR6   0   0.370  -0.3790  -0.5563  -4.1432
 PU4  O1    O  O2    0  -0.471  -0.6593  -1.2952  -5.2335
 PU4  C7    C  CH3   0  -0.437   0.3962  -1.6288  -6.1124
 PU4  H181  H  HCH3  0   0.220   5.3151   1.2919   1.7520
 PU4  H182  H  HCH3  0   0.230   6.2211  -0.2092   1.5822
 PU4  H183  H  HCH3  0   0.220   5.2046   0.0513   2.9968
 PU4  H171  H  HCH2  0   0.219   4.2110  -0.2690   0.1123
 PU4  H172  H  HCH2  0   0.222   4.0965  -1.4949   1.3548
 PU4  H161  H  HCH2  0   0.235   2.6323   0.0272   2.7126
 PU4  H162  H  HCH2  0   0.228   2.7503   1.2468   1.4568
 PU4  H151  H  HCH2  0   0.263   1.7234  -0.4003  -0.1776
 PU4  H152  H  HCH2  0   0.271   1.5464  -1.5482   1.1296
 PU4  H14   H  HCR6  0   0.248  -1.0933  -2.0697   4.8606
 PU4  H5N1  H  HNH2  0   0.400  -4.2982   0.9559   4.0842
 PU4  H5N2  H  HNH2  0   0.407  -3.8189   1.8521   2.6978
 PU4  H9C1  H  HCH2  0   0.293  -0.3238   2.7658  -0.6814
 PU4  H9C2  H  HCH2  0   0.277   1.2595   2.0571  -0.4630
 PU4  H6    H  HCR6  0   0.252  -2.1074   0.6815  -1.5078
 PU4  H5    H  HCR6  0   0.263  -2.4382  -0.6516  -3.5381
 PU4  H2    H  HCR6  0   0.259   2.0508   1.0547  -2.4337
 PU4  H3    H  HCR6  0   0.278   1.7425  -0.2634  -4.4525
 PU4  H7C1  H  HCH3  0   0.260  -0.0439  -2.2138  -6.9162
 PU4  H7C2  H  HCH3  0   0.228   0.8685  -0.7414  -6.5415
 PU4  H7C3  H  HCH3  0   0.228   1.1631  -2.2322  -5.6195

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
 PU4  C18  C17   single    1.522  0.020  1.522
 PU4  C18  H181  single    0.970  0.020  1.090
 PU4  C18  H182  single    0.970  0.020  1.090
 PU4  C18  H183  single    0.970  0.020  1.090
 PU4  C17  C16   single    1.523  0.020  1.523
 PU4  C17  H171  single    0.970  0.020  1.090
 PU4  C17  H172  single    0.970  0.020  1.090
 PU4  C16  C15   single    1.522  0.020  1.522
 PU4  C16  H161  single    0.970  0.020  1.090
 PU4  C16  H162  single    0.970  0.020  1.090
 PU4  C15  N2    single    1.450  0.020  1.450
 PU4  C15  H151  single    0.970  0.020  1.090
 PU4  C15  H152  single    0.970  0.020  1.090
 PU4  N2   C12   aromatic  1.362  0.020  1.362
 PU4  N2   C10   aromatic  1.372  0.020  1.372
 PU4  C12  N4    aromatic  1.332  0.020  1.332
 PU4  C12  C11   aromatic  1.386  0.020  1.386
 PU4  N4   C14   aromatic  1.322  0.020  1.322
 PU4  C14  N3    aromatic  1.331  0.020  1.331
 PU4  C14  H14   single    0.930  0.020  1.080
 PU4  N3   C13   aromatic  1.338  0.020  1.338
 PU4  C11  C13   aromatic  1.405  0.020  1.405
 PU4  C11  N1    aromatic  1.370  0.020  1.370
 PU4  C13  N5    single    1.338  0.020  1.338
 PU4  N5   H5N1  single    0.860  0.020  1.020
 PU4  N5   H5N2  single    0.860  0.020  1.020
 PU4  N1   C10   aromatic  1.306  0.020  1.306
 PU4  C10  C9    single    1.490  0.020  1.490
 PU4  C9   C1    single    1.512  0.020  1.512
 PU4  C9   H9C1  single    0.970  0.020  1.090
 PU4  C9   H9C2  single    0.970  0.020  1.090
 PU4  C1   C6    aromatic  1.396  0.020  1.396
 PU4  C1   C2    aromatic  1.386  0.020  1.386
 PU4  C6   C5    aromatic  1.381  0.020  1.381
 PU4  C6   H6    single    0.930  0.020  1.080
 PU4  C5   C4    aromatic  1.398  0.020  1.398
 PU4  C5   H5    single    0.930  0.020  1.080
 PU4  C2   C3    aromatic  1.392  0.020  1.392
 PU4  C2   H2    single    0.930  0.020  1.080
 PU4  C3   C4    aromatic  1.391  0.020  1.391
 PU4  C3   H3    single    0.930  0.020  1.080
