# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:07:50 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 8-(1,3-benzodioxol-5-ylmethyl)-9-butyl-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCn1c(Cc2ccc3OCOc3c2)nc4c(N)ncnc14
#
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
 PU6  PU6  8-(1,3-benzodioxol-5-ylmethyl)-9-butyl-9H-purin-6-amine  ligand  43  24  .  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_PU6
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
 PU6  C18   C  CH3   0  -0.662   5.2534   0.1218   1.6488
 PU6  C17   C  CH2   0  -0.428   4.0050  -0.4513   0.9941
 PU6  C16   C  CH2   0  -0.427   2.7245   0.1751   1.5301
 PU6  C15   C  CH2   0  -0.320   1.4903  -0.4282   0.8749
 PU6  N2    N  NR5   0  -0.527   0.2555   0.1528   1.3647
 PU6  C12   C  CR56  0   0.479  -0.3975  -0.2228   2.4998
 PU6  N4    N  N     0  -0.460  -0.0924  -1.2151   3.3335
 PU6  C14   C  CR16  0   0.034  -0.9559  -1.2987   4.3308
 PU6  N3    N  N     0  -0.473  -2.0246  -0.5409   4.5651
 PU6  C11   C  CR56  0  -0.003  -1.4692   0.6486   2.6146
 PU6  C13   C  CR6   0   0.436  -2.3154   0.4539   3.7192
 PU6  N5    N  NH2   0  -0.818  -3.3765   1.2313   3.9643
 PU6  N1    N  N     0  -0.466  -1.4740   1.5450   1.5789
 PU6  C10   C  CR5   0   0.464  -0.4327   1.2260   0.8584
 PU6  C9    C  CH2   0  -0.611  -0.0409   1.9118  -0.4047
 PU6  C1    C  CR6   0   0.083  -0.2500   1.0560  -1.6352
 PU6  C6    C  CR16  0  -0.404   0.7751   0.9553  -2.5880
 PU6  C5    C  CR56  0   0.310   0.5371   0.1744  -3.6921
 PU6  C2    C  CR16  0  -0.287  -1.4504   0.3849  -1.8293
 PU6  O3    O  O     0  -0.486   1.3505  -0.0642  -4.7495
 PU6  C3    C  CR16  0  -0.327  -1.6802  -0.4084  -2.9588
 PU6  C4    C  CR56  0   0.287  -0.6615  -0.4948  -3.8749
 PU6  O1    O  O     0  -0.486  -0.6254  -1.1683  -5.0516
 PU6  C7    C  CH2   0   0.068   0.7195  -1.0911  -5.5043
 PU6  H181  H  HCH3  0   0.230   6.1573  -0.3388   1.2496
 PU6  H182  H  HCH3  0   0.220   5.3285   1.1979   1.4830
 PU6  H183  H  HCH3  0   0.220   5.2452  -0.0451   2.7273
 PU6  H171  H  HCH2  0   0.220   4.0570  -0.3026  -0.0887
 PU6  H172  H  HCH2  0   0.222   3.9725  -1.5335   1.1510
 PU6  H161  H  HCH2  0   0.234   2.6654   0.0309   2.6127
 PU6  H162  H  HCH2  0   0.228   2.7410   1.2561   1.3585
 PU6  H151  H  HCH2  0   0.267   1.5252  -0.3000  -0.2070
 PU6  H152  H  HCH2  0   0.269   1.4463  -1.5018   1.0614
 PU6  H14   H  HCR6  0   0.248  -0.7757  -2.0859   5.0555
 PU6  H5N1  H  HNH2  0   0.400  -4.0261   0.9699   4.6861
 PU6  H5N2  H  HNH2  0   0.407  -3.6884   1.8937   3.2757
 PU6  H9C1  H  HCH2  0   0.295  -0.6408   2.8211  -0.4715
 PU6  H9C2  H  HCH2  0   0.279   1.0020   2.2342  -0.3530
 PU6  H6    H  HCR6  0   0.274   1.7171   1.4733  -2.4567
 PU6  H2    H  HCR6  0   0.255  -2.2351   0.4705  -1.0878
 PU6  H3    H  HCR6  0   0.274  -2.6199  -0.9255  -3.0990
