# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 23:52:35 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 2'-deoxy-2-fluoroadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(F)nc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO)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
 2FD  2FD  2'-deoxy-2-fluoroadenosine  ligand  31  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2FD
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
 2FD  O5'   O  OH1   0  -0.670  -4.5753   1.6130  -0.8868
 2FD  C5'   C  CH2   0  -0.153  -3.9400   1.0464   0.2317
 2FD  C4'   C  CH1   0   0.006  -3.3250  -0.2739  -0.1624
 2FD  O4'   O  O2    0  -0.497  -2.3341  -0.0928  -1.1786
 2FD  C1'   C  CH1   0   0.190  -1.1612  -0.7769  -0.8671
 2FD  N9    N  NR5   0  -0.533  -0.1404   0.2027  -0.4636
 2FD  C4    C  CR56  0   0.496   1.1499  -0.0806  -0.1456
 2FD  N3    N  N     0  -0.490   1.7460  -1.2767  -0.0890
 2FD  C2    C  CR6   0   0.568   2.9984  -1.1459   0.2468
 2FD  F     F  F     0  -0.288   3.6765  -2.2890   0.3301
 2FD  N1    N  N     0  -0.504   3.7149  -0.0808   0.5205
 2FD  C6    C  CR6   0   0.474   3.1109   1.1140   0.4601
 2FD  N6    N  NH2   0  -0.808   3.8106   2.2083   0.7378
 2FD  C5    C  CR56  0  -0.005   1.7478   1.1438   0.1062
 2FD  N7    N  N     0  -0.448   0.8521   2.1633  -0.0681
 2FD  C8    C  CR15  0   0.102  -0.2523   1.5673  -0.4120
 2FD  C2'   C  CH2   0  -0.544  -1.5105  -1.7346   0.2598
 2FD  C3'   C  CH1   0   0.009  -2.6088  -0.9714   0.9926
 2FD  O3'   O  OH1   0  -0.661  -3.5179  -1.7612   1.7063
 2FD  H5'   H  HOH1  0   0.459  -4.9425   2.4622  -0.6259
 2FD  H5'1  H  HCH2  0   0.214  -4.6455   0.8475   1.0493
 2FD  H5'2  H  HCH2  0   0.196  -3.1610   1.7042   0.6404
 2FD  H4'   H  HCH1  0   0.242  -4.1050  -0.9392  -0.5548
 2FD  H1'   H  HCH1  0   0.284  -0.7815  -1.2853  -1.7555
 2FD  HN61  H  HNH2  0   0.410   4.7914   2.1479   0.9518
 2FD  HN62  H  HNH2  0   0.417   3.3924   3.1200   0.6726
 2FD  H8    H  HCR5  0   0.297  -1.1727   2.0741  -0.6527
 2FD  H2'1  H  HCH2  0   0.268  -1.9210  -2.6516  -0.1694
 2FD  H2'2  H  HCH2  0   0.283  -0.6595  -2.0025   0.8835
 2FD  H3'   H  HCH1  0   0.226  -2.1480  -0.2168   1.6467
 2FD  H1    H  HOH1  0   0.461  -3.0960  -2.0501   2.5210

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
 2FD  O5'  C5'   single    1.406  0.020  1.406
 2FD  O5'  H5'   single    0.850  0.020  0.980
 2FD  C5'  C4'   single    1.509  0.020  1.509
 2FD  C5'  H5'1  single    0.970  0.020  1.090
 2FD  C5'  H5'2  single    0.970  0.020  1.090
 2FD  C4'  O4'   single    1.431  0.020  1.431
 2FD  C4'  C3'   single    1.527  0.020  1.527
 2FD  C4'  H4'   single    0.970  0.020  1.090
 2FD  O4'  C1'   single    1.393  0.020  1.393
