# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 22:02:57 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)C(F)(F)[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 ATF  ATF  5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine  ligand  49  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_ATF
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
 ATF  PG    P  P     0   1.315  24.4641  32.2104  14.0885
 ATF  O1G   O  O     0  -0.667  24.2145  31.4118  12.8767
 ATF  O2G   O  OH1   0  -0.737  25.9704  32.1036  14.5812
 ATF  O3G   O  OH1   0  -0.737  24.0122  33.7359  14.1090
 ATF  PB    P  P     0   1.349  23.8010  32.6833  17.0961
 ATF  O1B   O  O     0  -0.667  25.1798  33.2110  17.0887
 ATF  O2B   O  OH1   0  -0.696  22.7003  33.8048  17.1740
 ATF  C3B   C  CT    0   0.266  23.4603  31.6780  15.5616
 ATF  F1B   F  F     0  -0.319  23.7623  30.3818  15.8183
 ATF  F2B   F  F     0  -0.320  22.1433  31.7417  15.2562
 ATF  PA    P  P     0   1.498  24.3665  30.5269  18.9877
 ATF  O1A   O  O     0  -0.665  25.5903  30.2533  18.2264
 ATF  O2A   O  OH1   0  -0.702  23.4076  29.2885  19.1338
 ATF  O3A   O  O2    0  -0.694  23.4262  31.6824  18.3013
 ATF  O5'   O  O2    0  -0.579  24.5196  31.0500  20.4750
 ATF  C5'   C  CH2   0  -0.229  25.2130  32.2652  20.8096
 ATF  C4'   C  CH1   0   0.012  26.4494  31.9866  21.6332
 ATF  O4'   O  O2    0  -0.490  26.0900  31.2843  22.8212
 ATF  C3'   C  CH1   0  -0.052  27.5406  31.1606  20.9467
 ATF  O3'   O  OH1   0  -0.666  28.7826  31.6632  21.3706
 ATF  C2'   C  CH1   0  -0.025  27.2889  29.7649  21.5102
 ATF  O2'   O  OH1   0  -0.656  28.4375  28.9768  21.4587
 ATF  C1'   C  CH1   0   0.196  26.8363  30.1035  22.9356
 ATF  N9    N  NR5   0  -0.546  26.0253  29.0913  23.5558
 ATF  C8    C  CR15  0   0.118  24.8083  28.6217  23.1342
 ATF  N7    N  N     0  -0.447  24.3101  27.7096  23.9125
 ATF  C5    C  CR56  0  -0.010  25.2425  27.5620  24.9075
 ATF  C6    C  CR6   0   0.461  25.3012  26.7414  26.0493
 ATF  N6    N  NH2   0  -0.816  24.3425  25.8690  26.3606
 ATF  N1    N  N     0  -0.474  26.3730  26.8497  26.8428
 ATF  C2    C  CR16  0   0.047  27.3297  27.7173  26.5246
 ATF  N3    N  N     0  -0.457  27.3877  28.5336  25.4866
 ATF  C4    C  CR56  0   0.490  26.3151  28.4157  24.7086
 ATF  HOG2  H  HOH1  0   0.499  26.1681  32.5995  15.3966
 ATF  HOG3  H  HOH1  0   0.514  24.3796  34.3054  13.4166
 ATF  HOB2  H  HOH1  0   0.518  21.7751  33.5512  17.3072
 ATF  HOA2  H  HOH1  0   0.515  22.5693  29.4124  19.6022
 ATF  H5'1  H  HCH2  0   0.254  25.5029  32.8318  19.9210
 ATF  H5'2  H  HCH2  0   0.286  24.5114  32.8749  21.3779
 ATF  H4'   H  HCH1  0   0.275  26.8577  32.9689  21.8964
 ATF  H3'   H  HCH1  0   0.258  27.4499  31.1829  19.8548
 ATF  HO3'  H  HOH1  0   0.456  29.4719  31.0578  21.0762
 ATF  H2'   H  HCH1  0   0.243  26.4604  29.3022  20.9613
 ATF  HO2'  H  HOH1  0   0.470  28.1892  28.0483  21.4742
 ATF  H1'   H  HCH1  0   0.262  27.7109  30.2322  23.5824
 ATF  H8    H  HCR5  0   0.282  24.3298  28.9995  22.2437
 ATF  HN61  H  HNH2  0   0.404  24.4015  25.3302  27.2074
 ATF  HN62  H  HNH2  0   0.412  23.5118  25.7883  25.8012
 ATF  H2    H  HCR6  0   0.253  28.1700  27.7552  27.2094

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
 ATF  PG   O1G   double    1.473  0.020  1.473
 ATF  PG   O2G   single    1.588  0.020  1.588
 ATF  PG   O3G   single    1.591  0.020  1.591
 ATF  PG   C3B   single    1.860  0.020  1.860
 ATF  O2G  HOG2  single    0.850  0.020  0.980
 ATF  O3G  HOG3  single    0.850  0.020  0.980
 ATF  PB   O1B   double    1.476  0.020  1.476
 ATF  PB   O2B   single    1.573  0.020  1.573
 ATF  PB   C3B   single    1.866  0.020  1.866
 ATF  PB   O3A   single    1.611  0.020  1.611
 ATF  O2B  HOB2  single    0.850  0.020  0.980
 ATF  C3B  F1B   single    1.355  0.020  1.355
 ATF  C3B  F2B   single    1.353  0.020  1.353
