# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 00:00:01 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (2R,3R,4R)-2-(6-amino-9H-purin-9-yl)tetrahydrofuran-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3OC[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
 CC5  CC5  (2R,3R,4R)-2-(6-amino-9H-purin-9-yl)tetrahydrofuran-3,4-diol  ligand  28  17  .  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_CC5
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
 CC5  N1    N  N     0  -0.474   3.5264   1.0202  -0.2212
 CC5  C2    C  CR16  0   0.039   2.5599   1.8613   0.1378
 CC5  N3    N  N     0  -0.458   1.3010   1.5885   0.4339
 CC5  C4    C  CR56  0   0.485   1.0482   0.2838   0.3422
 CC5  N9    N  NR5   0  -0.533  -0.1293  -0.3630   0.5742
 CC5  C8    C  CR15  0   0.101   0.1132  -1.6910   0.3530
 CC5  N7    N  N     0  -0.451   1.3412  -1.9386  -0.0009
 CC5  C5    C  CR56  0  -0.003   1.9460  -0.7098  -0.0147
 CC5  C6    C  CR6   0   0.459   3.2556  -0.2870  -0.3101
 CC5  N6    N  NH2   0  -0.817   4.2239  -1.1319  -0.6661
 CC5  C1'   C  CH1   0   0.160  -1.3828   0.2763   0.9650
 CC5  C2'   C  CH1   0  -0.031  -2.0467   0.9593  -0.2282
 CC5  C3'   C  CH1   0  -0.029  -2.8266  -0.2117  -0.8232
 CC5  C4'   C  CH2   0  -0.193  -3.2943  -0.9318   0.4442
 CC5  O4'   O  O2    0  -0.489  -2.2735  -0.6951   1.4150
 CC5  O2'   O  OH1   0  -0.663  -2.9021   1.9433   0.2863
 CC5  O3'   O  OH1   0  -0.663  -3.8508   0.2645  -1.6468
 CC5  H2    H  HCR6  0   0.252   2.8477   2.9058   0.1908
 CC5  H8    H  HCR5  0   0.299  -0.6529  -2.4409   0.4759
 CC5  H6N1  H  HNH2  0   0.403   5.1397  -0.7863  -0.8950
 CC5  H6N2  H  HNH2  0   0.411   4.0435  -2.1143  -0.7733
 CC5  H1'   H  HCH1  0   0.289  -1.1532   0.9855   1.7643
 CC5  H2'   H  HCH1  0   0.260  -1.3119   1.3797  -0.9252
 CC5  H3'   H  HCH1  0   0.236  -2.1334  -0.8544  -1.3814
 CC5  H4'1  H  HCH2  0   0.249  -3.4100  -2.0081   0.3062
 CC5  H4'2  H  HCH2  0   0.236  -4.2459  -0.5217   0.7941
 CC5  HA    H  HOH1  0   0.457  -3.5867   2.1233  -0.3680
 CC5  HB    H  HOH1  0   0.468  -4.3430  -0.4804  -2.0053

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
 CC5  N1   C2    aromatic  1.331  0.020  1.331
 CC5  N1   C6    aromatic  1.338  0.020  1.338
 CC5  C2   N3    aromatic  1.322  0.020  1.322
 CC5  C2   H2    single    0.930  0.020  1.080
 CC5  N3   C4    aromatic  1.332  0.020  1.332
 CC5  C4   N9    aromatic  1.363  0.020  1.363
 CC5  C4   C5    aromatic  1.386  0.020  1.386
 CC5  N9   C8    aromatic  1.368  0.020  1.368
 CC5  N9   C1'   single    1.460  0.020  1.460
 CC5  C8   N7    aromatic  1.302  0.020  1.302
 CC5  C8   H8    single    0.930  0.020  1.080
 CC5  N7   C5    aromatic  1.370  0.020  1.370
 CC5  C5   C6    aromatic  1.407  0.020  1.407
 CC5  C6   N6    single    1.333  0.020  1.333
 CC5  N6   H6N1  single    0.860  0.020  1.020
 CC5  N6   H6N2  single    0.860  0.020  1.020
 CC5  C1'  C2'   single    1.527  0.020  1.527
 CC5  C1'  O4'   single    1.393  0.020  1.393
 CC5  C1'  H1'   single    0.970  0.020  1.090
 CC5  C2'  C3'   single    1.528  0.020  1.528
 CC5  C2'  O2'   single    1.402  0.020  1.402
 CC5  C2'  H2'   single    0.970  0.020  1.090
 CC5  C3'  C4'   single    1.531  0.020  1.531
 CC5  C3'  O3'   single    1.398  0.020  1.398
 CC5  C3'  H3'   single    0.970  0.020  1.090
 CC5  C4'  O4'   single    1.428  0.020  1.428
 CC5  C4'  H4'1  single    0.970  0.020  1.090
 CC5  C4'  H4'2  single    0.970  0.020  1.090
 CC5  O2'  HA    single    0.850  0.020  0.980
 CC5  O3'  HB    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
 CC5  C6    N1   C2    119.24  3.000
 CC5  H2    C2   N3    116.14  3.000
 CC5  H2    C2   N1    115.41  3.000
 CC5  N3    C2   N1    128.45  3.000
 CC5  C4    N3   C2    111.56  3.000
 CC5  C5    C4   N9    105.26  3.000
 CC5  C5    C4   N3    126.65  3.000
 CC5  N9    C4   N3    128.09  3.000
