# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 18:12:48 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 2',5'-dideoxy-5'-fluoroadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CF)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
 5F1  5F1  2',5'-dideoxy-5'-fluoroadenosine  ligand  30  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5F1
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
 5F1  C2'   C  CH2   0  -0.543  -1.4834  -1.7250   0.4901
 5F1  C3'   C  CH1   0   0.005  -2.6818  -0.9194   0.9834
 5F1  O3'   O  OH1   0  -0.659  -3.7809  -1.6773   1.4028
 5F1  C4'   C  CH1   0  -0.028  -3.0518  -0.1337  -0.2731
 5F1  C5'   C  CH2   0  -0.007  -3.7406   1.1664   0.0381
 5F1  F19   F  F     0  -0.374  -4.1256   1.8060  -1.1345
 5F1  O4'   O  O2    0  -0.494  -1.8241   0.1122  -0.9419
 5F1  C1'   C  CH1   0   0.177  -0.8403  -0.8088  -0.5481
 5F1  N9    N  NR5   0  -0.526   0.3096  -0.0708  -0.0543
 5F1  C8    C  CR15  0   0.111   0.3239   1.0074   0.7873
 5F1  N7    N  N     0  -0.449   1.5205   1.4438   1.0497
 5F1  C5    C  CR56  0  -0.008   2.3486   0.6085   0.3465
 5F1  C4    C  CR56  0   0.489   1.6148  -0.3406  -0.3479
 5F1  N3    N  N     0  -0.459   2.1022  -1.3016  -1.1304
 5F1  C2    C  CR16  0   0.045   3.4216  -1.2589  -1.1914
 5F1  N1    N  N     0  -0.474   4.2510  -0.4110  -0.5886
 5F1  C6    C  CR6   0   0.458   3.7465   0.5481   0.1960
 5F1  N6    N  NH2   0  -0.816   4.5755   1.3970   0.8047
 5F1  H2'1  H  HCH2  0   0.272  -1.8428  -2.6293  -0.0049
 5F1  H2'2  H  HCH2  0   0.284  -0.7908  -2.0216   1.2771
 5F1  H3'   H  HCH1  0   0.225  -2.3678  -0.2236   1.7750
 5F1  HA    H  HOH1  0   0.463  -3.5883  -2.0384   2.2733
 5F1  H4'   H  HCH1  0   0.250  -3.7032  -0.7564  -0.9015
 5F1  H5'1  H  HCH2  0   0.221  -4.6326   0.9725   0.6360
 5F1  H5'2  H  HCH2  0   0.210  -3.0806   1.8369   0.5935
 5F1  H1'   H  HCH1  0   0.272  -0.4746  -1.3736  -1.4082
 5F1  H8    H  HCR5  0   0.288  -0.5829   1.4479   1.1734
 5F1  H2    H  HCR6  0   0.252   3.8958  -2.0109  -1.8129
 5F1  H6N1  H  HNH2  0   0.403   5.5642   1.3529   0.6278
 5F1  H6N2  H  HNH2  0   0.411   4.2242   2.1624   1.3529

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
 5F1  C2'  C3'   single    1.526  0.020  1.526
 5F1  C2'  C1'   single    1.527  0.020  1.527
 5F1  C2'  H2'1  single    0.970  0.020  1.090
 5F1  C2'  H2'2  single    0.970  0.020  1.090
 5F1  C3'  O3'   single    1.399  0.020  1.399
 5F1  C3'  C4'   single    1.527  0.020  1.527
 5F1  C3'  H3'   single    0.970  0.020  1.090
 5F1  O3'  HA    single    0.850  0.020  0.980
 5F1  C4'  C5'   single    1.504  0.020  1.504
 5F1  C4'  O4'   single    1.419  0.020  1.419
 5F1  C4'  H4'   single    0.970  0.020  1.090
 5F1  C5'  F19   single    1.390  0.020  1.390
 5F1  C5'  H5'1  single    0.970  0.020  1.090
 5F1  C5'  H5'2  single    0.970  0.020  1.090
 5F1  O4'  C1'   single    1.404  0.020  1.404
 5F1  C1'  N9    single    1.453  0.020  1.453
 5F1  C1'  H1'   single    0.970  0.020  1.090
 5F1  N9   C8    aromatic  1.368  0.020  1.368
 5F1  N9   C4    aromatic  1.365  0.020  1.365
 5F1  C8   N7    aromatic  1.301  0.020  1.301
 5F1  C8   H8    single    0.930  0.020  1.080
 5F1  N7   C5    aromatic  1.370  0.020  1.370
 5F1  C5   C4    aromatic  1.386  0.020  1.386
 5F1  C5   C6    aromatic  1.407  0.020  1.407
 5F1  C4   N3    aromatic  1.332  0.020  1.332
 5F1  N3   C2    aromatic  1.321  0.020  1.321
 5F1  C2   N1    aromatic  1.331  0.020  1.331
 5F1  C2   H2    single    0.930  0.020  1.080
 5F1  N1   C6    aromatic  1.338  0.020  1.338
 5F1  C6   N6    single    1.334  0.020  1.334
 5F1  N6   H6N1  single    0.860  0.020  1.020
 5F1  N6   H6N2  single    0.860  0.020  1.020

