# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:12:39 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 7-[(5R)-5-C-phenyl-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]([C@@H](O)[C@H]3O)[C@H](O)c4ccccc4
#
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
 F5J  F5J  7-[(5R)-5-C-phenyl-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  43  25  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F5J
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
 F5J  C7   C  CR15  0  -0.003  -1.1155   0.5559  -1.3646
 F5J  C6   C  CR15  0  -0.439  -2.1310   1.4579  -1.4220
 F5J  C1   C  CR16  0  -0.268   3.7586   3.1363   1.0365
 F5J  C5   C  CR16  0  -0.320   4.1232   0.7669   0.8141
 F5J  C4   C  CR16  0  -0.310   2.4438   1.8452  -0.5087
 F5J  C3   C  CR16  0  -0.239   4.4413   1.9830   1.4021
 F5J  C2   C  CR16  0  -0.241   2.7568   3.0641   0.0784
 F5J  C8   C  CR16  0   0.044  -4.0620   0.0632   1.8533
 F5J  C9   C  CR56  0  -0.085  -2.9917   1.1619  -0.3221
 F5J  C10  C  CR6   0   0.169   3.1193   0.6848  -0.1483
 F5J  C11  C  CR56  0   0.517  -2.4392   0.0745   0.3565
 F5J  C12  C  CR6   0   0.440  -4.1886   1.6682   0.2206
 F5J  C13  C  CR15  0  -0.017   1.3764  -2.7757  -0.4286
 F5J  C14  C  CR15  0  -0.060   0.0215  -2.2984  -0.9534
 F5J  C15  C  CR15  0  -0.029   1.9270  -1.4948   0.1882
 F5J  C16  C  CR15  0   0.210  -0.4008  -1.3245   0.1441
 F5J  C17  C  CH1   0  -0.090   2.7568  -0.6407  -0.7804
 F5J  N18  N  N     0  -0.465  -2.9426  -0.5031   1.4483
 F5J  N19  N  N     0  -0.477  -4.7029   1.0971   1.3131
 F5J  N20  N  NR5   0  -0.556  -1.2987  -0.2948  -0.2922
 F5J  N21  N  NH2   0  -0.821  -4.8513   2.6954  -0.3304
 F5J  O22  O  O     0  -0.488   0.7925  -0.7497   0.6211
 F5J  O23  O  OH1   0  -0.671   1.2149  -3.7217   0.5985
 F5J  O24  O  OH1   0  -0.654  -0.9427  -3.2991  -1.0964
 F5J  O25  O  OH1   0  -0.649   3.8784  -1.3521  -1.2436
 F5J  H1   H  HCR5  0   0.291  -0.2692   0.4527  -2.0242
 F5J  H2   H  HCR5  0   0.261  -2.2398   2.2314  -2.1650
 F5J  H4   H  HCR6  0   0.245   4.6702  -0.1164   1.1254
 F5J  H5   H  HCR6  0   0.243   1.6641   1.8008  -1.2594
 F5J  H6   H  HCR6  0   0.258   5.2242   2.0293   2.1476
 F5J  H7   H  HCR6  0   0.257   2.2191   3.9567  -0.2148
 F5J  H8   H  HCR6  0   0.247  -4.5225  -0.3620   2.7388
 F5J  H9   H  HCR5  0   0.253   2.0154  -3.1573  -1.2331
 F5J  H10  H  HCR5  0   0.248   0.1794  -1.7611  -1.8970
 F5J  H11  H  HCR5  0   0.258   2.5430  -1.7354   1.0642
 F5J  H12  H  HCR5  0   0.258  -0.9172  -1.8663   0.9428
 F5J  H13  H  HCH1  0   0.251   2.1533  -0.4342  -1.6706
 F5J  H14  H  HNH2  0   0.406  -4.4249   3.2575  -1.0459
 F5J  H15  H  HNH2  0   0.398  -5.6191   3.1058   0.1735
 F5J  H16  H  HOH1  0   0.449   0.5974  -4.3950   0.2897