 CC5  C1'   N9   C8    128.34  3.000
 CC5  C1'   N9   C4    125.39  3.000
 CC5  C8    N9   C4    106.26  3.000
 CC5  H8    C8   N7    124.65  3.000
 CC5  H8    C8   N9    122.03  3.000
 CC5  N7    C8   N9    113.32  3.000
 CC5  C5    N7   C8    104.40  3.000
 CC5  C6    C5   N7    133.04  3.000
 CC5  C6    C5   C4    116.19  3.000
 CC5  N7    C5   C4    110.77  3.000
 CC5  N6    C6   C5    122.77  3.000
 CC5  N6    C6   N1    119.33  3.000
 CC5  C5    C6   N1    117.90  3.000
 CC5  H6N2  N6   H6N1  118.39  3.000
 CC5  H6N2  N6   C6    121.18  3.000
 CC5  H6N1  N6   C6    120.30  3.000
 CC5  H1'   C1'  O4'   110.53  3.000
 CC5  H1'   C1'  C2'   111.88  3.000
 CC5  O4'   C1'  C2'   106.65  3.000
 CC5  H1'   C1'  N9    107.42  3.000
 CC5  O4'   C1'  N9    109.28  3.000
 CC5  C2'   C1'  N9    111.09  3.000
 CC5  H2'   C2'  O2'   111.91  3.000
 CC5  H2'   C2'  C3'   112.86  3.000
 CC5  O2'   C2'  C3'   111.69  3.000
 CC5  H2'   C2'  C1'   112.14  3.000
 CC5  O2'   C2'  C1'   107.01  3.000
 CC5  C3'   C2'  C1'   100.57  3.000
 CC5  H3'   C3'  O3'   111.25  3.000
 CC5  H3'   C3'  C4'   109.79  3.000
 CC5  O3'   C3'  C4'   115.10  3.000
 CC5  H3'   C3'  C2'   108.93  3.000
 CC5  O3'   C3'  C2'   110.02  3.000
 CC5  C4'   C3'  C2'   101.19  3.000
 CC5  H4'2  C4'  H4'1  108.54  3.000
 CC5  H4'2  C4'  O4'   110.01  3.000
 CC5  H4'1  C4'  O4'   108.97  3.000
 CC5  H4'2  C4'  C3'   110.75  3.000
 CC5  H4'1  C4'  C3'   113.06  3.000
 CC5  O4'   C4'  C3'   105.45  3.000
 CC5  C4'   O4'  C1'   110.67  3.000
 CC5  HA    O2'  C2'   108.38  3.000
 CC5  HB    O3'  C3'   109.31  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
 CC5  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 CC5  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 CC5  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 CC5  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 CC5  CONST_05  N9    C4   N3   C2   180.00   0.0  0
 CC5  CONST_06  C5    C4   N3   C2     0.00   0.0  0
 CC5  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 CC5  CONST_08  C8    N9   C4   N3   180.00   0.0  0
 CC5  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 CC5  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 CC5  CONST_11  N7    C8   N9   C4     0.00   0.0  0
 CC5  CONST_12  C8    N7   C5   C4     0.00   0.0  0
 CC5  CONST_13  N7    C5   C4   N9     0.00   0.0  0
 CC5  CONST_14  C6    C5   C4   N9   180.00   0.0  0
 CC5  CONST_15  C5    N7   C8   N9     0.00   0.0  0
 CC5  CONST_16  C5    C4   N9   C8     0.00   0.0  0
 CC5  CONST_17  C6    C5   N7   C8   180.00   0.0  0
 CC5  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 CC5  CONST_19  C1'   N9   C8   N7   180.00   0.0  0
 CC5  CONST_20  C1'   N9   C4   C5   180.00   0.0  0
 CC5  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 CC5  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 CC5  CONST_23  N6    C6   C5   N7     0.00   0.0  0
 CC5  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 CC5  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 CC5  CONST_26  H6N1  N6   C6   N1     0.00   0.0  0
 CC5  CONST_27  H6N2  N6   C6   N1   180.00   0.0  0
 CC5  Var_01    C3'   C4'  O4'  C1'   11.06  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
 CC5  chir_01  C1'  N9   C2'  O4'  negativ
 CC5  chir_02  C2'  O2'  C3'  C1'  positiv
 CC5  chir_03  C3'  O3'  C2'  C4'  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
 CC5  plan-1  N1    0.020
 CC5  plan-1  C2    0.020
 CC5  plan-1  N3    0.020
 CC5  plan-1  C4    0.020
 CC5  plan-1  N9    0.020
 CC5  plan-1  C8    0.020
 CC5  plan-1  N7    0.020
 CC5  plan-1  C5    0.020
 CC5  plan-1  C6    0.020
 CC5  plan-1  N6    0.020
 CC5  plan-1  C1'   0.020
 CC5  plan-1  H2    0.020
 CC5  plan-1  H8    0.020
 CC5  plan-2  C6    0.020
 CC5  plan-2  N6    0.020
 CC5  plan-2  H6N1  0.020
 CC5  plan-2  H6N2  0.020

