# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:35:14 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)-~{N}-prop-2-ynyl-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)NCC#C
#
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
 DKW  DKW  (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)-~{N}-prop-2-ynyl-oxolane-2-carboxamide  ligand  37  23  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DKW
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
 DKW  N3   N  N     0  -0.459   3.2591   1.3476   0.1621
 DKW  C4   C  CR56  0   0.485   2.5858   0.1984   0.1533
 DKW  C5   C  CR56  0  -0.001   3.0559  -1.0346  -0.2686
 DKW  C6   C  CR6   0   0.455   4.3838  -1.0651  -0.7341
 DKW  C8   C  CR15  0   0.089   1.0640  -1.3591   0.3601
 DKW  C2   C  CR16  0   0.039   4.4895   1.1925  -0.2955
 DKW  N1   N  N     0  -0.474   5.0749   0.0803  -0.7322
 DKW  CAK  C  CR15  0   0.172   0.4182   0.9986   1.0984
 DKW  CAM  C  CR15  0  -0.064  -1.8665   0.6471   0.9478
 DKW  CAN  C  CR15  0  -0.040  -1.3983   1.2101  -0.4015
 DKW  CAP  C  CR15  0  -0.043  -0.1101   1.9318   0.0109
 DKW  CAR  C  C     0   0.538  -2.6797  -0.6277   0.7841
 DKW  CAU  C  CH2   0  -0.387  -4.8426  -1.5010   0.0688
 DKW  CAV  C  CSP   0   0.232  -5.9085  -1.0641  -0.8227
 DKW  CAW  C  CSP1  0  -0.499  -6.7890  -0.7014  -1.5541
 DKW  N6   N  NH2   0  -0.816   4.9659  -2.1786  -1.1832
 DKW  N7   N  N     0  -0.453   2.0890  -1.9950  -0.1305
 DKW  N9   N  NR5   0  -0.540   1.3006  -0.0241   0.5515
 DKW  NAT  N  NH1   0  -0.636  -3.9244  -0.4124   0.3376
 DKW  OAL  O  O     0  -0.484  -0.6941   0.3877   1.6847
 DKW  OAO  O  OH1   0  -0.652  -2.3766   2.0545  -0.9311
 DKW  OAQ  O  OH1   0  -0.661  -0.3966   3.1596   0.6170
 DKW  OAS  O  O     0  -0.475  -2.2256  -1.7378   1.0038
 DKW  H1   H  HCR5  0   0.305   0.1144  -1.8084   0.6078
 DKW  H2   H  HCR6  0   0.252   5.1066   2.0843  -0.3214
 DKW  H3   H  HCR5  0   0.290   0.9857   1.5478   1.8543
 DKW  H4   H  HCR5  0   0.281  -2.4745   1.4007   1.4644
 DKW  H5   H  HCR5  0   0.267  -1.1562   0.3929  -1.0917
 DKW  H6   H  HCR5  0   0.269   0.5978   2.0344  -0.8197
 DKW  H7   H  HCH2  0   0.286  -5.2778  -1.8848   0.9962
 DKW  H8   H  HCH2  0   0.288  -4.3002  -2.3289  -0.3913
 DKW  H9   H  H     0   0.283  -7.5717  -0.3821  -2.2036
 DKW  H10  H  HNH2  0   0.411   4.4994  -3.0665  -1.1219
 DKW  H11  H  HNH2  0   0.403   5.9358  -2.1697  -1.4479
 DKW  H12  H  HNH1  0   0.412  -4.2572   0.5324   0.2244
 DKW  H13  H  HOH1  0   0.474  -2.2923   2.0734  -1.8896
 DKW  H14  H  HOH1  0   0.455  -1.0844   3.5954   0.0989

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
 DKW  CAW  CAV  triple    1.201  0.020  1.201
 DKW  CAV  CAU  single    1.457  0.020  1.457
 DKW  N6   C6   single    1.334  0.020  1.334
 DKW  N7   C5   aromatic  1.370  0.020  1.370
 DKW  N7   C8   aromatic  1.302  0.020  1.302
 DKW  C6   C5   aromatic  1.407  0.020  1.407
 DKW  C6   N1   aromatic  1.338  0.020  1.338
 DKW  OAS  CAR  double    1.219  0.020  1.219
 DKW  C5   C4   aromatic  1.385  0.020  1.385
 DKW  C8   N9   aromatic  1.369  0.020  1.369
 DKW  CAU  NAT  single    1.449  0.020  1.449
