# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:53:26 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolane-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnn2c1ccc2[C@@]3(O[C@H](CO)[C@@H](O)[C@H]3O)C#N
#
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
 U08  U08  (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolane-2-carbonitrile  ligand  34  21  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U08
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
 U08  C8   C  CSP   0   0.141  16.8549  -2.0413   3.5475
 U08  C5   C  CR5   0   0.412  18.9908  -2.2422   4.6685
 U08  C6   C  CH2   0  -0.168  20.3727  -3.3366   1.0053
 U08  N1   N  N     0  -0.417  18.6788  -3.1930   5.5803
 U08  C2   C  CR15  0  -0.026  18.8169  -1.0001   2.4659
 U08  N3   N  NS    0  -0.260  15.7277  -1.9315   3.7433
 U08  C4   C  CR15  0  -0.027  18.9043  -3.0108   1.2316
 U08  O2   O  OH1   0  -0.644  18.1495   0.1962   2.6868
 U08  N2   N  N     0  -0.273  17.7605  -4.1614   5.4070
 U08  N4   N  N     0  -0.479  18.3167  -4.9285   7.5922
 U08  C7   C  CR15  0  -0.382  19.9782  -1.4447   5.2283
 U08  C1   C  CR5   0   0.049  18.3147  -2.1814   3.3389
 U08  C10  C  CR15  0  -0.374  20.2685  -1.9343   6.5071
 U08  C11  C  CR6   0   0.432  19.2193  -3.9780   7.7501
 U08  C12  C  CR16  0   0.067  17.6462  -4.9534   6.4273
 U08  C3   C  CR15  0  -0.023  18.5685  -1.5389   1.0587
 U08  C9   C  CR56  0   0.322  19.4459  -3.0288   6.7082
 U08  N5   N  NH2   0  -0.812  19.9128  -3.9090   8.8800
 U08  O1   O  O     0  -0.485  18.5680  -3.3401   2.5867
 U08  O3   O  OH1   0  -0.655  17.2192  -1.4310   0.6909
 U08  H1   H  HCH2  0   0.224  20.5529  -4.3665   1.3363
 U08  H2   H  HCH2  0   0.201  21.0031  -2.6857   1.6263
 U08  H3   H  HCR5  0   0.274  19.8986  -0.9052   2.6148
 U08  H4   H  HCR5  0   0.268  18.2936  -3.6278   0.5657
 U08  H5   H  HOH1  0   0.471  18.5853   0.6923   3.3860
 U08  H6   H  HOH1  0   0.463  21.5767  -3.3104  -0.5120
 U08  H7   H  HCR5  0   0.272  20.4506  -0.5947   4.7616
 U08  H8   H  HCR5  0   0.268  20.9916  -1.5341   7.1994
 U08  H9   H  HCR6  0   0.277  16.9105  -5.7398   6.3127
 U08  H10  H  HCR5  0   0.260  19.2300  -1.0554   0.3311
 U08  H11  H  HNH2  0   0.412  19.7367  -4.5728   9.6156
 U08  H12  H  HNH2  0   0.420  20.6076  -3.2013   9.0422
 U08  H13  H  HOH1  0   0.457  16.9710  -0.5000   0.6885
 U08  O4   O  OH1   0  -0.667  20.6371  -3.1696  -0.3660

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
 U08  O4   C6   single    1.407  0.020  1.407
 U08  O3   C3   single    1.403  0.020  1.403
 U08  C6   C4   single    1.521  0.020  1.521
 U08  C3   C4   single    1.520  0.020  1.520
 U08  C3   C2   single    1.527  0.020  1.527
 U08  C4   O1   single    1.435  0.020  1.435
 U08  C2   O2   single    1.388  0.020  1.388
