# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 17:52:14 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)-~{N}-piperidin-4-yl-oxolane-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]([C@@H](O)[C@H]3O)C(=O)NC4CCNCC4
#
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
 NWZ  NWZ  (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)-~{N}-piperidin-4-yl-oxolane-2-carboxamide  ligand  47  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NWZ
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
 NWZ  C13  C  CH1   0  -0.070  -0.9778   1.3431   0.5413
 NWZ  C17  C  CH2   0  -0.431  -5.5806   0.1630   0.9300
 NWZ  C20  C  CH2   0  -0.299  -5.7987  -1.7802  -1.1955
 NWZ  C21  C  CH2   0  -0.419  -4.6137  -0.8252  -1.1554
 NWZ  C02  C  CR6   0   0.455   5.0421  -1.5653  -0.1336
 NWZ  C03  C  CR56  0  -0.003   3.7068  -1.2376   0.1664
 NWZ  C05  C  CR15  0   0.084   1.6481  -1.1204   0.6314
 NWZ  C07  C  CH1   0   0.170   1.3331   1.4101   0.7248
 NWZ  C08  C  CH1   0  -0.044   0.9632   2.0546  -0.6091
 NWZ  C09  C  CH1   0  -0.040  -0.4029   1.4141  -0.8794
 NWZ  C14  C  C     0   0.529  -1.9712   0.2004   0.6862
 NWZ  C16  C  CH1   0  -0.080  -4.3229  -0.4106   0.2860
 NWZ  C18  C  CH2   0  -0.298  -6.7266  -0.8324   0.8073
 NWZ  C23  C  CR56  0   0.485   3.4117   0.1140   0.2416
 NWZ  C25  C  CR16  0   0.038   5.4779   0.6935  -0.2155
 NWZ  N04  N  N     0  -0.454   2.5906  -1.9923   0.4131
 NWZ  N06  N  NR5   0  -0.538   2.0828   0.1749   0.5422
 NWZ  N15  N  NH1   0  -0.629  -3.2258   0.5344   0.3649
 NWZ  N19  N  NH1   0  -0.596  -6.9593  -1.1536  -0.5889
 NWZ  N24  N  N     0  -0.459   4.2589   1.1252   0.0581
 NWZ  N26  N  N     0  -0.474   5.9070  -0.5617  -0.3203
 NWZ  O10  O  OH1   0  -0.650  -1.2372   2.1769  -1.6980
 NWZ  O11  O  OH1   0  -0.662   0.8346   3.4314  -0.3922
 NWZ  O12  O  O2    0  -0.485   0.1324   1.1336   1.3864
 NWZ  O22  O  O     0  -0.481  -1.6196  -0.9216   1.0198
 NWZ  H1   H  HCH1  0   0.274  -1.4621   2.2965   0.7867
 NWZ  H3   H  HCH2  0   0.222  -5.8559   1.0985   0.4316
 NWZ  H4   H  HCH2  0   0.236  -6.0343  -2.0386  -2.2295
 NWZ  H5   H  HCH2  0   0.190  -5.5135  -2.7177  -0.6896
 NWZ  H6   H  HCH2  0   0.238  -3.7345  -1.3009  -1.5951
 NWZ  H7   H  HCH2  0   0.220  -4.8415   0.0636  -1.7521
 NWZ  H8   H  HCR5  0   0.310   0.6222  -1.3574   0.8672
 NWZ  H9   H  HCH1  0   0.287   1.9544   2.0759   1.3291
 NWZ  H10  H  HCH1  0   0.267   1.6973   1.8287  -1.3921
 NWZ  H11  H  HCH1  0   0.263  -0.2566   0.4021  -1.2774
 NWZ  H12  H  HCH1  0   0.244  -4.0184  -1.2959   0.8493
 NWZ  H13  H  HCH2  0   0.190  -6.4833  -1.7228   1.4107
 NWZ  H14  H  HCH2  0   0.237  -7.6368  -0.4035   1.2301
 NWZ  H15  H  HCR6  0   0.252   6.2302   1.4576  -0.3789
 NWZ  H16  H  HNH2  0   0.403   6.4334  -3.0189  -0.4465
 NWZ  H17  H  HNH2  0   0.411   4.8468  -3.5987  -0.0885
