# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 04:27:34 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (2~{R},3~{R},4~{R},5~{R})-2-[(6-aminopurin-9-yl)methyl]-5-azanyl-oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CO[C@H](Cn2cnc3c(N)ncnc23)[C@H](O)[C@@H]1O
#
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
 NXB  NXB  (2~{R},3~{R},4~{R},5~{R})-2-[(6-aminopurin-9-yl)methyl]-5-azanyl-oxane-3,4-diol  ligand  36  20  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXB
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
 NXB  C10  C  CR16  0   0.038  -3.2400  -2.0096  -0.4058
 NXB  C17  C  CH1   0  -0.011   2.5652  -0.9198   0.6648
 NXB  C02  C  CH1   0  -0.169   3.6178   0.4238  -1.1675
 NXB  C03  C  CH2   0  -0.194   2.2252   0.9679  -1.4601
 NXB  C05  C  CH1   0   0.016   1.2275  -0.3083   0.2295
 NXB  C06  C  CH2   0  -0.336   0.2649  -0.1843   1.3965
 NXB  C08  C  CR56  0   0.479  -2.0309  -0.3642   0.4008
 NXB  C12  C  CR6   0   0.452  -4.1752   0.0913  -0.5051
 NXB  C14  C  CR56  0  -0.004  -3.0026   0.5788   0.1002
 NXB  C16  C  CR15  0   0.113  -1.4106   1.6430   0.9809
 NXB  C19  C  CH1   0   0.038   3.4666  -0.9798  -0.5707
 NXB  N01  N  NH2   0  -0.813   4.3156   1.2858  -0.2154
 NXB  N07  N  NR5   0  -0.491  -1.0163   0.3375   0.9781
 NXB  N09  N  N     0  -0.459  -2.0979  -1.6744   0.1677
 NXB  N11  N  N     0  -0.475  -4.2571  -1.2218  -0.7476
 NXB  N13  N  NH2   0  -0.818  -5.2003   0.8806  -0.8336
 NXB  N15  N  N     0  -0.458  -2.5945   1.8332   0.4734
 NXB  O04  O  O2    0  -0.482   1.4038   0.9784  -0.3151
 NXB  O18  O  OH1   0  -0.693   3.1457  -0.2120   1.7285
 NXB  O20  O  OH1   0  -0.666   4.7008  -1.5493  -0.2082
 NXB  H1   H  HCR6  0   0.250  -3.3715  -3.0628  -0.6309
 NXB  H2   H  HCH1  0   0.243   2.3665  -1.9427   1.0080
 NXB  H3   H  HCH1  0   0.243   4.1417   0.3500  -2.1324
 NXB  H5   H  HCH2  0   0.218   1.7734   0.3613  -2.2576
 NXB  H6   H  HCH1  0   0.222   0.7777  -0.9783  -0.5217
 NXB  H7   H  HCH2  0   0.279   0.1095  -1.1634   1.8498
 NXB  H8   H  HCH2  0   0.278   0.6694   0.4753   2.1631
 NXB  H9   H  HCR5  0   0.289  -0.7751   2.4154   1.3877
 NXB  H10  H  HCH1  0   0.218   2.9539  -1.6034  -1.3184
 NXB  H11  H  HNH2  0   0.366   5.2819   0.9942  -0.1357
 NXB  H12  H  HNH2  0   0.367   4.3357   2.2402  -0.5545
 NXB  H14  H  HNH2  0   0.402  -5.9933   0.5025  -1.3225
 NXB  H15  H  HNH2  0   0.410  -5.1447   1.8770  -0.7177
 NXB  H16  H  HOH1  0   0.445   3.5718   0.5729   1.3194
 NXB  H17  H  HOH1  0   0.453   5.2166  -1.6795  -1.0108
 NXB  H4   H  HCH2  0   0.250   2.2826   1.9962  -1.8230

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
 NXB  N15  C16  aromatic  1.302  0.020  1.302
 NXB  N15  C14  aromatic  1.371  0.020  1.371
 NXB  C16  N07  aromatic  1.364  0.020  1.364
 NXB  C03  C02  single    1.523  0.020  1.523
 NXB  C03  O04  single    1.409  0.020  1.409
 NXB  C02  C19  single    1.533  0.020  1.533
 NXB  C02  N01  single    1.462  0.020  1.462
 NXB  N13  C12  single    1.335  0.020  1.335
