# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:03:15 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2R,4S,5S)-2-(6-aminopurin-9-yl)-5-[bis(fluoranyl)methyl]oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C(F)F)[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
 Y3J  Y3J  (2R,4S,5S)-2-(6-aminopurin-9-yl)-5-[bis(fluoranyl)methyl]oxolane-3,4-diol  ligand  31  20  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y3J
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
 Y3J  N1    N  N     0  -0.474  -4.5806  -0.3828   0.8239
 Y3J  C2    C  CR16  0   0.048  -3.6795  -1.2545   1.2676
 Y3J  N3    N  N     0  -0.458  -2.3755  -1.2706   1.0500
 Y3J  C4    C  CR56  0   0.495  -1.9930  -0.2529   0.2841
 Y3J  C5    C  CR56  0  -0.011  -2.8086   0.7312  -0.2483
 Y3J  C6    C  CR6   0   0.462  -4.1798   0.6351   0.0535
 Y3J  N6    N  NH2   0  -0.816  -5.0820   1.5055  -0.3994
 Y3J  N7    N  N     0  -0.446  -2.0746   1.6294  -0.9812
 Y3J  C8    C  CR15  0   0.114  -0.8542   1.1967  -0.8961
 Y3J  N9    N  NR5   0  -0.542  -0.7324   0.0542  -0.1480
 Y3J  FAB   F  F     0  -0.338   3.0724   2.2527   0.9395
 Y3J  FAG   F  F     0  -0.339   4.5472   1.1048  -0.1955
 Y3J  CAH   C  CH1   0   0.547   3.2133   1.2510   0.0324
 Y3J  CAI   C  CH1   0  -0.136   2.6673  -0.0416   0.6088
 Y3J  OAJ   O  O2    0  -0.490   1.3051   0.1631   0.9577
 Y3J  CAK   C  CH1   0   0.200   0.4694  -0.6584   0.1796
 Y3J  CAQ   C  CH1   0  -0.054   2.6917  -1.2080  -0.3890
 Y3J  CAR   C  CH1   0  -0.014   1.3099  -1.0635  -1.0279
 Y3J  OAS   O  OH1   0  -0.662   2.7393  -2.4470   0.2611
 Y3J  OAT   O  OH1   0  -0.649   0.7685  -2.1990  -1.6143
 Y3J  H2    H  HCR6  0   0.254  -4.0702  -2.0532   1.8890
 Y3J  HN6   H  HNH2  0   0.404  -6.0443   1.4288  -0.1187
 Y3J  HN6A  H  HNH2  0   0.412  -4.8065   2.3085  -0.9371
 Y3J  H8    H  HCR5  0   0.296   0.0001   1.6733  -1.3534
 Y3J  HAH   H  HCH1  0   0.193   2.7340   1.5622  -0.8981
 Y3J  HAI   H  HCH1  0   0.289   3.2440  -0.2843   1.5088
 Y3J  HAK   H  HCH1  0   0.270   0.1547  -1.5467   0.7370
 Y3J  HAQ   H  HCH1  0   0.270   3.4963  -1.1046  -1.1260
 Y3J  HOAS  H  HOH1  0   0.462   3.5959  -2.5352   0.6914
 Y3J  HAR   H  HCH1  0   0.246   1.3591  -0.2240  -1.7367
 Y3J  HAT   H  HOH1  0   0.467   1.2107  -2.3589  -2.4540

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
 Y3J  N1   C2    aromatic  1.330  0.020  1.330
 Y3J  N1   C6    aromatic  1.338  0.020  1.338
 Y3J  C2   N3    aromatic  1.322  0.020  1.322
 Y3J  N3   C4    aromatic  1.330  0.020  1.330
 Y3J  C4   C5    aromatic  1.385  0.020  1.385
 Y3J  C4   N9    aromatic  1.367  0.020  1.367
 Y3J  C5   C6    aromatic  1.407  0.020  1.407
