# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:17:00 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 9-butyl-8-(3-methoxybenzyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCn1c(Cc2cccc(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
 PU5  PU5  9-butyl-8-(3-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_PU5
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
 PU5  C18   C  CH3   0  -0.662   5.2366   0.1809   0.8057
 PU5  C17   C  CH2   0  -0.428   3.9297  -0.4197   0.3090
 PU5  C16   C  CH2   0  -0.426   2.7114   0.1869   0.9928
 PU5  C15   C  CH2   0  -0.319   1.4193  -0.4562   0.5099
 PU5  N2    N  NR5   0  -0.526   0.2430   0.1308   1.1220
 PU5  C12   C  CR56  0   0.479  -0.2523  -0.1931   2.3491
 PU5  N4    N  N     0  -0.460   0.1793  -1.1330   3.1883
 PU5  C14   C  CR16  0   0.034  -0.5420  -1.1687   4.2953
 PU5  N3    N  N     0  -0.474  -1.5827  -0.4092   4.6292
 PU5  C11   C  CR56  0  -0.004  -1.3174   0.6688   2.5558
 PU5  C13   C  CR6   0   0.440  -2.0044   0.5294   3.7739
 PU5  N5    N  NH2   0  -0.818  -3.0593   1.2824   4.0989
 PU5  N1    N  N     0  -0.465  -1.4722   1.5090   1.4857
 PU5  C10   C  CR5   0   0.460  -0.5250   1.1667   0.6547
 PU5  C1    C  CR16  0  -0.298  -1.8199   0.1139  -1.8110
 PU5  C6    C  CR6   0   0.115  -0.6445   0.8654  -1.8279
 PU5  C5    C  CR16  0  -0.411   0.2082   0.7734  -2.9156
 PU5  C2    C  CR16  0  -0.225  -2.1159  -0.7142  -2.8790
 PU5  C3    C  CR16  0  -0.396  -1.2645  -0.8142  -3.9747
 PU5  C4    C  CR6   0   0.397  -0.0933  -0.0623  -3.9944
 PU5  O1    O  O2    0  -0.472   0.8049  -0.0777  -4.9968
 PU5  C7    C  CH3   0  -0.436   0.5579  -0.9117  -6.1113
 PU5  H181  H  HCH3  0   0.220   5.3573   0.0268   1.8794
 PU5  H182  H  HCH3  0   0.220   5.2732   1.2561   0.6220
 PU5  H183  H  HCH3  0   0.230   6.0952  -0.2694   0.3073
 PU5  H171  H  HCH2  0   0.222   3.9370  -1.5012   0.4737
 PU5  H172  H  HCH2  0   0.220   3.8473  -0.2775  -0.7728
 PU5  H161  H  HCH2  0   0.228   2.6771   1.2639   0.8016
 PU5  H162  H  HCH2  0   0.234   2.7935   0.0635   2.0766
 PU5  H151  H  HCH2  0   0.269   1.4150  -1.5226   0.7380
 PU5  H152  H  HCH2  0   0.266   1.3239  -0.3666  -0.5723
 PU5  H14   H  HCR6  0   0.248  -0.2513  -1.9101   5.0326
 PU5  H9C1  H  HCH2  0   0.278   0.7196   2.1473  -0.7758
 PU5  H9C2  H  HCH2  0   0.298  -0.9485   2.6750  -0.7221
 PU5  H5N1  H  HNH2  0   0.401  -3.4604   1.2165   5.0184
 PU5  H5N2  H  HNH2  0   0.409  -3.3425   2.0494   3.5148
 PU5  H5    H  HCR6  0   0.261   1.1238   1.3539  -2.9382
 PU5  H2    H  HCR6  0   0.260  -3.0260  -1.3002  -2.8680
 PU5  H3    H  HCR6  0   0.279  -1.5284  -1.4767  -4.7877
 PU5  H7C1  H  HCH3  0   0.260   1.3905  -0.7686  -6.7954
 PU5  H7C2  H  HCH3  0   0.229   0.5122  -1.9666  -5.8288
 PU5  H7C3  H  HCH3  0   0.228  -0.3695  -0.6441  -6.6242
 PU5  C9    C  CH2   0  -0.611  -0.3095   1.7912  -0.6801
