# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 10:34:40 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: azanylidene-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[2-oxidanylidene-2-(prop-2-ynylamino)ethyl]sulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino]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)NCC#C)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
 E9W  E9W  azanylidene-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[2-oxidanylidene-2-(prop-2-ynylamino)ethyl]sulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino]azanium  ligand  47  29  .  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_E9W
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
 E9W  C2   C  CR16  0   0.016   3.9643   3.5658  -0.4233
 E9W  C4   C  CR56  0   0.505   2.4113   2.0218  -0.2935
 E9W  C5   C  CR56  0   0.037   1.3939   2.9449  -0.4519
 E9W  C6   C  CR6   0   0.383   1.7866   4.2863  -0.5991
 E9W  N9   N  NR5   0  -0.537   1.7840   0.8088  -0.1678
 E9W  C8   C  CR5   0   0.318   0.4355   1.0693  -0.2680
 E9W  CAA  C  CSP1  0  -0.496  -7.9726   0.6930  -0.1189
 E9W  CAB  C  CSP   0   0.185  -6.9631   0.0666   0.0552
 E9W  CAC  C  CH2   0  -0.362  -5.7379  -0.6915   0.2754
 E9W  CAE  C  C     0   0.590  -3.3410  -0.3281   0.0535
 E9W  CAG  C  CH2   0  -0.689  -2.2398   0.7116  -0.0144
 E9W  CAK  C  CR15  0   0.177   2.4545  -0.4316   0.1163
 E9W  CAM  C  CR15  0   0.023   1.9333  -2.6899   0.0676
 E9W  CAN  C  CH2   0  -0.373   0.5410  -3.2348   0.3248
 E9W  CAR  C  CR15  0  -0.001   2.6531  -2.3990   1.3958
 E9W  CAT  C  CR15  0  -0.059   2.3468  -0.9066   1.5639
 E9W  N1   N  N     0  -0.476   3.0966   4.5600  -0.5779
 E9W  N3   N  N     0  -0.405   3.7142   2.2751  -0.2717
 E9W  N6   N  NH2   0  -0.752   0.9143   5.2820  -0.7689
 E9W  N7   N  N     0  -0.464   0.1676   2.3287  -0.4423
 E9W  NAD  N  NH1   0  -0.708  -4.5785   0.1703   0.1477
 E9W  NAO  N  N     0  -0.201  -0.2218  -3.2380  -0.9382
 E9W  NAP  N  N     1   0.636  -1.2290  -3.7632  -1.1320
 E9W  NAQ  N  N     0  -0.314  -2.3014  -4.1382  -1.4050
 E9W  OAF  O  O     0  -0.457  -3.0938  -1.5241   0.0242
 E9W  OAL  O  O     0  -0.500   1.8776  -1.4606  -0.6476
 E9W  OAS  O  OH1   0  -0.659   4.0385  -2.5466   1.2860
 E9W  OAU  O  OH1   0  -0.668   3.2198  -0.1825   2.3626
 E9W  SAH  S  S2    0   0.100  -0.7166  -0.2314  -0.2237
 E9W  H1   H  HCR6  0   0.239   5.0099   3.8535  -0.4171
 E9W  H2   H  H     0   0.307  -8.8698   1.2475  -0.2739
 E9W  H3   H  HCH2  0   0.309  -5.7712  -1.1575   1.2646
 E9W  H4   H  HCH2  0   0.306  -5.6737  -1.5012  -0.4543
 E9W  H5   H  HCH2  0   0.323  -2.3917   1.3945  -0.8507
 E9W  H6   H  HCH2  0   0.331  -2.2071   1.3025   0.9026
 E9W  H7   H  HCR5  0   0.290   3.5056  -0.2708  -0.1468
 E9W  H8   H  HCR5  0   0.266   2.4888  -3.4193  -0.5284
 E9W  H9   H  HCH2  0   0.347   0.5906  -4.2607   0.6914
 E9W  H10  H  HCH2  0   0.316  -0.0405  -2.6361   1.0272
