# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:58:47 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (4S,5S)-4-(6-amino-9H-purin-9-yl)-3-fluoro-5-hydroxy-2-(hydroxymethyl)cyclopent-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3[C@H](O)C(=O)C(=C3F)CO
#
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
 AFX  AFX  (4S,5S)-4-(6-amino-9H-purin-9-yl)-3-fluoro-5-hydroxy-2-(hydroxymethyl)cyclopent-2-en-1-one  ligand  30  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AFX
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
 AFX  C1    C  CH2   0  -0.167  -4.2363  -1.1453  -0.0262
 AFX  F1    F  F     0  -0.254  -1.2726  -1.9316   0.5729
 AFX  N1    N  N     0  -0.474   4.3455   0.2035   0.8607
 AFX  O1    O  OH1   0  -0.660  -3.9963  -2.4765   0.3368
 AFX  C2    C  CR16  0   0.048   3.3855   0.5997   1.6916
 AFX  N3    N  N     0  -0.456   2.0796   0.6235   1.4863
 AFX  C4    C  CR56  0   0.499   1.7677   0.1805   0.2725
 AFX  C5    C  CR56  0  -0.011   2.6488  -0.2640  -0.6993
 AFX  C6    C  CR6   0   0.463   4.0140  -0.2407  -0.3572
 AFX  N6    N  NH2   0  -0.815   4.9753  -0.6299  -1.1951
 AFX  N7    N  N     0  -0.444   1.9750  -0.6513  -1.8291
 AFX  C8    C  CR15  0   0.108   0.7245  -0.4449  -1.5472
 AFX  N9    N  NR5   0  -0.518   0.5289   0.0603  -0.2886
 AFX  C1'   C  CR15  0  -0.288  -0.7231   0.3982   0.3379
 AFX  C2'   C  CR15  0  -0.035  -1.4975   1.5452  -0.3185
 AFX  O2'   O  OH1   0  -0.646  -1.2334   2.7599   0.3015
 AFX  C3'   C  CR5   0   0.329  -2.9500   1.0831  -0.2110
 AFX  O3'   O  O     0  -0.385  -3.9112   1.8088  -0.3049
 AFX  C4'   C  CR5   0  -0.216  -2.9712  -0.3649   0.0162
 AFX  C5'   C  CR5   0   0.520  -1.7173  -0.7231   0.2983
 AFX  H1    H  HCH2  0   0.233  -4.6566  -1.0589  -1.0375
 AFX  H1A   H  HCH2  0   0.232  -4.9546  -0.6544   0.6439
 AFX  HO1   H  HOH1  0   0.465  -4.8422  -2.9335   0.3573
 AFX  HN6   H  HNH2  0   0.404   5.9315  -0.6606  -0.8858
 AFX  HN6A  H  HNH2  0   0.412   4.7511  -1.0427  -2.0835
 AFX  H8    H  HCR5  0   0.308  -0.1025  -0.6424  -2.2145
 AFX  H1'   H  HCR5  0   0.344  -0.4997   0.6552   1.3781
 AFX  H2'   H  HCR5  0   0.281  -1.2541   1.5629  -1.3909
 AFX  HO2'  H  HOH1  0   0.469  -1.5799   3.4708  -0.2476
 AFX  H2    H  HCR6  0   0.254   3.7232   0.9463   2.6623

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
 AFX  C1   O1    single    1.401  0.020  1.401
 AFX  C1   C4'   single    1.487  0.020  1.487
 AFX  F1   C5'   single    1.317  0.020  1.317
 AFX  N1   C2    aromatic  1.330  0.020  1.330
 AFX  N1   C6    aromatic  1.338  0.020  1.338
 AFX  C2   N3    aromatic  1.322  0.020  1.322
 AFX  N3   C4    aromatic  1.329  0.020  1.329
 AFX  C4   C5    aromatic  1.385  0.020  1.385
 AFX  C4   N9    aromatic  1.365  0.020  1.365
 AFX  C5   C6    aromatic  1.408  0.020  1.408
 AFX  C5   N7    aromatic  1.371  0.020  1.371
 AFX  C6   N6    single    1.333  0.020  1.333
 AFX  N7   C8    aromatic  1.298  0.020  1.298
 AFX  C8   N9    aromatic  1.370  0.020  1.370
 AFX  N9   C1'   single    1.440  0.020  1.440
 AFX  C1'  C2'   single    1.532  0.020  1.532
 AFX  C1'  C5'   single    1.499  0.020  1.499
 AFX  C2'  O2'   single    1.389  0.020  1.389
 AFX  C2'  C3'   single    1.528  0.020  1.528
 AFX  C3'  O3'   double    1.208  0.020  1.208
 AFX  C3'  C4'   single    1.466  0.020  1.466
 AFX  C4'  C5'   double    1.334  0.020  1.334
 AFX  C1   H1    single    0.970  0.020  1.090
 AFX  C1   H1A   single    0.970  0.020  1.090
 AFX  O1   HO1   single    0.850  0.020  0.980
 AFX  C2   H2    single    0.930  0.020  1.080
 AFX  N6   HN6   single    0.860  0.020  1.020
 AFX  N6   HN6A  single    0.860  0.020  1.020
 AFX  C8   H8    single    0.930  0.020  1.080
 AFX  C1'  H1'   single    0.970  0.020  1.090
 AFX  C2'  H2'   single    0.970  0.020  1.090
 AFX  O2'  HO2'  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
 AFX  H1A   C1   H1   106.04  3.000
 AFX  H1A   C1   C4'  107.73  3.000
 AFX  H1    C1   C4'  108.08  3.000
 AFX  H1A   C1   O1   112.26  3.000
 AFX  H1    C1   O1   112.27  3.000
 AFX  C4'   C1   O1   110.22  3.000
 AFX  C6    N1   C2   119.26  3.000
