# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:56:19 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 6-[(2S)-tetrahydrofuran-2-ylmethoxy]-9H-purin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2[nH]cnc2c(OC[C@@H]3CCCO3)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
 NRT  NRT  6-[(2S)-tetrahydrofuran-2-ylmethoxy]-9H-purin-2-amine  ligand  30  17  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NRT
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
 NRT  C2    C  CR6   0   0.536   1.8932  -0.1137  -2.2086
 NRT  C4    C  CR56  0   0.482  -0.1630  -0.0920  -3.0149
 NRT  C5    C  CR56  0  -0.043  -0.7383   0.0450  -1.7542
 NRT  C4'   C  CH1   0   0.034  -0.0906   0.4701   2.8920
 NRT  O4'   O  O2    0  -0.500  -0.9066  -0.6513   3.1590
 NRT  C3'   C  CH2   0  -0.481   0.0968  -0.1552   5.2205
 NRT  C2'   C  CH2   0  -0.494   0.8417   0.5993   4.1058
 NRT  N9    N  NR15  0  -0.651  -1.2169  -0.1216  -3.8705
 NRT  N3    N  N     0  -0.492   1.1315  -0.1762  -3.2955
 NRT  N2    N  NH2   0  -0.821   3.2350  -0.1456  -2.3777
 NRT  N1    N  N     0  -0.525   1.4661   0.0151  -0.9357
 NRT  C6    C  CR6   0   0.517   0.1777   0.0943  -0.6970
 NRT  O6    O  O2    0  -0.458  -0.2745   0.2204   0.5368
 NRT  C60   C  CH2   0  -0.197   0.6688   0.2655   1.6081
 NRT  C14   C  CH2   0  -0.182  -1.2005  -0.6026   4.5409
 NRT  N7    N  N     0  -0.440  -2.1088   0.0972  -1.8422
 NRT  C8    C  CR15  0   0.094  -2.3493  -0.0047  -3.1143
 NRT  H4'   H  HCH1  0   0.222  -0.7119   1.3752   2.8106
 NRT  H3'1  H  HCH2  0   0.243   0.6753  -1.0136   5.5620
 NRT  H3'2  H  HCH2  0   0.244  -0.1021   0.4710   6.0895
 NRT  H2'1  H  HCH2  0   0.244   1.8121   0.1404   3.9040
 NRT  H2'2  H  HCH2  0   0.251   1.0232   1.6447   4.3510
 NRT  H9    H  HNR5  0   0.423  -1.1776  -0.2067  -4.8744
 NRT  H2N1  H  HNH2  0   0.393   3.8036  -0.3513  -1.5745
 NRT  H2N2  H  HNH2  0   0.393   3.5895  -0.4640  -3.2633
 NRT  H601  H  HCH2  0   0.237   1.2458  -0.6628   1.6470
 NRT  H602  H  HCH2  0   0.245   1.3693   1.0914   1.4644
 NRT  H141  H  HCH2  0   0.235  -1.5439  -1.5876   4.8584
 NRT  H142  H  HCH2  0   0.204  -2.0043   0.1188   4.7383
 NRT  H8    H  HCR5  0   0.286  -3.3277  -0.0020  -3.5696

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
 NRT  C2   N3    aromatic  1.329  0.020  1.329
 NRT  C2   N2    single    1.353  0.020  1.353
 NRT  C2   N1    aromatic  1.349  0.020  1.349
 NRT  C4   C5    aromatic  1.392  0.020  1.392
 NRT  C4   N9    aromatic  1.358  0.020  1.358
 NRT  C4   N3    aromatic  1.327  0.020  1.327
 NRT  C5   C6    aromatic  1.400  0.020  1.400
 NRT  C5   N7    aromatic  1.374  0.020  1.374
