# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 06:45:31 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(F)nc2n(cnc12)[C@H]3C[C@H](O)[C@@](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)(O3)C#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
 6FN  6FN  '2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogen triphosphate)'  ligand  48  33  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6FN
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
 6FN  C4   C  CR56  0   0.498  -40.7971  -2.9442  -27.8024
 6FN  N3   N  N     0  -0.491  -39.4757  -3.1317  -27.7354
 6FN  C2   C  CR6   0   0.573  -38.9914  -3.3714  -28.9222
 6FN  F32  F  F     0  -0.287  -37.6763  -3.5724  -28.9584
 6FN  N1   N  N     0  -0.504  -39.5756  -3.4477  -30.0947
 6FN  C6   C  CR6   0   0.475  -40.9011  -3.2568  -30.1514
 6FN  N6   N  NH2   0  -0.807  -41.5147  -3.3281  -31.3266
 6FN  C5   C  CR56  0  -0.007  -41.5768  -2.9843  -28.9458
 6FN  N7   N  N     0  -0.446  -42.8901  -2.7420  -28.6434
 6FN  C8   C  CR15  0   0.104  -42.8994  -2.5584  -27.3565
 6FN  N9   N  NR5   0  -0.528  -41.6572  -2.6728  -26.7856
 6FN  C1'  C  CH1   0   0.179  -41.2704  -2.5027  -25.3927
 6FN  C2'  C  CH2   0  -0.539  -40.8960  -1.0641  -25.0417
 6FN  C3'  C  CH1   0   0.019  -42.1853  -0.5203  -24.4504
 6FN  O3'  O  OH1   0  -0.672  -41.9877   0.5777  -23.6277
 6FN  C4'  C  CT    0  -0.017  -42.7054  -1.7835  -23.7168
 6FN  C33  C  CSP   0   0.383  -42.0188  -1.9576  -22.4319
 6FN  C34  C  CSP1  0  -0.553  -41.4723  -2.1248  -21.3761
 6FN  O4'  O  O2    0  -0.483  -42.3758  -2.8481  -24.5929
 6FN  C5'  C  CH2   0  -0.183  -44.2011  -1.8045  -23.4359
 6FN  O5'  O  O2    0  -0.592  -44.8880  -1.5729  -24.6634
 6FN  PA   P  P     0   1.523  -46.4437  -1.3170  -24.8432
 6FN  O3A  O  O2    0  -0.696  -46.6388   0.2816  -24.6338
 6FN  PB   P  P     0   1.532  -45.9726   1.4199  -23.7305
 6FN  O3B  O  O2    0  -0.670  -46.8133   2.7015  -24.1717
 6FN  PG   P  P     0   1.468  -48.3484   2.8736  -24.7097
 6FN  O3G  O  O     0  -0.672  -48.5594   2.3674  -26.0719
 6FN  O2G  O  OH1   0  -0.711  -48.5713   4.4203  -24.4563
 6FN  O1G  O  OH1   0  -0.728  -49.1366   2.1952  -23.5167
 6FN  O2B  O  OH1   0  -0.713  -46.4599   0.9932  -22.2917
 6FN  O1B  O  O     0  -0.662  -44.5293   1.6458  -23.9110
 6FN  O2A  O  O     0  -0.650  -46.9259  -1.7345  -26.1621
 6FN  O1A  O  OH1   0  -0.724  -47.1709  -1.8426  -23.5394
 6FN  H1   H  HNH2  0   0.411  -40.9950  -3.5315  -32.1632
 6FN  H2   H  HNH2  0   0.418  -42.5094  -3.2031  -31.4013
 6FN  H3   H  HCR5  0   0.293  -43.7807  -2.3509  -26.7714
 6FN  H4   H  HCH1  0   0.285  -40.4438  -3.1943  -25.2185
 6FN  H5   H  HCH2  0   0.276  -40.1028  -1.0605  -24.2912
 6FN  H6   H  HCH2  0   0.290  -40.5443  -0.5046  -25.9074