 ATF  PA   O1A   double    1.467  0.020  1.467
 ATF  PA   O2A   single    1.573  0.020  1.573
 ATF  PA   O3A   single    1.640  0.020  1.640
 ATF  PA   O5'   single    1.584  0.020  1.584
 ATF  O2A  HOA2  single    0.850  0.020  0.980
 ATF  O5'  C5'   single    1.439  0.020  1.439
 ATF  C5'  C4'   single    1.511  0.020  1.511
 ATF  C5'  H5'1  single    0.970  0.020  1.090
 ATF  C5'  H5'2  single    0.970  0.020  1.090
 ATF  C4'  O4'   single    1.426  0.020  1.426
 ATF  C4'  C3'   single    1.531  0.020  1.531
 ATF  C4'  H4'   single    0.970  0.020  1.090
 ATF  O4'  C1'   single    1.402  0.020  1.402
 ATF  C3'  O3'   single    1.405  0.020  1.405
 ATF  C3'  C2'   single    1.526  0.020  1.526
 ATF  C3'  H3'   single    0.970  0.020  1.090
 ATF  O3'  HO3'  single    0.850  0.020  0.980
 ATF  C2'  O2'   single    1.394  0.020  1.394
 ATF  C2'  C1'   single    1.533  0.020  1.533
 ATF  C2'  H2'   single    0.970  0.020  1.090
 ATF  O2'  HO2'  single    0.850  0.020  0.980
 ATF  C1'  N9    single    1.438  0.020  1.438
 ATF  C1'  H1'   single    0.970  0.020  1.090
 ATF  N9   C8    aromatic  1.371  0.020  1.371
 ATF  N9   C4    aromatic  1.367  0.020  1.367
 ATF  C8   N7    aromatic  1.298  0.020  1.298
 ATF  C8   H8    single    0.930  0.020  1.080
 ATF  N7   C5    aromatic  1.372  0.020  1.372
 ATF  C5   C6    aromatic  1.407  0.020  1.407
 ATF  C5   C4    aromatic  1.385  0.020  1.385
 ATF  C6   N6    single    1.333  0.020  1.333
 ATF  C6   N1    aromatic  1.338  0.020  1.338
 ATF  N6   HN61  single    0.860  0.020  1.020
 ATF  N6   HN62  single    0.860  0.020  1.020
 ATF  N1   C2    aromatic  1.330  0.020  1.330
 ATF  C2   N3    aromatic  1.322  0.020  1.322
 ATF  C2   H2    single    0.930  0.020  1.080
 ATF  N3   C4    aromatic  1.330  0.020  1.330

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
 ATF  C3B   PG   O3G    96.37  3.000
 ATF  C3B   PG   O2G   104.29  3.000
 ATF  O3G   PG   O2G   109.25  3.000
 ATF  C3B   PG   O1G   113.89  3.000
 ATF  O3G   PG   O1G   118.84  3.000
 ATF  O2G   PG   O1G   112.31  3.000
 ATF  HOG2  O2G  PG    114.69  3.000
 ATF  HOG3  O3G  PG    116.53  3.000
 ATF  O3A   PB   C3B   103.77  3.000
 ATF  O3A   PB   O2B   104.07  3.000
 ATF  C3B   PB   O2B   107.28  3.000
 ATF  O3A   PB   O1B   116.30  3.000
 ATF  C3B   PB   O1B   111.04  3.000
 ATF  O2B   PB   O1B   113.51  3.000
 ATF  HOB2  O2B  PB    119.24  3.000
 ATF  F2B   C3B  F1B   107.73  3.000
 ATF  F2B   C3B  PB    109.75  3.000
 ATF  F1B   C3B  PB    108.59  3.000
 ATF  F2B   C3B  PG    109.44  3.000
 ATF  F1B   C3B  PG    107.66  3.000
 ATF  PB    C3B  PG    113.48  3.000
 ATF  O5'   PA   O3A   102.46  3.000
 ATF  O5'   PA   O2A   103.40  3.000
 ATF  O3A   PA   O2A   104.13  3.000
 ATF  O5'   PA   O1A   117.91  3.000
 ATF  O3A   PA   O1A   113.11  3.000
 ATF  O2A   PA   O1A   114.20  3.000
 ATF  HOA2  O2A  PA    118.16  3.000
 ATF  PA    O3A  PB    128.13  3.000
 ATF  C5'   O5'  PA    122.95  3.000
 ATF  H5'2  C5'  H5'1  107.75  3.000
 ATF  H5'2  C5'  C4'   110.22  3.000
 ATF  H5'1  C5'  C4'   108.76  3.000
 ATF  H5'2  C5'  O5'   106.48  3.000
 ATF  H5'1  C5'  O5'   112.12  3.000
 ATF  C4'   C5'  O5'   111.43  3.000
 ATF  H4'   C4'  C3'   109.01  3.000
 ATF  H4'   C4'  O4'   109.59  3.000
 ATF  C3'   C4'  O4'   106.70  3.000
 ATF  H4'   C4'  C5'   105.69  3.000
 ATF  C3'   C4'  C5'   115.98  3.000
 ATF  O4'   C4'  C5'   109.79  3.000
 ATF  C1'   O4'  C4'   110.41  3.000
 ATF  H3'   C3'  C2'   111.89  3.000
 ATF  H3'   C3'  O3'   111.49  3.000
 ATF  C2'   C3'  O3'   111.19  3.000
 ATF  H3'   C3'  C4'   112.13  3.000
 ATF  C2'   C3'  C4'   102.14  3.000
 ATF  O3'   C3'  C4'   107.56  3.000
 ATF  HO3'  O3'  C3'   108.39  3.000
 ATF  H2'   C2'  C1'   109.60  3.000
 ATF  H2'   C2'  O2'   111.44  3.000
 ATF  C1'   C2'  O2'   113.73  3.000
 ATF  H2'   C2'  C3'   109.02  3.000