 NWZ  H18  H  HNH1  0   0.400  -3.4140   1.4846   0.0817
 NWZ  H19  H  HNH1  0   0.353  -7.7551  -1.7735  -0.6647
 NWZ  H21  H  HOH1  0   0.473  -1.0891   1.9285  -2.6159
 NWZ  H22  H  HOH1  0   0.454   0.2028   3.7742  -1.0364
 NWZ  N01  N  NH2   0  -0.817   5.4697  -2.8244  -0.2365
 NWZ  H2   H  HCH2  0   0.242  -5.3957   0.3908   1.9818

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
 NWZ  C18  N19  single    1.451  0.020  1.451
 NWZ  C18  C17  single    1.523  0.020  1.523
 NWZ  N19  C20  single    1.452  0.020  1.452
 NWZ  C20  C21  single    1.523  0.020  1.523
 NWZ  C17  C16  single    1.525  0.020  1.525
 NWZ  C16  C21  single    1.528  0.020  1.528
 NWZ  C16  N15  single    1.450  0.020  1.450
 NWZ  O22  C14  double    1.222  0.020  1.222
 NWZ  N04  C05  aromatic  1.302  0.020  1.302
 NWZ  N04  C03  aromatic  1.370  0.020  1.370
 NWZ  C05  N06  aromatic  1.369  0.020  1.369
 NWZ  N15  C14  single    1.337  0.020  1.337
 NWZ  C14  C13  single    1.521  0.020  1.521
 NWZ  N01  C02  single    1.334  0.020  1.334
 NWZ  C03  C02  aromatic  1.407  0.020  1.407
 NWZ  C03  C23  aromatic  1.385  0.020  1.385
 NWZ  N06  C07  single    1.456  0.020  1.456
 NWZ  N06  C23  aromatic  1.364  0.020  1.364
 NWZ  C08  C09  single    1.533  0.020  1.533
 NWZ  C08  C07  single    1.527  0.020  1.527
 NWZ  C08  O11  single    1.400  0.020  1.400
 NWZ  C02  N26  aromatic  1.338  0.020  1.338
 NWZ  O12  C13  single    1.411  0.020  1.411
 NWZ  O12  C07  single    1.398  0.020  1.398
 NWZ  C13  C09  single    1.534  0.020  1.534
 NWZ  C09  O10  single    1.396  0.020  1.396
 NWZ  C23  N24  aromatic  1.332  0.020  1.332
 NWZ  N26  C25  aromatic  1.331  0.020  1.331
 NWZ  N24  C25  aromatic  1.322  0.020  1.322
 NWZ  C13  H1   single    0.970  0.020  1.090
 NWZ  C17  H2   single    0.970  0.020  1.090
 NWZ  C17  H3   single    0.970  0.020  1.090
 NWZ  C20  H4   single    0.970  0.020  1.090
 NWZ  C20  H5   single    0.970  0.020  1.090
 NWZ  C21  H6   single    0.970  0.020  1.090
 NWZ  C21  H7   single    0.970  0.020  1.090
 NWZ  C05  H8   single    0.930  0.020  1.080
 NWZ  C07  H9   single    0.970  0.020  1.090
 NWZ  C08  H10  single    0.970  0.020  1.090
 NWZ  C09  H11  single    0.970  0.020  1.090
 NWZ  C16  H12  single    0.970  0.020  1.090
 NWZ  C18  H13  single    0.970  0.020  1.090
 NWZ  C18  H14  single    0.970  0.020  1.090
 NWZ  C25  H15  single    0.930  0.020  1.080
 NWZ  N01  H16  single    0.860  0.020  1.020
 NWZ  N01  H17  single    0.860  0.020  1.020
 NWZ  N15  H18  single    0.860  0.020  1.020
 NWZ  N19  H19  single    0.890  0.020  1.040
 NWZ  O10  H21  single    0.850  0.020  0.980
 NWZ  O11  H22  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
 NWZ  H1   C13  O12  110.02  3.000
 NWZ  H1   C13  C14  110.07  3.000
 NWZ  O12  C13  C14  110.20  3.000
 NWZ  H1   C13  C09  109.41  3.000
