# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 15:27:20 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-amino-9-[4-hydroxy-3-(hydroxymethyl)butyl]-1,9-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(CCC(CO)CO)cnc2C(=O)N1
#
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
 PE2  PE2  2-amino-9-[4-hydroxy-3-(hydroxymethyl)butyl]-1,9-dihydro-6H-purin-6-one  ligand  33  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PE2
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
 PE2  C2    C  CR6   0   0.682   1.6539  -0.2738  -2.2996
 PE2  C4    C  CR56  0   0.495  -0.2498   0.2655  -1.3116
 PE2  C5    C  CR56  0  -0.088  -1.0458   0.0118  -2.4156
 PE2  C4'   C  CH2   0  -0.129  -0.1268  -1.2248   4.1163
 PE2  O4'   O  OH1   0  -0.675  -0.2285  -1.0004   5.5058
 PE2  C3'   C  CH2   0  -0.166   0.6148   1.1616   3.7073
 PE2  O3'   O  OH1   0  -0.672   1.8871   0.7791   3.2329
 PE2  C2'   C  CH1   0  -0.312  -0.3956   0.0747   3.3684
 PE2  C12   C  CH2   0  -0.431  -0.4808  -0.2212   1.8692
 PE2  N9    N  NR5   0  -0.496  -1.1019   0.6787  -0.3402
 PE2  N3    N  N     0  -0.507   1.0814   0.1446  -1.1994
 PE2  N2    N  NH2   0  -0.834   2.9777  -0.4871  -2.3272
 PE2  N1    N  NR16  0  -0.727   0.9597  -0.5475  -3.4446
 PE2  C6    C  CR6   0   0.499  -0.4253  -0.4323  -3.6181
 PE2  O6    O  O     0  -0.478  -0.9406  -0.7000  -4.6920
 PE2  N7    N  N     0  -0.448  -2.3629   0.2598  -2.1293
 PE2  C8    C  CR15  0   0.089  -2.3552   0.6486  -0.8897
 PE2  H4'1  H  HCH2  0   0.196  -0.8556  -1.9777   3.7851
 PE2  H4'2  H  HCH2  0   0.197   0.8653  -1.6059   3.8448
 PE2  HO4'  H  HOH1  0   0.453   0.1220  -1.7712   5.9599
 PE2  H3'1  H  HCH2  0   0.204   0.2909   2.1095   3.2583
 PE2  H3'2  H  HCH2  0   0.212   0.6205   1.3203   4.7919
 PE2  HO3'  H  HOH1  0   0.454   2.5163   1.4640   3.4748
 PE2  H2'   H  HCH1  0   0.238  -1.3748   0.4518   3.6888
 PE2  H121  H  HCH2  0   0.239  -1.2852  -0.9428   1.7023
 PE2  H122  H  HCH2  0   0.242   0.4415  -0.6908   1.5202
 PE2  H1'1  H  HCH2  0   0.267   0.1050   1.6809   1.0033
 PE2  H1'2  H  HCH2  0   0.265  -1.5951   1.5854   1.4391
 PE2  HN21  H  HNH2  0   0.411   3.5230  -0.1461  -1.5540
 PE2  HN22  H  HNH2  0   0.414   3.4653  -0.6231  -3.1958
 PE2  HN1   H  HNR6  0   0.424   1.4774  -0.8626  -4.2554
 PE2  H8    H  HCR5  0   0.285  -3.2229   0.9347  -0.3139
 PE2  C1'   C  CH2   0  -0.306  -0.7593   1.0180   1.0274

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
 PE2  C2   N3    double    1.309  0.020  1.309
 PE2  C2   N2    single    1.341  0.020  1.341
 PE2  C2   N1    single    1.367  0.020  1.367
 PE2  C4   C5    aromatic  1.384  0.020  1.384