 6FN  H7   H  HCH1  0   0.250  -42.8856  -0.2893  -25.2627
 6FN  H8   H  HOH1  0   0.463  -42.8317   1.0550  -23.5733
 6FN  H9   H  H     0   0.287  -40.9795  -2.2719  -20.4419
 6FN  H10  H  HCH2  0   0.256  -44.4242  -1.0357  -22.6935
 6FN  H11  H  HCH2  0   0.291  -44.4911  -2.7715  -23.0217
 6FN  H12  H  HOH1  0   0.512  -48.3282   4.9904  -25.1995
 6FN  H13  H  HOH1  0   0.514  -49.9914   1.8145  -23.7624
 6FN  H14  H  HOH1  0   0.517  -46.0079   1.4308  -21.5551
 6FN  H15  H  HOH1  0   0.516  -47.4230  -2.7775  -23.5572

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
 6FN  N6   C6   single    1.328  0.020  1.328
 6FN  N1   C6   aromatic  1.340  0.020  1.340
 6FN  N1   C2   aromatic  1.312  0.020  1.312
 6FN  C6   C5   aromatic  1.409  0.020  1.409
 6FN  F32  C2   single    1.331  0.020  1.331
 6FN  C2   N3   aromatic  1.304  0.020  1.304
 6FN  C5   N7   aromatic  1.369  0.020  1.369
 6FN  C5   C4   aromatic  1.385  0.020  1.385
 6FN  N7   C8   aromatic  1.300  0.020  1.300
 6FN  N3   C4   aromatic  1.336  0.020  1.336
 6FN  C4   N9   aromatic  1.359  0.020  1.359
 6FN  C8   N9   aromatic  1.372  0.020  1.372
 6FN  N9   C1'  single    1.456  0.020  1.456
 6FN  O2A  PA   double    1.465  0.020  1.465
 6FN  O3G  PG   double    1.468  0.020  1.468
 6FN  O3A  PA   single    1.624  0.020  1.624
 6FN  O3A  PB   single    1.598  0.020  1.598
 6FN  C1'  C2'  single    1.527  0.020  1.527
 6FN  C1'  O4'  single    1.407  0.020  1.407
 6FN  C2'  C3'  single    1.519  0.020  1.519
 6FN  PA   O5'  single    1.587  0.020  1.587
 6FN  PA   O1A  single    1.583  0.020  1.583
 6FN  O5'  C5'  single    1.426  0.020  1.426
 6FN  O3B  PG   single    1.636  0.020  1.636
 6FN  O3B  PB   single    1.595  0.020  1.595
 6FN  O4'  C4'  single    1.418  0.020  1.418
 6FN  PG   O1G  single    1.583  0.020  1.583
 6FN  PG   O2G  single    1.583  0.020  1.583
 6FN  C3'  C4'  single    1.551  0.020  1.551
 6FN  C3'  O3'  single    1.386  0.020  1.386
 6FN  PB   O1B  double    1.472  0.020  1.472
 6FN  PB   O2B  single    1.578  0.020  1.578
 6FN  C4'  C5'  single    1.522  0.020  1.522
 6FN  C4'  C33  single    1.467  0.020  1.467
 6FN  C33  C34  triple    1.201  0.020  1.201
 6FN  N6   H1   single    0.868  0.020  1.013
 6FN  N6   H2   single    0.868  0.020  1.013
 6FN  C8   H3   single    0.929  0.020  1.085
 6FN  C1'  H4   single    0.939  0.020  1.096
 6FN  C2'  H5   single    0.939  0.020  1.096
 6FN  C2'  H6   single    0.939  0.020  1.096
 6FN  C3'  H7   single    0.939  0.020  1.096
 6FN  O3'  H8   single    0.832  0.020  0.971
 6FN  C34  H9   single    0.913  0.020  1.066
 6FN  C5'  H10  single    0.939  0.020  1.096
 6FN  C5'  H11  single    0.939  0.020  1.096
 6FN  O2G  H12  single    0.832  0.020  0.971
 6FN  O1G  H13  single    0.832  0.020  0.971
