# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 02:53:10 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 5-iodo-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cc(I)c12)[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
 5ID  5ID  5-iodo-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  33  20  .  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_5ID
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
 5ID  O5'   O  OH1   0  -0.668  -4.4521  -2.2623   2.1204
 5ID  C5'   C  CH2   0  -0.164  -4.4736  -2.0649   0.7291
 5ID  C4'   C  CR15  0  -0.015  -4.0424  -0.6580   0.4104
 5ID  O4'   O  O     0  -0.492  -2.6718  -0.4796   0.7272
 5ID  C1'   C  CR15  0   0.199  -2.2586   0.6966   0.0849
 5ID  N9    N  NR5   0  -0.563  -0.8306   0.6612  -0.0454
 5ID  C8    C  CR15  0   0.016  -0.1126  -0.3684  -0.6064
 5ID  C7    C  CR5   0  -0.406   1.2151  -0.0891  -0.5119
 5ID  C5    C  CR56  0  -0.034   1.3427   1.1683   0.1558
 5ID  C6    C  CR6   0   0.448   2.3627   2.0594   0.5584
 5ID  N1    N  N     0  -0.475   2.0218   3.2009   1.1637
 5ID  C2    C  CR16  0   0.051   0.7362   3.4651   1.3688
 5ID  N3    N  N     0  -0.462  -0.3050   2.7312   1.0339
 5ID  C4    C  CR56  0   0.529   0.0376   1.5962   0.4271
 5ID  N6    N  NH2   0  -0.824   3.6656   1.8396   0.3512
 5ID  C2'   C  CR15  0  -0.042  -3.0299   0.7705  -1.2481
 5ID  O2'   O  OH1   0  -0.659  -3.5310   2.0669  -1.3856
 5ID  C3'   C  CR15  0   0.003  -4.1185  -0.3150  -1.0805
 5ID  O3'   O  OH1   0  -0.663  -5.3736   0.1460  -1.4907
 5ID  IAE   I  I     0   0.072   2.7098  -1.3467  -1.2115
 5ID  H5'   H  HOH1  0   0.459  -4.8019  -3.1383   2.3061
 5ID  H5'1  H  HCH2  0   0.206  -5.4791  -2.2045   0.3101
 5ID  H5'2  H  HCH2  0   0.201  -3.8129  -2.7662   0.2005
 5ID  H4'   H  HCR5  0   0.235  -4.6570   0.0608   0.9734
 5ID  H1'   H  HCR5  0   0.266  -2.5019   1.5833   0.6822
 5ID  H8    H  HCR5  0   0.315  -0.6028  -1.2121  -1.0639
 5ID  H2    H  HCR6  0   0.252   0.5244   4.4006   1.8758
 5ID  H6N1  H  HNH2  0   0.403   4.3327   2.4967   0.7182
 5ID  H6N2  H  HNH2  0   0.406   4.0194   0.9532   0.0390
 5ID  H2'   H  HCR5  0   0.247  -2.3711   0.5066  -2.0852
 5ID  HA    H  HOH1  0   0.456  -4.1179   2.0859  -2.1491
 5ID  H3'   H  HCR5  0   0.238  -3.8065  -1.1940  -1.6580
 5ID  HB    H  HOH1  0   0.465  -5.8534  -0.5778  -1.9013

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
 5ID  O5'  C5'   single    1.405  0.020  1.405
 5ID  O5'  H5'   single    0.850  0.020  0.980
 5ID  C5'  C4'   single    1.506  0.020  1.506
 5ID  C5'  H5'1  single    0.970  0.020  1.090
 5ID  C5'  H5'2  single    0.970  0.020  1.090
 5ID  C4'  O4'   single    1.418  0.020  1.418
 5ID  C4'  C3'   single    1.532  0.020  1.532
 5ID  C4'  H4'   single    0.970  0.020  1.090
 5ID  O4'  C1'   single    1.402  0.020  1.402
 5ID  C1'  N9    single    1.434  0.020  1.434