 PU4  C4   O1    single    1.347  0.020  1.347
 PU4  O1   C7    single    1.413  0.020  1.413
 PU4  C7   H7C1  single    0.970  0.020  1.090
 PU4  C7   H7C2  single    0.970  0.020  1.090
 PU4  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
 PU4  H183  C18  H182  107.68  3.000
 PU4  H183  C18  H181  107.56  3.000
 PU4  H182  C18  H181  107.70  3.000
 PU4  H183  C18  C17   111.17  3.000
 PU4  H182  C18  C17   111.33  3.000
 PU4  H181  C18  C17   111.22  3.000
 PU4  H172  C17  H171  106.14  3.000
 PU4  H172  C17  C16   109.47  3.000
 PU4  H171  C17  C16   109.25  3.000
 PU4  H172  C17  C18   109.60  3.000
 PU4  H171  C17  C18   109.66  3.000
 PU4  C16   C17  C18   112.51  3.000
 PU4  H162  C16  H161  106.60  3.000
 PU4  H162  C16  C15   109.63  3.000
 PU4  H161  C16  C15   109.33  3.000
 PU4  H162  C16  C17   109.61  3.000
 PU4  H161  C16  C17   109.93  3.000
 PU4  C15   C16  C17   111.60  3.000
 PU4  H152  C15  H151  106.63  3.000
 PU4  H152  C15  N2    107.61  3.000
 PU4  H151  C15  N2    108.29  3.000
 PU4  H152  C15  C16   110.51  3.000
 PU4  H151  C15  C16   110.76  3.000
 PU4  N2    C15  C16   112.79  3.000
 PU4  C10   N2   C12   106.47  3.000
 PU4  C10   N2   C15   127.78  3.000
 PU4  C12   N2   C15   125.60  3.000
 PU4  C11   C12  N4    126.42  3.000
 PU4  C11   C12  N2    105.38  3.000
 PU4  N4    C12  N2    128.20  3.000
 PU4  C14   N4   C12   111.70  3.000
 PU4  H14   C14  N3    115.37  3.000
 PU4  H14   C14  N4    116.18  3.000
 PU4  N3    C14  N4    128.45  3.000
 PU4  C13   N3   C14   119.09  3.000
 PU4  N1    C11  C13   133.03  3.000
 PU4  N1    C11  C12   110.63  3.000
 PU4  C13   C11  C12   116.34  3.000
 PU4  N5    C13  C11   122.78  3.000
 PU4  N5    C13  N3    119.22  3.000
 PU4  C11   C13  N3    117.99  3.000
 PU4  H5N2  N5   H5N1  117.49  3.000
 PU4  H5N2  N5   C13   120.30  3.000
 PU4  H5N1  N5   C13   119.51  3.000
 PU4  C10   N1   C11   104.73  3.000
 PU4  C9    C10  N1    124.58  3.000
 PU4  C9    C10  N2    122.61  3.000
 PU4  N1    C10  N2    112.77  3.000
 PU4  H9C2  C9   H9C1  106.36  3.000
 PU4  H9C2  C9   C1    109.70  3.000
 PU4  H9C1  C9   C1    110.13  3.000
 PU4  H9C2  C9   C10   110.45  3.000
 PU4  H9C1  C9   C10   107.13  3.000
 PU4  C1    C9   C10   112.84  3.000
 PU4  C2    C1   C6    117.95  3.000
 PU4  C2    C1   C9    121.20  3.000
 PU4  C6    C1   C9    120.85  3.000
 PU4  H6    C6   C5    118.96  3.000
 PU4  H6    C6   C1    119.87  3.000
 PU4  C5    C6   C1    121.18  3.000
 PU4  H5    C5   C4    119.45  3.000
 PU4  H5    C5   C6    120.23  3.000
 PU4  C4    C5   C6    120.32  3.000
 PU4  H2    C2   C3    118.59  3.000
 PU4  H2    C2   C1    119.67  3.000
 PU4  C3    C2   C1    121.74  3.000
 PU4  H3    C3   C4    121.61  3.000
 PU4  H3    C3   C2    118.75  3.000
 PU4  C4    C3   C2    119.64  3.000
 PU4  O1    C4   C3    124.55  3.000
 PU4  O1    C4   C5    116.29  3.000
 PU4  C3    C4   C5    119.17  3.000
 PU4  C7    O1   C4    118.53  3.000
 PU4  H7C3  C7   H7C2  108.78  3.000
 PU4  H7C3  C7   H7C1  108.68  3.000
 PU4  H7C2  C7   H7C1  108.75  3.000
 PU4  H7C3  C7   O1    111.96  3.000
 PU4  H7C2  C7   O1    112.03  3.000
 PU4  H7C1  C7   O1    106.53  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
 PU4  CONST_01  C14   N4   C12  N2    180.00   0.0  0
 PU4  CONST_02  C13   C11  C12  N2    180.00   0.0  0