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
 5F1  H2'2  C2'  H2'1  108.14  3.000
 5F1  H2'2  C2'  C1'   112.76  3.000
 5F1  H2'1  C2'  C1'   109.11  3.000
 5F1  H2'2  C2'  C3'   114.17  3.000
 5F1  H2'1  C2'  C3'   108.98  3.000
 5F1  C1'   C2'  C3'   103.52  3.000
 5F1  H3'   C3'  C4'   109.63  3.000
 5F1  H3'   C3'  O3'   110.56  3.000
 5F1  C4'   C3'  O3'   109.57  3.000
 5F1  H3'   C3'  C2'   110.03  3.000
 5F1  C4'   C3'  C2'   101.29  3.000
 5F1  O3'   C3'  C2'   115.32  3.000
 5F1  HA    O3'  C3'   108.50  3.000
 5F1  H4'   C4'  O4'   109.96  3.000
 5F1  H4'   C4'  C5'   109.68  3.000
 5F1  O4'   C4'  C5'   110.12  3.000
 5F1  H4'   C4'  C3'   108.82  3.000
 5F1  O4'   C4'  C3'   105.50  3.000
 5F1  C5'   C4'  C3'   112.67  3.000
 5F1  H5'2  C5'  H5'1  108.93  3.000
 5F1  H5'2  C5'  F19   108.29  3.000
 5F1  H5'1  C5'  F19   108.52  3.000
 5F1  H5'2  C5'  C4'   111.04  3.000
 5F1  H5'1  C5'  C4'   109.52  3.000
 5F1  F19   C5'  C4'   110.49  3.000
 5F1  C1'   O4'  C4'   111.12  3.000
 5F1  H1'   C1'  N9    105.39  3.000
 5F1  H1'   C1'  O4'   110.67  3.000
 5F1  N9    C1'  O4'   108.47  3.000
 5F1  H1'   C1'  C2'   111.48  3.000
 5F1  N9    C1'  C2'   114.02  3.000
 5F1  O4'   C1'  C2'   106.81  3.000
 5F1  C4    N9   C8    106.15  3.000
 5F1  C4    N9   C1'   125.69  3.000
 5F1  C8    N9   C1'   128.16  3.000
 5F1  H8    C8   N7    124.32  3.000
 5F1  H8    C8   N9    122.20  3.000
 5F1  N7    C8   N9    113.47  3.000
 5F1  C5    N7   C8    104.35  3.000
 5F1  C6    C5   C4    116.29  3.000
 5F1  C6    C5   N7    132.94  3.000
 5F1  C4    C5   N7    110.77  3.000
 5F1  N3    C4   C5    126.49  3.000
 5F1  N3    C4   N9    128.25  3.000
 5F1  C5    C4   N9    105.26  3.000
 5F1  C2    N3   C4    111.67  3.000
 5F1  H2    C2   N1    115.39  3.000
 5F1  H2    C2   N3    116.14  3.000
 5F1  N1    C2   N3    128.47  3.000
 5F1  C6    N1   C2    119.17  3.000
 5F1  N6    C6   N1    119.31  3.000
 5F1  N6    C6   C5    122.77  3.000
 5F1  N1    C6   C5    117.91  3.000
 5F1  H6N2  N6   H6N1  118.24  3.000
 5F1  H6N2  N6   C6    121.10  3.000
 5F1  H6N1  N6   C6    120.20  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
 5F1  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 5F1  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 5F1  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 5F1  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 5F1  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 5F1  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 5F1  CONST_07  C4    C5  N7  C8     0.00  0.0  0
 5F1  CONST_08  C6    C5  N7  C8   180.00  0.0  0
 5F1  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 5F1  CONST_10  N3    C4  C5  N7   180.00  0.0  0
 5F1  CONST_11  N1    C6  C5  N7   180.00  0.0  0
 5F1  CONST_12  C2    N3  C4  C5     0.00  0.0  0
 5F1  CONST_13  C2    N1  C6  C5     0.00  0.0  0
 5F1  CONST_14  N1    C6  C5  C4     0.00  0.0  0
 5F1  CONST_15  N1    C2  N3  C4     0.00  0.0  0
 5F1  CONST_16  C6    C5  C4  N3     0.00  0.0  0
 5F1  CONST_17  C6    N1  C2  N3     0.00  0.0  0
 5F1  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 5F1  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 5F1  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 5F1  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 5F1  CONST_22  N6    C6  C5  C4   180.00  0.0  0
 5F1  CONST_23  N6    C6  N1  C2   180.00  0.0  0
 5F1  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 5F1  CONST_25  H2    C2  N3  C4   180.00  0.0  0
 5F1  CONST_26  H6N1  N6  C6  C5   180.00  0.0  0
 5F1  CONST_27  H6N2  N6  C6  C5     0.00  0.0  0

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
 5F1  chir_01  C3'  C2'  O3'  C4'  positiv
 5F1  chir_02  C4'  O4'  C3'  C5'  negativ
 5F1  chir_03  C1'  O4'  N9   C2'  negativ

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
 5F1  plan-1  C1'   0.020
 5F1  plan-1  N9    0.020
 5F1  plan-1  C8    0.020
 5F1  plan-1  N7    0.020
 5F1  plan-1  C5    0.020
 5F1  plan-1  C4    0.020
 5F1  plan-1  N3    0.020
 5F1  plan-1  C2    0.020
 5F1  plan-1  N1    0.020
 5F1  plan-1  C6    0.020
 5F1  plan-1  N6    0.020
 5F1  plan-1  H8    0.020
 5F1  plan-1  H2    0.020
 5F1  plan-2  C6    0.020
 5F1  plan-2  N6    0.020
 5F1  plan-2  H6N1  0.020
 5F1  plan-2  H6N2  0.020

