# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 10:21:36 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-(2-hydroxy-2-oxoethylsulfanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino-azanylidene-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=N)[C@@H](O)[C@H]3O)c(SCC(O)=O)nc12
#
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
 DVZ  DVZ  '[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-(2-hydroxy-2-oxoethylsulfanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino-azanylidene-azanium'  ligand  41  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DVZ
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
 DVZ  C2   C  CR16  0   0.045   4.1632   2.3803   0.5624
 DVZ  C4   C  CR56  0   0.496   2.3303   1.1937   0.3482
 DVZ  C5   C  CR56  0   0.007   3.0116   0.0013   0.5059
 DVZ  C6   C  CR6   0   0.450   4.4003   0.0960   0.6996
 DVZ  C8   C  CR5   0   0.334   0.9831  -0.5344   0.2427
 DVZ  N1   N  N     0  -0.470   4.9459   1.3184   0.7210
 DVZ  C1'  C  CH1   0   0.203  -0.0417   1.7668  -0.1259
 DVZ  C2'  C  CH1   0   0.005  -0.5245   1.7592  -1.5739
 DVZ  C3'  C  CH1   0  -0.056  -1.9032   2.4118  -1.4153
 DVZ  C4'  C  CH1   0  -0.011  -2.3523   1.8119  -0.0694
 DVZ  C5'  C  CH2   0  -0.371  -3.2453   0.6035  -0.3015
 DVZ  C82  C  CH2   0  -0.671   0.1444  -3.0721  -0.0878
 DVZ  C83  C  C     0   0.570  -1.0381  -3.9844  -0.2791
 DVZ  N3   N  N     0  -0.457   2.8544   2.4133   0.3688
 DVZ  N51  N  N     0  -0.120  -3.4359  -0.1026   0.9786
 DVZ  N52  N  N     1   0.542  -4.4470  -0.3947   1.4495
 DVZ  N53  N  N     0  -0.331  -5.3949  -0.8664   1.9431
 DVZ  N6   N  NH2   0  -0.817   5.1814  -0.9719   0.8721
 DVZ  N7   N  N     0  -0.455   2.1516  -1.0657   0.4442
 DVZ  N9   N  NR5   0  -0.587   1.0164   0.8407   0.1719
 DVZ  O2'  O  OH1   0  -0.646   0.3872   2.4314  -2.3749
 DVZ  O3'  O  OH1   0  -0.657  -1.7229   3.7950  -1.3376
 DVZ  O31  O  OH1   0  -0.580  -0.6577  -5.2380  -0.4402
 DVZ  O32  O  O     0  -0.426  -2.1814  -3.6067  -0.2803
 DVZ  O4'  O  O2    0  -0.492  -1.1757   1.4402   0.6361
 DVZ  S81  S  S2    0   0.073  -0.5193  -1.4049   0.1225
 DVZ  H1   H  HCR6  0   0.254   4.6655   3.3412   0.5944
 DVZ  H2   H  HCH1  0   0.278   0.3477   2.7578   0.1316
 DVZ  H3   H  HCH1  0   0.247  -0.6691   0.7198  -1.9001
 DVZ  H4   H  HCH1  0   0.271  -2.5880   2.1335  -2.2263
 DVZ  H5   H  HCH1  0   0.300  -2.9076   2.5469   0.5192
 DVZ  H6   H  HCH2  0   0.345  -4.2110   0.9029  -0.7059
 DVZ  H7   H  HCH2  0   0.329  -2.7857  -0.1368  -0.9565
 DVZ  H8   H  HCH2  0   0.331   0.7152  -3.3752   0.7908
 DVZ  H9   H  HCH2  0   0.331   0.8087  -3.1213  -0.9518
 DVZ  H10  H  H     0   0.498  -5.8943  -0.2701   2.6134
 DVZ  H11  H  HNH2  0   0.412   4.8107  -1.9030   0.8012
 DVZ  H12  H  HNH2  0   0.404   6.1783  -0.8616   0.9397
 DVZ  H13  H  HOH1  0   0.467   0.1868   2.2479  -3.2979
 DVZ  H14  H  HOH1  0   0.463  -2.5847   4.2140  -1.2462
 DVZ  H15  H  HOH1  0   0.491  -1.4296  -5.8124  -0.5615

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
 DVZ  N53  N52  double    1.168  0.020  1.168
 DVZ  O32  C83  double    1.204  0.020  1.204
 DVZ  N52  N51  double    1.153  0.020  1.153
 DVZ  N6   C6   single    1.334  0.020  1.334
 DVZ  C83  C82  single    1.506  0.020  1.506
 DVZ  C83  O31  single    1.320  0.020  1.320
 DVZ  C82  S81  single    1.807  0.020  1.807
 DVZ  N7   C5   aromatic  1.372  0.020  1.372
 DVZ  N7   C8   aromatic  1.299  0.020  1.299