 PU6  H7C1  H  HCH2  0   0.233   1.2270  -2.0461  -5.3289
 PU6  H7C2  H  HCH2  0   0.247   0.7394  -0.8364  -6.5636

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
 PU6  C18  C17   single    1.522  0.020  1.522
 PU6  C18  H181  single    0.970  0.020  1.090
 PU6  C18  H182  single    0.970  0.020  1.090
 PU6  C18  H183  single    0.970  0.020  1.090
 PU6  C17  C16   single    1.523  0.020  1.523
 PU6  C17  H171  single    0.970  0.020  1.090
 PU6  C17  H172  single    0.970  0.020  1.090
 PU6  C16  C15   single    1.522  0.020  1.522
 PU6  C16  H161  single    0.970  0.020  1.090
 PU6  C16  H162  single    0.970  0.020  1.090
 PU6  C15  N2    single    1.450  0.020  1.450
 PU6  C15  H151  single    0.970  0.020  1.090
 PU6  C15  H152  single    0.970  0.020  1.090
 PU6  N2   C12   aromatic  1.362  0.020  1.362
 PU6  N2   C10   aromatic  1.372  0.020  1.372
 PU6  C12  N4    aromatic  1.331  0.020  1.331
 PU6  C12  C11   aromatic  1.386  0.020  1.386
 PU6  N4   C14   aromatic  1.322  0.020  1.322
 PU6  C14  N3    aromatic  1.331  0.020  1.331
 PU6  C14  H14   single    0.930  0.020  1.080
 PU6  N3   C13   aromatic  1.338  0.020  1.338
 PU6  C11  C13   aromatic  1.405  0.020  1.405
 PU6  C11  N1    aromatic  1.370  0.020  1.370
 PU6  C13  N5    single    1.338  0.020  1.338
 PU6  N5   H5N1  single    0.860  0.020  1.020
 PU6  N5   H5N2  single    0.860  0.020  1.020
 PU6  N1   C10   aromatic  1.306  0.020  1.306
 PU6  C10  C9    single    1.490  0.020  1.490
 PU6  C9   C1    single    1.513  0.020  1.513
 PU6  C9   H9C1  single    0.970  0.020  1.090
 PU6  C9   H9C2  single    0.970  0.020  1.090
 PU6  C1   C6    aromatic  1.403  0.020  1.403
 PU6  C1   C2    aromatic  1.389  0.020  1.389
 PU6  C6   C5    aromatic  1.373  0.020  1.373
 PU6  C6   H6    single    0.930  0.020  1.080
 PU6  C5   O3    single    1.355  0.020  1.355
 PU6  C5   C4    aromatic  1.385  0.020  1.385
 PU6  C2   C3    aromatic  1.399  0.020  1.399
 PU6  C2   H2    single    0.930  0.020  1.080
 PU6  O3   C7    single    1.422  0.020  1.422
 PU6  C3   C4    aromatic  1.373  0.020  1.373
 PU6  C3   H3    single    0.930  0.020  1.080
 PU6  C4   O1    single    1.356  0.020  1.356
 PU6  O1   C7    single    1.421  0.020  1.421
 PU6  C7   H7C1  single    0.970  0.020  1.090
 PU6  C7   H7C2  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
 PU6  H183  C18  H182  107.55  3.000
 PU6  H183  C18  H181  107.67  3.000
 PU6  H182  C18  H181  107.69  3.000
 PU6  H183  C18  C17   111.19  3.000
 PU6  H182  C18  C17   111.25  3.000
 PU6  H181  C18  C17   111.31  3.000
 PU6  H172  C17  H171  106.12  3.000
 PU6  H172  C17  C16   109.36  3.000
 PU6  H171  C17  C16   109.41  3.000
 PU6  H172  C17  C18   109.59  3.000
 PU6  H171  C17  C18   109.61  3.000
 PU6  C16   C17  C18   112.55  3.000
 PU6  H162  C16  H161  106.63  3.000
 PU6  H162  C16  C15   109.65  3.000
