# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 00:25:35 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 2-fluoroadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(F)nc2n(cnc12)[C@@H]3O[C@H](CO)[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
 2FA  2FA  '2-fluoroadenosine        '  ligand  32  20  .  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_2FA
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
 2FA  O5'   O  OH1   0  -0.668  -4.5499   1.7450  -1.0968
 2FA  C5'   C  CH2   0  -0.154  -3.9331   1.2595   0.0689
 2FA  C4'   C  CR15  0   0.009  -3.2814  -0.0673  -0.2330
 2FA  O4'   O  O     0  -0.496  -2.2395   0.0844  -1.2006
 2FA  C1'   C  CR15  0   0.175  -1.0942  -0.6131  -0.8255
 2FA  N9    N  NR5   0  -0.537  -0.0613   0.3443  -0.4259
 2FA  C4    C  CR56  0   0.496   1.2328   0.0354  -0.1473
 2FA  N3    N  N     0  -0.489   1.8105  -1.1700  -0.1415
 2FA  C2    C  CR6   0   0.570   3.0722  -1.0668   0.1706
 2FA  F     F  F     0  -0.287   3.7351  -2.2207   0.2036
 2FA  N1    N  N     0  -0.504   3.8088  -0.0200   0.4599
 2FA  C6    C  CR6   0   0.476   3.2217   1.1847   0.4486
 2FA  N6    N  NH2   0  -0.807   3.9445   2.2603   0.7380
 2FA  C5    C  CR56  0  -0.005   1.8509   1.2435   0.1285
 2FA  N7    N  N     0  -0.446   0.9625   2.2781   0.0125
 2FA  C8    C  CR15  0   0.102  -0.1572   1.7081  -0.3224
 2FA  C2'   C  CR15  0  -0.040  -1.4915  -1.5210   0.3365
 2FA  O2'   O  OH1   0  -0.664  -1.9989  -2.7056  -0.2109
 2FA  C3'   C  CR15  0  -0.044  -2.6035  -0.6897   0.9840
 2FA  O3'   O  OH1   0  -0.655  -3.5224  -1.4472   1.7179
 2FA  H5'   H  HOH1  0   0.460  -4.9529   2.5934  -0.8920
 2FA  H5'1  H  HCH2  0   0.216  -4.6554   1.0904   0.8783
 2FA  H5'2  H  HCH2  0   0.197  -3.1796   1.9576   0.4581
 2FA  H4'   H  HCR5  0   0.248  -4.0362  -0.7567  -0.6312
 2FA  H1'   H  HCR5  0   0.289  -0.7000  -1.1830  -1.6712
 2FA  HN61  H  HNH2  0   0.411   4.9282   2.1790   0.9309
 2FA  HN62  H  HNH2  0   0.418   3.5384   3.1795   0.7119
 2FA  H8    H  HCR5  0   0.300  -1.0773   2.2339  -0.5204
 2FA  H2'   H  HCR5  0   0.263  -0.6575  -1.7115   1.0220
 2FA  H1    H  HOH1  0   0.452  -2.6680  -3.0482   0.3947
 2FA  H3'   H  HCR5  0   0.245  -2.1469   0.0971   1.5996
 2FA  H2    H  HOH1  0   0.470  -3.1707  -1.5903   2.6027

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
 2FA  O5'  C5'   single    1.405  0.020  1.405
 2FA  O5'  H5'   single    0.850  0.020  0.980
 2FA  C5'  C4'   single    1.509  0.020  1.509
 2FA  C5'  H5'1  single    0.970  0.020  1.090
 2FA  C5'  H5'2  single    0.970  0.020  1.090
 2FA  C4'  O4'   single    1.430  0.020  1.430
 2FA  C4'  C3'   single    1.526  0.020  1.526
 2FA  C4'  H4'   single    0.970  0.020  1.090