 Y3J  C5   N7    aromatic  1.372  0.020  1.372
 Y3J  C6   N6    single    1.333  0.020  1.333
 Y3J  N7   C8    aromatic  1.298  0.020  1.298
 Y3J  C8   N9    aromatic  1.371  0.020  1.371
 Y3J  N9   CAK   single    1.435  0.020  1.435
 Y3J  FAB  CAH   single    1.359  0.020  1.359
 Y3J  FAG  CAH   single    1.361  0.020  1.361
 Y3J  CAH  CAI   single    1.517  0.020  1.517
 Y3J  CAI  OAJ   single    1.421  0.020  1.421
 Y3J  CAI  CAQ   single    1.535  0.020  1.535
 Y3J  OAJ  CAK   single    1.407  0.020  1.407
 Y3J  CAK  CAR   single    1.526  0.020  1.526
 Y3J  CAQ  CAR   single    1.529  0.020  1.529
 Y3J  CAQ  OAS   single    1.400  0.020  1.400
 Y3J  CAR  OAT   single    1.388  0.020  1.388
 Y3J  C2   H2    single    0.930  0.020  1.080
 Y3J  N6   HN6   single    0.860  0.020  1.020
 Y3J  N6   HN6A  single    0.860  0.020  1.020
 Y3J  C8   H8    single    0.930  0.020  1.080
 Y3J  CAH  HAH   single    0.970  0.020  1.090
 Y3J  CAI  HAI   single    0.970  0.020  1.090
 Y3J  CAK  HAK   single    0.970  0.020  1.090
 Y3J  CAQ  HAQ   single    0.970  0.020  1.090
 Y3J  OAS  HOAS  single    0.850  0.020  0.980
 Y3J  CAR  HAR   single    0.970  0.020  1.090
 Y3J  OAT  HAT   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
 Y3J  C6    N1   C2   119.20  3.000
 Y3J  H2    C2   N3   116.13  3.000
 Y3J  H2    C2   N1   115.46  3.000
 Y3J  N3    C2   N1   128.41  3.000
 Y3J  C4    N3   C2   111.66  3.000
 Y3J  N9    C4   C5   105.18  3.000
 Y3J  N9    C4   N3   128.24  3.000
 Y3J  C5    C4   N3   126.58  3.000
 Y3J  N7    C5   C6   132.88  3.000
 Y3J  N7    C5   C4   110.83  3.000
 Y3J  C6    C5   C4   116.29  3.000
 Y3J  N6    C6   C5   122.82  3.000
 Y3J  N6    C6   N1   119.32  3.000
 Y3J  C5    C6   N1   117.86  3.000
 Y3J  HN6A  N6   HN6  118.22  3.000
 Y3J  HN6A  N6   C6   121.20  3.000
 Y3J  HN6   N6   C6   120.21  3.000
 Y3J  C8    N7   C5   104.46  3.000
 Y3J  H8    C8   N9   121.91  3.000
 Y3J  H8    C8   N7   124.68  3.000
 Y3J  N9    C8   N7   113.40  3.000
 Y3J  CAK   N9   C8   127.78  3.000
 Y3J  CAK   N9   C4   126.04  3.000
 Y3J  C8    N9   C4   106.12  3.000
 Y3J  HAH   CAH  CAI  114.12  3.000
 Y3J  HAH   CAH  FAG  108.54  3.000
 Y3J  CAI   CAH  FAG  108.95  3.000
 Y3J  HAH   CAH  FAB  108.26  3.000
 Y3J  CAI   CAH  FAB  109.71  3.000
 Y3J  FAG   CAH  FAB  107.01  3.000
 Y3J  HAI   CAI  CAQ  110.92  3.000
 Y3J  HAI   CAI  OAJ  109.55  3.000
 Y3J  CAQ   CAI  OAJ  106.52  3.000
 Y3J  HAI   CAI  CAH  108.14  3.000
 Y3J  CAQ   CAI  CAH  113.25  3.000
 Y3J  OAJ   CAI  CAH  108.39  3.000
 Y3J  CAK   OAJ  CAI  110.46  3.000
 Y3J  HAK   CAK  CAR  110.23  3.000
 Y3J  HAK   CAK  OAJ  111.28  3.000
 Y3J  CAR   CAK  OAJ  105.40  3.000
