# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 21:37:25 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (5R)-5-{[(2-amino-9H-purin-6-yl)oxy]methyl}pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2[nH]cnc2c(OC[C@H]3CCC(=O)N3)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
 UN4  UN4  (5R)-5-{[(2-amino-9H-purin-6-yl)oxy]methyl}pyrrolidin-2-one  ligand  30  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UN4
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
 UN4  C2    C  CR6   0   0.538   1.9050   0.2812  -2.3607
 UN4  C4    C  CR56  0   0.483  -0.1539   0.2786  -3.1626
 UN4  C5    C  CR56  0  -0.044  -0.7078  -0.1225  -1.9493
 UN4  C4'   C  CH1   0  -0.123  -0.0602  -1.1527   2.5883
 UN4  C3'   C  CH2   0  -0.589   0.6320   0.2881   4.4009
 UN4  C2'   C  CH2   0  -0.483   0.8350  -1.1163   3.8371
 UN4  N9    N  NR15  0  -0.651  -1.2162   0.4014  -3.9993
 UN4  N3    N  N     0  -0.493   1.1303   0.4898  -3.4206
 UN4  N2    N  NH2   0  -0.822   3.2295   0.5094  -2.4963
 UN4  N1    N  N     0  -0.523   1.4984  -0.1075  -1.1340
 UN4  C6    C  CR6   0   0.516   0.2199  -0.3098  -0.9191
 UN4  O6    O  O2    0  -0.460  -0.2119  -0.6929   0.2691
 UN4  C60   C  CH2   0  -0.149   0.7259  -0.8022   1.3379
 UN4  C14   C  C     0   0.517  -0.7285   0.7047   3.8795
 UN4  N7    N  N     0  -0.438  -2.0737  -0.2394  -2.0466
 UN4  C8    C  CR15  0   0.093  -2.3323   0.0805  -3.2784
 UN4  O14   O  O     0  -0.493  -1.3959   1.6529   4.2563
 UN4  N15   N  NH1   0  -0.614  -1.0646  -0.1593   2.9033
 UN4  H4'   H  HCH1  0   0.274  -0.5267  -2.1316   2.4588
 UN4  H3'1  H  HCH2  0   0.278   0.6670   0.3350   5.4885
 UN4  H3'2  H  HCH2  0   0.277   1.3739   0.9967   4.0226
 UN4  H2'1  H  HCH2  0   0.267   0.4888  -1.8620   4.5524
 UN4  H2'2  H  HCH2  0   0.262   1.8753  -1.3428   3.6061
 UN4  H9    H  HNR5  0   0.423  -1.1930   0.6795  -4.9684
 UN4  H2N1  H  HNH2  0   0.394   3.8505   0.1503  -1.7924
 UN4  H2N2  H  HNH2  0   0.394   3.6047   0.5945  -3.4251
 UN4  H601  H  HCH2  0   0.246   1.4584  -1.5859   1.1294
 UN4  H602  H  HCH2  0   0.236   1.2651   0.1409   1.4649
 UN4  H8    H  HCR5  0   0.286  -3.3135   0.1043  -3.7271
 UN4  H15   H  HNH1  0   0.397  -1.8975  -0.0388   2.3477

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
 UN4  C2   N3    aromatic  1.329  0.020  1.329
 UN4  C2   N2    single    1.351  0.020  1.351
 UN4  C2   N1    aromatic  1.350  0.020  1.350
 UN4  C4   C5    aromatic  1.393  0.020  1.393
 UN4  C4   N9    aromatic  1.358  0.020  1.358
 UN4  C4   N3    aromatic  1.327  0.020  1.327
 UN4  C5   C6    aromatic  1.399  0.020  1.399
 UN4  C5   N7    aromatic  1.374  0.020  1.374
 UN4  C4'  C2'   single    1.537  0.020  1.537
 UN4  C4'  C60   single    1.518  0.020  1.518