 2FD  C1'  N9    single    1.471  0.020  1.471
 2FD  C1'  C2'   single    1.520  0.020  1.520
 2FD  C1'  H1'   single    0.970  0.020  1.090
 2FD  N9   C4    aromatic  1.359  0.020  1.359
 2FD  N9   C8    aromatic  1.370  0.020  1.370
 2FD  C4   N3    aromatic  1.338  0.020  1.338
 2FD  C4   C5    aromatic  1.386  0.020  1.386
 2FD  N3   C2    aromatic  1.303  0.020  1.303
 2FD  C2   F     single    1.332  0.020  1.332
 2FD  C2   N1    aromatic  1.313  0.020  1.313
 2FD  N1   C6    aromatic  1.340  0.020  1.340
 2FD  C6   N6    single    1.328  0.020  1.328
 2FD  C6   C5    aromatic  1.409  0.020  1.409
 2FD  N6   HN61  single    0.860  0.020  1.020
 2FD  N6   HN62  single    0.860  0.020  1.020
 2FD  C5   N7    aromatic  1.368  0.020  1.368
 2FD  N7   C8    aromatic  1.301  0.020  1.301
 2FD  C8   H8    single    0.930  0.020  1.080
 2FD  C2'  C3'   single    1.525  0.020  1.525
 2FD  C2'  H2'1  single    0.970  0.020  1.090
 2FD  C2'  H2'2  single    0.970  0.020  1.090
 2FD  C3'  O3'   single    1.400  0.020  1.400
 2FD  C3'  H3'   single    0.970  0.020  1.090
 2FD  O3'  H1    single    0.850  0.020  0.980

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
 2FD  H5'   O5'  C5'   108.22  3.000
 2FD  H5'2  C5'  H5'1  106.68  3.000
 2FD  H5'2  C5'  C4'   109.40  3.000
 2FD  H5'1  C5'  C4'   107.33  3.000
 2FD  H5'2  C5'  O5'   112.04  3.000
 2FD  H5'1  C5'  O5'   112.03  3.000
 2FD  C4'   C5'  O5'   109.21  3.000
 2FD  H4'   C4'  C3'   109.07  3.000
 2FD  H4'   C4'  O4'   108.36  3.000
 2FD  C3'   C4'  O4'   105.68  3.000
 2FD  H4'   C4'  C5'   109.51  3.000
 2FD  C3'   C4'  C5'   113.15  3.000
 2FD  O4'   C4'  C5'   110.91  3.000
 2FD  C1'   O4'  C4'   111.23  3.000
 2FD  H1'   C1'  C2'   112.95  3.000
 2FD  H1'   C1'  N9    106.97  3.000
 2FD  C2'   C1'  N9    112.07  3.000
 2FD  H1'   C1'  O4'   109.85  3.000
 2FD  C2'   C1'  O4'   106.37  3.000
 2FD  N9    C1'  O4'   108.57  3.000
 2FD  C8    N9   C4    106.04  3.000
 2FD  C8    N9   C1'   128.09  3.000
 2FD  C4    N9   C1'   125.75  3.000
 2FD  C5    C4   N3    126.17  3.000
 2FD  C5    C4   N9    105.54  3.000
 2FD  N3    C4   N9    128.28  3.000
 2FD  C2    N3   C4    110.45  3.000
 2FD  N1    C2   F     113.93  3.000
 2FD  N1    C2   N3    131.28  3.000
 2FD  F     C2   N3    114.79  3.000
 2FD  C6    N1   C2    117.91  3.000
 2FD  C5    C6   N6    123.01  3.000
 2FD  C5    C6   N1    117.80  3.000
 2FD  N6    C6   N1    119.19  3.000
 2FD  HN62  N6   HN61  118.30  3.000
 2FD  HN62  N6   C6    120.97  3.000
 2FD  HN61  N6   C6    120.58  3.000
 2FD  N7    C5   C6    132.95  3.000
 2FD  N7    C5   C4    110.66  3.000
 2FD  C6    C5   C4    116.38  3.000
 2FD  C8    N7   C5    104.36  3.000
