# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:17:45 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC=Nc23
#
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
 NOS  NOS  9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-purin-6-one  ligand  31  19  .  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_NOS
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
 NOS  N9   N  NR5   0  -0.527  -0.2596  -0.1718   0.0162
 NOS  C4   C  CR56  0   0.490  -1.5365   0.1961  -0.2745
 NOS  N3   N  N     0  -0.447  -1.9310   1.3249  -0.8956
 NOS  C2   C  CR16  0   0.168  -3.2148   1.3920  -1.0355
 NOS  N1   N  NR16  0  -0.664  -4.0857   0.4501  -0.6099
 NOS  C6   C  CR6   0   0.514  -3.7525  -0.7425   0.0413
 NOS  O6   O  O     0  -0.465  -4.6062  -1.5364   0.3930
 NOS  C5   C  CR56  0  -0.064  -2.3323  -0.8305   0.1953
 NOS  N7   N  N     0  -0.441  -1.5672  -1.8140   0.7547
 NOS  C8   C  CR15  0   0.110  -0.3441  -1.3905   0.6307
 NOS  C4'  C  CH1   0  -0.043   3.1755  -0.0301  -0.4670
 NOS  O4'  O  O2    0  -0.491   1.8432  -0.2410  -0.9492
 NOS  C1'  C  CH1   0   0.204   0.9398   0.5798  -0.2701
 NOS  C2'  C  CH1   0  -0.011   1.6712   1.0612   0.9818
 NOS  O2'  O  OH1   0  -0.652   1.0707   2.2203   1.4603
 NOS  C3'  C  CH1   0  -0.044   3.0990   1.1900   0.4545
 NOS  O3'  O  OH1   0  -0.667   3.1909   2.4002  -0.2479
 NOS  H1   H  HCR6  0   0.306  -3.6594   2.2489  -1.5233
 NOS  H2   H  HNR6  0   0.436  -5.0703   0.6187  -0.7734
 NOS  H3   H  HCR5  0   0.296   0.5341  -1.9284   0.9547
 NOS  H6   H  HOH1  0   0.459   4.0487  -3.1086  -0.2287
 NOS  H8   H  HCH1  0   0.265   0.6258   1.4362  -0.8771
 NOS  H9   H  HCH1  0   0.244   1.6615   0.2613   1.7358
 NOS  H10  H  HOH1  0   0.465   1.4310   2.4200   2.3299
 NOS  H11  H  HCH1  0   0.255   3.8411   1.1306   1.2612
 NOS  H12  H  HOH1  0   0.457   4.0565   2.4445  -0.6666
 NOS  H7   H  HCH1  0   0.258   3.8184   0.1780  -1.3293
 NOS  C5'  C  CH2   0  -0.154   3.7004  -1.2645   0.2363
 NOS  H4   H  HCH2  0   0.195   3.1113  -1.4711   1.1414
 NOS  O5'  O  OH1   0  -0.666   3.6654  -2.3419  -0.6642
 NOS  H5   H  HCH2  0   0.215   4.7217  -1.0423   0.5713

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
 NOS  N1   C2   single    1.352  0.020  1.352
 NOS  N1   C6   single    1.399  0.020  1.399
 NOS  C2   N3   double    1.293  0.020  1.293
 NOS  O6   C6   double    1.218  0.020  1.218
 NOS  C6   C5   single    1.431  0.020  1.431
 NOS  N3   C4   single    1.347  0.020  1.347
 NOS  O2'  C2'  single    1.390  0.020  1.390
 NOS  C5   C4   aromatic  1.381  0.020  1.381
 NOS  C5   N7   aromatic  1.366  0.020  1.366
 NOS  C4   N9   aromatic  1.360  0.020  1.360
 NOS  N7   C8   aromatic  1.300  0.020  1.300
 NOS  N9   C8   aromatic  1.367  0.020  1.367
 NOS  N9   C1'  single    1.444  0.020  1.444
 NOS  C1'  C2'  single    1.528  0.020  1.528
 NOS  C1'  O4'  single    1.397  0.020  1.397
 NOS  C2'  C3'  single    1.528  0.020  1.528
 NOS  O4'  C4'  single    1.432  0.020  1.432
 NOS  C3'  O3'  single    1.402  0.020  1.402
 NOS  C3'  C4'  single    1.531  0.020  1.531
 NOS  C4'  C5'  single    1.515  0.020  1.515
 NOS  C5'  O5'  single    1.405  0.020  1.405
 NOS  C2   H1   single    0.930  0.020  1.080
 NOS  N1   H2   single    0.860  0.020  1.020
 NOS  C8   H3   single    0.930  0.020  1.080
 NOS  C5'  H4   single    0.970  0.020  1.090
 NOS  C5'  H5   single    0.970  0.020  1.090
 NOS  O5'  H6   single    0.850  0.020  0.980
 NOS  C4'  H7   single    0.970  0.020  1.090
 NOS  C1'  H8   single    0.970  0.020  1.090
 NOS  C2'  H9   single    0.970  0.020  1.090
