# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 07:13:42 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-[(4~{a}~{S},7~{a}~{S})-4-azanyl-1,4,4~{a},7~{a}-tetrahydropyrrolo[2,3-d]pyrimidin-7-yl]-5-(quinolin-7-yloxymethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1N=CN[C@@H]2[C@H]1C=CN2[C@@H]3O[C@H](COc4ccc5cccnc5c4)[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
 U6K  U6K  "(2~{R},3~{R},4~{S},5~{R})-2-[(4~{a}~{S},7~{a}~{S})-4-azanyl-1,4,4~{a},7~{a}-tetrahydropyrrolo[2,3-d]pyrimidin-7-yl]-5-(quinolin-7-yloxymethyl)oxolane-3,4-diol"
  ligand  52  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_U6K
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
 U6K  C1   C  CH1   0   0.065  -37.1123  -35.4062   -3.3664
 U6K  C2   C  C1    0   0.111  -35.9330  -33.8169   -2.1505
 U6K  C3   C  CH1   0   0.160  -34.7244  -34.8660   -3.9797
 U6K  C4   C  CH1   0  -0.391  -36.1234  -35.1736   -4.5228
 U6K  C5   C  C1    0  -0.344  -35.8585  -36.4423   -5.2866
 U6K  C6   C  C1    0   0.007  -34.7326  -36.9851   -4.8238
 U6K  C8   C  CH1   0  -0.010  -30.8342  -37.0271   -4.7122
 U6K  C11  C  CR16  0  -0.334  -28.4178  -40.4399   -6.7539
 U6K  C12  C  CR16  0  -0.290  -28.1727  -41.4802   -7.5974
 U6K  C13  C  CR66  0   0.047  -29.1442  -41.8903   -8.5412
 U6K  C14  C  CR16  0  -0.180  -28.9457  -42.9617   -9.4322
 U6K  C15  C  CR16  0  -0.334  -29.9404  -43.2922  -10.3116
 U6K  C16  C  CR16  0  -0.082  -31.1296  -42.5390  -10.2874
 U6K  C17  C  CR66  0   0.234  -30.3784  -41.1974   -8.5967
 U6K  C20  C  CH1   0  -0.059  -32.3066  -37.6418   -2.9678
 U6K  N1   N  NH2   0  -0.792  -38.4357  -35.5981   -3.9115
 U6K  N2   N  N     0  -0.446  -37.0640  -34.3552   -2.3676
 U6K  N3   N  NH1   0  -0.644  -34.7560  -34.1035   -2.7697
 U6K  N4   N  NT    0  -0.499  -34.1303  -36.2037   -3.8339
 U6K  C7   C  CH1   0   0.206  -32.7420  -36.3014   -3.5582
 U6K  O1   O  O2    0  -0.504  -31.9439  -36.1414   -4.7274
 U6K  C9   C  CH2   0  -0.214  -30.9909  -38.0275   -5.8485
 U6K  O2   O  O2    0  -0.469  -29.7765  -38.7489   -5.9207
 U6K  C10  C  CR6   0   0.395  -29.6564  -39.7490   -6.8071
 U6K  N5   N  N     0  -0.437  -31.3508  -41.5367   -9.4755
 U6K  C18  C  CR16  0  -0.439  -30.6186  -40.1178   -7.7146
 U6K  C19  C  CH1   0  -0.025  -30.8206  -37.6743   -3.3307
 U6K  O3   O  OH1   0  -0.667  -30.0730  -36.8589   -2.4642
 U6K  O4   O  OH1   0  -0.655  -32.5649  -37.6622   -1.5920
 U6K  H22  H  HCH1  0   0.224  -36.8274  -36.3476   -2.8785
 U6K  H3   H  H     0   0.258  -35.8494  -33.0403   -1.3935
 U6K  H4   H  HCH1  0   0.264  -34.1604  -34.2994   -4.7314
 U6K  H5   H  HCH1  0   0.258  -36.4836  -34.3428   -5.1360
 U6K  H6   H  H     0   0.246  -36.5373  -36.8971   -5.9901
 U6K  H7   H  H     0   0.278  -34.2993  -37.9341   -5.1092
 U6K  H9   H  HCH1  0   0.253  -29.9124  -36.4573   -4.8745
 U6K  H13  H  HCR6  0   0.266  -27.2271  -42.0065   -7.5516
 U6K  H14  H  HCR6  0   0.271  -28.0111  -43.5097   -9.4113
 U6K  H15  H  HCR6  0   0.268  -29.8310  -44.1076  -11.0128
 U6K  H16  H  HCR6  0   0.260  -31.9287  -42.7859  -10.9791
 U6K  H20  H  HCH1  0   0.247  -32.8181  -38.4660   -3.4810
 U6K  H23  H  HNH2  0   0.342  -39.0825  -35.8010   -3.1588
 U6K  H2   H  HNH2  0   0.333  -38.7555  -34.7275   -4.3221
 U6K  H24  H  HNH1  0   0.400  -33.9906  -33.4729   -2.5971
 U6K  H8   H  HCH1  0   0.238  -32.5045  -35.5087   -2.8377
 U6K  H11  H  HCH2  0   0.250  -31.1829  -37.4953   -6.7866
 U6K  H10  H  HCH2  0   0.235  -31.8349  -38.7050   -5.6702
 U6K  H17  H  HCR6  0   0.278  -31.5726  -39.6124   -7.7867
 U6K  H18  H  HCH1  0   0.244  -30.4258  -38.6978   -3.3577
 U6K  H19  H  HOH1  0   0.444  -30.3743  -37.0338   -1.5645
 U6K  H21  H  HOH1  0   0.464  -32.5715  -38.5762   -1.2899
