# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 01:46:59 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 7-(5-deoxy-beta-D-ribofuranosyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cc(I)c3c(N)ncnc23
#
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
 5I5  5I5  7-(5-deoxy-beta-D-ribofuranosyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  32  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5I5
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
 5I5  N1    N  N     0  -0.476  -2.7408   0.7796  -4.2577
 5I5  C1    C  CR6   0   0.448  -1.5265   0.5426  -4.7636
 5I5  C2    C  CR56  0  -0.019  -0.3889   0.8526  -3.9841
 5I5  C3    C  CR56  0   0.523  -0.6652   1.3995  -2.7252
 5I5  N2    N  N     0  -0.466  -1.8749   1.6371  -2.2155
 5I5  C4    C  CR16  0   0.044  -2.8458   1.3014  -3.0399
 5I5  C5    C  CR5   0  -0.411   1.0339   0.7846  -4.0737
 5I5  C6    C  CR15  0   0.001   1.5431   1.2777  -2.9094
 5I5  N3    N  NR5   0  -0.546   0.5072   1.6518  -2.0908
 5I5  I     I  I     0   0.065   2.2047   0.0977  -5.6440
 5I5  N4    N  NH2   0  -0.825  -1.4649   0.0208  -5.9918
 5I5  C7    C  CH1   0   0.014   1.7773   0.7140   0.6027
 5I5  C8    C  CH1   0  -0.053   0.3513   1.1805   0.3454
 5I5  C9    C  CH1   0   0.162   0.5926   2.2298  -0.7529
 5I5  O3    O  O2    0  -0.497   1.8749   2.7396  -0.5582
 5I5  C10   C  CH1   0   0.019   2.5649   2.0203   0.4706
 5I5  O2    O  OH1   0  -0.657   1.9075   0.0775   1.8377
 5I5  O1    O  OH1   0  -0.660  -0.1371   1.7784   1.5132
 5I5  C11   C  CH3   0  -0.688   4.0202   1.8498   0.1045
 5I5  H4    H  HCR6  0   0.251  -3.8582   1.4688  -2.6876
 5I5  H6    H  HCR5  0   0.317   2.5716   1.3959  -2.6136
 5I5  HN41  H  HNH2  0   0.403  -2.3188  -0.1702  -6.4876
 5I5  HN42  H  HNH2  0   0.407  -0.5981  -0.1848  -6.4548
 5I5  H7    H  HCH1  0   0.231   2.0641   0.0459  -0.2226
 5I5  H8    H  HCH1  0   0.263  -0.3007   0.3732  -0.0068
 5I5  H9    H  HCH1  0   0.277  -0.1532   3.0291  -0.7080
 5I5  H10   H  HCH1  0   0.236   2.4910   2.5827   1.4094
 5I5  HO2   H  HOH1  0   0.459   2.7331  -0.4160   1.8403
 5I5  HO1   H  HOH1  0   0.461  -1.0548   2.0305   1.3687
 5I5  H111  H  HCH3  0   0.250   4.5089   2.8114  -0.0523
 5I5  H112  H  HCH3  0   0.239   4.5456   1.3480   0.9184
 5I5  H113  H  HCH3  0   0.229   4.1435   1.2468  -0.7972

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
 5I5  N1   C4    aromatic  1.329  0.020  1.329
 5I5  N1   C1    aromatic  1.337  0.020  1.337
 5I5  C1   N4    single    1.336  0.020  1.336
 5I5  C1   C2    aromatic  1.413  0.020  1.413
 5I5  C2   C3    aromatic  1.400  0.020  1.400
 5I5  C2   C5    aromatic  1.427  0.020  1.427
 5I5  C3   N2    aromatic  1.334  0.020  1.334
 5I5  C3   N3    aromatic  1.357  0.020  1.357
 5I5  N2   C4    aromatic  1.317  0.020  1.317