 DKW  OAL  CAM  single    1.409  0.020  1.409
 DKW  OAL  CAK  single    1.398  0.020  1.398
 DKW  NAT  CAR  single    1.340  0.020  1.340
 DKW  CAR  CAM  single    1.521  0.020  1.521
 DKW  N1   C2   aromatic  1.331  0.020  1.331
 DKW  CAM  CAN  single    1.535  0.020  1.535
 DKW  C4   N9   aromatic  1.364  0.020  1.364
 DKW  C4   N3   aromatic  1.332  0.020  1.332
 DKW  N9   CAK  single    1.457  0.020  1.457
 DKW  C2   N3   aromatic  1.322  0.020  1.322
 DKW  CAK  CAP  single    1.527  0.020  1.527
 DKW  CAN  CAP  single    1.533  0.020  1.533
 DKW  CAN  OAO  single    1.397  0.020  1.397
 DKW  CAP  OAQ  single    1.399  0.020  1.399
 DKW  C8   H1   single    0.929  0.020  1.085
 DKW  C2   H2   single    0.929  0.020  1.085
 DKW  CAK  H3   single    0.939  0.020  1.096
 DKW  CAM  H4   single    0.939  0.020  1.096
 DKW  CAN  H5   single    0.939  0.020  1.096
 DKW  CAP  H6   single    0.939  0.020  1.096
 DKW  CAU  H7   single    0.939  0.020  1.096
 DKW  CAU  H8   single    0.939  0.020  1.096
 DKW  CAW  H9   single    0.913  0.020  1.066
 DKW  N6   H10  single    0.868  0.020  1.013
 DKW  N6   H11  single    0.868  0.020  1.013
 DKW  NAT  H12  single    0.868  0.020  1.013
 DKW  OAO  H13  single    0.832  0.020  0.971
 DKW  OAQ  H14  single    0.832  0.020  0.971

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
 DKW  C2   N3   C4   111.54  3.000
 DKW  N9   C4   C5   105.28  3.000
 DKW  N9   C4   N3   127.97  3.000
 DKW  C5   C4   N3   126.75  3.000
 DKW  N7   C5   C6   133.16  3.000
 DKW  C6   C5   C4   116.12  3.000
 DKW  N7   C5   C4   110.72  3.000
 DKW  N6   C6   N1   119.32  3.000
 DKW  N1   C6   C5   117.93  3.000
 DKW  N6   C6   C5   122.75  3.000
 DKW  H1   C8   N9   121.72  3.000
 DKW  H1   C8   N7   125.15  3.000
 DKW  N9   C8   N7   113.12  3.000
 DKW  H2   C2   N1   115.41  3.000
 DKW  H2   C2   N3   116.19  3.000
 DKW  N1   C2   N3   128.40  3.000
 DKW  C2   N1   C6   119.27  3.000
 DKW  H3   CAK  OAL  110.03  3.000
 DKW  H3   CAK  N9   107.32  3.000
 DKW  OAL  CAK  N9   109.42  3.000
 DKW  H3   CAK  CAP  111.40  3.000
 DKW  N9   CAK  CAP  111.78  3.000
 DKW  OAL  CAK  CAP  106.88  3.000
 DKW  H4   CAM  OAL  109.95  3.000
 DKW  H4   CAM  CAR  109.27  3.000
 DKW  OAL  CAM  CAR  110.30  3.000
 DKW  H4   CAM  CAN  109.32  3.000
 DKW  CAR  CAM  CAN  112.08  3.000
 DKW  OAL  CAM  CAN  105.87  3.000
 DKW  H5   CAN  OAO  111.50  3.000
 DKW  H5   CAN  CAP  109.54  3.000
 DKW  OAO  CAN  CAP  113.95  3.000
 DKW  H5   CAN  CAM  110.31  3.000
 DKW  OAO  CAN  CAM  109.97  3.000
 DKW  CAP  CAN  CAM  101.10  3.000
 DKW  H6   CAP  OAQ  112.23  3.000
 DKW  H6   CAP  CAN  112.51  3.000
 DKW  OAQ  CAP  CAN  110.95  3.000
 DKW  H6   CAP  CAK  111.92  3.000
 DKW  OAQ  CAP  CAK  107.38  3.000
 DKW  CAN  CAP  CAK  101.22  3.000
 DKW  OAS  CAR  NAT  123.53  3.000
 DKW  NAT  CAR  CAM  113.45  3.000
 DKW  OAS  CAR  CAM  122.99  3.000
 DKW  H8   CAU  H7   106.79  3.000
 DKW  H8   CAU  NAT  109.46  3.000
 DKW  H7   CAU  NAT  111.00  3.000
 DKW  H8   CAU  CAV  109.46  3.000
 DKW  H7   CAU  CAV  109.44  3.000
 DKW  NAT  CAU  CAV  110.60  3.000
 DKW  CAW  CAV  CAU  180.00  3.000