 DVZ  C6   C5   aromatic  1.405  0.020  1.405
 DVZ  C6   N1   aromatic  1.339  0.020  1.339
 DVZ  C5'  N51  single    1.474  0.020  1.474
 DVZ  C5'  C4'  single    1.520  0.020  1.520
 DVZ  S81  C8   single    1.740  0.020  1.740
 DVZ  C5   C4   aromatic  1.382  0.020  1.382
 DVZ  C8   N9   aromatic  1.377  0.020  1.377
 DVZ  O4'  C4'  single    1.421  0.020  1.421
 DVZ  O4'  C1'  single    1.405  0.020  1.405
 DVZ  N1   C2   aromatic  1.329  0.020  1.329
 DVZ  C4   N9   aromatic  1.372  0.020  1.372
 DVZ  C4   N3   aromatic  1.328  0.020  1.328
 DVZ  N9   C1'  single    1.437  0.020  1.437
 DVZ  C4'  C3'  single    1.541  0.020  1.541
 DVZ  C2   N3   aromatic  1.323  0.020  1.323
 DVZ  C1'  C2'  single    1.526  0.020  1.526
 DVZ  C3'  C2'  single    1.534  0.020  1.534
 DVZ  C3'  O3'  single    1.397  0.020  1.397
 DVZ  C2'  O2'  single    1.387  0.020  1.387
 DVZ  C2   H1   single    0.930  0.020  1.080
 DVZ  C1'  H2   single    0.970  0.020  1.090
 DVZ  C2'  H3   single    0.970  0.020  1.090
 DVZ  C3'  H4   single    0.970  0.020  1.090
 DVZ  C4'  H5   single    0.970  0.020  1.090
 DVZ  C5'  H6   single    0.970  0.020  1.090
 DVZ  C5'  H7   single    0.970  0.020  1.090
 DVZ  C82  H8   single    0.970  0.020  1.090
 DVZ  C82  H9   single    0.970  0.020  1.090
 DVZ  N53  H10  single    0.890  0.020  1.040
 DVZ  N6   H11  single    0.860  0.020  1.020
 DVZ  N6   H12  single    0.860  0.020  1.020
 DVZ  O2'  H13  single    0.850  0.020  0.980
 DVZ  O3'  H14  single    0.850  0.020  0.980
 DVZ  O31  H15  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
 DVZ  H1   C2   N3   116.12  3.000
 DVZ  H1   C2   N1   115.57  3.000
 DVZ  N3   C2   N1   128.31  3.000
 DVZ  N9   C4   N3   128.06  3.000
 DVZ  N3   C4   C5   126.59  3.000
 DVZ  N9   C4   C5   105.35  3.000
 DVZ  N7   C5   C6   132.69  3.000
 DVZ  C6   C5   C4   116.40  3.000
 DVZ  N7   C5   C4   110.91  3.000
 DVZ  N6   C6   N1   119.35  3.000
 DVZ  N1   C6   C5   117.80  3.000
 DVZ  N6   C6   C5   122.85  3.000
 DVZ  S81  C8   N9   121.11  3.000
 DVZ  N9   C8   N7   113.23  3.000
 DVZ  S81  C8   N7   125.63  3.000
 DVZ  C6   N1   C2   119.19  3.000
 DVZ  H2   C1'  O4'  111.70  3.000
 DVZ  H2   C1'  N9   105.81  3.000
 DVZ  O4'  C1'  N9   109.39  3.000
 DVZ  H2   C1'  C2'  109.87  3.000
 DVZ  N9   C1'  C2'  115.23  3.000
 DVZ  O4'  C1'  C2'  104.96  3.000
 DVZ  H3   C2'  O2'  111.92  3.000
 DVZ  H3   C2'  C3'  108.36  3.000
 DVZ  O2'  C2'  C3'  116.38  3.000
 DVZ  H3   C2'  C1'  109.14  3.000
 DVZ  O2'  C2'  C1'  109.72  3.000
 DVZ  C3'  C2'  C1'  100.61  3.000
 DVZ  H4   C3'  O3'  111.89  3.000
 DVZ  H4   C3'  C4'  111.40  3.000
 DVZ  O3'  C3'  C4'  112.00  3.000
 DVZ  H4   C3'  C2'  112.13  3.000
 DVZ  O3'  C3'  C2'  108.12  3.000
 DVZ  C4'  C3'  C2'  100.76  3.000
 DVZ  H5   C4'  O4'  109.21  3.000
 DVZ  H5   C4'  C5'  108.56  3.000
 DVZ  O4'  C4'  C5'  110.74  3.000
 DVZ  H5   C4'  C3'  110.90  3.000
 DVZ  O4'  C4'  C3'  107.11  3.000
 DVZ  C5'  C4'  C3'  110.33  3.000
 DVZ  H7   C5'  H6   109.73  3.000
 DVZ  H7   C5'  N51  104.54  3.000
 DVZ  H6   C5'  N51  109.84  3.000
 DVZ  H7   C5'  C4'  112.57  3.000
 DVZ  H6   C5'  C4'  111.04  3.000
 DVZ  N51  C5'  C4'  108.91  3.000
 DVZ  H9   C82  H8   107.87  3.000
 DVZ  H9   C82  S81  110.94  3.000
 DVZ  H8   C82  S81  110.79  3.000
 DVZ  H9   C82  C83  110.50  3.000
 DVZ  H8   C82  C83  110.18  3.000
 DVZ  S81  C82  C83  106.58  3.000
 DVZ  O32  C83  O31  124.85  3.000
 DVZ  O31  C83  C82  111.38  3.000