 U08  C2   C1   single    1.552  0.020  1.552
 U08  O1   C1   single    1.404  0.020  1.404
 U08  C1   C8   single    1.481  0.020  1.481
 U08  C1   C5   single    1.493  0.020  1.493
 U08  C8   N3   triple    1.149  0.020  1.149
 U08  C5   C7   aromatic  1.387  0.020  1.387
 U08  C5   N1   aromatic  1.354  0.020  1.354
 U08  C7   C10  aromatic  1.400  0.020  1.400
 U08  N2   N1   aromatic  1.346  0.020  1.346
 U08  N2   C12  aromatic  1.297  0.020  1.297
 U08  N1   C9   aromatic  1.374  0.020  1.374
 U08  C12  N4   aromatic  1.344  0.020  1.344
 U08  C10  C9   aromatic  1.384  0.020  1.384
 U08  C9   C11  aromatic  1.428  0.020  1.428
 U08  N4   C11  aromatic  1.320  0.020  1.320
 U08  C11  N5   single    1.328  0.020  1.328
 U08  C6   H1   single    0.970  0.020  1.090
 U08  C6   H2   single    0.970  0.020  1.090
 U08  C2   H3   single    0.970  0.020  1.090
 U08  C4   H4   single    0.970  0.020  1.090
 U08  O2   H5   single    0.850  0.020  0.980
 U08  O4   H6   single    0.850  0.020  0.980
 U08  C7   H7   single    0.930  0.020  1.080
 U08  C10  H8   single    0.930  0.020  1.080
 U08  C12  H9   single    0.930  0.020  1.080
 U08  C3   H10  single    0.970  0.020  1.090
 U08  N5   H11  single    0.860  0.020  1.020
 U08  N5   H12  single    0.860  0.020  1.020
 U08  O3   H13  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
 U08  C1   C8   N3   180.00  3.000
 U08  C1   C5   C7   131.17  3.000
 U08  C7   C5   N1   107.22  3.000
 U08  C1   C5   N1   121.61  3.000
 U08  H2   C6   H1   106.95  3.000
 U08  H2   C6   O4   111.90  3.000
 U08  H1   C6   O4   112.02  3.000
 U08  H2   C6   C4   110.05  3.000
 U08  H1   C6   C4   108.35  3.000
 U08  O4   C6   C4   107.52  3.000
 U08  C9   N1   N2   124.94  3.000
 U08  C9   N1   C5   109.90  3.000
 U08  N2   N1   C5   125.16  3.000
 U08  H3   C2   C3   108.43  3.000
 U08  H3   C2   C1   107.99  3.000
 U08  C3   C2   C1   101.37  3.000
 U08  H3   C2   O2   112.24  3.000
 U08  C1   C2   O2   114.27  3.000
 U08  C3   C2   O2   111.88  3.000
 U08  H4   C4   O1   108.34  3.000
 U08  H4   C4   C3   110.71  3.000
 U08  O1   C4   C3   106.15  3.000
 U08  H4   C4   C6   109.11  3.000
 U08  O1   C4   C6   108.52  3.000
 U08  C3   C4   C6   113.82  3.000
 U08  H5   O2   C2   110.03  3.000
 U08  C12  N2   N1   113.47  3.000
 U08  C12  N4   C11  117.26  3.000
 U08  H7   C7   C10  125.45  3.000
 U08  H7   C7   C5   126.17  3.000
 U08  C10  C7   C5   108.37  3.000
 U08  O1   C1   C2   105.56  3.000
 U08  O1   C1   C5   111.21  3.000
 U08  C2   C1   C5   112.67  3.000
 U08  C5   C1   C8   108.95  3.000
 U08  O1   C1   C8   109.34  3.000
 U08  C2   C1   C8   109.03  3.000
 U08  H8   C10  C9   126.80  3.000
 U08  H8   C10  C7   126.57  3.000
 U08  C9   C10  C7   106.63  3.000
 U08  N5   C11  C9   120.24  3.000
 U08  N5   C11  N4   119.76  3.000