 2FA  O4'  C1'   single    1.392  0.020  1.392
 2FA  C1'  N9    single    1.464  0.020  1.464
 2FA  C1'  C2'   single    1.527  0.020  1.527
 2FA  C1'  H1'   single    0.970  0.020  1.090
 2FA  N9   C4    aromatic  1.359  0.020  1.359
 2FA  N9   C8    aromatic  1.371  0.020  1.371
 2FA  C4   N3    aromatic  1.337  0.020  1.337
 2FA  C4   C5    aromatic  1.385  0.020  1.385
 2FA  N3   C2    aromatic  1.304  0.020  1.304
 2FA  C2   F     single    1.331  0.020  1.331
 2FA  C2   N1    aromatic  1.312  0.020  1.312
 2FA  N1   C6    aromatic  1.340  0.020  1.340
 2FA  C6   N6    single    1.328  0.020  1.328
 2FA  C6   C5    aromatic  1.409  0.020  1.409
 2FA  N6   HN61  single    0.860  0.020  1.020
 2FA  N6   HN62  single    0.860  0.020  1.020
 2FA  C5   N7    aromatic  1.369  0.020  1.369
 2FA  N7   C8    aromatic  1.300  0.020  1.300
 2FA  C8   H8    single    0.930  0.020  1.080
 2FA  C2'  O2'   single    1.400  0.020  1.400
 2FA  C2'  C3'   single    1.532  0.020  1.532
 2FA  C2'  H2'   single    0.970  0.020  1.090
 2FA  O2'  H1    single    0.850  0.020  0.980
 2FA  C3'  O3'   single    1.399  0.020  1.399
 2FA  C3'  H3'   single    0.970  0.020  1.090
 2FA  O3'  H2    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
 2FA  H5'   O5'  C5'   108.19  3.000
 2FA  H5'2  C5'  H5'1  106.74  3.000
 2FA  H5'2  C5'  C4'   109.48  3.000
 2FA  H5'1  C5'  C4'   107.24  3.000
 2FA  H5'2  C5'  O5'   112.05  3.000
 2FA  H5'1  C5'  O5'   112.08  3.000
 2FA  C4'   C5'  O5'   109.11  3.000
 2FA  H4'   C4'  C3'   109.81  3.000
 2FA  H4'   C4'  O4'   108.81  3.000
 2FA  C3'   C4'  O4'   105.03  3.000
 2FA  H4'   C4'  C5'   109.15  3.000
 2FA  C3'   C4'  C5'   113.02  3.000
 2FA  O4'   C4'  C5'   110.90  3.000
 2FA  C1'   O4'  C4'   111.34  3.000
 2FA  H1'   C1'  C2'   111.87  3.000
 2FA  H1'   C1'  N9    107.31  3.000
 2FA  C2'   C1'  N9    111.38  3.000
 2FA  H1'   C1'  O4'   110.45  3.000
 2FA  C2'   C1'  O4'   106.79  3.000
 2FA  N9    C1'  O4'   109.04  3.000
 2FA  C8    N9   C4    106.09  3.000
 2FA  C8    N9   C1'   128.44  3.000
 2FA  C4    N9   C1'   125.39  3.000
 2FA  C5    C4   N3    126.37  3.000
 2FA  C5    C4   N9    105.52  3.000
 2FA  N3    C4   N9    128.12  3.000
 2FA  C2    N3   C4    110.36  3.000
 2FA  N1    C2   F     113.98  3.000
 2FA  N1    C2   N3    131.23  3.000
 2FA  F     C2   N3    114.79  3.000
 2FA  C6    N1   C2    117.99  3.000
 2FA  C5    C6   N6    123.05  3.000
 2FA  C5    C6   N1    117.75  3.000
 2FA  N6    C6   N1    119.20  3.000
 2FA  HN62  N6   HN61  118.29  3.000
 2FA  HN62  N6   C6    121.01  3.000
 2FA  HN61  N6   C6    120.58  3.000
 2FA  N7    C5   C6    133.03  3.000
 2FA  N7    C5   C4    110.67  3.000
 2FA  C6    C5   C4    116.30  3.000
 2FA  C8    N7   C5    104.44  3.000