 NWZ  O12  C13  C09  105.47  3.000
 NWZ  C14  C13  C09  111.57  3.000
 NWZ  H3   C17  H2   107.62  3.000
 NWZ  H3   C17  C18  109.42  3.000
 NWZ  H2   C17  C18  109.96  3.000
 NWZ  H3   C17  C16  109.66  3.000
 NWZ  H2   C17  C16  110.22  3.000
 NWZ  C18  C17  C16  109.92  3.000
 NWZ  H5   C20  H4   106.81  3.000
 NWZ  H5   C20  N19  112.46  3.000
 NWZ  H4   C20  N19  108.99  3.000
 NWZ  H5   C20  C21  108.66  3.000
 NWZ  H4   C20  C21  109.96  3.000
 NWZ  N19  C20  C21  109.90  3.000
 NWZ  H7   C21  H6   107.57  3.000
 NWZ  H7   C21  C16  109.49  3.000
 NWZ  H6   C21  C16  110.17  3.000
 NWZ  H7   C21  C20  109.45  3.000
 NWZ  H6   C21  C20  110.04  3.000
 NWZ  C16  C21  C20  110.07  3.000
 NWZ  N26  C02  N01  119.35  3.000
 NWZ  N26  C02  C03  117.93  3.000
 NWZ  N01  C02  C03  122.72  3.000
 NWZ  N04  C03  C23  110.74  3.000
 NWZ  C23  C03  C02  116.16  3.000
 NWZ  N04  C03  C02  133.10  3.000
 NWZ  H8   C05  N06  121.59  3.000
 NWZ  H8   C05  N04  125.28  3.000
 NWZ  N06  C05  N04  113.12  3.000
 NWZ  H9   C07  O12  110.30  3.000
 NWZ  H9   C07  N06  107.06  3.000
 NWZ  O12  C07  N06  109.49  3.000
 NWZ  H9   C07  C08  111.32  3.000
 NWZ  O12  C07  C08  106.78  3.000
 NWZ  N06  C07  C08  111.91  3.000
 NWZ  H10  C08  O11  112.01  3.000
 NWZ  H10  C08  C09  112.62  3.000
 NWZ  O11  C08  C09  110.88  3.000
 NWZ  H10  C08  C07  112.00  3.000
 NWZ  O11  C08  C07  107.58  3.000
 NWZ  C09  C08  C07  101.16  3.000
 NWZ  H11  C09  O10  111.78  3.000
 NWZ  H11  C09  C08  109.30  3.000
 NWZ  O10  C09  C08  114.07  3.000
 NWZ  H11  C09  C13  110.07  3.000
 NWZ  O10  C09  C13  110.15  3.000
 NWZ  C08  C09  C13  100.95  3.000
 NWZ  O22  C14  N15  124.38  3.000
 NWZ  N15  C14  C13  113.71  3.000
 NWZ  O22  C14  C13  121.85  3.000
 NWZ  H12  C16  N15  106.80  3.000
 NWZ  H12  C16  C21  108.64  3.000
 NWZ  N15  C16  C21  111.85  3.000
 NWZ  H12  C16  C17  108.47  3.000
 NWZ  N15  C16  C17  110.85  3.000
 NWZ  C21  C16  C17  110.09  3.000
 NWZ  H14  C18  H13  106.82  3.000
 NWZ  H14  C18  N19  109.02  3.000
 NWZ  H13  C18  N19  112.53  3.000
 NWZ  H14  C18  C17  109.84  3.000
 NWZ  H13  C18  C17  108.52  3.000
 NWZ  N19  C18  C17  110.04  3.000
 NWZ  N24  C23  N06  128.04  3.000
 NWZ  N24  C23  C03  126.70  3.000
 NWZ  N06  C23  C03  105.25  3.000
 NWZ  H15  C25  N26  115.41  3.000
 NWZ  H15  C25  N24  116.15  3.000
 NWZ  N26  C25  N24  128.44  3.000
 NWZ  C05  N04  C03  104.54  3.000
 NWZ  C23  N06  C07  124.55  3.000
 NWZ  C23  N06  C05  106.34  3.000
 NWZ  C07  N06  C05  129.11  3.000
 NWZ  H18  N15  C16  117.21  3.000
 NWZ  H18  N15  C14  118.52  3.000
 NWZ  C16  N15  C14  124.06  3.000
 NWZ  H19  N19  C18  109.49  3.000
 NWZ  H19  N19  C20  109.46  3.000
 NWZ  C18  N19  C20  111.67  3.000
 NWZ  C25  N24  C23  111.54  3.000
 NWZ  C25  N26  C02  119.22  3.000
 NWZ  H21  O10  C09  109.05  3.000