 PU6  H161  C16  C15   109.27  3.000
 PU6  H162  C16  C17   109.78  3.000
 PU6  H161  C16  C17   109.85  3.000
 PU6  C15   C16  C17   111.55  3.000
 PU6  H152  C15  H151  106.67  3.000
 PU6  H152  C15  N2    107.60  3.000
 PU6  H151  C15  N2    108.38  3.000
 PU6  H152  C15  C16   110.45  3.000
 PU6  H151  C15  C16   110.77  3.000
 PU6  N2    C15  C16   112.73  3.000
 PU6  C10   N2   C12   106.43  3.000
 PU6  C10   N2   C15   128.03  3.000
 PU6  C12   N2   C15   125.39  3.000
 PU6  C11   C12  N4    126.43  3.000
 PU6  C11   C12  N2    105.44  3.000
 PU6  N4    C12  N2    128.13  3.000
 PU6  C14   N4   C12   111.71  3.000
 PU6  H14   C14  N3    115.39  3.000
 PU6  H14   C14  N4    116.19  3.000
 PU6  N3    C14  N4    128.42  3.000
 PU6  C13   N3   C14   119.12  3.000
 PU6  N1    C11  C13   133.08  3.000
 PU6  N1    C11  C12   110.58  3.000
 PU6  C13   C11  C12   116.34  3.000
 PU6  N5    C13  C11   122.76  3.000
 PU6  N5    C13  N3    119.25  3.000
 PU6  C11   C13  N3    117.98  3.000
 PU6  H5N2  N5   H5N1  117.55  3.000
 PU6  H5N2  N5   C13   120.23  3.000
 PU6  H5N1  N5   C13   119.52  3.000
 PU6  C10   N1   C11   104.75  3.000
 PU6  C9    C10  N1    124.41  3.000
 PU6  C9    C10  N2    122.76  3.000
 PU6  N1    C10  N2    112.80  3.000
 PU6  H9C2  C9   H9C1  106.36  3.000
 PU6  H9C2  C9   C1    109.70  3.000
 PU6  H9C1  C9   C1    110.21  3.000
 PU6  H9C2  C9   C10   110.29  3.000
 PU6  H9C1  C9   C10   106.91  3.000
 PU6  C1    C9   C10   113.12  3.000
 PU6  C2    C1   C6    120.12  3.000
 PU6  C2    C1   C9    120.42  3.000
 PU6  C6    C1   C9    119.46  3.000
 PU6  H6    C6   C5    121.34  3.000
 PU6  H6    C6   C1    121.26  3.000
 PU6  C5    C6   C1    117.40  3.000
 PU6  C4    C5   O3    109.36  3.000
 PU6  C4    C5   C6    122.06  3.000
 PU6  O3    C5   C6    128.57  3.000
 PU6  H2    C2   C3    118.59  3.000
 PU6  H2    C2   C1    119.50  3.000
 PU6  C3    C2   C1    121.92  3.000
 PU6  C7    O3   C5    105.96  3.000
 PU6  H3    C3   C4    121.88  3.000
 PU6  H3    C3   C2    121.22  3.000
 PU6  C4    C3   C2    116.90  3.000
 PU6  O1    C4   C3    129.05  3.000
 PU6  O1    C4   C5    109.35  3.000
 PU6  C3    C4   C5    121.59  3.000
 PU6  C7    O1   C4    105.93  3.000
 PU6  H7C2  C7   H7C1  110.54  3.000
 PU6  H7C2  C7   O1    109.86  3.000
 PU6  H7C1  C7   O1    109.88  3.000
 PU6  H7C2  C7   O3    109.82  3.000
 PU6  H7C1  C7   O3    109.81  3.000
 PU6  O1    C7   O3    106.86  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
 PU6  CONST_01  C14   N4   C12  N2    180.00   0.0  0
 PU6  CONST_02  C13   C11  C12  N2    180.00   0.0  0
 PU6  CONST_03  N1    C11  C12  N2      0.00   0.0  0
 PU6  CONST_04  C11   N1   C10  N2      0.00   0.0  0
 PU6  CONST_05  N1    C10  N2   C12     0.00   0.0  0
 PU6  CONST_06  N3    C14  N4   C12     0.00   0.0  0
 PU6  CONST_07  N3    C13  C11  C12     0.00   0.0  0