 PU4  CONST_03  N1    C11  C12  N2      0.00   0.0  0
 PU4  CONST_04  C11   N1   C10  N2      0.00   0.0  0
 PU4  CONST_05  N1    C10  N2   C12     0.00   0.0  0
 PU4  CONST_06  N3    C14  N4   C12     0.00   0.0  0
 PU4  CONST_07  N3    C13  C11  C12     0.00   0.0  0
 PU4  CONST_08  C10   N1   C11  C12     0.00   0.0  0
 PU4  CONST_09  C10   N2   C12  N4    180.00   0.0  0
 PU4  CONST_10  C13   C11  C12  N4      0.00   0.0  0
 PU4  CONST_11  N1    C11  C12  N4    180.00   0.0  0
 PU4  CONST_12  C13   N3   C14  N4      0.00   0.0  0
 PU4  CONST_13  C11   C12  N4   C14     0.00   0.0  0
 PU4  CONST_14  C11   C13  N3   C14     0.00   0.0  0
 PU4  CONST_15  N1    C11  C13  N3    180.00   0.0  0
 PU4  CONST_16  C10   N2   C12  C11     0.00   0.0  0
 PU4  CONST_17  C10   N1   C11  C13   180.00   0.0  0
 PU4  CONST_18  C4    C5   C6   C1      0.00   0.0  0
 PU4  CONST_19  C4    C3   C2   C1      0.00   0.0  0
 PU4  CONST_20  C3    C2   C1   C6      0.00   0.0  0
 PU4  CONST_21  C3    C4   C5   C6      0.00   0.0  0
 PU4  CONST_22  C2    C1   C6   C5      0.00   0.0  0
 PU4  CONST_23  C2    C3   C4   C5      0.00   0.0  0
 PU4  CONST_24  N4    C12  N2   C15     0.00   0.0  0
 PU4  CONST_25  C11   C12  N2   C15   180.00   0.0  0
 PU4  CONST_26  N1    C10  N2   C15   180.00   0.0  0
 PU4  CONST_27  C9    C10  N2   C12   180.00   0.0  0
 PU4  CONST_28  N5    C13  C11  C12   180.00   0.0  0
 PU4  CONST_29  N5    C13  N3   C14   180.00   0.0  0
 PU4  CONST_30  C9    C10  N1   C11   180.00   0.0  0
 PU4  CONST_31  N1    C11  C13  N5      0.00   0.0  0
 PU4  CONST_32  C5    C6   C1   C9    180.00   0.0  0
 PU4  CONST_33  C3    C2   C1   C9    180.00   0.0  0
 PU4  CONST_34  O1    C4   C5   C6    180.00   0.0  0
 PU4  CONST_35  O1    C4   C3   C2    180.00   0.0  0
 PU4  CONST_36  H14   C14  N4   C12   180.00   0.0  0
 PU4  CONST_37  H5    C5   C6   C1    180.00   0.0  0
 PU4  CONST_38  H3    C3   C2   C1    180.00   0.0  0
 PU4  CONST_39  H2    C2   C1   C6    180.00   0.0  0
 PU4  CONST_40  H6    C6   C1   C2    180.00   0.0  0
 PU4  CONST_41  H5N1  N5   C13  N3      0.00   0.0  0
 PU4  CONST_42  H5N2  N5   C13  N3    180.00   0.0  0
 PU4  Var_01    C1    C9   C10  N2     73.45  30.0  2
 PU4  Var_02    C6    C1   C9   C10    53.32  30.0  2
 PU4  Var_03    C12   N2   C15  C16   -85.39  30.0  2
 PU4  Var_04    N2    C15  C16  C17  -176.93  30.0  3
 PU4  Var_05    H7C1  C7   O1   C4   -179.65  30.0  3
 PU4  Var_06    C15   C16  C17  C18  -179.53  30.0  3
 PU4  Var_07    H181  C18  C17  C16   -59.46  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
 PU4  plan-1  C9    0.020
 PU4  plan-1  C1    0.020
 PU4  plan-1  C6    0.020
 PU4  plan-1  C5    0.020
 PU4  plan-1  C2    0.020
 PU4  plan-1  C3    0.020
 PU4  plan-1  C4    0.020
 PU4  plan-1  O1    0.020
 PU4  plan-1  H6    0.020
 PU4  plan-1  H5    0.020
 PU4  plan-1  H2    0.020
 PU4  plan-1  H3    0.020
 PU4  plan-2  C15   0.020
 PU4  plan-2  N2    0.020
 PU4  plan-2  C12   0.020
 PU4  plan-2  N4    0.020
 PU4  plan-2  C14   0.020
 PU4  plan-2  N3    0.020
 PU4  plan-2  C11   0.020
 PU4  plan-2  C13   0.020
 PU4  plan-2  N5    0.020
 PU4  plan-2  N1    0.020
 PU4  plan-2  C10   0.020
 PU4  plan-2  C9    0.020
 PU4  plan-2  H14   0.020
 PU4  plan-3  C13   0.020
 PU4  plan-3  N5    0.020
 PU4  plan-3  H5N1  0.020
 PU4  plan-3  H5N2  0.020