 PU5  H1    H  HCR6  0   0.249  -2.4977   0.1782  -0.9687

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
 PU5  C18  C17   single    1.522  0.020  1.522
 PU5  C18  H181  single    0.970  0.020  1.090
 PU5  C18  H182  single    0.970  0.020  1.090
 PU5  C18  H183  single    0.970  0.020  1.090
 PU5  C17  C16   single    1.523  0.020  1.523
 PU5  C17  H171  single    0.970  0.020  1.090
 PU5  C17  H172  single    0.970  0.020  1.090
 PU5  C16  C15   single    1.522  0.020  1.522
 PU5  C16  H161  single    0.970  0.020  1.090
 PU5  C16  H162  single    0.970  0.020  1.090
 PU5  C15  N2    single    1.450  0.020  1.450
 PU5  C15  H151  single    0.970  0.020  1.090
 PU5  C15  H152  single    0.970  0.020  1.090
 PU5  N2   C12   aromatic  1.362  0.020  1.362
 PU5  N2   C10   aromatic  1.372  0.020  1.372
 PU5  C12  N4    aromatic  1.332  0.020  1.332
 PU5  C12  C11   aromatic  1.386  0.020  1.386
 PU5  N4   C14   aromatic  1.322  0.020  1.322
 PU5  C14  N3    aromatic  1.331  0.020  1.331
 PU5  C14  H14   single    0.930  0.020  1.080
 PU5  C9   C10   single    1.489  0.020  1.489
 PU5  C9   C6    single    1.512  0.020  1.512
 PU5  C9   H9C1  single    0.970  0.020  1.090
 PU5  C9   H9C2  single    0.970  0.020  1.090
 PU5  N3   C13   aromatic  1.338  0.020  1.338
 PU5  C11  C13   aromatic  1.405  0.020  1.405
 PU5  C11  N1    aromatic  1.369  0.020  1.369
 PU5  C13  N5    single    1.336  0.020  1.336
 PU5  N5   H5N1  single    0.860  0.020  1.020
 PU5  N5   H5N2  single    0.860  0.020  1.020
 PU5  N1   C10   aromatic  1.306  0.020  1.306
 PU5  C1   C6    aromatic  1.395  0.020  1.395
 PU5  C1   C2    aromatic  1.383  0.020  1.383
 PU5  C1   H1    single    0.930  0.020  1.080
 PU5  C6   C5    aromatic  1.385  0.020  1.385
 PU5  C5   C4    aromatic  1.397  0.020  1.397
 PU5  C5   H5    single    0.930  0.020  1.080
 PU5  C2   C3    aromatic  1.391  0.020  1.391
 PU5  C2   H2    single    0.930  0.020  1.080
 PU5  C3   C4    aromatic  1.392  0.020  1.392
 PU5  C3   H3    single    0.930  0.020  1.080
 PU5  C4   O1    single    1.346  0.020  1.346
 PU5  O1   C7    single    1.414  0.020  1.414
 PU5  C7   H7C1  single    0.970  0.020  1.090
 PU5  C7   H7C2  single    0.970  0.020  1.090
 PU5  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
 PU5  H183  C18  H182  107.67  3.000
 PU5  H183  C18  H181  107.72  3.000
 PU5  H182  C18  H181  107.52  3.000
 PU5  H183  C18  C17   111.35  3.000
 PU5  H182  C18  C17   111.26  3.000
 PU5  H181  C18  C17   111.13  3.000
 PU5  H172  C17  H171  106.13  3.000
 PU5  H172  C17  C16   109.38  3.000
 PU5  H171  C17  C16   109.36  3.000
 PU5  H172  C17  C18   109.64  3.000
 PU5  H171  C17  C18   109.59  3.000
 PU5  C16   C17  C18   112.54  3.000
 PU5  H162  C16  H161  106.64  3.000
 PU5  H162  C16  C15   109.30  3.000
 PU5  H161  C16  C15   109.50  3.000
 PU5  H162  C16  C17   109.87  3.000
 PU5  H161  C16  C17   109.79  3.000