 NRT  C4'  O4'   single    1.412  0.020  1.412
 NRT  C4'  C2'   single    1.536  0.020  1.536
 NRT  C4'  C60   single    1.506  0.020  1.506
 NRT  C4'  H4'   single    0.970  0.020  1.090
 NRT  O4'  C14   single    1.414  0.020  1.414
 NRT  C3'  C2'   single    1.538  0.020  1.538
 NRT  C3'  C14   single    1.531  0.020  1.531
 NRT  C3'  H3'1  single    0.970  0.020  1.090
 NRT  C3'  H3'2  single    0.970  0.020  1.090
 NRT  C2'  H2'1  single    0.970  0.020  1.090
 NRT  C2'  H2'2  single    0.970  0.020  1.090
 NRT  N9   C8    aromatic  1.367  0.020  1.367
 NRT  N9   H9    single    0.860  0.020  1.020
 NRT  N2   H2N1  single    0.890  0.020  1.040
 NRT  N2   H2N2  single    0.890  0.020  1.040
 NRT  N1   C6    aromatic  1.313  0.020  1.313
 NRT  C6   O6    single    1.320  0.020  1.320
 NRT  O6   C60   single    1.428  0.020  1.428
 NRT  C60  H601  single    0.970  0.020  1.090
 NRT  C60  H602  single    0.970  0.020  1.090
 NRT  C14  H141  single    0.970  0.020  1.090
 NRT  C14  H142  single    0.970  0.020  1.090
 NRT  N7   C8    aromatic  1.299  0.020  1.299
 NRT  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
 NRT  N1    C2   N2    115.74  3.000
 NRT  N1    C2   N3    126.51  3.000
 NRT  N2    C2   N3    117.73  3.000
 NRT  N3    C4   N9    128.49  3.000
 NRT  N3    C4   C5    126.91  3.000
 NRT  N9    C4   C5    104.60  3.000
 NRT  N7    C5   C6    134.40  3.000
 NRT  N7    C5   C4    110.96  3.000
 NRT  C6    C5   C4    114.64  3.000
 NRT  H4'   C4'  C60   109.47  3.000
 NRT  H4'   C4'  C2'   109.38  3.000
 NRT  C60   C4'  C2'   112.28  3.000
 NRT  H4'   C4'  O4'   109.93  3.000
 NRT  C60   C4'  O4'   110.17  3.000
 NRT  C2'   C4'  O4'   105.55  3.000
 NRT  C14   O4'  C4'   106.12  3.000
 NRT  H3'2  C3'  H3'1  107.43  3.000
 NRT  H3'2  C3'  C14   111.55  3.000
 NRT  H3'1  C3'  C14   111.01  3.000
 NRT  H3'2  C3'  C2'   112.61  3.000
 NRT  H3'1  C3'  C2'   110.87  3.000
 NRT  C14   C3'  C2'   103.41  3.000
 NRT  H2'2  C2'  H2'1  107.27  3.000
 NRT  H2'2  C2'  C3'   112.85  3.000
 NRT  H2'1  C2'  C3'   110.97  3.000
 NRT  H2'2  C2'  C4'   111.09  3.000
 NRT  H2'1  C2'  C4'   110.97  3.000
 NRT  C3'   C2'  C4'   103.73  3.000
 NRT  H9    N9   C8    126.19  3.000
 NRT  H9    N9   C4    126.80  3.000
 NRT  C8    N9   C4    107.01  3.000
 NRT  C4    N3   C2    112.53  3.000
 NRT  H2N2  N2   H2N1  116.07  3.000
 NRT  H2N2  N2   C2    117.85  3.000
 NRT  H2N1  N2   C2    117.77  3.000
 NRT  C6    N1   C2    119.21  3.000
 NRT  O6    C6   N1    120.79  3.000
 NRT  O6    C6   C5    119.02  3.000
 NRT  N1    C6   C5    120.19  3.000
 NRT  C60   O6   C6    118.55  3.000
 NRT  H602  C60  H601  107.94  3.000