 NXB  C19  C17  single    1.531  0.020  1.531
 NXB  C19  O20  single    1.407  0.020  1.407
 NXB  C14  C12  aromatic  1.407  0.020  1.407
 NXB  C14  C08  aromatic  1.387  0.020  1.387
 NXB  C05  O04  single    1.408  0.020  1.408
 NXB  C05  C17  single    1.534  0.020  1.534
 NXB  C05  C06  single    1.518  0.020  1.518
 NXB  N07  C08  aromatic  1.362  0.020  1.362
 NXB  N07  C06  single    1.445  0.020  1.445
 NXB  C12  N11  aromatic  1.338  0.020  1.338
 NXB  C17  O18  single    1.403  0.020  1.403
 NXB  C08  N09  aromatic  1.332  0.020  1.332
 NXB  N11  C10  aromatic  1.331  0.020  1.331
 NXB  N09  C10  aromatic  1.321  0.020  1.321
 NXB  C10  H1   single    0.930  0.020  1.080
 NXB  C17  H2   single    0.970  0.020  1.090
 NXB  C02  H3   single    0.970  0.020  1.090
 NXB  C03  H4   single    0.970  0.020  1.090
 NXB  C03  H5   single    0.970  0.020  1.090
 NXB  C05  H6   single    0.970  0.020  1.090
 NXB  C06  H7   single    0.970  0.020  1.090
 NXB  C06  H8   single    0.970  0.020  1.090
 NXB  C16  H9   single    0.930  0.020  1.080
 NXB  C19  H10  single    0.970  0.020  1.090
 NXB  N01  H11  single    0.890  0.020  1.040
 NXB  N01  H12  single    0.890  0.020  1.040
 NXB  N13  H14  single    0.860  0.020  1.020
 NXB  N13  H15  single    0.860  0.020  1.020
 NXB  O18  H16  single    0.850  0.020  0.980
 NXB  O20  H17  single    0.850  0.020  0.980

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
 NXB  H1   C10  N11  115.37  3.000
 NXB  H1   C10  N09  116.18  3.000
 NXB  N11  C10  N09  128.45  3.000
 NXB  H2   C17  O18  107.94  3.000
 NXB  H2   C17  C19  108.82  3.000
 NXB  O18  C17  C19  112.83  3.000
 NXB  H2   C17  C05  107.61  3.000
 NXB  O18  C17  C05  112.01  3.000
 NXB  C19  C17  C05  107.47  3.000
 NXB  H3   C02  N01  112.55  3.000
 NXB  H3   C02  C19  109.09  3.000
 NXB  N01  C02  C19  109.48  3.000
 NXB  H3   C02  C03  106.90  3.000
 NXB  N01  C02  C03  110.54  3.000
 NXB  C19  C02  C03  108.16  3.000
 NXB  H5   C03  H4   107.47  3.000
 NXB  H5   C03  O04  110.73  3.000
 NXB  H4   C03  O04  107.08  3.000
 NXB  H5   C03  C02  108.54  3.000
 NXB  H4   C03  C02  110.62  3.000
 NXB  O04  C03  C02  112.30  3.000
 NXB  H6   C05  O04  110.05  3.000
 NXB  H6   C05  C06  108.35  3.000
 NXB  O04  C05  C06  107.58  3.000
 NXB  H6   C05  C17  107.87  3.000
 NXB  C06  C05  C17  111.55  3.000
 NXB  O04  C05  C17  111.39  3.000
 NXB  H8   C06  H7   107.71  3.000
 NXB  H8   C06  N07  108.32  3.000
 NXB  H7   C06  N07  108.56  3.000
 NXB  H8   C06  C05  110.80  3.000
 NXB  H7   C06  C05  109.68  3.000
 NXB  N07  C06  C05  111.66  3.000
 NXB  N09  C08  N07  128.19  3.000
 NXB  N09  C08  C14  126.53  3.000
 NXB  N07  C08  C14  105.27  3.000
 NXB  N13  C12  N11  119.25  3.000
 NXB  N11  C12  C14  117.98  3.000
 NXB  N13  C12  C14  122.76  3.000
 NXB  N15  C14  C12  133.03  3.000
 NXB  C12  C14  C08  116.21  3.000
 NXB  N15  C14  C08  110.77  3.000
 NXB  H9   C16  N15  125.27  3.000
 NXB  H9   C16  N07  121.02  3.000