 F5J  H17  H  HOH1  0   0.469  -0.8261  -3.7201  -1.9539
 F5J  H18  H  HOH1  0   0.453   4.3975  -1.6637  -0.4946
 F5J  H3   H  HCR6  0   0.257   4.0064   4.0846   1.4956

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
 F5J  O25  C17  single    1.407  0.020  1.407
 F5J  C2   C4   aromatic  1.389  0.020  1.389
 F5J  C2   C1   aromatic  1.388  0.020  1.388
 F5J  C4   C10  aromatic  1.390  0.020  1.390
 F5J  C1   C3   aromatic  1.389  0.020  1.389
 F5J  C3   C5   aromatic  1.388  0.020  1.388
 F5J  C10  C5   aromatic  1.393  0.020  1.393
 F5J  C10  C17  single    1.513  0.020  1.513
 F5J  C17  C15  single    1.535  0.020  1.535
 F5J  O22  C15  single    1.425  0.020  1.425
 F5J  O22  C16  single    1.408  0.020  1.408
 F5J  C15  C13  single    1.525  0.020  1.525
 F5J  C7   C6   aromatic  1.359  0.020  1.359
 F5J  C7   N20  aromatic  1.381  0.020  1.381
 F5J  C6   C9   aromatic  1.428  0.020  1.428
 F5J  N20  C16  single    1.434  0.020  1.434
 F5J  N20  C11  aromatic  1.363  0.020  1.363
 F5J  N21  C12  single    1.341  0.020  1.341
 F5J  C9   C12  aromatic  1.408  0.020  1.408
 F5J  C9   C11  aromatic  1.396  0.020  1.396
 F5J  C13  C14  single    1.529  0.020  1.529
 F5J  C13  O23  single    1.406  0.020  1.406
 F5J  C16  C14  single    1.527  0.020  1.527
 F5J  C12  N19  aromatic  1.336  0.020  1.336
 F5J  C11  N18  aromatic  1.334  0.020  1.334
 F5J  C14  O24  single    1.397  0.020  1.397
 F5J  N19  C8   aromatic  1.331  0.020  1.331
 F5J  N18  C8   aromatic  1.318  0.020  1.318
 F5J  C7   H1   single    0.930  0.020  1.080
 F5J  C6   H2   single    0.930  0.020  1.080
 F5J  C1   H3   single    0.930  0.020  1.080
 F5J  C5   H4   single    0.930  0.020  1.080
 F5J  C4   H5   single    0.930  0.020  1.080
 F5J  C3   H6   single    0.930  0.020  1.080
 F5J  C2   H7   single    0.930  0.020  1.080
 F5J  C8   H8   single    0.930  0.020  1.080
 F5J  C13  H9   single    0.970  0.020  1.090
 F5J  C14  H10  single    0.970  0.020  1.090
 F5J  C15  H11  single    0.970  0.020  1.090
 F5J  C16  H12  single    0.970  0.020  1.090
 F5J  C17  H13  single    0.970  0.020  1.090
 F5J  N21  H14  single    0.890  0.020  1.040
 F5J  N21  H15  single    0.890  0.020  1.040
 F5J  O23  H16  single    0.850  0.020  0.980
 F5J  O24  H17  single    0.850  0.020  0.980
 F5J  O25  H18  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
 F5J  H1   C7   N20  121.35  3.000
 F5J  H1   C7   C6   128.62  3.000
 F5J  N20  C7   C6   110.02  3.000
 F5J  H2   C6   C9   128.23  3.000
 F5J  H2   C6   C7   125.49  3.000
 F5J  C9   C6   C7   106.28  3.000
 F5J  H3   C1   C2   120.24  3.000
 F5J  H3   C1   C3   120.21  3.000
 F5J  C2   C1   C3   119.55  3.000
 F5J  H4   C5   C10  120.91  3.000
 F5J  H4   C5   C3   118.45  3.000