 UN4  C4'  N15   single    1.447  0.020  1.447
 UN4  C4'  H4'   single    0.970  0.020  1.090
 UN4  C3'  C2'   single    1.527  0.020  1.527
 UN4  C3'  C14   single    1.515  0.020  1.515
 UN4  C3'  H3'1  single    0.970  0.020  1.090
 UN4  C3'  H3'2  single    0.970  0.020  1.090
 UN4  C2'  H2'1  single    0.970  0.020  1.090
 UN4  C2'  H2'2  single    0.970  0.020  1.090
 UN4  N9   C8    aromatic  1.367  0.020  1.367
 UN4  N9   H9    single    0.860  0.020  1.020
 UN4  N2   H2N1  single    0.890  0.020  1.040
 UN4  N2   H2N2  single    0.890  0.020  1.040
 UN4  N1   C6    aromatic  1.312  0.020  1.312
 UN4  C6   O6    single    1.321  0.020  1.321
 UN4  O6   C60   single    1.426  0.020  1.426
 UN4  C60  H601  single    0.970  0.020  1.090
 UN4  C60  H602  single    0.970  0.020  1.090
 UN4  C14  O14   double    1.219  0.020  1.219
 UN4  C14  N15   single    1.346  0.020  1.346
 UN4  N7   C8    aromatic  1.299  0.020  1.299
 UN4  C8   H8    single    0.930  0.020  1.080
 UN4  N15  H15   single    0.860  0.020  1.020

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
 UN4  N1    C2   N2    115.80  3.000
 UN4  N1    C2   N3    126.47  3.000
 UN4  N2    C2   N3    117.70  3.000
 UN4  N3    C4   N9    128.53  3.000
 UN4  N3    C4   C5    126.88  3.000
 UN4  N9    C4   C5    104.58  3.000
 UN4  N7    C5   C6    134.42  3.000
 UN4  N7    C5   C4    110.98  3.000
 UN4  C6    C5   C4    114.60  3.000
 UN4  H4'   C4'  N15   110.15  3.000
 UN4  H4'   C4'  C60   109.30  3.000
 UN4  N15   C4'  C60   112.35  3.000
 UN4  H4'   C4'  C2'   111.49  3.000
 UN4  N15   C4'  C2'   102.19  3.000
 UN4  C60   C4'  C2'   111.24  3.000
 UN4  H3'2  C3'  H3'1  107.20  3.000
 UN4  H3'2  C3'  C14   108.17  3.000
 UN4  H3'1  C3'  C14   111.13  3.000
 UN4  H3'2  C3'  C2'   112.22  3.000
 UN4  H3'1  C3'  C2'   113.83  3.000
 UN4  C14   C3'  C2'   104.19  3.000
 UN4  H2'2  C2'  H2'1  107.47  3.000
 UN4  H2'2  C2'  C3'   113.36  3.000
 UN4  H2'1  C2'  C3'   110.17  3.000
 UN4  H2'2  C2'  C4'   112.27  3.000
 UN4  H2'1  C2'  C4'   109.39  3.000
 UN4  C3'   C2'  C4'   104.14  3.000
 UN4  H9    N9   C8    126.18  3.000
 UN4  H9    N9   C4    126.81  3.000
 UN4  C8    N9   C4    107.01  3.000
 UN4  C4    N3   C2    112.58  3.000
 UN4  H2N2  N2   H2N1  116.54  3.000
 UN4  H2N2  N2   C2    118.23  3.000
 UN4  H2N1  N2   C2    118.37  3.000
 UN4  C6    N1   C2    119.13  3.000
 UN4  O6    C6   N1    120.70  3.000
 UN4  O6    C6   C5    118.97  3.000
 UN4  N1    C6   C5    120.33  3.000
 UN4  C60   O6   C6    118.78  3.000
 UN4  H602  C60  H601  108.06  3.000
 UN4  H602  C60  O6    110.18  3.000
 UN4  H601  C60  O6    110.65  3.000
 UN4  H602  C60  C4'   111.02  3.000
 UN4  H601  C60  C4'   109.80  3.000
 UN4  O6    C60  C4'   107.13  3.000
 UN4  N15   C14  O14   125.92  3.000
