# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 07:52:21 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-ethynyl-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(C#C)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
 HO4  HO4  5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  35  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HO4
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
 HO4  C11  C  CSP1  0  -0.591  -2.5694  -3.8105   0.5256
 HO4  C10  C  CSP   0   0.222  -2.0623  -2.7468   0.2726
 HO4  C7   C  CR5   0  -0.111  -1.5076  -1.4782  -0.0118
 HO4  C8   C  CR15  0  -0.039  -0.1886  -1.2023  -0.2727
 HO4  C5   C  CR56  0  -0.095  -2.1998  -0.2269  -0.0934
 HO4  C6   C  CR6   0   0.423  -3.5217   0.2380   0.0543
 HO4  N6   N  NH2   0  -0.826  -4.5405  -0.5689   0.3651
 HO4  N1   N  N     0  -0.472  -3.7678   1.5416  -0.1080
 HO4  C2   C  CR16  0   0.041  -2.7558   2.3538  -0.4024
 HO4  N3   N  N     0  -0.467  -1.4834   2.0462  -0.5642
 HO4  C4   C  CR56  0   0.516  -1.2504   0.7430  -0.4018
 HO4  N9   N  NR5   0  -0.550  -0.0351   0.1356  -0.5057
 HO4  C1'  C  CH1   0   0.174   1.2063   0.8498  -0.7933
 HO4  O4'  O  O2    0  -0.494   2.1869  -0.0674  -1.1704
 HO4  C4'  C  CH1   0  -0.009   3.2182  -0.1496  -0.1831
 HO4  C5'  C  CH2   0  -0.156   3.6401  -1.5809   0.0332
 HO4  O5'  O  OH1   0  -0.667   4.1995  -2.0852  -1.1528
 HO4  C3'  C  CH1   0  -0.018   2.6127   0.5033   1.0629
 HO4  O3'  O  OH1   0  -0.662   3.5480   1.0622   1.9372
 HO4  C2'  C  CH1   0  -0.043   1.7328   1.5837   0.4399
 HO4  O2'  O  OH1   0  -0.663   2.4902   2.6685  -0.0242
 HO4  H1   H  H     0   0.283  -3.0089  -4.7579   0.7394
 HO4  H2   H  HCR5  0   0.316   0.6397  -1.8884  -0.3177
 HO4  H3   H  HNH2  0   0.410  -4.4254  -1.5664   0.4155
 HO4  H4   H  HNH2  0   0.403  -5.4765  -0.2020   0.3937
 HO4  H5   H  HCR6  0   0.251  -3.0160   3.4001  -0.5223
 HO4  H6   H  HCH1  0   0.284   0.9948   1.5472  -1.6081
 HO4  H7   H  HCH1  0   0.244   4.0840   0.4357  -0.5164
 HO4  H8   H  HCH2  0   0.209   4.3637  -1.5859   0.8600
 HO4  H9   H  HCH2  0   0.200   2.7779  -2.1749   0.3686
 HO4  H10  H  HOH1  0   0.460   4.5071  -2.9799  -0.9824
 HO4  H11  H  HCH1  0   0.238   1.9635  -0.2193   1.5777
 HO4  H12  H  HOH1  0   0.467   3.8759   0.3809   2.5310
 HO4  H13  H  HCH1  0   0.264   0.9239   1.9039   1.1063
 HO4  H14  H  HOH1  0   0.459   3.0199   3.0073   0.7056

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
 HO4  C11  C10  triple    1.205  0.020  1.205
 HO4  O2'  C2'  single    1.402  0.020  1.402
 HO4  C10  C7   single    1.413  0.020  1.413
 HO4  C2'  C3'  single    1.526  0.020  1.526
 HO4  C2'  C1'  single    1.529  0.020  1.529
 HO4  C7   C8   aromatic  1.373  0.020  1.373
 HO4  C7   C5   aromatic  1.432  0.020  1.432
 HO4  C8   N9   aromatic  1.367  0.020  1.367
 HO4  C3'  O3'  single    1.397  0.020  1.397
