# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:01:02 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 9-butyl-8-(3,4,5-trimethoxybenzyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCn1c(Cc2cc(OC)c(OC)c(OC)c2)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
 PU3  PU3  9-butyl-8-(3,4,5-trimethoxybenzyl)-9H-purin-6-amine  ligand  52  27  .  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_PU3
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
 PU3  C19   C  CH3   0  -0.438  -3.1684  -0.5794  -2.6641
 PU3  O3    O  O2    0  -0.463  -1.9117  -0.7709  -3.2837
 PU3  C5    C  CR6   0   0.349  -0.8303  -0.2003  -2.7275
 PU3  C6    C  CR16  0  -0.435  -0.8607   0.6027  -1.5903
 PU3  C4    C  CR6   0   0.162   0.3864  -0.4704  -3.3624
 PU3  O1    O  O2    0  -0.481   0.4216  -1.2859  -4.4492
 PU3  C7    C  CH3   0  -0.409   0.2721  -0.6079  -5.6897
 PU3  C3    C  CR6   0   0.346   1.5668   0.0818  -2.8621
 PU3  O2    O  O2    0  -0.462   2.6876  -0.2286  -3.5343
 PU3  C8    C  CH3   0  -0.439   3.9244   0.2313  -3.0270
 PU3  C2    C  CR16  0  -0.489   1.5305   0.8868  -1.7237
 PU3  C1    C  CR6   0   0.130   0.3199   1.1423  -1.0957
 PU3  C9    C  CH2   0  -0.616   0.2835   2.0128   0.1399
 PU3  C10   C  CR5   0   0.463  -0.4289   1.3700   1.2804
 PU3  N1    N  N     0  -0.465  -1.5761   1.7724   1.7574
 PU3  C11   C  CR56  0  -0.004  -1.8631   0.8908   2.7651
 PU3  C13   C  CR6   0   0.437  -2.9430   0.7699   3.6556
 PU3  N5    N  NH2   0  -0.818  -3.9753   1.6204   3.6633
 PU3  C12   C  CR56  0   0.477  -0.8586  -0.0567   2.8853
 PU3  N4    N  N     0  -0.460  -0.8179  -1.0583   3.7618
 PU3  C14   C  CR16  0   0.035  -1.8826  -1.0680   4.5448
 PU3  N3    N  N     0  -0.473  -2.9183  -0.2325   4.5414
 PU3  N2    N  NR5   0  -0.528   0.0523   0.2568   1.9221
 PU3  C15   C  CH2   0  -0.322   1.3044  -0.4359   1.6843
 PU3  C16   C  CH2   0  -0.431   2.4851   0.2064   2.3991
 PU3  C17   C  CH2   0  -0.427   3.7969  -0.4745   2.0301
 PU3  C18   C  CH3   0  -0.661   4.9928   0.1364   2.7455
 PU3  H191  H  HCH3  0   0.262  -3.8904  -1.1380  -3.2543
 PU3  H192  H  HCH3  0   0.229  -3.1812  -0.9618  -1.6402
 PU3  H193  H  HCH3  0   0.230  -3.4634   0.4729  -2.6529
 PU3  H6    H  HCR6  0   0.273  -1.7936   0.8163  -1.0849
 PU3  H7C1  H  HCH3  0   0.237   0.3188  -1.3595  -6.4756
 PU3  H7C2  H  HCH3  0   0.221  -0.6885  -0.0916  -5.7553
 PU3  H7C3  H  HCH3  0   0.221   1.0718   0.1187  -5.8532
 PU3  H8C1  H  HCH3  0   0.263   4.6924  -0.1512  -3.6945
 PU3  H8C2  H  HCH3  0   0.230   3.9829   1.3225  -3.0133
 PU3  H8C3  H  HCH3  0   0.227   4.1159  -0.1451  -2.0183
 PU3  H2    H  HCR6  0   0.279   2.4354   1.3129  -1.3105