 PU5  C15   C16  C17   111.62  3.000
 PU5  H152  C15  H151  106.72  3.000
 PU5  H152  C15  N2    108.35  3.000
 PU5  H151  C15  N2    107.72  3.000
 PU5  H152  C15  C16   110.77  3.000
 PU5  H151  C15  C16   110.50  3.000
 PU5  N2    C15  C16   112.56  3.000
 PU5  C10   N2   C12   106.43  3.000
 PU5  C10   N2   C15   128.03  3.000
 PU5  C12   N2   C15   125.37  3.000
 PU5  C11   C12  N4    126.45  3.000
 PU5  C11   C12  N2    105.42  3.000
 PU5  N4    C12  N2    128.13  3.000
 PU5  C14   N4   C12   111.72  3.000
 PU5  H14   C14  N3    115.39  3.000
 PU5  H14   C14  N4    116.19  3.000
 PU5  N3    C14  N4    128.41  3.000
 PU5  C13   N3   C14   119.11  3.000
 PU5  N1    C11  C13   133.08  3.000
 PU5  N1    C11  C12   110.61  3.000
 PU5  C13   C11  C12   116.31  3.000
 PU5  N5    C13  C11   122.74  3.000
 PU5  N5    C13  N3    119.25  3.000
 PU5  C11   C13  N3    118.01  3.000
 PU5  H5N2  N5   H5N1  117.98  3.000
 PU5  H5N2  N5   C13   120.75  3.000
 PU5  H5N1  N5   C13   120.03  3.000
 PU5  C10   N1   C11   104.75  3.000
 PU5  N1    C10  C9    124.44  3.000
 PU5  N1    C10  N2    112.79  3.000
 PU5  C9    C10  N2    122.75  3.000
 PU5  H1    C1   C2    120.13  3.000
 PU5  H1    C1   C6    120.31  3.000
 PU5  C2    C1   C6    119.56  3.000
 PU5  C5    C6   C1    119.50  3.000
 PU5  C5    C6   C9    120.02  3.000
 PU5  C1    C6   C9    120.48  3.000
 PU5  H5    C5   C4    119.09  3.000
 PU5  H5    C5   C6    120.04  3.000
 PU5  C4    C5   C6    120.87  3.000
 PU5  H2    C2   C3    118.92  3.000
 PU5  H2    C2   C1    119.74  3.000
 PU5  C3    C2   C1    121.33  3.000
 PU5  H3    C3   C4    121.71  3.000
 PU5  H3    C3   C2    119.13  3.000
 PU5  C4    C3   C2    119.16  3.000
 PU5  O1    C4   C3    124.46  3.000
 PU5  O1    C4   C5    115.96  3.000
 PU5  C3    C4   C5    119.58  3.000
 PU5  C7    O1   C4    118.51  3.000
 PU5  H7C3  C7   H7C2  108.79  3.000
 PU5  H7C3  C7   H7C1  108.80  3.000
 PU5  H7C2  C7   H7C1  108.77  3.000
 PU5  H7C3  C7   O1    111.94  3.000
 PU5  H7C2  C7   O1    111.89  3.000
 PU5  H7C1  C7   O1    106.54  3.000
 PU5  H9C2  C9   H9C1  106.50  3.000
 PU5  H9C2  C9   C6    109.68  3.000
 PU5  H9C1  C9   C6    109.97  3.000
 PU5  H9C2  C9   C10   106.81  3.000
 PU5  H9C1  C9   C10   110.57  3.000
 PU5  C6    C9   C10   113.05  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
 PU5  CONST_01  C14   N4   C12  N2    180.00   0.0  0
 PU5  CONST_02  C13   C11  C12  N2    180.00   0.0  0
 PU5  CONST_03  N1    C11  C12  N2      0.00   0.0  0
 PU5  CONST_04  C11   N1   C10  N2      0.00   0.0  0
 PU5  CONST_05  N1    C10  N2   C12     0.00   0.0  0
 PU5  CONST_06  N3    C14  N4   C12     0.00   0.0  0
 PU5  CONST_07  N3    C13  C11  C12     0.00   0.0  0
 PU5  CONST_08  C10   N1   C11  C12     0.00   0.0  0
 PU5  CONST_09  C10   N2   C12  N4    180.00   0.0  0
 PU5  CONST_10  C13   C11  C12  N4      0.00   0.0  0
