# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:34:21 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: 2-chloro-9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)nc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@@H]3F
#
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
 CFB  CFB  2-chloro-9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-9H-purin-6-amine  ligand  31  20  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CFB
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
 CFB  O5'   O   OH1   0  -0.668  -4.2686   1.8052  -1.0594
 CFB  C5'   C   CH2   0  -0.163  -4.1381   0.9423   0.0432
 CFB  C4'   C   CH1   0  -0.035  -3.5989  -0.3830  -0.4608
 CFB  O4'   O   O2    0  -0.494  -2.3769  -0.2147  -1.1819
 CFB  C3'   C   CH1   0  -0.066  -3.2695  -1.3664   0.6577
 CFB  O3'   O   OH1   0  -0.664  -3.3768  -2.6623   0.1285
 CFB  C2'   C   CH1   0   0.119  -1.8030  -1.0520   0.9447
 CFB  F     F   F     0  -0.358  -1.6971   0.0302   1.8016
 CFB  C1'   C   CH1   0   0.165  -1.2833  -0.6670  -0.4464
 CFB  N9    N   NR5   0  -0.535  -0.2870   0.3792  -0.3913
 CFB  C8    C   CR15  0   0.109  -0.4873   1.7316  -0.4712
 CFB  N7    N   N     0  -0.448   0.6044   2.4198  -0.3092
 CFB  C5    C   CR56  0   0.002   1.5750   1.4779  -0.0978
 CFB  C4    C   CR56  0   0.507   1.0373   0.2027  -0.1425
 CFB  N3    N   N     0  -0.433   1.6945  -0.9460   0.0268
 CFB  C2    C   CR6   0   0.277   2.9674  -0.7243   0.2399
 CFB  CL    CL  CL    0  -0.111   3.9358  -2.1476   0.4705
 CFB  N1    N   N     0  -0.452   3.6329   0.4103   0.3082
 CFB  C6    C   CR6   0   0.478   2.9598   1.5582   0.1425
 CFB  N6    N   NH2   0  -0.811   3.6182   2.7095   0.2153
 CFB  H5'   H   HOH1  0   0.460  -4.6009   2.6493  -0.7411
 CFB  H5'1  H   HCH2  0   0.222  -5.1042   0.7406   0.5244
 CFB  H5'2  H   HCH2  0   0.208  -3.4826   1.3668   0.8117
 CFB  H4'   H   HCH1  0   0.268  -4.3270  -0.8219  -1.1491
 CFB  H3'   H   HCH1  0   0.272  -3.8980  -1.2232   1.5448
 CFB  H1    H   HOH1  0   0.463  -3.1708  -3.2994   0.8209
 CFB  H2'   H   HCH1  0   0.273  -1.2507  -1.8846   1.3828
 CFB  H1'   H   HCH1  0   0.286  -0.8212  -1.5352  -0.9258
 CFB  H8    H   HCR5  0   0.298  -1.4594   2.1502  -0.6823
 CFB  HN61  H   HNH2  0   0.410   4.6133   2.7207   0.3608
 CFB  HN62  H   HNH2  0   0.418   3.1469   3.5861   0.0743

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
 CFB  O5'  C5'   single    1.406  0.020  1.406
 CFB  O5'  H5'   single    0.850  0.020  0.980
 CFB  C5'  C4'   single    1.517  0.020  1.517
 CFB  C5'  H5'1  single    0.970  0.020  1.090
 CFB  C5'  H5'2  single    0.970  0.020  1.090
 CFB  C4'  O4'   single    1.429  0.020  1.429
 CFB  C4'  C3'   single    1.525  0.020  1.525
 CFB  C4'  H4'   single    0.970  0.020  1.090
 CFB  O4'  C1'   single    1.393  0.020  1.393
 CFB  C3'  O3'   single    1.404  0.020  1.404
 CFB  C3'  C2'   single    1.527  0.020  1.527
 CFB  C3'  H3'   single    0.970  0.020  1.090
 CFB  O3'  H1    single    0.850  0.020  0.980
 CFB  C2'  F     single    1.384  0.020  1.384
 CFB  C2'  C1'   single    1.534  0.020  1.534
 CFB  C2'  H2'   single    0.970  0.020  1.090
 CFB  C1'  N9    single    1.446  0.020  1.446
 CFB  C1'  H1'   single    0.970  0.020  1.090
 CFB  N9   C8    aromatic  1.369  0.020  1.369
 CFB  N9   C4    aromatic  1.359  0.020  1.359
 CFB  C8   N7    aromatic  1.301  0.020  1.301
 CFB  C8   H8    single    0.930  0.020  1.080
 CFB  N7   C5    aromatic  1.369  0.020  1.369
 CFB  C5   C4    aromatic  1.385  0.020  1.385
 CFB  C5   C6    aromatic  1.408  0.020  1.408
 CFB  C4   N3    aromatic  1.334  0.020  1.334
 CFB  N3   C2    aromatic  1.310  0.020  1.310
 CFB  C2   CL    single    1.737  0.020  1.737
 CFB  C2   N1    aromatic  1.317  0.020  1.317
 CFB  N1   C6    aromatic  1.341  0.020  1.341
 CFB  C6   N6    single    1.328  0.020  1.328
 CFB  N6   HN61  single    0.860  0.020  1.020
 CFB  N6   HN62  single    0.860  0.020  1.020

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
 CFB  H5'   O5'  C5'   108.14  3.000
 CFB  H5'2  C5'  H5'1  106.87  3.000
 CFB  H5'2  C5'  C4'   111.03  3.000
 CFB  H5'1  C5'  C4'   107.33  3.000
 CFB  H5'2  C5'  O5'   111.57  3.000