 PU3  H9C1  H  HCH2  0   0.296  -0.2360   2.9478  -0.0772
 PU3  H9C2  H  HCH2  0   0.280   1.3015   2.2827   0.4323
 PU3  H5N1  H  HNH2  0   0.400  -4.7788   1.4203   4.2340
 PU3  H5N2  H  HNH2  0   0.408  -4.0803   2.3023   2.9324
 PU3  H14   H  HCR6  0   0.249  -1.9234  -1.8578   5.2872
 PU3  H151  H  HCH2  0   0.269   1.4788  -0.4698   0.6084
 PU3  H152  H  HCH2  0   0.272   1.1719  -1.4656   2.0158
 PU3  H161  H  HCH2  0   0.236   2.3279   0.1572   3.4804
 PU3  H162  H  HCH2  0   0.229   2.5433   1.2681   2.1407
 PU3  H171  H  HCH2  0   0.217   3.9429  -0.4081   0.9472
 PU3  H172  H  HCH2  0   0.223   3.7330  -1.5415   2.2621
 PU3  H181  H  HCH3  0   0.230   5.9227  -0.3500   2.4501
 PU3  H182  H  HCH3  0   0.220   5.0879   1.1996   2.5174
 PU3  H183  H  HCH3  0   0.221   4.8974   0.0391   3.8282

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
 PU3  C19  O3    single    1.414  0.020  1.414
 PU3  C19  H191  single    0.970  0.020  1.090
 PU3  C19  H192  single    0.970  0.020  1.090
 PU3  C19  H193  single    0.970  0.020  1.090
 PU3  O3   C5    single    1.343  0.020  1.343
 PU3  C5   C6    aromatic  1.392  0.020  1.392
 PU3  C5   C4    aromatic  1.399  0.020  1.399
 PU3  C6   C1    aromatic  1.389  0.020  1.389
 PU3  C6   H6    single    0.930  0.020  1.080
 PU3  C4   O1    single    1.359  0.020  1.359
 PU3  C4   C3    aromatic  1.396  0.020  1.396
 PU3  O1   C7    single    1.422  0.020  1.422
 PU3  C7   H7C1  single    0.970  0.020  1.090
 PU3  C7   H7C2  single    0.970  0.020  1.090
 PU3  C7   H7C3  single    0.970  0.020  1.090
 PU3  C3   O2    single    1.343  0.020  1.343
 PU3  C3   C2    aromatic  1.395  0.020  1.395
 PU3  O2   C8    single    1.414  0.020  1.414
 PU3  C8   H8C1  single    0.970  0.020  1.090
 PU3  C8   H8C2  single    0.970  0.020  1.090
 PU3  C8   H8C3  single    0.970  0.020  1.090
 PU3  C2   C1    aromatic  1.388  0.020  1.388
 PU3  C2   H2    single    0.930  0.020  1.080
 PU3  C1   C9    single    1.512  0.020  1.512
 PU3  C9   C10   single    1.490  0.020  1.490
 PU3  C9   H9C1  single    0.970  0.020  1.090
 PU3  C9   H9C2  single    0.970  0.020  1.090
 PU3  C10  N1    aromatic  1.306  0.020  1.306
 PU3  C10  N2    aromatic  1.372  0.020  1.372
 PU3  N1   C11   aromatic  1.369  0.020  1.369
 PU3  C11  C13   aromatic  1.405  0.020  1.405
 PU3  C11  C12   aromatic  1.386  0.020  1.386
 PU3  C13  N5    single    1.338  0.020  1.338
 PU3  C13  N3    aromatic  1.338  0.020  1.338
 PU3  N5   H5N1  single    0.860  0.020  1.020
 PU3  N5   H5N2  single    0.860  0.020  1.020
 PU3  C12  N4    aromatic  1.332  0.020  1.332
 PU3  C12  N2    aromatic  1.362  0.020  1.362
 PU3  N4   C14   aromatic  1.322  0.020  1.322