 NXB  N15  C16  N07  113.70  3.000
 NXB  H10  C19  O20  110.76  3.000
 NXB  H10  C19  C02  107.48  3.000
 NXB  O20  C19  C02  112.61  3.000
 NXB  H10  C19  C17  107.24  3.000
 NXB  O20  C19  C17  108.94  3.000
 NXB  C02  C19  C17  109.67  3.000
 NXB  H12  N01  H11  106.18  3.000
 NXB  H12  N01  C02  110.31  3.000
 NXB  H11  N01  C02  109.70  3.000
 NXB  C16  N07  C08  106.18  3.000
 NXB  C08  N07  C06  126.66  3.000
 NXB  C16  N07  C06  126.97  3.000
 NXB  C08  N09  C10  111.65  3.000
 NXB  C12  N11  C10  119.18  3.000
 NXB  H15  N13  H14  118.21  3.000
 NXB  H15  N13  C12  121.03  3.000
 NXB  H14  N13  C12  120.20  3.000
 NXB  C16  N15  C14  104.07  3.000
 NXB  C05  O04  C03  112.36  3.000
 NXB  H16  O18  C17  105.48  3.000
 NXB  H17  O20  C19  108.06  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
 NXB  CONST_01  C14  C12  N11  C10    0.00   0.0  0
 NXB  CONST_02  C14  C08  N09  C10    0.00   0.0  0
 NXB  CONST_03  N07  C08  N09  C10  180.00   0.0  0
 NXB  CONST_04  C16  N15  C14  C08    0.00   0.0  0
 NXB  CONST_05  N11  C12  C14  C08    0.00   0.0  0
 NXB  CONST_06  N15  C16  N07  C08    0.00   0.0  0
 NXB  CONST_07  N11  C10  N09  C08    0.00   0.0  0
 NXB  CONST_08  C16  N15  C14  C12  180.00   0.0  0
 NXB  CONST_09  N07  C08  C14  C12  180.00   0.0  0
 NXB  CONST_10  N09  C08  C14  C12    0.00   0.0  0
 NXB  CONST_11  N09  C10  N11  C12    0.00   0.0  0
 NXB  CONST_12  N07  C16  N15  C14    0.00   0.0  0
 NXB  CONST_13  C16  N07  C08  C14    0.00   0.0  0
 NXB  CONST_14  N09  C08  N07  C16  180.00   0.0  0
 NXB  CONST_15  N15  C14  C08  N07    0.00   0.0  0
 NXB  CONST_16  N15  C14  C08  N09  180.00   0.0  0
 NXB  CONST_17  N15  C14  C12  N11  180.00   0.0  0
 NXB  CONST_18  N13  C12  N11  C10  180.00   0.0  0
 NXB  CONST_19  N15  C16  N07  C06  180.00   0.0  0
 NXB  CONST_20  C14  C08  N07  C06  180.00   0.0  0
 NXB  CONST_21  N09  C08  N07  C06    0.00   0.0  0
 NXB  CONST_22  N13  C12  C14  C08  180.00   0.0  0
 NXB  CONST_23  N15  C14  C12  N13    0.00   0.0  0
 NXB  CONST_24  H9   C16  N07  C08  180.00   0.0  0
 NXB  CONST_25  H1   C10  N09  C08  180.00   0.0  0
 NXB  CONST_26  H14  N13  C12  C14  180.00   0.0  0
 NXB  CONST_27  H15  N13  C12  C14    0.00   0.0  0
 NXB  Var_01    C16  N07  C06  C05  -93.18  30.0  2
 NXB  Var_02    H4   C03  O04  C05  178.59  30.0  1

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
 NXB  chir_01  C17  C19  C05  O18  positiv
 NXB  chir_02  C02  N01  C19  C03  negativ
 NXB  chir_03  C05  O04  C06  C17  positiv
 NXB  chir_04  C19  O20  C17  C02  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
 NXB  plan-1  C10  0.020
 NXB  plan-1  C06  0.020
 NXB  plan-1  C08  0.020
 NXB  plan-1  C12  0.020
 NXB  plan-1  C14  0.020
 NXB  plan-1  C16  0.020
 NXB  plan-1  N07  0.020
 NXB  plan-1  N09  0.020
 NXB  plan-1  N11  0.020
 NXB  plan-1  N13  0.020
 NXB  plan-1  N15  0.020
 NXB  plan-1  H1   0.020
 NXB  plan-1  H9   0.020
 NXB  plan-2  C12  0.020
 NXB  plan-2  N13  0.020
 NXB  plan-2  H14  0.020
 NXB  plan-2  H15  0.020