 DVZ  O32  C83  C82  123.76  3.000
 DVZ  C4   N3   C2   111.70  3.000
 DVZ  N52  N51  C5'  126.11  3.000
 DVZ  N53  N52  N51  170.55  3.000
 DVZ  H10  N53  N52  115.84  3.000
 DVZ  H12  N6   H11  118.18  3.000
 DVZ  H12  N6   C6   120.09  3.000
 DVZ  H11  N6   C6   121.11  3.000
 DVZ  C8   N7   C5   104.64  3.000
 DVZ  C1'  N9   C8   129.50  3.000
 DVZ  C1'  N9   C4   124.46  3.000
 DVZ  C8   N9   C4   105.87  3.000
 DVZ  H13  O2'  C2'  108.94  3.000
 DVZ  H14  O3'  C3'  108.70  3.000
 DVZ  H15  O31  C83  110.39  3.000
 DVZ  C4'  O4'  C1'  109.76  3.000
 DVZ  C82  S81  C8    98.77  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
 DVZ  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 DVZ  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 DVZ  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 DVZ  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 DVZ  CONST_05  N1   C6   C5   C4      0.00   0.0  0
 DVZ  CONST_06  N7   C8   N9   C4      0.00   0.0  0
 DVZ  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 DVZ  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 DVZ  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 DVZ  CONST_10  C8   N7   C5   C6    180.00   0.0  0
 DVZ  CONST_11  N9   C4   C5   C6    180.00   0.0  0
 DVZ  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 DVZ  CONST_13  N3   C2   N1   C6      0.00   0.0  0
 DVZ  CONST_14  N3   C4   N9   C8    180.00   0.0  0
 DVZ  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 DVZ  CONST_16  N7   C5   C4   N3    180.00   0.0  0
 DVZ  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 DVZ  CONST_18  C1'  N9   C4   C5    180.00   0.0  0
 DVZ  CONST_19  N7   C8   N9   C1'   180.00   0.0  0
 DVZ  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 DVZ  CONST_21  N6   C6   N1   C2    180.00   0.0  0
 DVZ  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 DVZ  CONST_23  S81  C8   N9   C4    180.00   0.0  0
 DVZ  CONST_24  S81  C8   N7   C5    180.00   0.0  0
 DVZ  CONST_25  S81  C8   N9   C1'     0.00   0.0  0
 DVZ  CONST_26  N7   C5   C6   N6      0.00   0.0  0
 DVZ  CONST_27  H1   C2   N3   C4    180.00   0.0  0
 DVZ  CONST_28  H11  N6   C6   C5      0.00   0.0  0
 DVZ  CONST_29  H12  N6   C6   C5    180.00   0.0  0
 DVZ  CONST_30  H15  O31  C83  C82   180.00   0.0  0
 DVZ  Var_01    N7   C8   S81  C82   -14.31  30.0  2
 DVZ  Var_02    C83  C82  S81  C8   -177.34  30.0  1
 DVZ  Var_03    S81  C82  C83  O31  -179.86  30.0  3
 DVZ  Var_04    H6   C5'  N51  N52     5.49  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
 DVZ  chir_01  C1'  O4'  N9   C2'  negativ
 DVZ  chir_02  C2'  O2'  C1'  C3'  negativ
 DVZ  chir_03  C3'  O3'  C4'  C2'  positiv
 DVZ  chir_04  C4'  O4'  C3'  C5'  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
 DVZ  plan-1  C2   0.020
 DVZ  plan-1  C4   0.020
 DVZ  plan-1  C5   0.020
 DVZ  plan-1  C6   0.020
 DVZ  plan-1  C8   0.020
 DVZ  plan-1  N1   0.020
 DVZ  plan-1  C1'  0.020
 DVZ  plan-1  N3   0.020
 DVZ  plan-1  N6   0.020
 DVZ  plan-1  N7   0.020
 DVZ  plan-1  N9   0.020
 DVZ  plan-1  S81  0.020
 DVZ  plan-1  H1   0.020
 DVZ  plan-2  C6   0.020
 DVZ  plan-2  N6   0.020
 DVZ  plan-2  H11  0.020
 DVZ  plan-2  H12  0.020
 DVZ  plan-3  C82  0.020
 DVZ  plan-3  C83  0.020
 DVZ  plan-3  O31  0.020
 DVZ  plan-3  O32  0.020
 DVZ  plan-3  H15  0.020
 DVZ  plan-4  C5'  0.020
 DVZ  plan-4  N51  0.020
 DVZ  plan-4  N52  0.020
 DVZ  plan-4  N53  0.020
 DVZ  plan-4  H10  0.020