 NRT  H602  C60  O6    110.41  3.000
 NRT  H601  C60  O6    110.39  3.000
 NRT  H602  C60  C4'   109.45  3.000
 NRT  H601  C60  C4'   110.56  3.000
 NRT  O6    C60  C4'   108.11  3.000
 NRT  H142  C14  H141  108.10  3.000
 NRT  H142  C14  C3'   110.40  3.000
 NRT  H141  C14  C3'   113.67  3.000
 NRT  H142  C14  O4'   110.52  3.000
 NRT  H141  C14  O4'   108.60  3.000
 NRT  C3'   C14  O4'   105.53  3.000
 NRT  C8    N7   C5    104.15  3.000
 NRT  H8    C8   N7    125.52  3.000
 NRT  H8    C8   N9    121.20  3.000
 NRT  N7    C8   N9    113.28  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
 NRT  CONST_01  C5    C4   N3   C2     0.00   0.0  0
 NRT  CONST_02  N9    C4   N3   C2   180.00   0.0  0
 NRT  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 NRT  CONST_04  N1    C6   C5   C4     0.00   0.0  0
 NRT  CONST_05  C8    N7   C5   C4     0.00   0.0  0
 NRT  CONST_06  N7    C8   N9   C4     0.00   0.0  0
 NRT  CONST_07  N1    C2   N3   C4     0.00   0.0  0
 NRT  CONST_08  C8    N9   C4   C5     0.00   0.0  0
 NRT  CONST_09  N9    C8   N7   C5     0.00   0.0  0
 NRT  CONST_10  C6    C5   C4   N9   180.00   0.0  0
 NRT  CONST_11  N7    C5   C4   N9     0.00   0.0  0
 NRT  CONST_12  C6    N1   C2   N3     0.00   0.0  0
 NRT  CONST_13  C6    C5   C4   N3     0.00   0.0  0
 NRT  CONST_14  N7    C5   C4   N3   180.00   0.0  0
 NRT  CONST_15  C8    N9   C4   N3   180.00   0.0  0
 NRT  CONST_16  N7    C5   C6   N1   180.00   0.0  0
 NRT  CONST_17  C8    N7   C5   C6   180.00   0.0  0
 NRT  CONST_18  O6    C6   N1   C2   180.00   0.0  0
 NRT  CONST_19  O6    C6   C5   C4   180.00   0.0  0
 NRT  CONST_20  N2    C2   N3   C4   180.00   0.0  0
 NRT  CONST_21  C6    N1   C2   N2   180.00   0.0  0
 NRT  CONST_22  N7    C5   C6   O6     0.00   0.0  0
 NRT  CONST_23  H8    C8   N9   C4   180.00   0.0  0
 NRT  CONST_24  H9    N9   C4   C5   180.00   0.0  0
 NRT  Var_01    C3'   C14  O4'  C4'  -39.73  30.0  1
 NRT  Var_02    C14   C3'  C2'  C4'   -1.56  30.0  1
 NRT  Var_03    C2'   C3'  C14  O4'   24.31  30.0  1
 NRT  Var_04    H601  C60  O6   C6   -61.33  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
 NRT  chir_01  C4'  O4'  C2'  C60  negativ

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
 NRT  plan-1  C2    0.020
 NRT  plan-1  C4    0.020
 NRT  plan-1  C5    0.020
 NRT  plan-1  N9    0.020
 NRT  plan-1  N3    0.020
 NRT  plan-1  N2    0.020
 NRT  plan-1  N1    0.020
 NRT  plan-1  C6    0.020
 NRT  plan-1  O6    0.020
 NRT  plan-1  N7    0.020
 NRT  plan-1  C8    0.020
 NRT  plan-1  H9    0.020
 NRT  plan-1  H8    0.020
 NRT  plan-2  C2    0.020
 NRT  plan-2  N2    0.020
 NRT  plan-2  H2N1  0.020
 NRT  plan-2  H2N2  0.020