 PU5  CONST_11  N1    C11  C12  N4    180.00   0.0  0
 PU5  CONST_12  C13   N3   C14  N4      0.00   0.0  0
 PU5  CONST_13  C11   C12  N4   C14     0.00   0.0  0
 PU5  CONST_14  C11   C13  N3   C14     0.00   0.0  0
 PU5  CONST_15  N1    C11  C13  N3    180.00   0.0  0
 PU5  CONST_16  C10   N2   C12  C11     0.00   0.0  0
 PU5  CONST_17  C10   N1   C11  C13   180.00   0.0  0
 PU5  CONST_18  C4    C5   C6   C1      0.00   0.0  0
 PU5  CONST_19  C4    C3   C2   C1      0.00   0.0  0
 PU5  CONST_20  C3    C2   C1   C6      0.00   0.0  0
 PU5  CONST_21  C3    C4   C5   C6      0.00   0.0  0
 PU5  CONST_22  C2    C1   C6   C5      0.00   0.0  0
 PU5  CONST_23  C2    C3   C4   C5      0.00   0.0  0
 PU5  CONST_24  N4    C12  N2   C15     0.00   0.0  0
 PU5  CONST_25  C11   C12  N2   C15   180.00   0.0  0
 PU5  CONST_26  N1    C10  N2   C15   180.00   0.0  0
 PU5  CONST_27  C9    C10  N2   C12   180.00   0.0  0
 PU5  CONST_28  N5    C13  C11  C12   180.00   0.0  0
 PU5  CONST_29  N5    C13  N3   C14   180.00   0.0  0
 PU5  CONST_30  C11   N1   C10  C9    180.00   0.0  0
 PU5  CONST_31  C2    C1   C6   C9    180.00   0.0  0
 PU5  CONST_32  C4    C5   C6   C9    180.00   0.0  0
 PU5  CONST_33  N1    C11  C13  N5      0.00   0.0  0
 PU5  CONST_34  O1    C4   C5   C6    180.00   0.0  0
 PU5  CONST_35  O1    C4   C3   C2    180.00   0.0  0
 PU5  CONST_36  H14   C14  N4   C12   180.00   0.0  0
 PU5  CONST_37  H5    C5   C6   C1    180.00   0.0  0
 PU5  CONST_38  H3    C3   C2   C1    180.00   0.0  0
 PU5  CONST_39  H2    C2   C1   C6    180.00   0.0  0
 PU5  CONST_40  H1    C1   C6   C5    180.00   0.0  0
 PU5  CONST_41  H5N1  N5   C13  N3      0.00   0.0  0
 PU5  CONST_42  H5N2  N5   C13  N3    180.00   0.0  0
 PU5  Var_01    C6    C9   C10  N2     67.87  30.0  2
 PU5  Var_02    C1    C6   C9   C10    45.36  30.0  2
 PU5  Var_03    C12   N2   C15  C16   -82.46  30.0  2
 PU5  Var_04    N2    C15  C16  C17  -178.46  30.0  3
 PU5  Var_05    H7C1  C7   O1   C4    179.61  30.0  3
 PU5  Var_06    C15   C16  C17  C18  -178.37  30.0  3
 PU5  Var_07    H181  C18  C17  C16    59.67  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
 PU5  plan-1  C1    0.020
 PU5  plan-1  C6    0.020
 PU5  plan-1  C5    0.020
 PU5  plan-1  C2    0.020
 PU5  plan-1  C3    0.020
 PU5  plan-1  C4    0.020
 PU5  plan-1  O1    0.020
 PU5  plan-1  H5    0.020
 PU5  plan-1  H2    0.020
 PU5  plan-1  H3    0.020
 PU5  plan-1  C9    0.020
 PU5  plan-1  H1    0.020
 PU5  plan-2  C15   0.020
 PU5  plan-2  N2    0.020
 PU5  plan-2  C12   0.020
 PU5  plan-2  N4    0.020
 PU5  plan-2  C14   0.020
 PU5  plan-2  N3    0.020
 PU5  plan-2  C11   0.020
 PU5  plan-2  C13   0.020
 PU5  plan-2  N5    0.020
 PU5  plan-2  N1    0.020
 PU5  plan-2  C10   0.020
 PU5  plan-2  H14   0.020
 PU5  plan-2  C9    0.020
 PU5  plan-3  C13   0.020
 PU5  plan-3  N5    0.020
 PU5  plan-3  H5N1  0.020
 PU5  plan-3  H5N2  0.020

