# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:02:08 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(ccc12)[C@@H]3O[C@H](CO)[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
 TBN  TBN  7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  33  19  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TBN
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
 TBN  O5'   O  OH1   0  -0.667  -4.2594  -1.8680   1.0776
 TBN  C5'   C  CH2   0  -0.158  -3.6845  -1.3263  -0.0849
 TBN  C4'   C  CR15  0   0.010  -3.0316  -0.0086   0.2512
 TBN  O4'   O  O     0  -0.496  -1.9412  -0.1971   1.1500
 TBN  C1'   C  CR15  0   0.171  -0.8480   0.5991   0.7974
 TBN  N9    N  NR5   0  -0.548   0.2535  -0.2514   0.3702
 TBN  C8    C  CR15  0  -0.021   0.1884  -1.5326  -0.1331
 TBN  C7    C  CR15  0  -0.444   1.4365  -1.9604  -0.4743
 TBN  C5    C  CR56  0  -0.074   2.3240  -0.8864  -0.1714
 TBN  C6    C  CR6   0   0.439   3.7053  -0.6238  -0.2573
 TBN  N1    N  N     0  -0.478   4.1705   0.5625   0.1434
 TBN  C2    C  CR16  0   0.037   3.3080   1.4603   0.6165
 TBN  N3    N  N     0  -0.467   2.0020   1.3448   0.7497
 TBN  C4    C  CR56  0   0.509   1.5497   0.1540   0.3472
 TBN  N6    N  NH2   0  -0.822   4.5829  -1.5301  -0.7092
 TBN  C2'   C  CR15  0  -0.037  -1.3220   1.5316  -0.3182
 TBN  O2'   O  OH1   0  -0.666  -1.8625   2.6770   0.2820
 TBN  C3'   C  CR15  0  -0.043  -2.4224   0.6843  -0.9652
 TBN  O3'   O  OH1   0  -0.657  -3.3936   1.4364  -1.6363
 TBN  H5'   H  HOH1  0   0.459  -4.6847  -2.6976   0.8432
 TBN  H5'1  H  HCH2  0   0.213  -4.4349  -1.1302  -0.8619
 TBN  H5'2  H  HCH2  0   0.200  -2.9394  -2.0007  -0.5292
 TBN  H4'   H  HCR5  0   0.243  -3.7769   0.6511   0.7141
 TBN  H1'   H  HCR5  0   0.273  -0.4905   1.1690   1.6594
 TBN  H8    H  HCR5  0   0.299  -0.7464  -2.0622  -0.2008
 TBN  H7    H  HCR5  0   0.257   1.6770  -2.9298  -0.8803
 TBN  H2    H  HCR6  0   0.246   3.7412   2.4054   0.9274
 TBN  HN61  H  HNH2  0   0.398   5.5394  -1.2580  -0.8589
 TBN  HN62  H  HNH2  0   0.406   4.2726  -2.3790  -1.1476
 TBN  H2'   H  HCR5  0   0.256  -0.5103   1.7770  -1.0136
 TBN  H1    H  HOH1  0   0.451  -2.5463   3.0230  -0.3052
 TBN  H3'   H  HCR5  0   0.243  -1.9611  -0.0605  -1.6278
 TBN  H3    H  HOH1  0   0.469  -3.1048   1.5842  -2.5423

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
 TBN  O5'  C5'   single    1.405  0.020  1.405
 TBN  O5'  H5'   single    0.850  0.020  0.980
 TBN  C5'  C4'   single    1.509  0.020  1.509
 TBN  C5'  H5'1  single    0.970  0.020  1.090
 TBN  C5'  H5'2  single    0.970  0.020  1.090
 TBN  C4'  O4'   single    1.426  0.020  1.426
 TBN  C4'  C3'   single    1.527  0.020  1.527
 TBN  C4'  H4'   single    0.970  0.020  1.090
 TBN  O4'  C1'   single    1.398  0.020  1.398
 TBN  C1'  N9    single    1.456  0.020  1.456