 U08  C9   C11  N4   119.99  3.000
 U08  H9   C12  N4   116.36  3.000
 U08  H9   C12  N2   114.84  3.000
 U08  N4   C12  N2   128.80  3.000
 U08  H10  C3   O3   111.88  3.000
 U08  H10  C3   C4   111.69  3.000
 U08  O3   C3   C4   108.48  3.000
 U08  H10  C3   C2   110.97  3.000
 U08  C4   C3   C2   101.59  3.000
 U08  O3   C3   C2   111.77  3.000
 U08  C11  C9   C10  136.58  3.000
 U08  C11  C9   N1   115.53  3.000
 U08  C10  C9   N1   107.89  3.000
 U08  H12  N5   H11  117.88  3.000
 U08  H12  N5   C11  122.36  3.000
 U08  H11  N5   C11  119.76  3.000
 U08  C1   O1   C4   111.02  3.000
 U08  H13  O3   C3   108.83  3.000
 U08  H6   O4   C6   108.32  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
 U08  CONST_01  C9   C10  C7   C5     0.00  0.0  0
 U08  CONST_02  C12  N2   N1   C5   180.00  0.0  0
 U08  CONST_03  C10  C9   N1   C5     0.00  0.0  0
 U08  CONST_04  C11  C9   N1   C5   180.00  0.0  0
 U08  CONST_05  C10  C7   C5   N1     0.00  0.0  0
 U08  CONST_06  N4   C12  N2   N1     0.00  0.0  0
 U08  CONST_07  C7   C10  C9   N1     0.00  0.0  0
 U08  CONST_08  N4   C11  C9   N1     0.00  0.0  0
 U08  CONST_09  C7   C5   N1   N2   180.00  0.0  0
 U08  CONST_10  C10  C9   N1   N2   180.00  0.0  0
 U08  CONST_11  C11  C9   N1   N2     0.00  0.0  0
 U08  CONST_12  C11  N4   C12  N2     0.00  0.0  0
 U08  CONST_13  C10  C9   C11  N4   180.00  0.0  0
 U08  CONST_14  C9   N1   C5   C7     0.00  0.0  0
 U08  CONST_15  C11  C9   C10  C7   180.00  0.0  0
 U08  CONST_16  C9   N1   N2   C12    0.00  0.0  0
 U08  CONST_17  C9   C11  N4   C12    0.00  0.0  0
 U08  CONST_18  C1   C5   N1   N2     0.00  0.0  0
 U08  CONST_19  C10  C7   C5   C1   180.00  0.0  0
 U08  CONST_20  C9   N1   C5   C1   180.00  0.0  0
 U08  CONST_21  N5   C11  C9   N1   180.00  0.0  0
 U08  CONST_22  N5   C11  C9   C10    0.00  0.0  0
 U08  CONST_23  N5   C11  N4   C12  180.00  0.0  0
 U08  CONST_24  H8   C10  C7   C5   180.00  0.0  0
 U08  CONST_25  H7   C7   C5   N1   180.00  0.0  0
 U08  CONST_26  H9   C12  N2   N1   180.00  0.0  0
 U08  CONST_27  H11  N5   C11  N4     0.00  0.0  0
 U08  CONST_28  H12  N5   C11  N4   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
 U08  chir_01  C2  C3  O2  C1  negativ
 U08  chir_02  C4  O1  C3  C6  negativ
 U08  chir_03  C1  C5  O1  C2  positiv
 U08  chir_04  C3  O3  C2  C4  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
 U08  plan-1  C5   0.020
 U08  plan-1  N1   0.020
 U08  plan-1  N2   0.020
 U08  plan-1  N4   0.020
 U08  plan-1  C7   0.020
 U08  plan-1  C1   0.020
 U08  plan-1  C10  0.020
 U08  plan-1  C11  0.020
 U08  plan-1  C12  0.020
 U08  plan-1  C9   0.020
 U08  plan-1  N5   0.020
 U08  plan-1  H7   0.020
 U08  plan-1  H8   0.020
 U08  plan-1  H9   0.020
 U08  plan-2  C11  0.020
 U08  plan-2  N5   0.020
 U08  plan-2  H11  0.020
 U08  plan-2  H12  0.020