 6FN  O2B  H14  single    0.832  0.020  0.971
 6FN  O1A  H15  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
 6FN  N9   C4   C5   105.50  3.000
 6FN  N9   C4   N3   128.05  3.000
 6FN  C5   C4   N3   126.46  3.000
 6FN  C2   N3   C4   110.33  3.000
 6FN  N1   C2   F32  114.00  3.000
 6FN  F32  C2   N3   114.80  3.000
 6FN  N1   C2   N3   131.20  3.000
 6FN  C6   N1   C2   118.02  3.000
 6FN  C5   C6   N6   123.11  3.000
 6FN  C5   C6   N1   117.76  3.000
 6FN  N6   C6   N1   119.13  3.000
 6FN  H2   N6   H1   118.34  3.000
 6FN  H2   N6   C6   121.09  3.000
 6FN  H1   N6   C6   120.55  3.000
 6FN  N7   C5   C6   133.11  3.000
 6FN  N7   C5   C4   110.65  3.000
 6FN  C6   C5   C4   116.25  3.000
 6FN  C8   N7   C5   104.51  3.000
 6FN  H3   C8   N9   122.04  3.000
 6FN  H3   C8   N7   124.77  3.000
 6FN  N9   C8   N7   113.18  3.000
 6FN  C1'  N9   C8   128.98  3.000
 6FN  C1'  N9   C4   124.82  3.000
 6FN  C8   N9   C4   106.17  3.000
 6FN  H4   C1'  O4'  110.39  3.000
 6FN  H4   C1'  C2'  111.99  3.000
 6FN  O4'  C1'  C2'  107.04  3.000
 6FN  H4   C1'  N9   106.25  3.000
 6FN  O4'  C1'  N9   107.84  3.000
 6FN  C2'  C1'  N9   113.27  3.000
 6FN  H6   C2'  H5   108.07  3.000
 6FN  H6   C2'  C3'  113.55  3.000
 6FN  H5   C2'  C3'  110.35  3.000
 6FN  H6   C2'  C1'  112.36  3.000
 6FN  H5   C2'  C1'  109.82  3.000
 6FN  C3'  C2'  C1'  102.62  3.000
 6FN  H7   C3'  C4'  107.92  3.000
 6FN  H7   C3'  O3'  111.32  3.000
 6FN  C4'  C3'  O3'  114.35  3.000
 6FN  H7   C3'  C2'  109.20  3.000
 6FN  O3'  C3'  C2'  113.18  3.000
 6FN  C4'  C3'  C2'  100.21  3.000
 6FN  H8   O3'  C3'  107.37  3.000
 6FN  C5'  C4'  O4'  109.40  3.000
 6FN  C5'  C4'  C33  107.26  3.000
 6FN  O4'  C4'  C33  110.08  3.000
 6FN  C33  C4'  C3'  110.74  3.000
 6FN  C5'  C4'  C3'  115.35  3.000
 6FN  O4'  C4'  C3'  103.97  3.000
 6FN  C34  C33  C4'  180.00  3.000
 6FN  H9   C34  C33  180.00  3.000
 6FN  C4'  O4'  C1'  110.46  3.000
 6FN  H11  C5'  H10  108.15  3.000
 6FN  H11  C5'  O5'  110.04  3.000
 6FN  H10  C5'  O5'  111.88  3.000
 6FN  H11  C5'  C4'  110.08  3.000
 6FN  H10  C5'  C4'  108.46  3.000
 6FN  O5'  C5'  C4'  108.20  3.000
 6FN  PA   O5'  C5'  126.60  3.000
 6FN  O1A  PA   O2A  119.72  3.000
 6FN  O1A  PA   O3A   99.53  3.000
 6FN  O2A  PA   O3A  110.92  3.000
 6FN  O1A  PA   O5'  107.67  3.000
 6FN  O3A  PA   O5'  105.18  3.000
 6FN  O2A  PA   O5'  112.25  3.000
 6FN  PB   O3A  PA   136.36  3.000
 6FN  O1B  PB   O2B  117.14  3.000
 6FN  O2B  PB   O3B  107.87  3.000
 6FN  O1B  PB   O3B  111.07  3.000
 6FN  O2B  PB   O3A  101.19  3.000
 6FN  O1B  PB   O3A  116.65  3.000
 6FN  O3B  PB   O3A  101.32  3.000
 6FN  PG   O3B  PB   132.08  3.000
 6FN  O1G  PG   O2G  103.18  3.000
 6FN  O2G  PG   O3G  117.71  3.000
 6FN  O1G  PG   O3G  118.68  3.000
