# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 22:21:21 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 5'-deoxy-5'-fluoroadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CF)N2C=N[C@H]3[C@H]2N=CNC3=N
#
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
 5FD  5FD  5'-deoxy-5'-fluoroadenosine  ligand  33  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_5FD
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
 5FD  O2'   O  OH1   0  -0.677   1.4343   1.1480   2.4407
 5FD  C2'   C  CR15  0  -0.021   1.3130   0.7313   1.1238
 5FD  C3'   C  CR15  0  -0.051   2.1052  -0.5208   0.7885
 5FD  O3'   O  OH1   0  -0.668   3.3866  -0.3958   1.3475
 5FD  C4'   C  CR15  0  -0.059   2.1154  -0.4467  -0.7475
 5FD  C5'   C  CH2   0  -0.007   0.9896  -1.2540  -1.3499
 5FD  F19   F  F     0  -0.376   1.0013  -1.1193  -2.7332
 5FD  O4'   O  O     0  -0.498   1.9713   0.9273  -1.0944
 5FD  C1'   C  CR15  0   0.224   1.8650   1.7119   0.0834
 5FD  N9    N  NR5   0  -0.506   1.0561   2.8574  -0.1453
 5FD  C8    C  CR15  0   0.176   1.5256   4.0883  -0.4879
 5FD  N7    N  N     0  -0.445   0.6631   5.0064  -0.6773
 5FD  C5    C  CR15  0  -0.309  -0.6384   4.3439  -0.5356
 5FD  C4    C  CR15  0   0.048  -0.3544   3.0047   0.1765
 5FD  N3    N  N     0  -0.465  -0.5175   3.0014   1.6156
 5FD  C2    C  C1    0   0.179  -1.1911   3.9345   2.1521
 5FD  N1    N  NH1   0  -0.653  -1.7815   4.9813   1.5130
 5FD  C6    C  C     0   0.450  -1.6178   5.2456   0.1736
 5FD  N6    N  N     0  -0.607  -2.2346   6.2190  -0.3490
 5FD  HO2   H  HOH1  0   0.457   0.7584   1.8472   2.5294
 5FD  H2'   H  HCR5  0   0.233   0.2647   0.5156   0.8672
 5FD  H3''  H  HCR5  0   0.253   1.6025  -1.4300   1.1433
 5FD  HO3   H  HOH1  0   0.458   3.9248  -1.1348   1.0473
 5FD  H4'   H  HCR5  0   0.257   3.0666  -0.8246  -1.1413
 5FD  H5'1  H  HCH2  0   0.208   0.0153  -0.9218  -0.9844
 5FD  H5'2  H  HCH2  0   0.217   1.1167  -2.3103  -1.1060
 5FD  H1'   H  HCR5  0   0.236   2.8586   2.0627   0.3895
 5FD  HC8   H  HCR5  0   0.291   2.5946   4.2418  -0.5897
 5FD  H55   H  HCR5  0   0.300  -1.0390   4.1435  -1.5352
 5FD  H44   H  HCR5  0   0.293  -0.9517   2.1941  -0.2452
 5FD  HC2   H  H     0   0.295  -1.3390   3.9341   3.2263
 5FD  HN1   H  HNH1  0   0.418  -2.3484   5.6177   2.0532
 5FD  HN2   H  H     0   0.349  -2.0106   6.2937  -1.3355

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
 5FD  O2'  C2'   single  1.387  0.020  1.387
 5FD  O2'  HO2   single  0.850  0.020  0.980
 5FD  C2'  C3'   single  1.519  0.020  1.519
 5FD  C2'  C1'   single  1.533  0.020  1.533
 5FD  C2'  H2'   single  0.970  0.020  1.090
 5FD  C3'  O3'   single  1.404  0.020  1.404
 5FD  C3'  C4'   single  1.538  0.020  1.538
 5FD  C3'  H3''  single  0.970  0.020  1.090
 5FD  O3'  HO3   single  0.850  0.020  0.980
 5FD  C4'  C5'   single  1.511  0.020  1.511
 5FD  C4'  O4'   single  1.424  0.020  1.424
 5FD  C4'  H4'   single  0.970  0.020  1.090
 5FD  C5'  F19   single  1.390  0.020  1.390
 5FD  C5'  H5'1  single  0.970  0.020  1.090
 5FD  C5'  H5'2  single  0.970  0.020  1.090
 5FD  O4'  C1'   single  1.419  0.020  1.419
 5FD  C1'  N9    single  1.421  0.020  1.421
 5FD  C1'  H1'   single  0.970  0.020  1.090
 5FD  N9   C8    single  1.361  0.020  1.361
 5FD  N9   C4    single  1.454  0.020  1.454
 5FD  C8   N7    double  1.274  0.020  1.274
 5FD  C8   HC8   single  0.930  0.020  1.080
 5FD  N7   C5    single  1.467  0.020  1.467
 5FD  C5   C4    single  1.543  0.020  1.543
 5FD  C5   C6    single  1.508  0.020  1.508
 5FD  C5   H55   single  0.970  0.020  1.090
 5FD  C4   N3    single  1.448  0.020  1.448
 5FD  C4   H44   single  0.970  0.020  1.090
 5FD  N3   C2    double  1.270  0.020  1.270
 5FD  C2   N1    single  1.361  0.020  1.361
 5FD  C2   HC2   single  0.930  0.020  1.080
 5FD  N1   C6    single  1.375  0.020  1.375