 NOS  O2'  H10  single    0.850  0.020  0.980
 NOS  C3'  H11  single    0.970  0.020  1.090
 NOS  O3'  H12  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
 NOS  C1'  N9   C8   127.17  3.000
 NOS  C1'  N9   C4   126.62  3.000
 NOS  C8   N9   C4   106.21  3.000
 NOS  C5   C4   N3   127.64  3.000
 NOS  C5   C4   N9   105.49  3.000
 NOS  N3   C4   N9   126.86  3.000
 NOS  C2   N3   C4   112.58  3.000
 NOS  H1   C2   N1   115.42  3.000
 NOS  H1   C2   N3   119.87  3.000
 NOS  N1   C2   N3   124.72  3.000
 NOS  H2   N1   C6   116.67  3.000
 NOS  H2   N1   C2   117.38  3.000
 NOS  C6   N1   C2   125.95  3.000
 NOS  C5   C6   O6   128.65  3.000
 NOS  C5   C6   N1   109.81  3.000
 NOS  O6   C6   N1   121.54  3.000
 NOS  N7   C5   C6   130.10  3.000
 NOS  N7   C5   C4   110.59  3.000
 NOS  C6   C5   C4   119.30  3.000
 NOS  C8   N7   C5   104.67  3.000
 NOS  H3   C8   N7   125.05  3.000
 NOS  H3   C8   N9   121.92  3.000
 NOS  N7   C8   N9   113.03  3.000
 NOS  H7   C4'  C3'  110.59  3.000
 NOS  H7   C4'  O4'  107.99  3.000
 NOS  C3'  C4'  O4'  105.88  3.000
 NOS  H7   C4'  C5'  108.48  3.000
 NOS  C3'  C4'  C5'  112.79  3.000
 NOS  O4'  C4'  C5'  111.02  3.000
 NOS  C1'  O4'  C4'  110.57  3.000
 NOS  H8   C1'  C2'  110.18  3.000
 NOS  H8   C1'  O4'  112.04  3.000
 NOS  C2'  C1'  O4'  105.90  3.000
 NOS  H8   C1'  N9   106.17  3.000
 NOS  O4'  C1'  N9   109.13  3.000
 NOS  C2'  C1'  N9   113.53  3.000
 NOS  H9   C2'  C3'  107.84  3.000
 NOS  H9   C2'  O2'  111.52  3.000
 NOS  C3'  C2'  O2'  116.89  3.000
 NOS  H9   C2'  C1'  109.18  3.000
 NOS  C3'  C2'  C1'  101.02  3.000
 NOS  O2'  C2'  C1'  109.75  3.000
 NOS  H10  O2'  C2'  108.80  3.000
 NOS  H11  C3'  O3'  111.74  3.000
 NOS  H11  C3'  C2'  111.95  3.000
 NOS  O3'  C3'  C2'  107.87  3.000
 NOS  H11  C3'  C4'  111.44  3.000
 NOS  O3'  C3'  C4'  112.52  3.000
 NOS  C2'  C3'  C4'  100.79  3.000
 NOS  H12  O3'  C3'  108.45  3.000
 NOS  H5   C5'  H4   106.58  3.000
 NOS  H5   C5'  C4'  107.41  3.000
 NOS  H4   C5'  C4'  110.46  3.000
 NOS  H5   C5'  O5'  111.97  3.000
 NOS  H4   C5'  O5'  111.73  3.000
 NOS  C4'  C5'  O5'  108.59  3.000
 NOS  H6   O5'  C5'  108.14  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
 NOS  CONST_01  N7   C5  C4  N9    0.00  0.0  0
 NOS  CONST_02  C5   N7  C8  N9    0.00  0.0  0
 NOS  CONST_03  C8   N7  C5  C4    0.00  0.0  0
 NOS  CONST_04  N7   C8  N9  C4    0.00  0.0  0
 NOS  CONST_05  C8   N9  C4  C5    0.00  0.0  0
 NOS  CONST_06  C1'  N9  C4  N3    0.00  0.0  0
 NOS  CONST_07  C1'  N9  C4  C5  180.00  0.0  0
 NOS  CONST_08  C1'  N9  C8  N7  180.00  0.0  0
 NOS  CONST_09  N1   C2  N3  C4    0.00  0.0  0
 NOS  CONST_10  C6   N1  C2  N3    0.00  0.0  0
 NOS  CONST_11  C5   C6  N1  C2    0.00  0.0  0
 NOS  CONST_12  O6   C6  N1  C2  180.00  0.0  0
 NOS  CONST_13  H3   C8  N9  C4  180.00  0.0  0
 NOS  CONST_14  H1   C2  N3  C4  180.00  0.0  0
 NOS  CONST_15  H2   N1  C2  N3  180.00  0.0  0

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
 NOS  chir_01  C4'  O4'  C3'  C5'  negativ
 NOS  chir_02  C1'  O4'  N9   C2'  negativ
 NOS  chir_03  C2'  O2'  C1'  C3'  negativ
 NOS  chir_04  C3'  O3'  C4'  C2'  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
 NOS  plan-1  N9   0.020
 NOS  plan-1  C4   0.020
 NOS  plan-1  N3   0.020
 NOS  plan-1  C2   0.020
 NOS  plan-1  N1   0.020
 NOS  plan-1  C6   0.020
 NOS  plan-1  O6   0.020
 NOS  plan-1  C5   0.020
 NOS  plan-1  N7   0.020
 NOS  plan-1  C8   0.020
 NOS  plan-1  C1'  0.020
 NOS  plan-1  H1   0.020
 NOS  plan-1  H2   0.020
 NOS  plan-1  H3   0.020