 NWZ  H22  O11  C08  107.82  3.000
 NWZ  C07  O12  C13  111.28  3.000
 NWZ  H17  N01  H16  118.42  3.000
 NWZ  H17  N01  C02  121.16  3.000
 NWZ  H16  N01  C02  120.41  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
 NWZ  CONST_01  C05  N04  C03  C02  180.00   0.0  0
 NWZ  CONST_02  N06  C23  C03  C02  180.00   0.0  0
 NWZ  CONST_03  N24  C23  C03  C02    0.00   0.0  0
 NWZ  CONST_04  N24  C25  N26  C02    0.00   0.0  0
 NWZ  CONST_05  N06  C05  N04  C03    0.00   0.0  0
 NWZ  CONST_06  C25  N26  C02  C03    0.00   0.0  0
 NWZ  CONST_07  C05  N06  C23  C03    0.00   0.0  0
 NWZ  CONST_08  C25  N24  C23  C03    0.00   0.0  0
 NWZ  CONST_09  C23  C03  N04  C05    0.00   0.0  0
 NWZ  CONST_10  N24  C23  N06  C05  180.00   0.0  0
 NWZ  CONST_11  N26  C02  C03  C23    0.00   0.0  0
 NWZ  CONST_12  N04  C05  N06  C23    0.00   0.0  0
 NWZ  CONST_13  N26  C25  N24  C23    0.00   0.0  0
 NWZ  CONST_14  N06  C23  N24  C25  180.00   0.0  0
 NWZ  CONST_15  N26  C02  C03  N04  180.00   0.0  0
 NWZ  CONST_16  N06  C23  C03  N04    0.00   0.0  0
 NWZ  CONST_17  N24  C23  C03  N04  180.00   0.0  0
 NWZ  CONST_18  C07  N06  C23  C03  180.00   0.0  0
 NWZ  CONST_19  N04  C05  N06  C07  180.00   0.0  0
 NWZ  CONST_20  N24  C23  N06  C07    0.00   0.0  0
 NWZ  CONST_21  N01  C02  C03  C23  180.00   0.0  0
 NWZ  CONST_22  N01  C02  N26  C25  180.00   0.0  0
 NWZ  CONST_23  N04  C03  C02  N01    0.00   0.0  0
 NWZ  CONST_24  H15  C25  N26  C02  180.00   0.0  0
 NWZ  CONST_25  H8   C05  N04  C03  180.00   0.0  0
 NWZ  CONST_26  C16  N15  C14  C13  180.00   0.0  0
 NWZ  CONST_27  H16  N01  C02  C03  180.00   0.0  0
 NWZ  CONST_28  H17  N01  C02  C03    0.00   0.0  0
 NWZ  CONST_29  O22  C14  N15  C16    0.00   0.0  0
 NWZ  CONST_30  H18  N15  C14  C13    0.00   0.0  0
 NWZ  Var_01    C20  N19  C18  C17   61.81  30.0  1
 NWZ  Var_02    C18  N19  C20  C21  -61.68  30.0  1
 NWZ  Var_03    N19  C18  C17  C16  -57.54  30.0  1
 NWZ  Var_04    N19  C20  C21  C16   57.39  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
 NWZ  chir_01  C13  C14  O12  C09  negativ
 NWZ  chir_02  C07  O12  N06  C08  negativ
 NWZ  chir_03  C08  O11  C07  C09  negativ
 NWZ  chir_04  C09  O10  C13  C08  positiv
 NWZ  chir_05  C16  N15  C17  C21  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
 NWZ  plan-1  C13  0.020
 NWZ  plan-1  C14  0.020
 NWZ  plan-1  C16  0.020
 NWZ  plan-1  N15  0.020
 NWZ  plan-1  O22  0.020
 NWZ  plan-1  H18  0.020
 NWZ  plan-2  C02  0.020
 NWZ  plan-2  H16  0.020
 NWZ  plan-2  H17  0.020
 NWZ  plan-2  N01  0.020
 NWZ  plan-3  C02  0.020
 NWZ  plan-3  C03  0.020
 NWZ  plan-3  C05  0.020
 NWZ  plan-3  C07  0.020
 NWZ  plan-3  C23  0.020
 NWZ  plan-3  C25  0.020
 NWZ  plan-3  N04  0.020
 NWZ  plan-3  N06  0.020
 NWZ  plan-3  N24  0.020
 NWZ  plan-3  N26  0.020
 NWZ  plan-3  H8   0.020
 NWZ  plan-3  H15  0.020
 NWZ  plan-3  N01  0.020