 F5J  C10  C5   C3   120.63  3.000
 F5J  H5   C4   C10  119.68  3.000
 F5J  H5   C4   C2   119.42  3.000
 F5J  C10  C4   C2   120.90  3.000
 F5J  H6   C3   C5   119.69  3.000
 F5J  H6   C3   C1   120.09  3.000
 F5J  C5   C3   C1   120.22  3.000
 F5J  H7   C2   C4   119.82  3.000
 F5J  H7   C2   C1   120.17  3.000
 F5J  C4   C2   C1   120.01  3.000
 F5J  H8   C8   N19  115.56  3.000
 F5J  H8   C8   N18  116.29  3.000
 F5J  N19  C8   N18  128.16  3.000
 F5J  C12  C9   C11  115.42  3.000
 F5J  C11  C9   C6   107.30  3.000
 F5J  C12  C9   C6   137.28  3.000
 F5J  C17  C10  C4   120.44  3.000
 F5J  C17  C10  C5   120.87  3.000
 F5J  C4   C10  C5   118.69  3.000
 F5J  N20  C11  N18  126.02  3.000
 F5J  N18  C11  C9   125.86  3.000
 F5J  N20  C11  C9   108.12  3.000
 F5J  N21  C12  N19  118.25  3.000
 F5J  N19  C12  C9   119.26  3.000
 F5J  N21  C12  C9   122.49  3.000
 F5J  H9   C13  O23  111.66  3.000
 F5J  H9   C13  C15  112.27  3.000
 F5J  O23  C13  C15  108.14  3.000
 F5J  H9   C13  C14  111.92  3.000
 F5J  O23  C13  C14  111.03  3.000
 F5J  C15  C13  C14  101.34  3.000
 F5J  H10  C14  O24  111.23  3.000
 F5J  H10  C14  C16  110.22  3.000
 F5J  O24  C14  C16  109.85  3.000
 F5J  H10  C14  C13  108.69  3.000
 F5J  O24  C14  C13  115.03  3.000
 F5J  C16  C14  C13  101.39  3.000
 F5J  H11  C15  O22  108.61  3.000
 F5J  H11  C15  C17  108.80  3.000
 F5J  O22  C15  C17  109.34  3.000
 F5J  H11  C15  C13  109.96  3.000
 F5J  O22  C15  C13  105.95  3.000
 F5J  C17  C15  C13  114.04  3.000
 F5J  H12  C16  O22  110.77  3.000
 F5J  H12  C16  N20  106.38  3.000
 F5J  O22  C16  N20  109.91  3.000
 F5J  H12  C16  C14  109.84  3.000
 F5J  N20  C16  C14  114.36  3.000
 F5J  O22  C16  C14  105.64  3.000
 F5J  H13  C17  O25  105.49  3.000
 F5J  H13  C17  C15  108.66  3.000
 F5J  O25  C17  C15  110.94  3.000
 F5J  H13  C17  C10  107.85  3.000
 F5J  C15  C17  C10  110.70  3.000
 F5J  O25  C17  C10  112.94  3.000
 F5J  C11  N18  C8   112.71  3.000
 F5J  C12  N19  C8   118.60  3.000
 F5J  C16  N20  C11  125.00  3.000
 F5J  C11  N20  C7   108.28  3.000
 F5J  C16  N20  C7   126.55  3.000
 F5J  H15  N21  H14  116.90  3.000
 F5J  H15  N21  C12  118.94  3.000
 F5J  H14  N21  C12  120.75  3.000
 F5J  C16  O22  C15  111.01  3.000
 F5J  H16  O23  C13  108.03  3.000
 F5J  H17  O24  C14  108.71  3.000
 F5J  H18  O25  C17  109.72  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
 F5J  CONST_01  C12  C9   C6   C7   180.00  0.0  0
 F5J  CONST_02  C11  C9   C6   C7     0.00  0.0  0
 F5J  CONST_03  C9   C11  N20  C7     0.00  0.0  0
 F5J  CONST_04  N18  C11  N20  C7   180.00  0.0  0
 F5J  CONST_05  C11  N20  C7   C6     0.00  0.0  0
 F5J  CONST_06  N19  C12  C9   C6   180.00  0.0  0
 F5J  CONST_07  N20  C11  C9   C6     0.00  0.0  0