 Y3J  HAK   CAK  N9   106.16  3.000
 Y3J  CAR   CAK  N9   114.36  3.000
 Y3J  OAJ   CAK  N9   109.50  3.000
 Y3J  HAQ   CAQ  OAS  111.77  3.000
 Y3J  HAQ   CAQ  CAR  111.93  3.000
 Y3J  OAS   CAQ  CAR  107.96  3.000
 Y3J  HAQ   CAQ  CAI  112.15  3.000
 Y3J  OAS   CAQ  CAI  111.78  3.000
 Y3J  CAR   CAQ  CAI  100.68  3.000
 Y3J  HAR   CAR  OAT  111.69  3.000
 Y3J  HAR   CAR  CAQ  107.52  3.000
 Y3J  OAT   CAR  CAQ  116.85  3.000
 Y3J  HAR   CAR  CAK  109.39  3.000
 Y3J  OAT   CAR  CAK  109.67  3.000
 Y3J  CAQ   CAR  CAK  101.09  3.000
 Y3J  HOAS  OAS  CAQ  108.60  3.000
 Y3J  HAT   OAT  CAR  108.99  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
 Y3J  CONST_01  C4    N3  C2  N1    0.00  0.0  0
 Y3J  CONST_02  C4    C5  C6  N1    0.00  0.0  0
 Y3J  CONST_03  N7    C5  C6  N1  180.00  0.0  0
 Y3J  CONST_04  C5    C6  N1  C2    0.00  0.0  0
 Y3J  CONST_05  C5    C4  N3  C2    0.00  0.0  0
 Y3J  CONST_06  N9    C4  N3  C2  180.00  0.0  0
 Y3J  CONST_07  C6    N1  C2  N3    0.00  0.0  0
 Y3J  CONST_08  C6    C5  C4  N3    0.00  0.0  0
 Y3J  CONST_09  N7    C5  C4  N3  180.00  0.0  0
 Y3J  CONST_10  C8    N9  C4  N3  180.00  0.0  0
 Y3J  CONST_11  C8    N7  C5  C4    0.00  0.0  0
 Y3J  CONST_12  N7    C8  N9  C4    0.00  0.0  0
 Y3J  CONST_13  C8    N9  C4  C5    0.00  0.0  0
 Y3J  CONST_14  N9    C8  N7  C5    0.00  0.0  0
 Y3J  CONST_15  N9    C4  C5  C6  180.00  0.0  0
 Y3J  CONST_16  C8    N7  C5  C6  180.00  0.0  0
 Y3J  CONST_17  N9    C4  C5  N7    0.00  0.0  0
 Y3J  CONST_18  CAK   N9  C4  N3    0.00  0.0  0
 Y3J  CONST_19  CAK   N9  C4  C5  180.00  0.0  0
 Y3J  CONST_20  CAK   N9  C8  N7  180.00  0.0  0
 Y3J  CONST_21  N6    C6  N1  C2  180.00  0.0  0
 Y3J  CONST_22  N6    C6  C5  C4  180.00  0.0  0
 Y3J  CONST_23  N7    C5  C6  N6    0.00  0.0  0
 Y3J  CONST_24  H2    C2  N3  C4  180.00  0.0  0
 Y3J  CONST_25  H8    C8  N9  C4  180.00  0.0  0
 Y3J  CONST_26  HN6   N6  C6  N1    0.00  0.0  0
 Y3J  CONST_27  HN6A  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
 Y3J  chir_01  CAI  CAH  OAJ  CAQ  negativ
 Y3J  chir_02  CAK  OAJ  N9   CAR  negativ
 Y3J  chir_03  CAQ  OAS  CAR  CAI  negativ
 Y3J  chir_04  CAR  OAT  CAK  CAQ  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
 Y3J  plan-1  N1    0.020
 Y3J  plan-1  C2    0.020
 Y3J  plan-1  N3    0.020
 Y3J  plan-1  C4    0.020
 Y3J  plan-1  C5    0.020
 Y3J  plan-1  C6    0.020
 Y3J  plan-1  N6    0.020
 Y3J  plan-1  N7    0.020
 Y3J  plan-1  C8    0.020
 Y3J  plan-1  N9    0.020
 Y3J  plan-1  CAK   0.020
 Y3J  plan-1  H2    0.020
 Y3J  plan-1  H8    0.020
 Y3J  plan-2  C6    0.020
 Y3J  plan-2  N6    0.020
 Y3J  plan-2  HN6   0.020
 Y3J  plan-2  HN6A  0.020