 ATF  C1'   C2'  C3'   100.95  3.000
 ATF  O2'   C2'  C3'   111.57  3.000
 ATF  HO2'  O2'  C2'   109.43  3.000
 ATF  H1'   C1'  N9    106.16  3.000
 ATF  H1'   C1'  C2'   109.83  3.000
 ATF  N9    C1'  C2'   114.34  3.000
 ATF  H1'   C1'  O4'   111.98  3.000
 ATF  N9    C1'  O4'   109.15  3.000
 ATF  C2'   C1'  O4'   105.50  3.000
 ATF  C4    N9   C8    106.15  3.000
 ATF  C4    N9   C1'   126.31  3.000
 ATF  C8    N9   C1'   127.53  3.000
 ATF  H8    C8   N7    124.78  3.000
 ATF  H8    C8   N9    121.84  3.000
 ATF  N7    C8   N9    113.38  3.000
 ATF  C5    N7   C8    104.46  3.000
 ATF  C4    C5   C6    116.33  3.000
 ATF  C4    C5   N7    110.84  3.000
 ATF  C6    C5   N7    132.82  3.000
 ATF  N1    C6   N6    119.38  3.000
 ATF  N1    C6   C5    117.86  3.000
 ATF  N6    C6   C5    122.76  3.000
 ATF  HN62  N6   HN61  118.31  3.000
 ATF  HN62  N6   C6    121.14  3.000
 ATF  HN61  N6   C6    120.35  3.000
 ATF  C2    N1   C6    119.15  3.000
 ATF  H2    C2   N3    116.11  3.000
 ATF  H2    C2   N1    115.41  3.000
 ATF  N3    C2   N1    128.48  3.000
 ATF  C4    N3   C2    111.66  3.000
 ATF  N3    C4   C5    126.51  3.000
 ATF  N3    C4   N9    128.33  3.000
 ATF  C5    C4   N9    105.16  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
 ATF  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 ATF  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 ATF  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 ATF  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 ATF  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 ATF  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 ATF  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 ATF  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 ATF  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 ATF  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 ATF  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 ATF  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 ATF  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 ATF  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 ATF  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 ATF  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 ATF  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 ATF  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 ATF  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 ATF  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 ATF  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 ATF  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 ATF  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 ATF  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 ATF  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 ATF  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 ATF  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 ATF  Var_01    C4'   C5'  O5'  PA   -115.08  30.0  3
 ATF  Var_02    O1B   PB   C3B  PG    -28.37  30.0  2
 ATF  Var_03    PB    C3B  PG   O1G   179.28  30.0  3
 ATF  Var_04    O1A   PA   O3A  PB    -11.58  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
 ATF  chir_03  C4'  C5'  O4'  C3'  negativ
 ATF  chir_04  C3'  O3'  C4'  C2'  positiv
 ATF  chir_05  C2'  O2'  C3'  C1'  positiv
 ATF  chir_06  C1'  O4'  N9   C2'  negativ
 ATF  chir_07  PB   O2B  C3B  O3A  both
 ATF  chir_08  PA   O2A  O3A  O5'  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
 ATF  plan-1  C1'   0.020
 ATF  plan-1  N9    0.020
 ATF  plan-1  C8    0.020
 ATF  plan-1  N7    0.020
 ATF  plan-1  C5    0.020
 ATF  plan-1  C6    0.020
 ATF  plan-1  N6    0.020
 ATF  plan-1  N1    0.020
 ATF  plan-1  C2    0.020
 ATF  plan-1  N3    0.020
 ATF  plan-1  C4    0.020
 ATF  plan-1  H8    0.020
 ATF  plan-1  H2    0.020
 ATF  plan-2  C6    0.020
 ATF  plan-2  N6    0.020
 ATF  plan-2  HN61  0.020
 ATF  plan-2  HN62  0.020