 AFX  HO1   O1   C1   107.85  3.000
 AFX  H2    C2   N3   116.16  3.000
 AFX  H2    C2   N1   115.44  3.000
 AFX  N3    C2   N1   128.40  3.000
 AFX  C4    N3   C2   111.57  3.000
 AFX  N9    C4   C5   105.10  3.000
 AFX  N9    C4   N3   128.14  3.000
 AFX  C5    C4   N3   126.75  3.000
 AFX  N7    C5   C6   132.96  3.000
 AFX  N7    C5   C4   110.87  3.000
 AFX  C6    C5   C4   116.18  3.000
 AFX  N6    C6   C5   122.80  3.000
 AFX  N6    C6   N1   119.36  3.000
 AFX  C5    C6   N1   117.84  3.000
 AFX  HN6A  N6   HN6  118.13  3.000
 AFX  HN6A  N6   C6   120.98  3.000
 AFX  HN6   N6   C6   120.08  3.000
 AFX  C8    N7   C5   104.44  3.000
 AFX  H8    C8   N9   121.68  3.000
 AFX  H8    C8   N7   125.01  3.000
 AFX  N9    C8   N7   113.30  3.000
 AFX  C1'   N9   C8   127.60  3.000
 AFX  C1'   N9   C4   126.11  3.000
 AFX  C8    N9   C4   106.29  3.000
 AFX  H1'   C1'  C5'  109.64  3.000
 AFX  H1'   C1'  C2'  109.55  3.000
 AFX  C5'   C1'  C2'  102.33  3.000
 AFX  H1'   C1'  N9   106.92  3.000
 AFX  C5'   C1'  N9   112.93  3.000
 AFX  C2'   C1'  N9   115.39  3.000
 AFX  H2'   C2'  C3'  106.49  3.000
 AFX  H2'   C2'  O2'  112.27  3.000
 AFX  C3'   C2'  O2'  114.44  3.000
 AFX  H2'   C2'  C1'  108.55  3.000
 AFX  C3'   C2'  C1'  102.94  3.000
 AFX  O2'   C2'  C1'  111.56  3.000
 AFX  HO2'  O2'  C2'  108.83  3.000
 AFX  C4'   C3'  O3'  126.44  3.000
 AFX  C4'   C3'  C2'  108.87  3.000
 AFX  O3'   C3'  C2'  124.69  3.000
 AFX  C5'   C4'  C3'  106.52  3.000
 AFX  C5'   C4'  C1   131.66  3.000
 AFX  C3'   C4'  C1   121.75  3.000
 AFX  C4'   C5'  C1'  115.34  3.000
 AFX  C4'   C5'  F1   127.44  3.000
 AFX  C1'   C5'  F1   117.20  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
 AFX  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 AFX  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 AFX  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 AFX  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 AFX  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 AFX  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 AFX  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 AFX  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 AFX  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 AFX  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 AFX  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 AFX  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 AFX  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 AFX  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 AFX  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 AFX  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 AFX  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 AFX  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 AFX  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 AFX  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 AFX  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 AFX  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 AFX  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 AFX  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 AFX  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 AFX  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 AFX  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 AFX  Var_01    C3'   C4'  C5'  C1'    1.64  30.0  1
 AFX  Var_02    C5'   C4'  C3'  C2'   11.42  30.0  1

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
 AFX  chir_01  C1'  N9   C2'  C5'  negativ
 AFX  chir_02  C2'  O2'  C1'  C3'  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
 AFX  plan-1  N1    0.020
 AFX  plan-1  C2    0.020
 AFX  plan-1  N3    0.020
 AFX  plan-1  C4    0.020
 AFX  plan-1  C5    0.020
 AFX  plan-1  C6    0.020
 AFX  plan-1  N6    0.020
 AFX  plan-1  N7    0.020
 AFX  plan-1  C8    0.020
 AFX  plan-1  N9    0.020
 AFX  plan-1  C1'   0.020
 AFX  plan-1  H8    0.020
 AFX  plan-1  H2    0.020
 AFX  plan-2  C6    0.020
 AFX  plan-2  N6    0.020
 AFX  plan-2  HN6   0.020
 AFX  plan-2  HN6A  0.020
 AFX  plan-3  C2'   0.020
 AFX  plan-3  C3'   0.020
 AFX  plan-3  O3'   0.020
 AFX  plan-3  C4'   0.020