 PU3  C14  N3    aromatic  1.331  0.020  1.331
 PU3  C14  H14   single    0.930  0.020  1.080
 PU3  N2   C15   single    1.451  0.020  1.451
 PU3  C15  C16   single    1.522  0.020  1.522
 PU3  C15  H151  single    0.970  0.020  1.090
 PU3  C15  H152  single    0.970  0.020  1.090
 PU3  C16  C17   single    1.523  0.020  1.523
 PU3  C16  H161  single    0.970  0.020  1.090
 PU3  C16  H162  single    0.970  0.020  1.090
 PU3  C17  C18   single    1.522  0.020  1.522
 PU3  C17  H171  single    0.970  0.020  1.090
 PU3  C17  H172  single    0.970  0.020  1.090
 PU3  C18  H181  single    0.970  0.020  1.090
 PU3  C18  H182  single    0.970  0.020  1.090
 PU3  C18  H183  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
 PU3  H193  C19  H192  108.91  3.000
 PU3  H193  C19  H191  108.73  3.000
 PU3  H192  C19  H191  108.73  3.000
 PU3  H193  C19  O3    112.01  3.000
 PU3  H192  C19  O3    111.93  3.000
 PU3  H191  C19  O3    106.42  3.000
 PU3  C5    O3   C19   118.45  3.000
 PU3  C4    C5   C6    120.07  3.000
 PU3  C4    C5   O3    115.49  3.000
 PU3  C6    C5   O3    124.44  3.000
 PU3  H6    C6   C1    119.32  3.000
 PU3  H6    C6   C5    120.93  3.000
 PU3  C1    C6   C5    119.76  3.000
 PU3  C3    C4   O1    120.13  3.000
 PU3  C3    C4   C5    119.77  3.000
 PU3  O1    C4   C5    120.09  3.000
 PU3  C7    O1   C4    114.13  3.000
 PU3  H7C3  C7   H7C2  108.68  3.000
 PU3  H7C3  C7   H7C1  108.65  3.000
 PU3  H7C2  C7   H7C1  108.70  3.000
 PU3  H7C3  C7   O1    111.76  3.000
 PU3  H7C2  C7   O1    111.73  3.000
 PU3  H7C1  C7   O1    107.23  3.000
 PU3  C2    C3   O2    124.30  3.000
 PU3  C2    C3   C4    119.93  3.000
 PU3  O2    C3   C4    115.77  3.000
 PU3  C8    O2   C3    118.37  3.000
 PU3  H8C3  C8   H8C2  108.83  3.000
 PU3  H8C3  C8   H8C1  108.75  3.000
 PU3  H8C2  C8   H8C1  108.74  3.000
 PU3  H8C3  C8   O2    111.85  3.000
 PU3  H8C2  C8   O2    112.10  3.000
 PU3  H8C1  C8   O2    106.45  3.000
 PU3  H2    C2   C1    118.96  3.000
 PU3  H2    C2   C3    121.14  3.000
 PU3  C1    C2   C3    119.89  3.000
 PU3  C9    C1   C2    119.80  3.000
 PU3  C9    C1   C6    119.62  3.000
 PU3  C2    C1   C6    120.58  3.000
 PU3  H9C2  C9   H9C1  106.55  3.000
 PU3  H9C2  C9   C10   110.31  3.000
 PU3  H9C1  C9   C10   107.11  3.000
 PU3  H9C2  C9   C1    109.78  3.000
 PU3  H9C1  C9   C1    110.00  3.000
 PU3  C10   C9   C1    112.87  3.000
 PU3  N2    C10  N1    112.78  3.000
 PU3  N2    C10  C9    122.69  3.000
 PU3  N1    C10  C9    124.51  3.000
 PU3  C11   N1   C10   104.75  3.000
 PU3  C12   C11  C13   116.31  3.000
 PU3  C12   C11  N1    110.61  3.000
 PU3  C13   C11  N1    133.07  3.000
 PU3  N3    C13  N5    119.14  3.000
