# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 16:08:32 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)C(F)(F)[P](O)(=O)O[P](O)(O)=O)O3
#
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
 F3A  F3A  2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine  ligand  48  32  .  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_F3A
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
 F3A  N1    N  N     0  -0.474   9.8286   6.9246   8.5380
 F3A  C2    C  CR16  0   0.038   8.6812   6.8634   7.8666
 F3A  N3    N  N     0  -0.459   7.4492   6.9609   8.3345
 F3A  C4    C  CR56  0   0.485   7.4393   7.1467   9.6540
 F3A  C5    C  CR56  0  -0.002   8.5452   7.2325  10.4853
 F3A  C6    C  CR6   0   0.455   9.8012   7.1107   9.8625
 F3A  N6    N  NH2   0  -0.817  10.9504   7.1814  10.5364
 F3A  N7    N  N     0  -0.454   8.1602   7.4268  11.7850
 F3A  C8    C  CR15  0   0.100   6.8587   7.4544  11.7366
 F3A  N9    N  NR5   0  -0.529   6.3604   7.2907  10.4742
 F3A  PA    P  P     0   1.369   4.2593   6.5842  15.3034
 F3A  PB    P  P     0   1.383   3.8583   3.4793  14.9898
 F3A  PG    P  P     0   1.470   4.6311   0.6831  15.0744
 F3A  C1'   C  CH1   0   0.191   4.9685   7.2427  10.0303
 F3A  F1A   F  F     0  -0.325   6.0261   4.8359  14.4495
 F3A  O1A   O  OH1   0  -0.740   2.7708   6.3216  15.8044
 F3A  O1B   O  O     0  -0.657   3.0575   3.6953  13.7691
 F3A  O1G   O  OH1   0  -0.709   5.8505   0.0762  14.2707
 F3A  C2'   C  CH2   0  -0.538   4.4922   5.8153   9.7823
 F3A  F2A   F  F     0  -0.322   5.5529   4.6902  16.5833
 F3A  O2A   O  O     0  -0.651   5.0849   7.5653  16.0263
 F3A  O2B   O  OH1   0  -0.722   3.0800   3.2170  16.3424
 F3A  O2G   O  O     0  -0.681   3.2667   0.3270  14.6592
 F3A  C3'   C  CH1   0   0.011   3.8968   5.4408  11.1300
 F3A  O3'   O  OH1   0  -0.684   2.9923   4.3827  11.0407
 F3A  C3A   C  CT    0   0.256   5.0152   4.8840  15.3555
 F3A  O3B   O  O2    0  -0.695   4.9321   2.2897  14.9601
 F3A  O3G   O  OH1   0  -0.717   5.0600   0.4364  16.5754
 F3A  C4'   C  CH1   0   0.006   3.2501   6.7773  11.5127
 F3A  O4'   O  O2    0  -0.498   4.1594   7.7682  11.0450
 F3A  C5'   C  CH2   0  -0.201   2.9301   6.9955  12.9670
 F3A  O5'   O  O2    0  -0.598   4.1188   6.7895  13.7431
 F3A  H2    H  HCR6  0   0.251   8.7759   6.7130   6.7963
 F3A  HN6   H  HNH2  0   0.403  11.8258   7.0419  10.0624
 F3A  HN6A  H  HNH2  0   0.410  10.9592   7.2626  11.5378
 F3A  H8    H  HCR5  0   0.290   6.2158   7.6005  12.5886
 F3A  H1'   H  HCH1  0   0.276   4.9070   7.8639   9.1343
 F3A  HO1A  H  HOH1  0   0.517   2.5721   6.6181  16.7048
 F3A  HO1G  H  HOH1  0   0.512   5.7325   0.0476  13.3104
 F3A  H2'   H  HCH2  0   0.267   3.7087   5.8211   9.0206
 F3A  H2'A  H  HCH2  0   0.282   5.2916   5.1574   9.4450
 F3A  HO2B  H  HOH1  0   0.517   2.1406   3.4524  16.3402
 F3A  H3'   H  HCH1  0   0.221   4.7077   5.2085  11.8334
 F3A  HO3'  H  HOH1  0   0.461   2.8975   4.0101  11.9297
 F3A  HO3G  H  HOH1  0   0.515   4.5995  -0.2956  17.0096
 F3A  H4'   H  HCH1  0   0.251   2.2946   6.8659  10.9771
 F3A  H5'   H  HCH2  0   0.275   2.5601   8.0079  13.1361
 F3A  H5'A  H  HCH2  0   0.259   2.1492   6.2925  13.2592

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
 F3A  C2   N1    aromatic  1.331  0.020  1.331
 F3A  N1   C6    aromatic  1.338  0.020  1.338
 F3A  C2   N3    aromatic  1.321  0.020  1.321
 F3A  C2   H2    single    0.930  0.020  1.080
 F3A  N3   C4    aromatic  1.333  0.020  1.333
 F3A  C4   C5    aromatic  1.386  0.020  1.386
 F3A  C4   N9    aromatic  1.363  0.020  1.363
 F3A  C6   C5    aromatic  1.407  0.020  1.407
 F3A  C5   N7    aromatic  1.369  0.020  1.369
 F3A  C6   N6    single    1.334  0.020  1.334
 F3A  N6   HN6   single    0.860  0.020  1.020