 CFB  H5'1  C5'  O5'   112.01  3.000
 CFB  C4'   C5'  O5'   107.97  3.000
 CFB  H4'   C4'  C3'   110.28  3.000
 CFB  H4'   C4'  O4'   107.40  3.000
 CFB  C3'   C4'  O4'   105.15  3.000
 CFB  H4'   C4'  C5'   108.84  3.000
 CFB  C3'   C4'  C5'   113.35  3.000
 CFB  O4'   C4'  C5'   111.64  3.000
 CFB  C1'   O4'  C4'   111.50  3.000
 CFB  H3'   C3'  C2'   111.81  3.000
 CFB  H3'   C3'  O3'   112.44  3.000
 CFB  C2'   C3'  O3'   109.53  3.000
 CFB  H3'   C3'  C4'   112.66  3.000
 CFB  C2'   C3'  C4'   102.27  3.000
 CFB  O3'   C3'  C4'   107.59  3.000
 CFB  H1    O3'  C3'   108.86  3.000
 CFB  H2'   C2'  C1'   112.60  3.000
 CFB  H2'   C2'  F     108.02  3.000
 CFB  C1'   C2'  F     109.82  3.000
 CFB  H2'   C2'  C3'   113.86  3.000
 CFB  C1'   C2'  C3'   101.92  3.000
 CFB  F     C2'  C3'   110.53  3.000
 CFB  H1'   C1'  N9    107.45  3.000
 CFB  H1'   C1'  C2'   109.95  3.000
 CFB  N9    C1'  C2'   112.36  3.000
 CFB  H1'   C1'  O4'   110.96  3.000
 CFB  N9    C1'  O4'   109.03  3.000
 CFB  C2'   C1'  O4'   107.11  3.000
 CFB  C4    N9   C8    106.35  3.000
 CFB  C4    N9   C1'   125.77  3.000
 CFB  C8    N9   C1'   127.71  3.000
 CFB  H8    C8   N7    125.11  3.000
 CFB  H8    C8   N9    121.75  3.000
 CFB  N7    C8   N9    113.11  3.000
 CFB  C5    N7   C8    104.49  3.000
 CFB  C6    C5   C4    116.10  3.000
 CFB  C6    C5   N7    133.20  3.000
 CFB  C4    C5   N7    110.70  3.000
 CFB  N3    C4   C5    126.70  3.000
 CFB  N3    C4   N9    127.95  3.000
 CFB  C5    C4   N9    105.35  3.000
 CFB  C2    N3   C4    110.71  3.000
 CFB  N1    C2   CL    114.67  3.000
 CFB  N1    C2   N3    130.19  3.000
 CFB  CL    C2   N3    115.14  3.000
 CFB  C6    N1   C2    118.52  3.000
 CFB  N6    C6   N1    119.11  3.000
 CFB  N6    C6   C5    123.12  3.000
 CFB  N1    C6   C5    117.77  3.000
 CFB  HN62  N6   HN61  118.33  3.000
 CFB  HN62  N6   C6    121.05  3.000
 CFB  HN61  N6   C6    120.53  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
 CFB  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 CFB  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 CFB  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 CFB  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 CFB  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 CFB  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 CFB  CONST_07  C4    C5  N7  C8     0.00  0.0  0
 CFB  CONST_08  C6    C5  N7  C8   180.00  0.0  0
 CFB  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 CFB  CONST_10  N3    C4  C5  N7   180.00  0.0  0
 CFB  CONST_11  N1    C6  C5  N7   180.00  0.0  0
 CFB  CONST_12  C2    N3  C4  C5     0.00  0.0  0
 CFB  CONST_13  C2    N1  C6  C5     0.00  0.0  0
 CFB  CONST_14  N1    C6  C5  C4     0.00  0.0  0
 CFB  CONST_15  N1    C2  N3  C4     0.00  0.0  0
 CFB  CONST_16  C6    C5  C4  N3     0.00  0.0  0
 CFB  CONST_17  C6    N1  C2  N3     0.00  0.0  0
 CFB  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 CFB  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 CFB  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 CFB  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 CFB  CONST_22  N6    C6  C5  C4   180.00  0.0  0
 CFB  CONST_23  CL    C2  N3  C4   180.00  0.0  0
 CFB  CONST_24  N6    C6  N1  C2   180.00  0.0  0
 CFB  CONST_25  C6    N1  C2  CL   180.00  0.0  0
 CFB  CONST_26  H8    C8  N9  C1'    0.00  0.0  0
 CFB  CONST_27  HN61  N6  C6  C5   180.00  0.0  0
 CFB  CONST_28  HN62  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
 CFB  chir_01  C4'  C5'  O4'  C3'  negativ
 CFB  chir_02  C3'  O3'  C4'  C2'  positiv
 CFB  chir_03  C2'  F    C3'  C1'  negativ
 CFB  chir_04  C1'  O4'  N9   C2'  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
 CFB  plan-1  C1'   0.020
 CFB  plan-1  N9    0.020
 CFB  plan-1  C8    0.020
 CFB  plan-1  N7    0.020
 CFB  plan-1  C5    0.020
 CFB  plan-1  C4    0.020
 CFB  plan-1  N3    0.020
 CFB  plan-1  C2    0.020
 CFB  plan-1  CL    0.020
 CFB  plan-1  N1    0.020
 CFB  plan-1  C6    0.020
 CFB  plan-1  N6    0.020
 CFB  plan-1  H8    0.020
 CFB  plan-2  C6    0.020
 CFB  plan-2  N6    0.020
 CFB  plan-2  HN61  0.020
 CFB  plan-2  HN62  0.020