 E9W  H11  H  HCR5  0   0.242   2.2429  -3.0001   2.2177
 E9W  H12  H  HCR5  0   0.282   1.3046  -0.8010   1.8965
 E9W  H13  H  HNH2  0   0.397  -0.0760   5.1170  -0.7343
 E9W  H14  H  HNH2  0   0.363   1.2369   6.2329  -0.8141
 E9W  H15  H  HNH1  0   0.406  -4.7091   1.1661   0.2311
 E9W  H17  H  HOH1  0   0.467   4.2427  -3.4820   1.1880
 E9W  H18  H  HOH1  0   0.453   3.0076  -0.3473   3.2864
 E9W  H16  H  H     0   0.508  -2.3552  -5.0912  -1.7822

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
 E9W  CAA  CAB  triple    1.201  0.020  1.201
 E9W  CAB  CAC  single    1.458  0.020  1.458
 E9W  CAC  NAD  single    1.450  0.020  1.450
 E9W  NAD  CAE  single    1.337  0.020  1.337
 E9W  OAF  CAE  double    1.222  0.020  1.222
 E9W  CAE  CAG  single    1.516  0.020  1.516
 E9W  N6   C6   single    1.335  0.020  1.335
 E9W  CAG  SAH  single    1.804  0.020  1.804
 E9W  N7   C5   aromatic  1.372  0.020  1.372
 E9W  N7   C8   aromatic  1.299  0.020  1.299
 E9W  C6   C5   aromatic  1.405  0.020  1.405
 E9W  C6   N1   aromatic  1.339  0.020  1.339
 E9W  C5   C4   aromatic  1.383  0.020  1.383
 E9W  SAH  C8   single    1.738  0.020  1.738
 E9W  NAO  NAP  double    1.152  0.020  1.152
 E9W  NAO  CAN  single    1.476  0.020  1.476
 E9W  C8   N9   aromatic  1.377  0.020  1.377
 E9W  N1   C2   aromatic  1.329  0.020  1.329
 E9W  NAP  NAQ  double    1.168  0.020  1.168
 E9W  OAL  CAM  single    1.423  0.020  1.423
 E9W  OAL  CAK  single    1.405  0.020  1.405
 E9W  C4   N9   aromatic  1.371  0.020  1.371
 E9W  C4   N3   aromatic  1.327  0.020  1.327
 E9W  N9   CAK  single    1.438  0.020  1.438
 E9W  C2   N3   aromatic  1.323  0.020  1.323
 E9W  CAM  CAN  single    1.517  0.020  1.517
 E9W  CAM  CAR  single    1.538  0.020  1.538
 E9W  CAK  CAT  single    1.527  0.020  1.527
 E9W  CAR  CAT  single    1.533  0.020  1.533
 E9W  CAR  OAS  single    1.397  0.020  1.397
 E9W  CAT  OAU  single    1.387  0.020  1.387
 E9W  C2   H1   single    0.929  0.020  1.085
 E9W  CAA  H2   single    0.913  0.020  1.066
 E9W  CAC  H3   single    0.939  0.020  1.096
 E9W  CAC  H4   single    0.939  0.020  1.096
 E9W  CAG  H5   single    0.939  0.020  1.096
 E9W  CAG  H6   single    0.939  0.020  1.096
 E9W  CAK  H7   single    0.939  0.020  1.096
 E9W  CAM  H8   single    0.939  0.020  1.096
 E9W  CAN  H9   single    0.939  0.020  1.096
 E9W  CAN  H10  single    0.939  0.020  1.096
 E9W  CAR  H11  single    0.939  0.020  1.096
 E9W  CAT  H12  single    0.939  0.020  1.096
 E9W  N6   H13  single    0.868  0.020  1.013
 E9W  N6   H14  single    0.868  0.020  1.013
 E9W  NAD  H15  single    0.868  0.020  1.013
 E9W  OAS  H17  single    0.832  0.020  0.971
 E9W  OAU  H18  single    0.832  0.020  0.971
 E9W  NAQ  H16  single    0.872  0.020  1.018

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
 E9W  H1   C2   N3   116.12  3.000
 E9W  H1   C2   N1   115.59  3.000