 PE2  C4   N9    aromatic  1.357  0.020  1.357
 PE2  C4   N3    single    1.341  0.020  1.341
 PE2  C5   C6    single    1.424  0.020  1.424
 PE2  C5   N7    aromatic  1.371  0.020  1.371
 PE2  C4'  O4'   single    1.411  0.020  1.411
 PE2  C4'  C2'   single    1.523  0.020  1.523
 PE2  C4'  H4'1  single    0.970  0.020  1.090
 PE2  C4'  H4'2  single    0.970  0.020  1.090
 PE2  O4'  HO4'  single    0.850  0.020  0.980
 PE2  C3'  O3'   single    1.411  0.020  1.411
 PE2  C3'  C2'   single    1.522  0.020  1.522
 PE2  C3'  H3'1  single    0.970  0.020  1.090
 PE2  C3'  H3'2  single    0.970  0.020  1.090
 PE2  O3'  HO3'  single    0.850  0.020  0.980
 PE2  C2'  C12   single    1.530  0.020  1.530
 PE2  C2'  H2'   single    0.970  0.020  1.090
 PE2  C12  C1'   single    1.524  0.020  1.524
 PE2  C12  H121  single    0.970  0.020  1.090
 PE2  C12  H122  single    0.970  0.020  1.090
 PE2  C1'  N9    single    1.450  0.020  1.450
 PE2  C1'  H1'1  single    0.970  0.020  1.090
 PE2  C1'  H1'2  single    0.970  0.020  1.090
 PE2  N9   C8    aromatic  1.369  0.020  1.369
 PE2  N2   HN21  single    0.890  0.020  1.040
 PE2  N2   HN22  single    0.890  0.020  1.040
 PE2  N1   C6    single    1.401  0.020  1.401
 PE2  N1   HN1   single    0.860  0.020  1.020
 PE2  C6   O6    double    1.221  0.020  1.221
 PE2  N7   C8    aromatic  1.299  0.020  1.299
 PE2  C8   H8    single    0.930  0.020  1.080

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
 PE2  N1    C2   N2    116.89  3.000
 PE2  N1    C2   N3    123.10  3.000
 PE2  N2    C2   N3    119.99  3.000
 PE2  N3    C4   N9    126.22  3.000
 PE2  N3    C4   C5    128.37  3.000
 PE2  N9    C4   C5    105.41  3.000
 PE2  N7    C5   C6    130.66  3.000
 PE2  N7    C5   C4    110.66  3.000
 PE2  C6    C5   C4    118.68  3.000
 PE2  H4'2  C4'  H4'1  106.69  3.000
 PE2  H4'2  C4'  C2'   109.53  3.000
 PE2  H4'1  C4'  C2'   108.63  3.000
 PE2  H4'2  C4'  O4'   111.36  3.000
 PE2  H4'1  C4'  O4'   110.98  3.000
 PE2  C2'   C4'  O4'   109.58  3.000
 PE2  HO4'  O4'  C4'   108.15  3.000
 PE2  H3'2  C3'  H3'1  106.34  3.000
 PE2  H3'2  C3'  C2'   109.09  3.000
 PE2  H3'1  C3'  C2'   109.25  3.000
 PE2  H3'2  C3'  O3'   111.55  3.000
 PE2  H3'1  C3'  O3'   111.26  3.000
 PE2  C2'   C3'  O3'   109.28  3.000
 PE2  HO3'  O3'  C3'   108.21  3.000
 PE2  H2'   C2'  C12   107.63  3.000
 PE2  H2'   C2'  C3'   106.38  3.000
 PE2  C12   C2'  C3'   113.15  3.000
 PE2  H2'   C2'  C4'   107.89  3.000
 PE2  C12   C2'  C4'   109.02  3.000
 PE2  C3'   C2'  C4'   112.50  3.000
 PE2  H122  C12  H121  106.78  3.000
 PE2  H122  C12  C1'   109.11  3.000
 PE2  H121  C12  C1'   108.54  3.000
 PE2  H122  C12  C2'   110.43  3.000