 6FN  O2G  PG   O3B  100.50  3.000
 6FN  O1G  PG   O3B  100.04  3.000
 6FN  O3G  PG   O3B  113.81  3.000
 6FN  H12  O2G  PG   114.66  3.000
 6FN  H13  O1G  PG   114.66  3.000
 6FN  H14  O2B  PB   115.29  3.000
 6FN  H15  O1A  PA   115.15  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
 6FN  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 6FN  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 6FN  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 6FN  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 6FN  CONST_05  C6   N1   C2   N3      0.00   0.0  0
 6FN  CONST_06  C6   C5   C4   N3      0.00   0.0  0
 6FN  CONST_07  N7   C5   C4   N3    180.00   0.0  0
 6FN  CONST_08  C8   N9   C4   N3    180.00   0.0  0
 6FN  CONST_09  C5   C6   N1   C2      0.00   0.0  0
 6FN  CONST_10  C5   C4   N3   C2      0.00   0.0  0
 6FN  CONST_11  N9   C4   N3   C2    180.00   0.0  0
 6FN  CONST_12  N7   C5   C6   N1    180.00   0.0  0
 6FN  CONST_13  C8   N7   C5   C6    180.00   0.0  0
 6FN  CONST_14  N9   C4   C5   C6    180.00   0.0  0
 6FN  CONST_15  N9   C8   N7   C5      0.00   0.0  0
 6FN  CONST_16  C8   N9   C4   C5      0.00   0.0  0
 6FN  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 6FN  CONST_18  C1'  N9   C4   N3      0.00   0.0  0
 6FN  CONST_19  C1'  N9   C4   C5    180.00   0.0  0
 6FN  CONST_20  C1'  N9   C8   N7    180.00   0.0  0
 6FN  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 6FN  CONST_22  F32  C2   N3   C4    180.00   0.0  0
 6FN  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 6FN  CONST_24  C6   N1   C2   F32   180.00   0.0  0
 6FN  CONST_25  N7   C5   C6   N6      0.00   0.0  0
 6FN  CONST_26  H3   C8   N9   C4    180.00   0.0  0
 6FN  CONST_27  H1   N6   C6   N1      0.00   0.0  0
 6FN  CONST_28  H2   N6   C6   N1    180.00   0.0  0
 6FN  Var_01    O2A  PA   O5'  C5'  -152.94  30.0  1
 6FN  Var_02    O3B  PB   O3A  PA   -179.16  30.0  3
 6FN  Var_03    O3G  PG   O3B  PB    -71.52  30.0  3
 6FN  Var_04    H10  C5'  O5'  PA    -51.97  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
 6FN  chir_01  C1'  N9   C2'  O4'  negativ
 6FN  chir_02  C3'  O3'  C4'  C2'  positiv
 6FN  chir_03  C4'  C3'  O4'  C33  negativ
 6FN  chir_04  PA   O3A  O5'  O1A  both
 6FN  chir_05  PB   O3B  O1B  O2B  both

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
 6FN  plan-1  C4   0.020
 6FN  plan-1  N3   0.020
 6FN  plan-1  C2   0.020
 6FN  plan-1  F32  0.020
 6FN  plan-1  N1   0.020
 6FN  plan-1  C6   0.020
 6FN  plan-1  N6   0.020
 6FN  plan-1  C5   0.020
 6FN  plan-1  N7   0.020
 6FN  plan-1  C8   0.020
 6FN  plan-1  N9   0.020
 6FN  plan-1  C1'  0.020
 6FN  plan-1  H3   0.020
 6FN  plan-2  C6   0.020
 6FN  plan-2  N6   0.020
 6FN  plan-2  H1   0.020
 6FN  plan-2  H2   0.020