 PU3  N3    C13  C11   118.03  3.000
 PU3  N5    C13  C11   122.83  3.000
 PU3  H5N2  N5   H5N1  117.67  3.000
 PU3  H5N2  N5   C13   120.52  3.000
 PU3  H5N1  N5   C13   119.56  3.000
 PU3  N2    C12  N4    128.17  3.000
 PU3  N2    C12  C11   105.42  3.000
 PU3  N4    C12  C11   126.40  3.000
 PU3  C14   N4   C12   111.77  3.000
 PU3  H14   C14  N3    115.44  3.000
 PU3  H14   C14  N4    116.17  3.000
 PU3  N3    C14  N4    128.38  3.000
 PU3  C14   N3   C13   119.11  3.000
 PU3  C15   N2   C12   125.68  3.000
 PU3  C15   N2   C10   127.84  3.000
 PU3  C12   N2   C10   106.43  3.000
 PU3  H152  C15  H151  106.87  3.000
 PU3  H152  C15  C16   110.50  3.000
 PU3  H151  C15  C16   110.63  3.000
 PU3  H152  C15  N2    107.24  3.000
 PU3  H151  C15  N2    108.34  3.000
 PU3  C16   C15  N2    113.02  3.000
 PU3  H162  C16  H161  106.55  3.000
 PU3  H162  C16  C17   109.31  3.000
 PU3  H161  C16  C17   110.07  3.000
 PU3  H162  C16  C15   109.86  3.000
 PU3  H161  C16  C15   109.49  3.000
 PU3  C17   C16  C15   111.44  3.000
 PU3  H172  C17  H171  106.06  3.000
 PU3  H172  C17  C18   109.74  3.000
 PU3  H171  C17  C18   109.63  3.000
 PU3  H172  C17  C16   109.53  3.000
 PU3  H171  C17  C16   109.11  3.000
 PU3  C18   C17  C16   112.55  3.000
 PU3  H183  C18  H182  107.57  3.000
 PU3  H183  C18  H181  107.67  3.000
 PU3  H182  C18  H181  107.68  3.000
 PU3  H183  C18  C17   111.22  3.000
 PU3  H182  C18  C17   111.18  3.000
 PU3  H181  C18  C17   111.34  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
 PU3  CONST_01  C2    C1   C6   C5      0.00   0.0  0
 PU3  CONST_02  C2    C3   C4   C5      0.00   0.0  0
 PU3  CONST_03  C3    C4   C5   C6      0.00   0.0  0
 PU3  CONST_04  C3    C2   C1   C6      0.00   0.0  0
 PU3  CONST_05  C1    C6   C5   C4      0.00   0.0  0
 PU3  CONST_06  C1    C2   C3   C4      0.00   0.0  0
 PU3  CONST_07  C13   C11  N1   C10   180.00   0.0  0
 PU3  CONST_08  C12   C11  N1   C10     0.00   0.0  0
 PU3  CONST_09  C11   C12  N2   C10     0.00   0.0  0
 PU3  CONST_10  N4    C12  N2   C10   180.00   0.0  0
 PU3  CONST_11  C12   N2   C10  N1      0.00   0.0  0
 PU3  CONST_12  N3    C13  C11  N1    180.00   0.0  0
 PU3  CONST_13  N4    C12  C11  N1    180.00   0.0  0
 PU3  CONST_14  N2    C12  C11  N1      0.00   0.0  0
 PU3  CONST_15  N2    C10  N1   C11     0.00   0.0  0
 PU3  CONST_16  C14   N3   C13  C11     0.00   0.0  0
 PU3  CONST_17  C14   N4   C12  C11     0.00   0.0  0
 PU3  CONST_18  N4    C12  C11  C13     0.00   0.0  0
 PU3  CONST_19  N2    C12  C11  C13   180.00   0.0  0
 PU3  CONST_20  N4    C14  N3   C13     0.00   0.0  0
 PU3  CONST_21  N3    C13  C11  C12     0.00   0.0  0