 HO4  C3'  C4'  single    1.531  0.020  1.531
 HO4  N6   C6   single    1.336  0.020  1.336
 HO4  C5   C6   aromatic  1.409  0.020  1.409
 HO4  C5   C4   aromatic  1.392  0.020  1.392
 HO4  N9   C1'  single    1.461  0.020  1.461
 HO4  N9   C4   aromatic  1.363  0.020  1.363
 HO4  C1'  O4'  single    1.395  0.020  1.395
 HO4  C6   N1   aromatic  1.336  0.020  1.336
 HO4  C4   N3   aromatic  1.334  0.020  1.334
 HO4  C4'  C5'  single    1.508  0.020  1.508
 HO4  C4'  O4'  single    1.430  0.020  1.430
 HO4  C5'  O5'  single    1.405  0.020  1.405
 HO4  N1   C2   aromatic  1.331  0.020  1.331
 HO4  N3   C2   aromatic  1.319  0.020  1.319
 HO4  C11  H1   single    0.913  0.020  1.066
 HO4  C8   H2   single    0.929  0.020  1.085
 HO4  N6   H3   single    0.868  0.020  1.013
 HO4  N6   H4   single    0.868  0.020  1.013
 HO4  C2   H5   single    0.929  0.020  1.085
 HO4  C1'  H6   single    0.939  0.020  1.096
 HO4  C4'  H7   single    0.939  0.020  1.096
 HO4  C5'  H8   single    0.939  0.020  1.096
 HO4  C5'  H9   single    0.939  0.020  1.096
 HO4  O5'  H10  single    0.832  0.020  0.971
 HO4  C3'  H11  single    0.939  0.020  1.096
 HO4  O3'  H12  single    0.832  0.020  0.971
 HO4  C2'  H13  single    0.939  0.020  1.096
 HO4  O2'  H14  single    0.832  0.020  0.971

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
 HO4  H1   C11  C10  180.00  3.000
 HO4  C7   C10  C11  180.00  3.000
 HO4  C5   C7   C8   106.14  3.000
 HO4  C5   C7   C10  127.29  3.000
 HO4  C8   C7   C10  126.57  3.000
 HO4  H2   C8   N9   122.03  3.000
 HO4  H2   C8   C7   128.26  3.000
 HO4  N9   C8   C7   109.70  3.000
 HO4  C4   C5   C6   115.68  3.000
 HO4  C4   C5   C7   106.96  3.000
 HO4  C6   C5   C7   137.36  3.000
 HO4  N1   C6   N6   118.48  3.000
 HO4  N1   C6   C5   118.81  3.000
 HO4  N6   C6   C5   122.71  3.000
 HO4  H4   N6   H3   117.84  3.000
 HO4  H4   N6   C6   119.72  3.000
 HO4  H3   N6   C6   121.57  3.000
 HO4  C2   N1   C6   118.83  3.000
 HO4  H5   C2   N3   116.27  3.000
 HO4  H5   C2   N1   115.52  3.000
 HO4  N3   C2   N1   128.21  3.000
 HO4  C4   N3   C2   112.42  3.000
 HO4  N9   C4   N3   125.60  3.000
 HO4  N3   C4   C5   126.06  3.000
 HO4  N9   C4   C5   108.34  3.000
 HO4  C1'  N9   C4   123.71  3.000
 HO4  C4   N9   C8   108.86  3.000
 HO4  C1'  N9   C8   127.42  3.000
 HO4  H6   C1'  C2'  111.20  3.000
 HO4  H6   C1'  O4'  110.73  3.000
 HO4  C2'  C1'  O4'  106.97  3.000
 HO4  H6   C1'  N9   107.11  3.000
 HO4  O4'  C1'  N9   109.22  3.000
 HO4  C2'  C1'  N9   111.63  3.000
 HO4  C4'  O4'  C1'  110.98  3.000
 HO4  H7   C4'  C3'  109.38  3.000
 HO4  H7   C4'  C5'  109.22  3.000
 HO4  C3'  C4'  C5'  113.49  3.000
 HO4  H7   C4'  O4'  109.19  3.000
 HO4  C5'  C4'  O4'  110.82  3.000
 HO4  C3'  C4'  O4'  104.60  3.000
 HO4  H9   C5'  H8   106.52  3.000
 HO4  H9   C5'  O5'  112.08  3.000
 HO4  H8   C5'  O5'  111.80  3.000