 UN4  N15   C14  C3'   107.29  3.000
 UN4  O14   C14  C3'   126.79  3.000
 UN4  C8    N7   C5    104.13  3.000
 UN4  H8    C8   N7    125.51  3.000
 UN4  H8    C8   N9    121.19  3.000
 UN4  N7    C8   N9    113.30  3.000
 UN4  H15   N15  C14   121.93  3.000
 UN4  H15   N15  C4'   122.37  3.000
 UN4  C14   N15  C4'   115.16  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
 UN4  CONST_01  C5    C4   N3   C2     0.00   0.0  0
 UN4  CONST_02  N9    C4   N3   C2   180.00   0.0  0
 UN4  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 UN4  CONST_04  N1    C6   C5   C4     0.00   0.0  0
 UN4  CONST_05  C8    N7   C5   C4     0.00   0.0  0
 UN4  CONST_06  N7    C8   N9   C4     0.00   0.0  0
 UN4  CONST_07  N1    C2   N3   C4     0.00   0.0  0
 UN4  CONST_08  C8    N9   C4   C5     0.00   0.0  0
 UN4  CONST_09  N9    C8   N7   C5     0.00   0.0  0
 UN4  CONST_10  C6    C5   C4   N9   180.00   0.0  0
 UN4  CONST_11  N7    C5   C4   N9     0.00   0.0  0
 UN4  CONST_12  C6    N1   C2   N3     0.00   0.0  0
 UN4  CONST_13  C6    C5   C4   N3     0.00   0.0  0
 UN4  CONST_14  N7    C5   C4   N3   180.00   0.0  0
 UN4  CONST_15  C8    N9   C4   N3   180.00   0.0  0
 UN4  CONST_16  N7    C5   C6   N1   180.00   0.0  0
 UN4  CONST_17  C8    N7   C5   C6   180.00   0.0  0
 UN4  CONST_18  C3'   C14  N15  C4'    0.00   0.0  0
 UN4  CONST_19  O6    C6   N1   C2   180.00   0.0  0
 UN4  CONST_20  O6    C6   C5   C4   180.00   0.0  0
 UN4  CONST_21  N2    C2   N3   C4   180.00   0.0  0
 UN4  CONST_22  C6    N1   C2   N2   180.00   0.0  0
 UN4  CONST_23  N7    C5   C6   O6     0.00   0.0  0
 UN4  CONST_24  O14   C14  N15  C4'  180.00   0.0  0
 UN4  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 UN4  CONST_26  H9    N9   C4   C5   180.00   0.0  0
 UN4  CONST_27  H15   N15  C14  C3'  180.00   0.0  0
 UN4  CONST_28  H2N1  N2   C2   N3   180.00   0.0  0
 UN4  Var_01    C14   C3'  C2'  C4'   24.43  30.0  1
 UN4  Var_02    N15   C14  C3'  C2'  -14.12  30.0  1
 UN4  Var_03    H601  C60  O6   C6   -64.53  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 UN4  chir_01  C4'  C2'  C60  N15  positiv

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
 UN4  plan-1  C2    0.020
 UN4  plan-1  C4    0.020
 UN4  plan-1  C5    0.020
 UN4  plan-1  N9    0.020
 UN4  plan-1  N3    0.020
 UN4  plan-1  N2    0.020
 UN4  plan-1  N1    0.020
 UN4  plan-1  C6    0.020
 UN4  plan-1  O6    0.020
 UN4  plan-1  N7    0.020
 UN4  plan-1  C8    0.020
 UN4  plan-1  H9    0.020
 UN4  plan-1  H8    0.020
 UN4  plan-2  C2    0.020
 UN4  plan-2  N2    0.020
 UN4  plan-2  H2N1  0.020
 UN4  plan-2  H2N2  0.020
 UN4  plan-3  C4'   0.020
 UN4  plan-3  C3'   0.020
 UN4  plan-3  C14   0.020
 UN4  plan-3  O14   0.020
 UN4  plan-3  N15   0.020
 UN4  plan-3  H15   0.020