 PU6  CONST_08  C10   N1   C11  C12     0.00   0.0  0
 PU6  CONST_09  C10   N2   C12  N4    180.00   0.0  0
 PU6  CONST_10  C13   C11  C12  N4      0.00   0.0  0
 PU6  CONST_11  N1    C11  C12  N4    180.00   0.0  0
 PU6  CONST_12  C13   N3   C14  N4      0.00   0.0  0
 PU6  CONST_13  C11   C12  N4   C14     0.00   0.0  0
 PU6  CONST_14  C11   C13  N3   C14     0.00   0.0  0
 PU6  CONST_15  N1    C11  C13  N3    180.00   0.0  0
 PU6  CONST_16  C10   N2   C12  C11     0.00   0.0  0
 PU6  CONST_17  C10   N1   C11  C13   180.00   0.0  0
 PU6  CONST_18  C4    C5   C6   C1      0.00   0.0  0
 PU6  CONST_19  C4    C3   C2   C1      0.00   0.0  0
 PU6  CONST_20  C3    C2   C1   C6      0.00   0.0  0
 PU6  CONST_21  C3    C4   C5   C6      0.00   0.0  0
 PU6  CONST_22  C2    C1   C6   C5      0.00   0.0  0
 PU6  CONST_23  C2    C3   C4   C5      0.00   0.0  0
 PU6  CONST_24  N4    C12  N2   C15     0.00   0.0  0
 PU6  CONST_25  C11   C12  N2   C15   180.00   0.0  0
 PU6  CONST_26  N1    C10  N2   C15   180.00   0.0  0
 PU6  CONST_27  C9    C10  N2   C12   180.00   0.0  0
 PU6  CONST_28  N5    C13  C11  C12   180.00   0.0  0
 PU6  CONST_29  N5    C13  N3   C14   180.00   0.0  0
 PU6  CONST_30  C9    C10  N1   C11   180.00   0.0  0
 PU6  CONST_31  N1    C11  C13  N5      0.00   0.0  0
 PU6  CONST_32  C5    C6   C1   C9    180.00   0.0  0
 PU6  CONST_33  C3    C2   C1   C9    180.00   0.0  0
 PU6  CONST_34  H14   C14  N4   C12   180.00   0.0  0
 PU6  CONST_35  H3    C3   C2   C1    180.00   0.0  0
 PU6  CONST_36  H2    C2   C1   C6    180.00   0.0  0
 PU6  CONST_37  H6    C6   C1   C2    180.00   0.0  0
 PU6  CONST_38  H5N1  N5   C13  N3      0.00   0.0  0
 PU6  CONST_39  H5N2  N5   C13  N3    180.00   0.0  0
 PU6  Var_01    O1    C7   O3   C5     15.49  30.0  1
 PU6  Var_02    C1    C9   C10  N2     68.34  30.0  2
 PU6  Var_03    C6    C1   C9   C10  -132.57  30.0  2
 PU6  Var_04    C12   N2   C15  C16   -83.55  30.0  2
 PU6  Var_05    N2    C15  C16  C17  -179.86  30.0  3
 PU6  Var_06    C15   C16  C17  C18  -179.18  30.0  3
 PU6  Var_07    H181  C18  C17  C16  -179.90  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
 PU6  plan-1  C15   0.020
 PU6  plan-1  N2    0.020
 PU6  plan-1  C12   0.020
 PU6  plan-1  N4    0.020
 PU6  plan-1  C14   0.020
 PU6  plan-1  N3    0.020
 PU6  plan-1  C11   0.020
 PU6  plan-1  C13   0.020
 PU6  plan-1  N5    0.020
 PU6  plan-1  N1    0.020
 PU6  plan-1  C10   0.020
 PU6  plan-1  C9    0.020
 PU6  plan-1  H14   0.020
 PU6  plan-2  C9    0.020
 PU6  plan-2  C1    0.020
 PU6  plan-2  C6    0.020
 PU6  plan-2  C5    0.020
 PU6  plan-2  C2    0.020
 PU6  plan-2  O3    0.020
 PU6  plan-2  C3    0.020
 PU6  plan-2  C4    0.020
 PU6  plan-2  O1    0.020
 PU6  plan-2  H6    0.020
 PU6  plan-2  H2    0.020
 PU6  plan-2  H3    0.020
 PU6  plan-3  C13   0.020
 PU6  plan-3  N5    0.020
 PU6  plan-3  H5N1  0.020
 PU6  plan-3  H5N2  0.020