 HO4  H9   C5'  C4'  109.71  3.000
 HO4  H8   C5'  C4'  107.25  3.000
 HO4  O5'  C5'  C4'  109.33  3.000
 HO4  H10  O5'  C5'  108.17  3.000
 HO4  H11  C3'  C2'  108.42  3.000
 HO4  H11  C3'  O3'  111.43  3.000
 HO4  C2'  C3'  O3'  110.99  3.000
 HO4  H11  C3'  C4'  109.52  3.000
 HO4  O3'  C3'  C4'  114.52  3.000
 HO4  C2'  C3'  C4'  101.40  3.000
 HO4  H12  O3'  C3'  109.36  3.000
 HO4  H13  C2'  O2'  111.97  3.000
 HO4  H13  C2'  C3'  112.59  3.000
 HO4  O2'  C2'  C3'  111.80  3.000
 HO4  H13  C2'  C1'  112.12  3.000
 HO4  C3'  C2'  C1'  100.83  3.000
 HO4  O2'  C2'  C1'  106.89  3.000
 HO4  H14  O2'  C2'  108.57  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
 HO4  CONST_01  C4   N9  C8  C7     0.00  0.0  0
 HO4  CONST_02  N1   C6  C5  C7   180.00  0.0  0
 HO4  CONST_03  N9   C4  C5  C7     0.00  0.0  0
 HO4  CONST_04  N3   C4  C5  C7   180.00  0.0  0
 HO4  CONST_05  C6   C5  C7  C8   180.00  0.0  0
 HO4  CONST_06  C4   C5  C7  C8     0.00  0.0  0
 HO4  CONST_07  C5   C4  N9  C8     0.00  0.0  0
 HO4  CONST_08  N3   C4  N9  C8   180.00  0.0  0
 HO4  CONST_09  N9   C8  C7  C5     0.00  0.0  0
 HO4  CONST_10  C2   N1  C6  C5     0.00  0.0  0
 HO4  CONST_11  C2   N3  C4  C5     0.00  0.0  0
 HO4  CONST_12  N9   C4  C5  C6   180.00  0.0  0
 HO4  CONST_13  N3   C4  C5  C6     0.00  0.0  0
 HO4  CONST_14  N3   C2  N1  C6     0.00  0.0  0
 HO4  CONST_15  C4   C5  C6  N1     0.00  0.0  0
 HO4  CONST_16  C4   N3  C2  N1     0.00  0.0  0
 HO4  CONST_17  N9   C4  N3  C2   180.00  0.0  0
 HO4  CONST_18  C1'  N9  C8  C7   180.00  0.0  0
 HO4  CONST_19  C1'  N9  C4  C5   180.00  0.0  0
 HO4  CONST_20  C1'  N9  C4  N3     0.00  0.0  0
 HO4  CONST_21  N9   C8  C7  C10  180.00  0.0  0
 HO4  CONST_22  C6   C5  C7  C10    0.00  0.0  0
 HO4  CONST_23  C4   C5  C7  C10  180.00  0.0  0
 HO4  CONST_24  N6   C6  C5  C7     0.00  0.0  0
 HO4  CONST_25  C4   C5  C6  N6   180.00  0.0  0
 HO4  CONST_26  C2   N1  C6  N6   180.00  0.0  0
 HO4  CONST_27  H2   C8  C7  C5   180.00  0.0  0
 HO4  CONST_28  H5   C2  N1  C6   180.00  0.0  0
 HO4  CONST_29  H3   N6  C6  C5     0.00  0.0  0
 HO4  CONST_30  H4   N6  C6  C5   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
 HO4  chir_01  C1'  C2'  N9   O4'  positiv
 HO4  chir_02  C4'  O4'  C5'  C3'  positiv
 HO4  chir_03  C3'  O3'  C4'  C2'  positiv
 HO4  chir_04  C2'  O2'  C3'  C1'  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
 HO4  plan-1  C11  0.020
 HO4  plan-1  C10  0.020
 HO4  plan-1  C7   0.020
 HO4  plan-1  C8   0.020
 HO4  plan-1  C5   0.020
 HO4  plan-1  C6   0.020
 HO4  plan-1  N6   0.020
 HO4  plan-1  N1   0.020
 HO4  plan-1  C2   0.020
 HO4  plan-1  N3   0.020
 HO4  plan-1  C4   0.020
 HO4  plan-1  N9   0.020
 HO4  plan-1  C1'  0.020
 HO4  plan-1  H2   0.020
 HO4  plan-1  H5   0.020
 HO4  plan-2  C6   0.020
 HO4  plan-2  N6   0.020
 HO4  plan-2  H3   0.020
 HO4  plan-2  H4   0.020