 5I5  C4   H4    single    0.930  0.020  1.080
 5I5  C5   C6    aromatic  1.363  0.020  1.363
 5I5  C5   I     single    2.076  0.020  2.076
 5I5  C6   N3    aromatic  1.372  0.020  1.372
 5I5  C6   H6    single    0.930  0.020  1.080
 5I5  N3   C9    single    1.460  0.020  1.460
 5I5  N4   HN41  single    0.860  0.020  1.020
 5I5  N4   HN42  single    0.860  0.020  1.020
 5I5  C7   O2    single    1.395  0.020  1.395
 5I5  C7   C8    single    1.522  0.020  1.522
 5I5  C7   C10   single    1.531  0.020  1.531
 5I5  C7   H7    single    0.970  0.020  1.090
 5I5  C8   O1    single    1.400  0.020  1.400
 5I5  C8   C9    single    1.538  0.020  1.538
 5I5  C8   H8    single    0.970  0.020  1.090
 5I5  C9   O3    single    1.394  0.020  1.394
 5I5  C9   H9    single    0.970  0.020  1.090
 5I5  O3   C10   single    1.432  0.020  1.432
 5I5  C10  C11   single    1.510  0.020  1.510
 5I5  C10  H10   single    0.970  0.020  1.090
 5I5  O2   HO2   single    0.850  0.020  0.980
 5I5  O1   HO1   single    0.850  0.020  0.980
 5I5  C11  H111  single    0.970  0.020  1.090
 5I5  C11  H112  single    0.970  0.020  1.090
 5I5  C11  H113  single    0.970  0.020  1.090

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
 5I5  C4    N1   C1    119.22  3.000
 5I5  N4    C1   C2    123.75  3.000
 5I5  C2    C1   N1    118.92  3.000
 5I5  N4    C1   N1    117.33  3.000
 5I5  C5    C2   C3    105.77  3.000
 5I5  C5    C2   C1    139.23  3.000
 5I5  C3    C2   C1    115.00  3.000
 5I5  N3    C3   N2    124.87  3.000
 5I5  N3    C3   C2    108.82  3.000
 5I5  N2    C3   C2    126.31  3.000
 5I5  C4    N2   C3    112.57  3.000
 5I5  H4    C4   N2    116.44  3.000
 5I5  H4    C4   N1    115.59  3.000
 5I5  N2    C4   N1    127.97  3.000
 5I5  I     C5   C6    123.72  3.000
 5I5  I     C5   C2    128.72  3.000
 5I5  C6    C5   C2    107.55  3.000
 5I5  H6    C6   N3    121.82  3.000
 5I5  H6    C6   C5    129.14  3.000
 5I5  N3    C6   C5    109.04  3.000
 5I5  C9    N3   C6    127.62  3.000
 5I5  C9    N3   C3    123.55  3.000
 5I5  C6    N3   C3    108.82  3.000
 5I5  HN42  N4   HN41  117.82  3.000
 5I5  HN42  N4   C1    122.94  3.000
 5I5  HN41  N4   C1    119.23  3.000
 5I5  H7    C7   O2    111.27  3.000
 5I5  H7    C7   C10   108.62  3.000
 5I5  O2    C7   C10   114.68  3.000
 5I5  H7    C7   C8    107.67  3.000
 5I5  C10   C7   C8    101.88  3.000
 5I5  O2    C7   C8    112.14  3.000
 5I5  H8    C8   O1    112.03  3.000
 5I5  H8    C8   C9    111.50  3.000
 5I5  O1    C8   C9    111.04  3.000
 5I5  H8    C8   C7    112.70  3.000
 5I5  C9    C8   C7    100.54  3.000
 5I5  O1    C8   C7    108.46  3.000
 5I5  H9    C9   O3    110.74  3.000
 5I5  H9    C9   C8    111.23  3.000
 5I5  O3    C9   C8    107.11  3.000
 5I5  H9    C9   N3    106.68  3.000
 5I5  O3    C9   N3    109.07  3.000