 5FD  C6   N6    double  1.265  0.020  1.265
 5FD  HN1  N1    single  0.860  0.020  1.020
 5FD  HN2  N6    single  0.890  0.020  1.040

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
 5FD  HO2   O2'  C2'   103.94  3.000
 5FD  H2'   C2'  C1'   108.07  3.000
 5FD  H2'   C2'  C3'   106.48  3.000
 5FD  C1'   C2'  C3'   100.93  3.000
 5FD  H2'   C2'  O2'   111.33  3.000
 5FD  C1'   C2'  O2'   114.89  3.000
 5FD  C3'   C2'  O2'   114.31  3.000
 5FD  H3''  C3'  C4'   111.46  3.000
 5FD  H3''  C3'  O3'   111.29  3.000
 5FD  C4'   C3'  O3'   112.80  3.000
 5FD  H3''  C3'  C2'   111.86  3.000
 5FD  C4'   C3'  C2'   100.61  3.000
 5FD  O3'   C3'  C2'   108.34  3.000
 5FD  HO3   O3'  C3'   108.53  3.000
 5FD  H4'   C4'  O4'   109.44  3.000
 5FD  H4'   C4'  C5'   108.60  3.000
 5FD  O4'   C4'  C5'   110.06  3.000
 5FD  H4'   C4'  C3'   110.35  3.000
 5FD  O4'   C4'  C3'   106.80  3.000
 5FD  C5'   C4'  C3'   111.57  3.000
 5FD  H5'2  C5'  H5'1  108.87  3.000
 5FD  H5'2  C5'  F19   108.37  3.000
 5FD  H5'1  C5'  F19   108.12  3.000
 5FD  H5'2  C5'  C4'   109.96  3.000
 5FD  H5'1  C5'  C4'   111.64  3.000
 5FD  F19   C5'  C4'   109.80  3.000
 5FD  C1'   O4'  C4'   109.80  3.000
 5FD  H1'   C1'  N9    107.62  3.000
 5FD  H1'   C1'  O4'   109.91  3.000
 5FD  N9    C1'  O4'   110.78  3.000
 5FD  H1'   C1'  C2'   109.96  3.000
 5FD  N9    C1'  C2'   114.83  3.000
 5FD  O4'   C1'  C2'   103.69  3.000
 5FD  C4    N9   C8    107.38  3.000
 5FD  C4    N9   C1'   126.75  3.000
 5FD  C8    N9   C1'   124.97  3.000
 5FD  HC8   C8   N7    123.46  3.000
 5FD  HC8   C8   N9    119.44  3.000
 5FD  N7    C8   N9    117.10  3.000
 5FD  C5    N7   C8    105.12  3.000
 5FD  H55   C5   C6    107.51  3.000
 5FD  H55   C5   C4    109.25  3.000
 5FD  C6    C5   C4    114.92  3.000
 5FD  H55   C5   N7    108.60  3.000
 5FD  C6    C5   N7    110.57  3.000
 5FD  C4    C5   N7    105.85  3.000
 5FD  H44   C4   N3    108.70  3.000
 5FD  H44   C4   C5    111.43  3.000
 5FD  N3    C4   C5    116.09  3.000
 5FD  H44   C4   N9    111.72  3.000
 5FD  N3    C4   N9    109.20  3.000
 5FD  C5    C4   N9     99.46  3.000
 5FD  C2    N3   C4    118.55  3.000
 5FD  HC2   C2   N1    113.97  3.000
 5FD  HC2   C2   N3    119.39  3.000
 5FD  N1    C2   N3    126.64  3.000
 5FD  HN1   N1   C6    117.85  3.000
 5FD  HN1   N1   C2    118.50  3.000
 5FD  C6    N1   C2    123.61  3.000
 5FD  N6    C6   N1    119.48  3.000
 5FD  N6    C6   C5    125.61  3.000
 5FD  N1    C6   C5    114.86  3.000
 5FD  HN2   N6   C6    110.53  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
 5FD  CONST_01  N7   C8  N9  C1'  180.00  0.0  0
 5FD  CONST_02  C5   N7  C8  N9     0.00  0.0  0
 5FD  CONST_03  C4   N9  C8  N7     0.00  0.0  0
 5FD  CONST_04  C2   N1  C6  C5     0.00  0.0  0
 5FD  CONST_05  N1   C2  N3  C4     0.00  0.0  0
 5FD  CONST_06  C6   N1  C2  N3     0.00  0.0  0
 5FD  CONST_07  N6   C6  N1  C2   180.00  0.0  0
 5FD  CONST_08  HC8  C8  N9  C1'    0.00  0.0  0
 5FD  CONST_09  HN1  N1  C6  C5   180.00  0.0  0
 5FD  CONST_10  HC2  C2  N3  C4   180.00  0.0  0
 5FD  CONST_11  HN2  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
 5FD  chir_01  C2'  O2'  C3'  C1'  positiv
 5FD  chir_02  C3'  O3'  C4'  C2'  positiv
 5FD  chir_03  C4'  O4'  C3'  C5'  negativ
 5FD  chir_04  C1'  O4'  N9   C2'  negativ
 5FD  chir_05  C5   N7   C4   C6   negativ
 5FD  chir_06  C4   N3   N9   C5   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
 5FD  plan-1  C1'  0.020
 5FD  plan-1  N9   0.020
 5FD  plan-1  C8   0.020
 5FD  plan-1  N7   0.020
 5FD  plan-1  C5   0.020
 5FD  plan-1  C4   0.020
 5FD  plan-1  HC8  0.020
 5FD  plan-2  C5   0.020
 5FD  plan-2  C4   0.020
 5FD  plan-2  N3   0.020
 5FD  plan-2  C2   0.020
 5FD  plan-2  N1   0.020
 5FD  plan-2  C6   0.020
 5FD  plan-2  N6   0.020
 5FD  plan-2  HC2  0.020
 5FD  plan-2  HN1  0.020
 5FD  plan-2  HN2  0.020