 DKW  H9   CAW  CAV  180.00  3.000
 DKW  H11  N6   H10  118.15  3.000
 DKW  H11  N6   C6   120.14  3.000
 DKW  H10  N6   C6   120.95  3.000
 DKW  C8   N7   C5   104.55  3.000
 DKW  CAK  N9   C8   129.20  3.000
 DKW  CAK  N9   C4   124.45  3.000
 DKW  C8   N9   C4   106.33  3.000
 DKW  H12  NAT  CAU  118.30  3.000
 DKW  H12  NAT  CAR  119.65  3.000
 DKW  CAU  NAT  CAR  121.98  3.000
 DKW  CAM  OAL  CAK  111.24  3.000
 DKW  H13  OAO  CAN  109.17  3.000
 DKW  H14  OAQ  CAP  108.04  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
 DKW  CONST_01  N7   C5   C4   N3    180.00   0.0  0
 DKW  CONST_02  C6   C5   C4   N3      0.00   0.0  0
 DKW  CONST_03  C8   N9   C4   N3    180.00   0.0  0
 DKW  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 DKW  CONST_05  C8   N7   C5   C4      0.00   0.0  0
 DKW  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 DKW  CONST_07  N7   C8   N9   C4      0.00   0.0  0
 DKW  CONST_08  N1   C2   N3   C4      0.00   0.0  0
 DKW  CONST_09  N9   C8   N7   C5      0.00   0.0  0
 DKW  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 DKW  CONST_11  C8   N9   C4   C5      0.00   0.0  0
 DKW  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 DKW  CONST_13  C8   N7   C5   C6    180.00   0.0  0
 DKW  CONST_14  N9   C4   C5   C6    180.00   0.0  0
 DKW  CONST_15  N9   C4   N3   C2    180.00   0.0  0
 DKW  CONST_16  N7   C5   C6   N1    180.00   0.0  0
 DKW  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 DKW  CONST_18  CAK  N9   C4   N3      0.00   0.0  0
 DKW  CONST_19  CAK  N9   C4   C5    180.00   0.0  0
 DKW  CONST_20  N7   C8   N9   CAK   180.00   0.0  0
 DKW  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 DKW  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 DKW  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 DKW  CONST_24  H1   C8   N9   C4    180.00   0.0  0
 DKW  CONST_25  H2   C2   N3   C4    180.00   0.0  0
 DKW  CONST_26  H10  N6   C6   C5      0.00   0.0  0
 DKW  CONST_27  H11  N6   C6   C5    180.00   0.0  0
 DKW  CONST_28  CAU  NAT  CAR  CAM   180.00   0.0  0
 DKW  CONST_29  H12  NAT  CAR  CAM     0.00   0.0  0
 DKW  CONST_30  OAS  CAR  NAT  CAU     0.00   0.0  0
 DKW  Var_01    CAV  CAU  NAT  CAR  -159.91  30.0  1
 DKW  Var_02    NAT  CAU  CAV  CAW   -71.19  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
 DKW  chir_01  CAK  OAL  N9   CAP  negativ
 DKW  chir_02  CAM  OAL  CAR  CAN  positiv
 DKW  chir_03  CAN  OAO  CAM  CAP  positiv
 DKW  chir_04  CAP  OAQ  CAN  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
 DKW  plan-1  N3   0.020
 DKW  plan-1  C4   0.020
 DKW  plan-1  C5   0.020
 DKW  plan-1  C6   0.020
 DKW  plan-1  C8   0.020
 DKW  plan-1  C2   0.020
 DKW  plan-1  N1   0.020
 DKW  plan-1  CAK  0.020
 DKW  plan-1  N6   0.020
 DKW  plan-1  N7   0.020
 DKW  plan-1  N9   0.020
 DKW  plan-1  H1   0.020
 DKW  plan-1  H2   0.020
 DKW  plan-2  C6   0.020
 DKW  plan-2  N6   0.020
 DKW  plan-2  H10  0.020
 DKW  plan-2  H11  0.020
 DKW  plan-3  CAM  0.020
 DKW  plan-3  CAR  0.020
 DKW  plan-3  CAU  0.020
 DKW  plan-3  NAT  0.020
 DKW  plan-3  OAS  0.020
 DKW  plan-3  H12  0.020