 TBN  C1'  C2'   single    1.529  0.020  1.529
 TBN  C1'  H1'   single    0.970  0.020  1.090
 TBN  N9   C8    aromatic  1.378  0.020  1.378
 TBN  N9   C4    aromatic  1.358  0.020  1.358
 TBN  C8   C7    aromatic  1.363  0.020  1.363
 TBN  C8   H8    single    0.930  0.020  1.080
 TBN  C7   C5    aromatic  1.426  0.020  1.426
 TBN  C7   H7    single    0.930  0.020  1.080
 TBN  C5   C6    aromatic  1.409  0.020  1.409
 TBN  C5   C4    aromatic  1.397  0.020  1.397
 TBN  C6   N1    aromatic  1.336  0.020  1.336
 TBN  C6   N6    single    1.340  0.020  1.340
 TBN  N1   C2    aromatic  1.332  0.020  1.332
 TBN  C2   N3    aromatic  1.318  0.020  1.318
 TBN  C2   H2    single    0.930  0.020  1.080
 TBN  N3   C4    aromatic  1.336  0.020  1.336
 TBN  N6   HN61  single    0.860  0.020  1.020
 TBN  N6   HN62  single    0.860  0.020  1.020
 TBN  C2'  O2'   single    1.402  0.020  1.402
 TBN  C2'  C3'   single    1.532  0.020  1.532
 TBN  C2'  H2'   single    0.970  0.020  1.090
 TBN  O2'  H1    single    0.850  0.020  0.980
 TBN  C3'  O3'   single    1.400  0.020  1.400
 TBN  C3'  H3'   single    0.970  0.020  1.090
 TBN  O3'  H3    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
 TBN  H5'   O5'  C5'   108.17  3.000
 TBN  H5'2  C5'  H5'1  106.68  3.000
 TBN  H5'2  C5'  C4'   109.43  3.000
 TBN  H5'1  C5'  C4'   107.30  3.000
 TBN  H5'2  C5'  O5'   112.04  3.000
 TBN  H5'1  C5'  O5'   112.00  3.000
 TBN  C4'   C5'  O5'   109.23  3.000
 TBN  H4'   C4'  C3'   109.52  3.000
 TBN  H4'   C4'  O4'   109.44  3.000
 TBN  C3'   C4'  O4'   104.90  3.000
 TBN  H4'   C4'  C5'   108.97  3.000
 TBN  C3'   C4'  C5'   113.05  3.000
 TBN  O4'   C4'  C5'   110.86  3.000
 TBN  C1'   O4'  C4'   111.34  3.000
 TBN  H1'   C1'  C2'   111.01  3.000
 TBN  H1'   C1'  N9    106.77  3.000
 TBN  C2'   C1'  N9    112.13  3.000
 TBN  H1'   C1'  O4'   110.72  3.000
 TBN  C2'   C1'  O4'   106.79  3.000
 TBN  N9    C1'  O4'   109.46  3.000
 TBN  C4    N9   C8    108.44  3.000
 TBN  C4    N9   C1'   123.55  3.000
 TBN  C8    N9   C1'   127.92  3.000
 TBN  H8    C8   C7    128.69  3.000
 TBN  H8    C8   N9    121.43  3.000
 TBN  C7    C8   N9    109.88  3.000
 TBN  H7    C7   C5    128.20  3.000
 TBN  H7    C7   C8    125.51  3.000
 TBN  C5    C7   C8    106.29  3.000
 TBN  C4    C5   C6    115.30  3.000
 TBN  C4    C5   C7    107.15  3.000
 TBN  C6    C5   C7    137.55  3.000
 TBN  N6    C6   N1    118.28  3.000
 TBN  N6    C6   C5    122.46  3.000
 TBN  N1    C6   C5    119.26  3.000
 TBN  C2    N1   C6    118.67  3.000
 TBN  H2    C2   N3    116.30  3.000
 TBN  H2    C2   N1    115.49  3.000
 TBN  N3    C2   N1    128.21  3.000
 TBN  C4    N3   C2    112.53  3.000
 TBN  N3    C4   C5    126.02  3.000
 TBN  N3    C4   N9    125.73  3.000
 TBN  C5    C4   N9    108.24  3.000
 TBN  HN62  N6   HN61  117.22  3.000