 2FD  H8    C8   N7    124.63  3.000
 2FD  H8    C8   N9    121.98  3.000
 2FD  N7    C8   N9    113.38  3.000
 2FD  H2'2  C2'  H2'1  108.20  3.000
 2FD  H2'2  C2'  C3'   114.26  3.000
 2FD  H2'1  C2'  C3'   109.77  3.000
 2FD  H2'2  C2'  C1'   113.60  3.000
 2FD  H2'1  C2'  C1'   108.90  3.000
 2FD  C3'   C2'  C1'   101.92  3.000
 2FD  H3'   C3'  O3'   110.85  3.000
 2FD  H3'   C3'  C2'   109.11  3.000
 2FD  O3'   C3'  C2'   115.49  3.000
 2FD  H3'   C3'  C4'   109.45  3.000
 2FD  O3'   C3'  C4'   109.79  3.000
 2FD  C2'   C3'  C4'   101.70  3.000
 2FD  H1    O3'  C3'   108.45  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
 2FD  CONST_01  C2    N3  C4  N9   180.00  0.0  0
 2FD  CONST_02  C6    C5  C4  N9   180.00  0.0  0
 2FD  CONST_03  N7    C5  C4  N9     0.00  0.0  0
 2FD  CONST_04  C5    N7  C8  N9     0.00  0.0  0
 2FD  CONST_05  N7    C8  N9  C4     0.00  0.0  0
 2FD  CONST_06  N1    C2  N3  C4     0.00  0.0  0
 2FD  CONST_07  N1    C6  C5  C4     0.00  0.0  0
 2FD  CONST_08  C8    N7  C5  C4     0.00  0.0  0
 2FD  CONST_09  C8    N9  C4  N3   180.00  0.0  0
 2FD  CONST_10  C6    C5  C4  N3     0.00  0.0  0
 2FD  CONST_11  N7    C5  C4  N3   180.00  0.0  0
 2FD  CONST_12  C6    N1  C2  N3     0.00  0.0  0
 2FD  CONST_13  C5    C4  N3  C2     0.00  0.0  0
 2FD  CONST_14  C5    C6  N1  C2     0.00  0.0  0
 2FD  CONST_15  N7    C5  C6  N1   180.00  0.0  0
 2FD  CONST_16  C8    N7  C5  C6   180.00  0.0  0
 2FD  CONST_17  C8    N9  C4  C5     0.00  0.0  0
 2FD  CONST_18  N3    C4  N9  C1'    0.00  0.0  0
 2FD  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 2FD  CONST_20  N7    C8  N9  C1'  180.00  0.0  0
 2FD  CONST_21  F     C2  N3  C4   180.00  0.0  0
 2FD  CONST_22  N6    C6  C5  C4   180.00  0.0  0
 2FD  CONST_23  N6    C6  N1  C2   180.00  0.0  0
 2FD  CONST_24  C6    N1  C2  F    180.00  0.0  0
 2FD  CONST_25  N7    C5  C6  N6     0.00  0.0  0
 2FD  CONST_26  H8    C8  N9  C1'    0.00  0.0  0
 2FD  CONST_27  HN61  N6  C6  N1     0.00  0.0  0
 2FD  CONST_28  HN62  N6  C6  N1   180.00  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
 2FD  chir_01  C4'  C5'  O4'  C3'  negativ
 2FD  chir_02  C1'  O4'  N9   C2'  negativ
 2FD  chir_03  C3'  O3'  C4'  C2'  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
 2FD  plan-1  C1'   0.020
 2FD  plan-1  N9    0.020
 2FD  plan-1  C4    0.020
 2FD  plan-1  N3    0.020
 2FD  plan-1  C2    0.020
 2FD  plan-1  F     0.020
 2FD  plan-1  N1    0.020
 2FD  plan-1  C6    0.020
 2FD  plan-1  N6    0.020
 2FD  plan-1  C5    0.020
 2FD  plan-1  N7    0.020
 2FD  plan-1  C8    0.020
 2FD  plan-1  H8    0.020
 2FD  plan-2  C6    0.020
 2FD  plan-2  N6    0.020
 2FD  plan-2  HN61  0.020
 2FD  plan-2  HN62  0.020