 F5J  CONST_08  N18  C11  C9   C6   180.00  0.0  0
 F5J  CONST_09  C10  C4   C2   C1     0.00  0.0  0
 F5J  CONST_10  C10  C5   C3   C1     0.00  0.0  0
 F5J  CONST_11  C2   C1   C3   C5     0.00  0.0  0
 F5J  CONST_12  C2   C4   C10  C5     0.00  0.0  0
 F5J  CONST_13  C3   C1   C2   C4     0.00  0.0  0
 F5J  CONST_14  C3   C5   C10  C4     0.00  0.0  0
 F5J  CONST_15  C9   C12  N19  C8     0.00  0.0  0
 F5J  CONST_16  N20  C11  N18  C8   180.00  0.0  0
 F5J  CONST_17  C9   C11  N18  C8     0.00  0.0  0
 F5J  CONST_18  N20  C7   C6   C9     0.00  0.0  0
 F5J  CONST_19  N19  C12  C9   C11    0.00  0.0  0
 F5J  CONST_20  N19  C8   N18  C11    0.00  0.0  0
 F5J  CONST_21  N20  C11  C9   C12  180.00  0.0  0
 F5J  CONST_22  N18  C11  C9   C12    0.00  0.0  0
 F5J  CONST_23  N18  C8   N19  C12    0.00  0.0  0
 F5J  CONST_24  C16  N20  C7   C6   180.00  0.0  0
 F5J  CONST_25  C16  N20  C11  C9   180.00  0.0  0
 F5J  CONST_26  N18  C11  N20  C16    0.00  0.0  0
 F5J  CONST_27  N21  C12  C9   C6     0.00  0.0  0
 F5J  CONST_28  C17  C10  C5   C3   180.00  0.0  0
 F5J  CONST_29  C17  C10  C4   C2   180.00  0.0  0
 F5J  CONST_30  N21  C12  N19  C8   180.00  0.0  0
 F5J  CONST_31  N21  C12  C9   C11  180.00  0.0  0
 F5J  CONST_32  H5   C4   C2   C1   180.00  0.0  0
 F5J  CONST_33  H4   C5   C3   C1   180.00  0.0  0
 F5J  CONST_34  H3   C1   C3   C5   180.00  0.0  0
 F5J  CONST_35  H7   C2   C1   C3   180.00  0.0  0
 F5J  CONST_36  H6   C3   C1   C2   180.00  0.0  0
 F5J  CONST_37  H1   C7   C6   C9   180.00  0.0  0
 F5J  CONST_38  H2   C6   C9   C11  180.00  0.0  0
 F5J  CONST_39  H8   C8   N18  C11  180.00  0.0  0
 F5J  CONST_40  H14  N21  C12  C9     0.00  0.0  0
 F5J  CONST_41  H15  N21  C12  C9   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
 F5J  chir_01  C13  C15  C14  O23  positiv
 F5J  chir_02  C14  O24  C13  C16  positiv
 F5J  chir_03  C15  O22  C17  C13  positiv
 F5J  chir_04  C16  O22  N20  C14  negativ
 F5J  chir_05  C17  O25  C15  C10  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
 F5J  plan-1  C1   0.020
 F5J  plan-1  C5   0.020
 F5J  plan-1  C4   0.020
 F5J  plan-1  C3   0.020
 F5J  plan-1  C2   0.020
 F5J  plan-1  C10  0.020
 F5J  plan-1  C17  0.020
 F5J  plan-1  H4   0.020
 F5J  plan-1  H5   0.020
 F5J  plan-1  H6   0.020
 F5J  plan-1  H7   0.020
 F5J  plan-1  H3   0.020
 F5J  plan-2  C7   0.020
 F5J  plan-2  C6   0.020
 F5J  plan-2  C8   0.020
 F5J  plan-2  C9   0.020
 F5J  plan-2  C11  0.020
 F5J  plan-2  C12  0.020
 F5J  plan-2  C16  0.020
 F5J  plan-2  N18  0.020
 F5J  plan-2  N19  0.020
 F5J  plan-2  N20  0.020
 F5J  plan-2  N21  0.020
 F5J  plan-2  H1   0.020
 F5J  plan-2  H2   0.020
 F5J  plan-2  H8   0.020
 F5J  plan-3  C12  0.020
 F5J  plan-3  N21  0.020
 F5J  plan-3  H14  0.020
 F5J  plan-3  H15  0.020