 E9W  N3   C2   N1   128.29  3.000
 E9W  N3   C4   N9   128.04  3.000
 E9W  N3   C4   C5   126.63  3.000
 E9W  N9   C4   C5   105.33  3.000
 E9W  N7   C5   C6   132.76  3.000
 E9W  C6   C5   C4   116.33  3.000
 E9W  N7   C5   C4   110.91  3.000
 E9W  N6   C6   N1   119.28  3.000
 E9W  N1   C6   C5   117.84  3.000
 E9W  N6   C6   C5   122.88  3.000
 E9W  CAK  N9   C8   129.35  3.000
 E9W  CAK  N9   C4   124.59  3.000
 E9W  C8   N9   C4   105.89  3.000
 E9W  SAH  C8   N7   126.30  3.000
 E9W  SAH  C8   N9   120.37  3.000
 E9W  N7   C8   N9   113.27  3.000
 E9W  H2   CAA  CAB  180.00  3.000
 E9W  CAC  CAB  CAA  180.00  3.000
 E9W  H4   CAC  H3   106.86  3.000
 E9W  H4   CAC  NAD  109.56  3.000
 E9W  H3   CAC  NAD  110.93  3.000
 E9W  H4   CAC  CAB  109.52  3.000
 E9W  H3   CAC  CAB  109.43  3.000
 E9W  NAD  CAC  CAB  110.47  3.000
 E9W  OAF  CAE  NAD  123.62  3.000
 E9W  OAF  CAE  CAG  121.56  3.000
 E9W  NAD  CAE  CAG  114.82  3.000
 E9W  H6   CAG  H5   108.03  3.000
 E9W  H6   CAG  SAH  110.81  3.000
 E9W  H5   CAG  SAH  110.86  3.000
 E9W  H6   CAG  CAE  110.82  3.000
 E9W  H5   CAG  CAE  111.26  3.000
 E9W  SAH  CAG  CAE  105.08  3.000
 E9W  H7   CAK  OAL  111.77  3.000
 E9W  H7   CAK  CAT  109.94  3.000
 E9W  OAL  CAK  CAT  104.98  3.000
 E9W  H7   CAK  N9   105.86  3.000
 E9W  CAT  CAK  N9   114.99  3.000
 E9W  OAL  CAK  N9   109.43  3.000
 E9W  H8   CAM  OAL  108.79  3.000
 E9W  H8   CAM  CAR  111.04  3.000
 E9W  OAL  CAM  CAR  106.79  3.000
 E9W  H8   CAM  CAN  108.60  3.000
 E9W  CAR  CAM  CAN  110.55  3.000
 E9W  OAL  CAM  CAN  111.07  3.000
 E9W  H10  CAN  H9   108.91  3.000
 E9W  H10  CAN  NAO  106.07  3.000
 E9W  H9   CAN  NAO  108.01  3.000
 E9W  H10  CAN  CAM  113.66  3.000
 E9W  H9   CAN  CAM  110.68  3.000
 E9W  NAO  CAN  CAM  109.28  3.000
 E9W  H11  CAR  OAS  111.80  3.000
 E9W  H11  CAR  CAT  112.11  3.000
 E9W  OAS  CAR  CAT  108.03  3.000
 E9W  H11  CAR  CAM  111.59  3.000
 E9W  OAS  CAR  CAM  112.09  3.000
 E9W  CAT  CAR  CAM  100.68  3.000
 E9W  H12  CAT  OAU  111.86  3.000
 E9W  H12  CAT  CAR  108.44  3.000
 E9W  OAU  CAT  CAR  116.46  3.000
 E9W  H12  CAT  CAK  108.89  3.000
 E9W  OAU  CAT  CAK  109.81  3.000
 E9W  CAR  CAT  CAK  100.64  3.000
 E9W  C6   N1   C2   119.21  3.000
 E9W  C4   N3   C2   111.69  3.000
 E9W  H14  N6   H13  118.25  3.000
 E9W  H14  N6   C6   120.12  3.000
 E9W  H13  N6   C6   121.15  3.000
 E9W  C8   N7   C5   104.59  3.000
 E9W  H15  NAD  CAE  119.60  3.000
 E9W  H15  NAD  CAC  118.44  3.000
 E9W  CAE  NAD  CAC  121.64  3.000
 E9W  NAP  NAO  CAN  126.65  3.000
 E9W  NAQ  NAP  NAO  171.04  3.000
 E9W  H16  NAQ  NAP  115.59  3.000
 E9W  CAM  OAL  CAK  110.07  3.000
 E9W  H17  OAS  CAR  108.72  3.000
 E9W  H18  OAU  CAT  108.94  3.000
 E9W  CAG  SAH  C8    99.87  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