 F3A  N6   HN6A  single    0.860  0.020  1.020
 F3A  N7   C8    aromatic  1.303  0.020  1.303
 F3A  N9   C8    aromatic  1.367  0.020  1.367
 F3A  C8   H8    single    0.930  0.020  1.080
 F3A  C1'  N9    single    1.462  0.020  1.462
 F3A  O5'  PA    single    1.580  0.020  1.580
 F3A  C3A  PA    single    1.861  0.020  1.861
 F3A  PA   O2A   double    1.472  0.020  1.472
 F3A  PA   O1A   single    1.592  0.020  1.592
 F3A  O1B  PB    double    1.476  0.020  1.476
 F3A  PB   O2B   single    1.582  0.020  1.582
 F3A  PB   C3A   single    1.856  0.020  1.856
 F3A  PB   O3B   single    1.603  0.020  1.603
 F3A  O3B  PG    single    1.639  0.020  1.639
 F3A  PG   O2G   double    1.470  0.020  1.470
 F3A  PG   O3G   single    1.580  0.020  1.580
 F3A  PG   O1G   single    1.582  0.020  1.582
 F3A  C2'  C1'   single    1.525  0.020  1.525
 F3A  C1'  O4'   single    1.400  0.020  1.400
 F3A  C1'  H1'   single    0.970  0.020  1.090
 F3A  F1A  C3A   single    1.358  0.020  1.358
 F3A  O1A  HO1A  single    0.850  0.020  0.980
 F3A  O1G  HO1G  single    0.850  0.020  0.980
 F3A  C2'  C3'   single    1.520  0.020  1.520
 F3A  C2'  H2'   single    0.970  0.020  1.090
 F3A  C2'  H2'A  single    0.970  0.020  1.090
 F3A  C3A  F2A   single    1.354  0.020  1.354
 F3A  O2B  HO2B  single    0.850  0.020  0.980
 F3A  O3'  C3'   single    1.395  0.020  1.395
 F3A  C3'  C4'   single    1.533  0.020  1.533
 F3A  C3'  H3'   single    0.970  0.020  1.090
 F3A  O3'  HO3'  single    0.850  0.020  0.980
 F3A  O3G  HO3G  single    0.850  0.020  0.980
 F3A  O4'  C4'   single    1.424  0.020  1.424
 F3A  C4'  C5'   single    1.505  0.020  1.505
 F3A  C4'  H4'   single    0.970  0.020  1.090
 F3A  C5'  O5'   single    1.434  0.020  1.434
 F3A  C5'  H5'   single    0.970  0.020  1.090
 F3A  C5'  H5'A  single    0.970  0.020  1.090

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
 F3A  C6    N1   C2   119.22  3.000
 F3A  H2    C2   N3   116.16  3.000
 F3A  H2    C2   N1   115.39  3.000
 F3A  N3    C2   N1   128.45  3.000
 F3A  C4    N3   C2   111.58  3.000
 F3A  N9    C4   C5   105.31  3.000
 F3A  N9    C4   N3   128.07  3.000
 F3A  C5    C4   N3   126.62  3.000
 F3A  N7    C5   C6   133.10  3.000
 F3A  N7    C5   C4   110.71  3.000
 F3A  C6    C5   C4   116.19  3.000
 F3A  N6    C6   C5   122.73  3.000
 F3A  N6    C6   N1   119.33  3.000
 F3A  C5    C6   N1   117.94  3.000
 F3A  HN6A  N6   HN6  118.26  3.000
 F3A  HN6A  N6   C6   121.02  3.000
 F3A  HN6   N6   C6   120.30  3.000
 F3A  C8    N7   C5   104.40  3.000
 F3A  H8    C8   N9   121.94  3.000
 F3A  H8    C8   N7   124.73  3.000
 F3A  N9    C8   N7   113.32  3.000
 F3A  C1'   N9   C8   129.16  3.000
 F3A  C1'   N9   C4   124.58  3.000
 F3A  C8    N9   C4   106.25  3.000
 F3A  O5'   PA   C3A  100.51  3.000
 F3A  C3A   PA   O2A  111.55  3.000
 F3A  O5'   PA   O2A  116.63  3.000
 F3A  O2A   PA   O1A  118.67  3.000
 F3A  C3A   PA   O1A  102.72  3.000
 F3A  O5'   PA   O1A  104.42  3.000
 F3A  O3B   PB   C3A   98.50  3.000
 F3A  O3B   PB   O2B  102.84  3.000
 F3A  C3A   PB   O2B  105.28  3.000
 F3A  O3B   PB   O1B  117.19  3.000
 F3A  C3A   PB   O1B  112.98  3.000
 F3A  O2B   PB   O1B  117.67  3.000
 F3A  O3G   PG   O3B   99.75  3.000
 F3A  O3G   PG   O2G  118.84  3.000
 F3A  O3B   PG   O2G  112.85  3.000
 F3A  O3G   PG   O1G  102.32  3.000
 F3A  O2G   PG   O1G  118.63  3.000
 F3A  O3B   PG   O1G  101.49  3.000
 F3A  H1'   C1'  O4'  110.40  3.000
 F3A  H1'   C1'  C2'  112.42  3.000
 F3A  O4'   C1'  C2'  106.77  3.000
 F3A  H1'   C1'  N9   106.51  3.000
 F3A  O4'   C1'  N9   108.53  3.000
 F3A  C2'   C1'  N9   112.18  3.000
 F3A  HO1A  O1A  PA   115.70  3.000
 F3A  HO1G  O1G  PG   114.93  3.000
 F3A  H2'A  C2'  H2'  108.28  3.000
 F3A  H2'A  C2'  C3'  114.42  3.000
 F3A  H2'   C2'  C3'  109.78  3.000