 PE2  H121  C12  C2'   108.55  3.000
 PE2  C1'   C12  C2'   113.21  3.000
 PE2  C8    N9   C1'   126.88  3.000
 PE2  C8    N9   C4    106.31  3.000
 PE2  C1'   N9   C4    126.74  3.000
 PE2  C4    N3   C2    113.11  3.000
 PE2  HN22  N2   HN21  116.57  3.000
 PE2  HN22  N2   C2    121.20  3.000
 PE2  HN21  N2   C2    117.74  3.000
 PE2  HN1   N1   C6    115.60  3.000
 PE2  HN1   N1   C2    118.27  3.000
 PE2  C6    N1   C2    126.13  3.000
 PE2  O6    C6   N1    120.55  3.000
 PE2  O6    C6   C5    128.85  3.000
 PE2  N1    C6   C5    110.60  3.000
 PE2  C8    N7   C5    104.35  3.000
 PE2  H8    C8   N7    125.68  3.000
 PE2  H8    C8   N9    121.05  3.000
 PE2  N7    C8   N9    113.27  3.000
 PE2  H1'2  C1'  H1'1  107.44  3.000
 PE2  H1'2  C1'  N9    107.25  3.000
 PE2  H1'1  C1'  N9    107.99  3.000
 PE2  H1'2  C1'  C12   110.77  3.000
 PE2  H1'1  C1'  C12   111.23  3.000
 PE2  N9    C1'  C12   111.96  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
 PE2  CONST_01  C8    N7   C5   C4      0.00   0.0  0
 PE2  CONST_02  N7    C8   N9   C4      0.00   0.0  0
 PE2  CONST_03  C8    N9   C4   C5      0.00   0.0  0
 PE2  CONST_04  N9    C8   N7   C5      0.00   0.0  0
 PE2  CONST_05  N7    C5   C4   N9      0.00   0.0  0
 PE2  CONST_06  C5    C6   N1   C2      0.00   0.0  0
 PE2  CONST_07  N1    C2   N3   C4      0.00   0.0  0
 PE2  CONST_08  C6    N1   C2   N3      0.00   0.0  0
 PE2  CONST_09  C1'   N9   C4   C5    180.00   0.0  0
 PE2  CONST_10  N3    C4   N9   C1'     0.00   0.0  0
 PE2  CONST_11  N7    C8   N9   C1'   180.00   0.0  0
 PE2  CONST_12  O6    C6   N1   C2    180.00   0.0  0
 PE2  CONST_13  N2    C2   N3   C4    180.00   0.0  0
 PE2  CONST_14  C6    N1   C2   N2    180.00   0.0  0
 PE2  CONST_15  H8    C8   N9   C4    180.00   0.0  0
 PE2  CONST_16  HN1   N1   C6   C5    180.00   0.0  0
 PE2  CONST_17  HN21  N2   C2   N3      0.00   0.0  0
 PE2  CONST_18  HN22  N2   C2   N3    180.00   0.0  0
 PE2  Var_01    C12   C1'  N9   C4    -75.14  30.0  2
 PE2  Var_02    N9    C1'  C12  C2'  -168.35  30.0  3
 PE2  Var_03    O3'   C3'  C2'  C4'    66.22  30.0  3
 PE2  Var_04    C1'   C12  C2'  C4'   179.56  30.0  3
 PE2  Var_05    C3'   C2'  C4'  O4'    61.66  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
 PE2  plan-1  C2    0.020
 PE2  plan-1  C4    0.020
 PE2  plan-1  C5    0.020
 PE2  plan-1  N9    0.020
 PE2  plan-1  N3    0.020
 PE2  plan-1  N2    0.020
 PE2  plan-1  N1    0.020
 PE2  plan-1  C6    0.020
 PE2  plan-1  O6    0.020
 PE2  plan-1  N7    0.020
 PE2  plan-1  C8    0.020
 PE2  plan-1  HN21  0.020
 PE2  plan-1  HN22  0.020
 PE2  plan-1  HN1   0.020
 PE2  plan-1  H8    0.020
 PE2  plan-1  C1'   0.020