 5ID  C1'  C2'   single    1.542  0.020  1.542
 5ID  C1'  H1'   single    0.970  0.020  1.090
 5ID  N9   C8    aromatic  1.375  0.020  1.375
 5ID  N9   C4    aromatic  1.361  0.020  1.361
 5ID  C8   C7    aromatic  1.360  0.020  1.360
 5ID  C8   H8    single    0.930  0.020  1.080
 5ID  C7   C5    aromatic  1.429  0.020  1.429
 5ID  C7   IAE   single    2.075  0.020  2.075
 5ID  C5   C6    aromatic  1.413  0.020  1.413
 5ID  C5   C4    aromatic  1.400  0.020  1.400
 5ID  C6   N1    aromatic  1.336  0.020  1.336
 5ID  C6   N6    single    1.337  0.020  1.337
 5ID  N1   C2    aromatic  1.328  0.020  1.328
 5ID  C2   N3    aromatic  1.317  0.020  1.317
 5ID  C2   H2    single    0.930  0.020  1.080
 5ID  N3   C4    aromatic  1.332  0.020  1.332
 5ID  N6   H6N1  single    0.860  0.020  1.020
 5ID  N6   H6N2  single    0.860  0.020  1.020
 5ID  C2'  O2'   single    1.397  0.020  1.397
 5ID  C2'  C3'   single    1.546  0.020  1.546
 5ID  C2'  H2'   single    0.970  0.020  1.090
 5ID  O2'  HA    single    0.850  0.020  0.980
 5ID  C3'  O3'   single    1.399  0.020  1.399
 5ID  C3'  H3'   single    0.970  0.020  1.090
 5ID  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
 5ID  H5'   O5'  C5'   108.28  3.000
 5ID  H5'2  C5'  H5'1  106.61  3.000
 5ID  H5'2  C5'  C4'   108.80  3.000
 5ID  H5'1  C5'  C4'   107.47  3.000
 5ID  H5'2  C5'  O5'   112.16  3.000
 5ID  H5'1  C5'  O5'   111.96  3.000
 5ID  C4'   C5'  O5'   109.66  3.000
 5ID  H4'   C4'  C3'   108.89  3.000
 5ID  H4'   C4'  O4'   110.08  3.000
 5ID  C3'   C4'  O4'   103.73  3.000
 5ID  H4'   C4'  C5'   110.01  3.000
 5ID  C3'   C4'  C5'   113.64  3.000
 5ID  O4'   C4'  C5'   110.31  3.000
 5ID  C1'   O4'  C4'   106.74  3.000
 5ID  H1'   C1'  C2'   108.73  3.000
 5ID  H1'   C1'  N9    106.88  3.000
 5ID  C2'   C1'  N9    114.88  3.000
 5ID  H1'   C1'  O4'   111.31  3.000
 5ID  C2'   C1'  O4'   106.79  3.000
 5ID  N9    C1'  O4'   108.31  3.000
 5ID  C4    N9   C8    108.85  3.000
 5ID  C4    N9   C1'   125.93  3.000
 5ID  C8    N9   C1'   125.13  3.000
 5ID  H8    C8   C7    129.37  3.000
 5ID  H8    C8   N9    121.46  3.000
 5ID  C7    C8   N9    109.13  3.000
 5ID  IAE   C7   C5    128.78  3.000
 5ID  IAE   C7   C8    123.74  3.000
 5ID  C5    C7   C8    107.47  3.000
 5ID  C4    C5   C6    115.15  3.000
 5ID  C4    C5   C7    106.03  3.000
 5ID  C6    C5   C7    138.79  3.000
 5ID  N6    C6   N1    117.33  3.000
 5ID  N6    C6   C5    123.74  3.000
 5ID  N1    C6   C5    118.92  3.000
 5ID  C2    N1   C6    119.13  3.000
 5ID  H2    C2   N3    116.42  3.000
 5ID  H2    C2   N1    115.63  3.000
 5ID  N3    C2   N1    127.95  3.000
 5ID  C4    N3   C2    112.79  3.000
 5ID  N3    C4   C5    126.06  3.000
 5ID  N3    C4   N9    125.43  3.000
 5ID  C5    C4   N9    108.51  3.000
 5ID  H6N2  N6   H6N1  117.17  3.000
 5ID  H6N2  N6   C6    122.44  3.000