 F3A  H2'A  C2'  C1'  112.74  3.000
 F3A  H2'   C2'  C1'  109.41  3.000
 F3A  C3'   C2'  C1'  102.05  3.000
 F3A  HO2B  O2B  PB   115.78  3.000
 F3A  H3'   C3'  C4'  109.63  3.000
 F3A  H3'   C3'  O3'  111.05  3.000
 F3A  C4'   C3'  O3'  113.81  3.000
 F3A  H3'   C3'  C2'  109.31  3.000
 F3A  C4'   C3'  C2'   99.89  3.000
 F3A  O3'   C3'  C2'  112.59  3.000
 F3A  HO3'  O3'  C3'  107.25  3.000
 F3A  F2A   C3A  F1A  107.70  3.000
 F3A  F2A   C3A  PB   108.53  3.000
 F3A  F1A   C3A  PB   107.80  3.000
 F3A  F2A   C3A  PA   108.50  3.000
 F3A  F1A   C3A  PA   108.42  3.000
 F3A  PB    C3A  PA   115.63  3.000
 F3A  PG    O3B  PB   127.11  3.000
 F3A  HO3G  O3G  PG   114.52  3.000
 F3A  H4'   C4'  C5'  105.93  3.000
 F3A  H4'   C4'  O4'  109.82  3.000
 F3A  C5'   C4'  O4'  110.63  3.000
 F3A  H4'   C4'  C3'  108.37  3.000
 F3A  C5'   C4'  C3'  117.21  3.000
 F3A  O4'   C4'  C3'  104.79  3.000
 F3A  C4'   O4'  C1'  110.24  3.000
 F3A  H5'A  C5'  H5'  108.29  3.000
 F3A  H5'A  C5'  O5'  110.85  3.000
 F3A  H5'   C5'  O5'  109.29  3.000
 F3A  H5'A  C5'  C4'  108.52  3.000
 F3A  H5'   C5'  C4'  110.88  3.000
 F3A  O5'   C5'  C4'  109.01  3.000
 F3A  C5'   O5'  PA   128.80  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
 F3A  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 F3A  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 F3A  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 F3A  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 F3A  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 F3A  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 F3A  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 F3A  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 F3A  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 F3A  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 F3A  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 F3A  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 F3A  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 F3A  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 F3A  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 F3A  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 F3A  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 F3A  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 F3A  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 F3A  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 F3A  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 F3A  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 F3A  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 F3A  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 F3A  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 F3A  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 F3A  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 F3A  Var_01    C4'   C5'  O5'  PA  -165.20  30.0  1
 F3A  Var_02    O1B   PB   C3A  PA    48.86  30.0  1
 F3A  Var_03    O5'   PA   C3A  PB   -74.93  30.0  3
 F3A  Var_04    O2G   PG   O3B  PB    24.04  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
 F3A  chir_03  C1'  N9   C2'  O4'  negativ
 F3A  chir_04  C3'  O3'  C4'  C2'  positiv
 F3A  chir_05  C4'  O4'  C3'  C5'  negativ
 F3A  chir_06  PA   C3A  O2A  O1A  both
 F3A  chir_07  PB   O2B  O1B  C3A  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
 F3A  plan-1  N1    0.020
 F3A  plan-1  C2    0.020
 F3A  plan-1  N3    0.020
 F3A  plan-1  C4    0.020
 F3A  plan-1  C5    0.020
 F3A  plan-1  C6    0.020
 F3A  plan-1  N6    0.020
 F3A  plan-1  N7    0.020
 F3A  plan-1  C8    0.020
 F3A  plan-1  N9    0.020
 F3A  plan-1  C1'   0.020
 F3A  plan-1  H2    0.020
 F3A  plan-1  H8    0.020
 F3A  plan-2  C6    0.020
 F3A  plan-2  N6    0.020
 F3A  plan-2  HN6   0.020
 F3A  plan-2  HN6A  0.020