 5I5  C8    C9   N3    112.03  3.000
 5I5  C10   O3   C9    111.09  3.000
 5I5  H10   C10  C11   109.28  3.000
 5I5  H10   C10  O3    108.95  3.000
 5I5  C11   C10  O3    110.29  3.000
 5I5  H10   C10  C7    109.21  3.000
 5I5  C11   C10  C7    114.85  3.000
 5I5  O3    C10  C7    104.04  3.000
 5I5  HO2   O2   C7    108.45  3.000
 5I5  HO1   O1   C8    108.62  3.000
 5I5  H113  C11  H112  107.92  3.000
 5I5  H113  C11  H111  108.53  3.000
 5I5  H112  C11  H111  107.29  3.000
 5I5  H113  C11  C10   111.80  3.000
 5I5  H112  C11  C10   109.59  3.000
 5I5  H111  C11  C10   111.55  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
 5I5  CONST_01  C3    N2  C4  N1    0.00  0.0  0
 5I5  CONST_02  C3    C2  C1  N1    0.00  0.0  0
 5I5  CONST_03  C5    C2  C1  N1  180.00  0.0  0
 5I5  CONST_04  N2    C4  N1  C1    0.00  0.0  0
 5I5  CONST_05  N2    C3  C2  C1    0.00  0.0  0
 5I5  CONST_06  N3    C3  C2  C1  180.00  0.0  0
 5I5  CONST_07  C6    C5  C2  C1  180.00  0.0  0
 5I5  CONST_08  C4    N1  C1  C2    0.00  0.0  0
 5I5  CONST_09  C4    N2  C3  C2    0.00  0.0  0
 5I5  CONST_10  C6    N3  C3  C2    0.00  0.0  0
 5I5  CONST_11  N3    C6  C5  C2    0.00  0.0  0
 5I5  CONST_12  C6    C5  C2  C3    0.00  0.0  0
 5I5  CONST_13  C5    C6  N3  C3    0.00  0.0  0
 5I5  CONST_14  C5    C2  C3  N2  180.00  0.0  0
 5I5  CONST_15  C6    N3  C3  N2  180.00  0.0  0
 5I5  CONST_16  N3    C3  N2  C4  180.00  0.0  0
 5I5  CONST_17  N3    C3  C2  C5    0.00  0.0  0
 5I5  CONST_18  C9    N3  C3  C2  180.00  0.0  0
 5I5  CONST_19  C9    N3  C3  N2    0.00  0.0  0
 5I5  CONST_20  C9    N3  C6  C5  180.00  0.0  0
 5I5  CONST_21  I     C5  C2  C1    0.00  0.0  0
 5I5  CONST_22  N4    C1  C2  C3  180.00  0.0  0
 5I5  CONST_23  I     C5  C2  C3  180.00  0.0  0
 5I5  CONST_24  N4    C1  N1  C4  180.00  0.0  0
 5I5  CONST_25  N4    C1  C2  C5    0.00  0.0  0
 5I5  CONST_26  I     C5  C6  N3  180.00  0.0  0
 5I5  CONST_27  H4    C4  N1  C1  180.00  0.0  0
 5I5  CONST_28  H6    C6  C5  C2  180.00  0.0  0
 5I5  CONST_29  HN41  N4  C1  N1    0.00  0.0  0
 5I5  CONST_30  HN42  N4  C1  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
 5I5  chir_01  C7   O2  C8   C10  negativ
 5I5  chir_02  C8   O1  C7   C9   positiv
 5I5  chir_03  C9   O3  N3   C8   negativ
 5I5  chir_04  C10  O3  C11  C7   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
 5I5  plan-1  N1    0.020
 5I5  plan-1  C1    0.020
 5I5  plan-1  C2    0.020
 5I5  plan-1  C3    0.020
 5I5  plan-1  N2    0.020
 5I5  plan-1  C4    0.020
 5I5  plan-1  C5    0.020
 5I5  plan-1  C6    0.020
 5I5  plan-1  N3    0.020
 5I5  plan-1  I     0.020
 5I5  plan-1  N4    0.020
 5I5  plan-1  C9    0.020
 5I5  plan-1  H4    0.020
 5I5  plan-1  H6    0.020
 5I5  plan-2  C1    0.020
 5I5  plan-2  N4    0.020
 5I5  plan-2  HN41  0.020
 5I5  plan-2  HN42  0.020