 5ID  H6N1  N6   C6    118.83  3.000
 5ID  H2'   C2'  C3'   109.66  3.000
 5ID  H2'   C2'  O2'   111.31  3.000
 5ID  C3'   C2'  O2'   114.19  3.000
 5ID  H2'   C2'  C1'   110.34  3.000
 5ID  C3'   C2'  C1'   102.99  3.000
 5ID  O2'   C2'  C1'   108.01  3.000
 5ID  HA    O2'  C2'   108.36  3.000
 5ID  H3'   C3'  O3'   111.40  3.000
 5ID  H3'   C3'  C2'   107.77  3.000
 5ID  O3'   C3'  C2'   111.63  3.000
 5ID  H3'   C3'  C4'   108.59  3.000
 5ID  O3'   C3'  C4'   113.82  3.000
 5ID  C2'   C3'  C4'   103.16  3.000
 5ID  HB    O3'  C3'   108.98  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
 5ID  CONST_01  C5    C7  C8  N9     0.00  0.0  0
 5ID  CONST_02  C7    C5  C4  N9     0.00  0.0  0
 5ID  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 5ID  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 5ID  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 5ID  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 5ID  CONST_07  C6    C5  C7  C8   180.00  0.0  0
 5ID  CONST_08  C4    C5  C7  C8     0.00  0.0  0
 5ID  CONST_09  C4    N9  C8  C7     0.00  0.0  0
 5ID  CONST_10  N1    C6  C5  C7   180.00  0.0  0
 5ID  CONST_11  N3    C4  C5  C7   180.00  0.0  0
 5ID  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 5ID  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 5ID  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 5ID  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 5ID  CONST_16  C4    C5  C6  N1     0.00  0.0  0
 5ID  CONST_17  C4    N3  C2  N1     0.00  0.0  0
 5ID  CONST_18  C7    C8  N9  C1'  180.00  0.0  0
 5ID  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 5ID  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 5ID  CONST_21  IAE   C7  C8  N9   180.00  0.0  0
 5ID  CONST_22  N6    C6  C5  C7     0.00  0.0  0
 5ID  CONST_23  IAE   C7  C5  C6     0.00  0.0  0
 5ID  CONST_24  N6    C6  N1  C2   180.00  0.0  0
 5ID  CONST_25  IAE   C7  C5  C4   180.00  0.0  0
 5ID  CONST_26  N6    C6  C5  C4   180.00  0.0  0
 5ID  CONST_27  H8    C8  N9  C1'    0.00  0.0  0
 5ID  CONST_28  H2    C2  N1  C6   180.00  0.0  0
 5ID  CONST_29  H6N1  N6  C6  C5   180.00  0.0  0
 5ID  CONST_30  H6N2  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
 5ID  chir_01  C4'  C5'  O4'  C3'  negativ
 5ID  chir_02  C1'  O4'  N9   C2'  negativ
 5ID  chir_03  C2'  O2'  C1'  C3'  negativ
 5ID  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
 5ID  plan-1  C1'   0.020
 5ID  plan-1  N9    0.020
 5ID  plan-1  C8    0.020
 5ID  plan-1  C7    0.020
 5ID  plan-1  C5    0.020
 5ID  plan-1  C6    0.020
 5ID  plan-1  N1    0.020
 5ID  plan-1  C2    0.020
 5ID  plan-1  N3    0.020
 5ID  plan-1  C4    0.020
 5ID  plan-1  N6    0.020
 5ID  plan-1  IAE   0.020
 5ID  plan-1  H8    0.020
 5ID  plan-1  H2    0.020
 5ID  plan-2  C6    0.020
 5ID  plan-2  N6    0.020
 5ID  plan-2  H6N1  0.020
 5ID  plan-2  H6N2  0.020