 PU3  CONST_22  N3    C14  N4   C12     0.00   0.0  0
 PU3  CONST_23  N2    C12  N4   C14   180.00   0.0  0
 PU3  CONST_24  C1    C6   C5   O3    180.00   0.0  0
 PU3  CONST_25  C3    C4   C5   O3    180.00   0.0  0
 PU3  CONST_26  C9    C1   C6   C5    180.00   0.0  0
 PU3  CONST_27  O2    C3   C4   C5    180.00   0.0  0
 PU3  CONST_28  O1    C4   C5   C6    180.00   0.0  0
 PU3  CONST_29  C2    C3   C4   O1    180.00   0.0  0
 PU3  CONST_30  C9    C1   C2   C3    180.00   0.0  0
 PU3  CONST_31  C1    C2   C3   O2    180.00   0.0  0
 PU3  CONST_32  C11   N1   C10  C9    180.00   0.0  0
 PU3  CONST_33  C12   N2   C10  C9    180.00   0.0  0
 PU3  CONST_34  C15   N2   C10  N1    180.00   0.0  0
 PU3  CONST_35  N5    C13  C11  N1      0.00   0.0  0
 PU3  CONST_36  C15   N2   C12  C11   180.00   0.0  0
 PU3  CONST_37  C12   C11  C13  N5    180.00   0.0  0
 PU3  CONST_38  C14   N3   C13  N5    180.00   0.0  0
 PU3  CONST_39  C15   N2   C12  N4      0.00   0.0  0
 PU3  CONST_40  H2    C2   C1   C6    180.00   0.0  0
 PU3  CONST_41  H6    C6   C5   C4    180.00   0.0  0
 PU3  CONST_42  H14   C14  N3   C13   180.00   0.0  0
 PU3  CONST_43  H5N1  N5   C13  C11   180.00   0.0  0
 PU3  CONST_44  H5N2  N5   C13  C11     0.00   0.0  0
 PU3  Var_01    C10   C9   C1   C6     51.98  30.0  2
 PU3  Var_02    N1    C10  C9   C1   -111.39  30.0  2
 PU3  Var_03    C6    C5   O3   C19    -1.67  30.0  2
 PU3  Var_04    C3    C4   O1   C7    -90.57  30.0  2
 PU3  Var_05    C2    C3   O2   C8      3.24  30.0  2
 PU3  Var_06    C16   C15  N2   C10    82.84  30.0  2
 PU3  Var_07    C17   C16  C15  N2   -175.08  30.0  3
 PU3  Var_08    H191  C19  O3   C5   -178.65  30.0  3
 PU3  Var_09    H7C1  C7   O1   C4    179.89  30.0  3
 PU3  Var_10    H8C1  C8   O2   C3    178.30  30.0  3
 PU3  Var_11    C18   C17  C16  C15  -179.24  30.0  3
 PU3  Var_12    H181  C18  C17  C16  -178.70  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
 PU3  plan-1  O3    0.020
 PU3  plan-1  C5    0.020
 PU3  plan-1  C6    0.020
 PU3  plan-1  C4    0.020
 PU3  plan-1  O1    0.020
 PU3  plan-1  C3    0.020
 PU3  plan-1  O2    0.020
 PU3  plan-1  C2    0.020
 PU3  plan-1  C1    0.020
 PU3  plan-1  C9    0.020
 PU3  plan-1  H6    0.020
 PU3  plan-1  H2    0.020
 PU3  plan-2  C9    0.020
 PU3  plan-2  C10   0.020
 PU3  plan-2  N1    0.020
 PU3  plan-2  C11   0.020
 PU3  plan-2  C13   0.020
 PU3  plan-2  N5    0.020
 PU3  plan-2  C12   0.020
 PU3  plan-2  N4    0.020
 PU3  plan-2  C14   0.020
 PU3  plan-2  N3    0.020
 PU3  plan-2  N2    0.020
 PU3  plan-2  C15   0.020
 PU3  plan-2  H14   0.020
 PU3  plan-3  C13   0.020
 PU3  plan-3  N5    0.020
 PU3  plan-3  H5N1  0.020
 PU3  plan-3  H5N2  0.020