 2FA  H8    C8   N7    124.64  3.000
 2FA  H8    C8   N9    122.08  3.000
 2FA  N7    C8   N9    113.28  3.000
 2FA  H2'   C2'  C3'   112.48  3.000
 2FA  H2'   C2'  O2'   111.91  3.000
 2FA  C3'   C2'  O2'   111.18  3.000
 2FA  H2'   C2'  C1'   112.41  3.000
 2FA  C3'   C2'  C1'   100.83  3.000
 2FA  O2'   C2'  C1'   107.44  3.000
 2FA  H1    O2'  C2'   107.83  3.000
 2FA  H3'   C3'  O3'   111.52  3.000
 2FA  H3'   C3'  C2'   108.90  3.000
 2FA  O3'   C3'  C2'   113.88  3.000
 2FA  H3'   C3'  C4'   109.85  3.000
 2FA  O3'   C3'  C4'   110.34  3.000
 2FA  C2'   C3'  C4'   101.93  3.000
 2FA  H2    O3'  C3'   108.83  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
 2FA  CONST_01  C2    N3  C4  N9   180.00  0.0  0
 2FA  CONST_02  C6    C5  C4  N9   180.00  0.0  0
 2FA  CONST_03  N7    C5  C4  N9     0.00  0.0  0
 2FA  CONST_04  C5    N7  C8  N9     0.00  0.0  0
 2FA  CONST_05  N7    C8  N9  C4     0.00  0.0  0
 2FA  CONST_06  N1    C2  N3  C4     0.00  0.0  0
 2FA  CONST_07  N1    C6  C5  C4     0.00  0.0  0
 2FA  CONST_08  C8    N7  C5  C4     0.00  0.0  0
 2FA  CONST_09  C8    N9  C4  N3   180.00  0.0  0
 2FA  CONST_10  C6    C5  C4  N3     0.00  0.0  0
 2FA  CONST_11  N7    C5  C4  N3   180.00  0.0  0
 2FA  CONST_12  C6    N1  C2  N3     0.00  0.0  0
 2FA  CONST_13  C5    C4  N3  C2     0.00  0.0  0
 2FA  CONST_14  C5    C6  N1  C2     0.00  0.0  0
 2FA  CONST_15  N7    C5  C6  N1   180.00  0.0  0
 2FA  CONST_16  C8    N7  C5  C6   180.00  0.0  0
 2FA  CONST_17  C8    N9  C4  C5     0.00  0.0  0
 2FA  CONST_18  N3    C4  N9  C1'    0.00  0.0  0
 2FA  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 2FA  CONST_20  N7    C8  N9  C1'  180.00  0.0  0
 2FA  CONST_21  F     C2  N3  C4   180.00  0.0  0
 2FA  CONST_22  N6    C6  C5  C4   180.00  0.0  0
 2FA  CONST_23  N6    C6  N1  C2   180.00  0.0  0
 2FA  CONST_24  C6    N1  C2  F    180.00  0.0  0
 2FA  CONST_25  N7    C5  C6  N6     0.00  0.0  0
 2FA  CONST_26  H8    C8  N9  C1'    0.00  0.0  0
 2FA  CONST_27  HN61  N6  C6  N1     0.00  0.0  0
 2FA  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
 2FA  chir_01  C4'  C5'  O4'  C3'  negativ
 2FA  chir_02  C1'  O4'  N9   C2'  negativ
 2FA  chir_03  C2'  O2'  C1'  C3'  negativ
 2FA  chir_04  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
 2FA  plan-1  C1'   0.020
 2FA  plan-1  N9    0.020
 2FA  plan-1  C4    0.020
 2FA  plan-1  N3    0.020
 2FA  plan-1  C2    0.020
 2FA  plan-1  F     0.020
 2FA  plan-1  N1    0.020
 2FA  plan-1  C6    0.020
 2FA  plan-1  N6    0.020
 2FA  plan-1  C5    0.020
 2FA  plan-1  N7    0.020
 2FA  plan-1  C8    0.020
 2FA  plan-1  H8    0.020
 2FA  plan-2  C6    0.020
 2FA  plan-2  N6    0.020
 2FA  plan-2  HN61  0.020
 2FA  plan-2  HN62  0.020