 TBN  HN62  N6   C6    121.09  3.000
 TBN  HN61  N6   C6    119.34  3.000
 TBN  H2'   C2'  C3'   112.81  3.000
 TBN  H2'   C2'  O2'   111.97  3.000
 TBN  C3'   C2'  O2'   110.85  3.000
 TBN  H2'   C2'  C1'   111.69  3.000
 TBN  C3'   C2'  C1'   101.15  3.000
 TBN  O2'   C2'  C1'   107.79  3.000
 TBN  H1    O2'  C2'   107.79  3.000
 TBN  H3'   C3'  O3'   111.50  3.000
 TBN  H3'   C3'  C2'   109.15  3.000
 TBN  O3'   C3'  C2'   113.80  3.000
 TBN  H3'   C3'  C4'   109.91  3.000
 TBN  O3'   C3'  C4'   110.43  3.000
 TBN  C2'   C3'  C4'   101.60  3.000
 TBN  H3    O3'  C3'   109.01  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
 TBN  CONST_01  C5    C7  C8  N9     0.00  0.0  0
 TBN  CONST_02  C7    C5  C4  N9     0.00  0.0  0
 TBN  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 TBN  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 TBN  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 TBN  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 TBN  CONST_07  C6    C5  C7  C8   180.00  0.0  0
 TBN  CONST_08  C4    C5  C7  C8     0.00  0.0  0
 TBN  CONST_09  C4    N9  C8  C7     0.00  0.0  0
 TBN  CONST_10  N1    C6  C5  C7   180.00  0.0  0
 TBN  CONST_11  N3    C4  C5  C7   180.00  0.0  0
 TBN  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 TBN  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 TBN  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 TBN  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 TBN  CONST_16  C4    C5  C6  N1     0.00  0.0  0
 TBN  CONST_17  C4    N3  C2  N1     0.00  0.0  0
 TBN  CONST_18  C7    C8  N9  C1'  180.00  0.0  0
 TBN  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 TBN  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 TBN  CONST_21  N6    C6  C5  C7     0.00  0.0  0
 TBN  CONST_22  N6    C6  N1  C2   180.00  0.0  0
 TBN  CONST_23  N6    C6  C5  C4   180.00  0.0  0
 TBN  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 TBN  CONST_25  H7    C7  C8  N9   180.00  0.0  0
 TBN  CONST_26  H2    C2  N1  C6   180.00  0.0  0
 TBN  CONST_27  HN61  N6  C6  C5   180.00  0.0  0
 TBN  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
 TBN  chir_01  C4'  C5'  O4'  C3'  negativ
 TBN  chir_02  C1'  O4'  N9   C2'  negativ
 TBN  chir_03  C2'  O2'  C1'  C3'  negativ
 TBN  chir_04  C3'  O3'  C4'  C2'  positiv

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
 TBN  plan-1  C1'   0.020
 TBN  plan-1  N9    0.020
 TBN  plan-1  C8    0.020
 TBN  plan-1  C7    0.020
 TBN  plan-1  C5    0.020
 TBN  plan-1  C6    0.020
 TBN  plan-1  N1    0.020
 TBN  plan-1  C2    0.020
 TBN  plan-1  N3    0.020
 TBN  plan-1  C4    0.020
 TBN  plan-1  N6    0.020
 TBN  plan-1  H8    0.020
 TBN  plan-1  H7    0.020
 TBN  plan-1  H2    0.020
 TBN  plan-2  C6    0.020
 TBN  plan-2  N6    0.020
 TBN  plan-2  HN61  0.020
 TBN  plan-2  HN62  0.020

