# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 02:44:31 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: [(2S,5R)-5-(6-amino-2-chloro-9H-purin-9-yl)tetrahydrofuran-2-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)nc2n(cnc12)[C@H]3CC[C@@H](CO)O3
#
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
 CDY  CDY  '[(2S,5R)-5-(6-amino-2-chloro-9H-purin-9-yl)tetrahydrofuran-2-yl]methanol'  ligand  30  18  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CDY
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
 CDY  O5'   O   OH1   0  -0.670   0.5218  -1.0532  -5.3229
 CDY  C5'   C   CH2   0  -0.156   0.4797   0.1773  -4.6427
 CDY  C4'   C   CH1   0   0.020  -0.7285   0.2058  -3.7403
 CDY  O4'   O   O2    0  -0.500  -0.6359  -0.8204  -2.7375
 CDY  C3'   C   CH2   0  -0.504  -0.8930   1.5062  -2.9696
 CDY  C2'   C   CH2   0  -0.508  -1.6461   1.0366  -1.7336
 CDY  C1'   C   CH1   0   0.194  -1.0302  -0.3385  -1.4949
 CDY  N9    N   NR5   0  -0.531   0.1480  -0.2582  -0.6206
 CDY  C8    C   CR15  0   0.100   1.4691  -0.3935  -0.9451
 CDY  N7    N   N     0  -0.450   2.2687  -0.2681   0.0761
 CDY  C5    C   CR56  0   0.005   1.4328  -0.0412   1.1340
 CDY  C4    C   CR56  0   0.503   0.1110  -0.0352   0.7191
 CDY  N3    N   N     0  -0.434  -0.9628   0.1493   1.4926
 CDY  C2    C   CR6   0   0.272  -0.6115   0.3308   2.7400
 CDY  CL    CL  CL    0  -0.113  -1.9267   0.5794   3.8483
 CDY  N1    N   N     0  -0.453   0.5841   0.3547   3.2937
 CDY  C6    C   CR6   0   0.474   1.6548   0.1686   2.5084
 CDY  N6    N   NH2   0  -0.812   2.8667   0.1922   3.0528
 CDY  HO5   H   HOH1  0   0.458   1.3050  -1.0620  -5.8804
 CDY  HC51  H   HCH2  0   0.211   0.3912   1.0268  -5.3326
 CDY  HC52  H   HCH2  0   0.197   1.3860   0.3462  -4.0466
 CDY  H4'   H   HCH1  0   0.238  -1.6266   0.0131  -4.3405
 CDY  HC31  H   HCH2  0   0.272  -1.4409   2.2535  -3.5408
 CDY  HC32  H   HCH2  0   0.246   0.0783   1.9326  -2.7015
 CDY  HC21  H   HCH2  0   0.264  -2.7083   0.9153  -1.9534
 CDY  HC22  H   HCH2  0   0.275  -1.5558   1.6992  -0.8751
 CDY  H1'   H   HCH1  0   0.277  -1.7228  -1.0358  -1.0183
 CDY  HC8   H   HCR5  0   0.297   1.7922  -0.5992  -1.9525
 CDY  HN61  H   HNH2  0   0.410   2.9792   0.3193   4.0442
 CDY  HN62  H   HNH2  0   0.417   3.6884   0.0328   2.4962

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
 CDY  O5'  C5'   single    1.407  0.020  1.407
 CDY  O5'  HO5   single    0.850  0.020  0.980
 CDY  C5'  C4'   single    1.508  0.020  1.508
 CDY  C5'  HC51  single    0.970  0.020  1.090
 CDY  C5'  HC52  single    0.970  0.020  1.090
 CDY  C4'  O4'   single    1.438  0.020  1.438
 CDY  C4'  C3'   single    1.521  0.020  1.521
 CDY  C4'  H4'   single    0.970  0.020  1.090
 CDY  O4'  C1'   single    1.390  0.020  1.390
 CDY  C3'  C2'   single    1.522  0.020  1.522
 CDY  C3'  HC31  single    0.970  0.020  1.090
 CDY  C3'  HC32  single    0.970  0.020  1.090
 CDY  C2'  C1'   single    1.525  0.020  1.525
 CDY  C2'  HC21  single    0.970  0.020  1.090
 CDY  C2'  HC22  single    0.970  0.020  1.090
 CDY  C1'  N9    single    1.469  0.020  1.469
 CDY  C1'  H1'   single    0.970  0.020  1.090
 CDY  N9   C8    aromatic  1.367  0.020  1.367
 CDY  N9   C4    aromatic  1.359  0.020  1.359
 CDY  C8   N7    aromatic  1.303  0.020  1.303
 CDY  C8   HC8   single    0.930  0.020  1.080
 CDY  N7   C5    aromatic  1.367  0.020  1.367
 CDY  C5   C4    aromatic  1.385  0.020  1.385
 CDY  C5   C6    aromatic  1.408  0.020  1.408
 CDY  C4   N3    aromatic  1.336  0.020  1.336
 CDY  N3   C2    aromatic  1.309  0.020  1.309
 CDY  C2   CL    single    1.738  0.020  1.738
 CDY  C2   N1    aromatic  1.318  0.020  1.318
 CDY  N1   C6    aromatic  1.341  0.020  1.341
 CDY  C6   N6    single    1.329  0.020  1.329
 CDY  N6   HN61  single    0.860  0.020  1.020
 CDY  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
 CDY  HO5   O5'  C5'   108.22  3.000
 CDY  HC52  C5'  HC51  106.78  3.000
 CDY  HC52  C5'  C4'   109.48  3.000
 CDY  HC51  C5'  C4'   107.26  3.000
 CDY  HC52  C5'  O5'   111.87  3.000
 CDY  HC51  C5'  O5'   112.05  3.000