 E9W  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 E9W  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 E9W  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 E9W  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 E9W  CONST_05  N1   C6   C5   C4      0.00   0.0  0
 E9W  CONST_06  N7   C8   N9   C4      0.00   0.0  0
 E9W  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 E9W  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 E9W  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 E9W  CONST_10  C8   N7   C5   C6    180.00   0.0  0
 E9W  CONST_11  N9   C4   C5   C6    180.00   0.0  0
 E9W  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 E9W  CONST_13  N3   C2   N1   C6      0.00   0.0  0
 E9W  CONST_14  N7   C5   C4   N9      0.00   0.0  0
 E9W  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 E9W  CONST_16  N7   C5   C6   N1    180.00   0.0  0
 E9W  CONST_17  N7   C5   C4   N3    180.00   0.0  0
 E9W  CONST_18  CAK  N9   C4   C5    180.00   0.0  0
 E9W  CONST_19  N7   C8   N9   CAK   180.00   0.0  0
 E9W  CONST_20  N3   C4   N9   CAK     0.00   0.0  0
 E9W  CONST_21  N6   C6   N1   C2    180.00   0.0  0
 E9W  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 E9W  CONST_23  SAH  C8   N9   C4    180.00   0.0  0
 E9W  CONST_24  SAH  C8   N7   C5    180.00   0.0  0
 E9W  CONST_25  SAH  C8   N9   CAK     0.00   0.0  0
 E9W  CONST_26  N7   C5   C6   N6      0.00   0.0  0
 E9W  CONST_27  H1   C2   N3   C4    180.00   0.0  0
 E9W  CONST_28  H13  N6   C6   C5      0.00   0.0  0
 E9W  CONST_29  H14  N6   C6   C5    180.00   0.0  0
 E9W  CONST_30  OAF  CAE  NAD  CAC     0.00   0.0  0
 E9W  CONST_31  CAG  CAE  NAD  CAC   180.00   0.0  0
 E9W  CONST_32  H15  NAD  CAE  CAG     0.00   0.0  0
 E9W  Var_01    N7   C8   SAH  CAG   -15.00  30.0  2
 E9W  Var_02    CAE  CAG  SAH  C8   -179.46  30.0  1
 E9W  Var_03    NAD  CAC  CAB  CAA   -87.68  30.0  3
 E9W  Var_04    CAE  NAD  CAC  CAB  -167.13  30.0  3
 E9W  Var_05    SAH  CAG  CAE  NAD  -177.05  30.0  3
 E9W  Var_06    H9   CAN  NAO  NAP    47.35  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
 E9W  chir_01  CAK  OAL  N9   CAT  negativ
 E9W  chir_02  CAM  OAL  CAN  CAR  positiv
 E9W  chir_03  CAR  OAS  CAM  CAT  positiv
 E9W  chir_04  CAT  OAU  CAR  CAK  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
 E9W  plan-1  C2   0.020
 E9W  plan-1  C4   0.020
 E9W  plan-1  C5   0.020
 E9W  plan-1  C6   0.020
 E9W  plan-1  N9   0.020
 E9W  plan-1  C8   0.020
 E9W  plan-1  CAK  0.020
 E9W  plan-1  N1   0.020
 E9W  plan-1  N3   0.020
 E9W  plan-1  N6   0.020
 E9W  plan-1  N7   0.020
 E9W  plan-1  SAH  0.020
 E9W  plan-1  H1   0.020
 E9W  plan-2  C6   0.020
 E9W  plan-2  N6   0.020
 E9W  plan-2  H13  0.020
 E9W  plan-2  H14  0.020
 E9W  plan-3  CAC  0.020
 E9W  plan-3  CAE  0.020
 E9W  plan-3  CAG  0.020
 E9W  plan-3  NAD  0.020
 E9W  plan-3  OAF  0.020
 E9W  plan-3  H15  0.020
 E9W  plan-4  CAN  0.020
 E9W  plan-4  NAO  0.020
 E9W  plan-4  NAP  0.020
 E9W  plan-4  NAQ  0.020
 E9W  plan-4  H16  0.020