 CDY  C4'   C5'  O5'   109.26  3.000
 CDY  H4'   C4'  C3'   109.82  3.000
 CDY  H4'   C4'  O4'   107.99  3.000
 CDY  C3'   C4'  O4'   105.30  3.000
 CDY  H4'   C4'  C5'   108.97  3.000
 CDY  C3'   C4'  C5'   113.96  3.000
 CDY  O4'   C4'  C5'   110.62  3.000
 CDY  C1'   O4'  C4'   110.97  3.000
 CDY  HC32  C3'  HC31  107.93  3.000
 CDY  HC32  C3'  C2'   111.14  3.000
 CDY  HC31  C3'  C2'   112.89  3.000
 CDY  HC32  C3'  C4'   111.19  3.000
 CDY  HC31  C3'  C4'   112.06  3.000
 CDY  C2'   C3'  C4'   101.61  3.000
 CDY  HC22  C2'  HC21  107.90  3.000
 CDY  HC22  C2'  C1'   113.08  3.000
 CDY  HC21  C2'  C1'   108.92  3.000
 CDY  HC22  C2'  C3'   114.32  3.000
 CDY  HC21  C2'  C3'   110.63  3.000
 CDY  C1'   C2'  C3'   101.85  3.000
 CDY  H1'   C1'  N9    106.48  3.000
 CDY  H1'   C1'  C2'   112.81  3.000
 CDY  N9    C1'  C2'   111.56  3.000
 CDY  H1'   C1'  O4'   110.41  3.000
 CDY  N9    C1'  O4'   108.87  3.000
 CDY  C2'   C1'  O4'   106.69  3.000
 CDY  C4    N9   C8    106.06  3.000
 CDY  C4    N9   C1'   125.02  3.000
 CDY  C8    N9   C1'   128.92  3.000
 CDY  HC8   C8   N7    124.54  3.000
 CDY  HC8   C8   N9    122.03  3.000
 CDY  N7    C8   N9    113.42  3.000
 CDY  C5    N7   C8    104.31  3.000
 CDY  C6    C5   C4    116.24  3.000
 CDY  C6    C5   N7    133.13  3.000
 CDY  C4    C5   N7    110.63  3.000
 CDY  N3    C4   C5    126.44  3.000
 CDY  N3    C4   N9    127.98  3.000
 CDY  C5    C4   N9    105.58  3.000
 CDY  C2    N3   C4    110.81  3.000
 CDY  N1    C2   CL    114.59  3.000
 CDY  N1    C2   N3    130.28  3.000
 CDY  CL    C2   N3    115.13  3.000
 CDY  C6    N1   C2    118.42  3.000
 CDY  N6    C6   N1    119.07  3.000
 CDY  N6    C6   C5    123.12  3.000
 CDY  N1    C6   C5    117.81  3.000
 CDY  HN62  N6   HN61  118.32  3.000
 CDY  HN62  N6   C6    121.05  3.000
 CDY  HN61  N6   C6    120.54  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
 CDY  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 CDY  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 CDY  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 CDY  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 CDY  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 CDY  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 CDY  CONST_07  C4    C5   N7   C8     0.00   0.0  0
 CDY  CONST_08  C6    C5   N7   C8   180.00   0.0  0
 CDY  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 CDY  CONST_10  N3    C4   C5   N7   180.00   0.0  0
 CDY  CONST_11  N1    C6   C5   N7   180.00   0.0  0
 CDY  CONST_12  C2    N3   C4   C5     0.00   0.0  0
 CDY  CONST_13  C2    N1   C6   C5     0.00   0.0  0
 CDY  CONST_14  N1    C6   C5   C4     0.00   0.0  0
 CDY  CONST_15  N1    C2   N3   C4     0.00   0.0  0
 CDY  CONST_16  C6    C5   C4   N3     0.00   0.0  0
 CDY  CONST_17  C6    N1   C2   N3     0.00   0.0  0
 CDY  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 CDY  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 CDY  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 CDY  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 CDY  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 CDY  CONST_23  CL    C2   N3   C4   180.00   0.0  0
 CDY  CONST_24  N6    C6   N1   C2   180.00   0.0  0
 CDY  CONST_25  C6    N1   C2   CL   180.00   0.0  0
 CDY  CONST_26  HC8   C8   N9   C1'    0.00   0.0  0
 CDY  CONST_27  HN61  N6   C6   C5   180.00   0.0  0
 CDY  CONST_28  HN62  N6   C6   C5     0.00   0.0  0
 CDY  Var_01    C1'   C2'  C3'  C4'   35.89  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
 CDY  chir_01  C4'  C5'  O4'  C3'  negativ
 CDY  chir_02  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
 CDY  plan-1  C1'   0.020
 CDY  plan-1  N9    0.020
 CDY  plan-1  C8    0.020
 CDY  plan-1  N7    0.020
 CDY  plan-1  C5    0.020
 CDY  plan-1  C4    0.020
 CDY  plan-1  N3    0.020
 CDY  plan-1  C2    0.020
 CDY  plan-1  CL    0.020
 CDY  plan-1  N1    0.020
 CDY  plan-1  C6    0.020
 CDY  plan-1  N6    0.020
 CDY  plan-1  HC8   0.020
 CDY  plan-2  C6    0.020
 CDY  plan-2  N6    0.020
 CDY  plan-2  HN61  0.020
 CDY  plan-2  HN62  0.020