 U6K  H12  H  HCR6  0   0.270  -27.6757  -40.1283   -6.0298

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
 U6K  C15  C16  aromatic  1.408  0.020  1.408
 U6K  C15  C14  aromatic  1.368  0.020  1.368
 U6K  C16  N5   aromatic  1.309  0.020  1.309
 U6K  C14  C13  aromatic  1.408  0.020  1.408
 U6K  N5   C17  aromatic  1.354  0.020  1.354
 U6K  C13  C17  aromatic  1.416  0.020  1.416
 U6K  C13  C12  aromatic  1.415  0.020  1.415
 U6K  C17  C18  aromatic  1.415  0.020  1.415
 U6K  C12  C11  aromatic  1.362  0.020  1.362
 U6K  C18  C10  aromatic  1.373  0.020  1.373
 U6K  C11  C10  aromatic  1.419  0.020  1.419
 U6K  C10  O2   single    1.342  0.020  1.342
 U6K  O2   C9   single    1.414  0.020  1.414
 U6K  C9   C8   single    1.522  0.020  1.522
 U6K  O1   C8   single    1.420  0.020  1.420
 U6K  O1   C7   single    1.425  0.020  1.425
 U6K  C8   C19  single    1.526  0.020  1.526
 U6K  C5   C4   single    1.504  0.020  1.504
 U6K  C5   C6   double    1.333  0.020  1.333
 U6K  C4   C3   single    1.532  0.020  1.532
 U6K  C4   C1   single    1.539  0.020  1.539
 U6K  C6   N4   single    1.398  0.020  1.398
 U6K  N1   C1   single    1.444  0.020  1.444
 U6K  N4   C3   single    1.471  0.020  1.471
 U6K  N4   C7   single    1.419  0.020  1.419
 U6K  C3   N3   single    1.431  0.020  1.431
 U6K  C7   C20  single    1.528  0.020  1.528
 U6K  C1   N2   single    1.451  0.020  1.451
 U6K  C19  C20  single    1.530  0.020  1.530
 U6K  C19  O3   single    1.405  0.020  1.405
 U6K  N2   C2   double    1.271  0.020  1.271
 U6K  C20  O4   single    1.400  0.020  1.400
 U6K  N3   C2   single    1.361  0.020  1.361
 U6K  C1   H22  single    0.970  0.020  1.090
 U6K  C2   H3   single    0.930  0.020  1.080
 U6K  C3   H4   single    0.970  0.020  1.090
 U6K  C4   H5   single    0.970  0.020  1.090
 U6K  C5   H6   single    0.930  0.020  1.080
 U6K  C6   H7   single    0.930  0.020  1.080
 U6K  C8   H9   single    0.970  0.020  1.090
 U6K  C11  H12  single    0.930  0.020  1.080
 U6K  C12  H13  single    0.930  0.020  1.080
 U6K  C14  H14  single    0.930  0.020  1.080
 U6K  C15  H15  single    0.930  0.020  1.080
 U6K  C16  H16  single    0.930  0.020  1.080
 U6K  C20  H20  single    0.970  0.020  1.090
 U6K  N1   H23  single    0.890  0.020  1.040
 U6K  N1   H2   single    0.890  0.020  1.040
 U6K  N3   H24  single    0.890  0.020  1.040
 U6K  C7   H8   single    0.970  0.020  1.090
 U6K  C9   H11  single    0.970  0.020  1.090
 U6K  C9   H10  single    0.970  0.020  1.090
 U6K  C18  H17  single    0.930  0.020  1.080
 U6K  C19  H18  single    0.970  0.020  1.090
 U6K  O3   H19  single    0.850  0.020  0.980
 U6K  O4   H21  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
 U6K  H22  C1   N2   107.85  3.000
 U6K  H22  C1   N1   106.96  3.000
 U6K  N2   C1   N1   112.75  3.000
 U6K  H22  C1   C4   107.26  3.000
 U6K  N2   C1   C4   112.73  3.000
 U6K  N1   C1   C4   108.98  3.000
 U6K  H3   C2   N3   113.63  3.000
 U6K  H3   C2   N2   119.31  3.000
 U6K  N3   C2   N2   127.06  3.000
 U6K  H4   C3   N4   109.26  3.000
 U6K  H4   C3   N3   108.39  3.000
 U6K  N4   C3   N3   114.19  3.000
 U6K  H4   C3   C4   109.28  3.000
 U6K  N3   C3   C4   112.75  3.000
 U6K  N4   C3   C4   102.79  3.000
 U6K  H5   C4   C5   114.45  3.000
 U6K  H5   C4   C3   110.31  3.000
 U6K  C5   C4   C3   100.86  3.000
 U6K  H5   C4   C1   108.93  3.000
 U6K  C3   C4   C1   110.53  3.000
 U6K  C5   C4   C1   111.54  3.000
 U6K  H6   C5   C6   125.91  3.000
 U6K  H6   C5   C4   125.18  3.000
 U6K  C6   C5   C4   108.42  3.000
 U6K  H7   C6   N4   120.32  3.000
 U6K  H7   C6   C5   127.17  3.000
 U6K  N4   C6   C5   112.47  3.000
 U6K  H9   C8   C19  110.32  3.000
 U6K  H9   C8   C9   108.53  3.000
 U6K  C19  C8   C9   113.46  3.000
 U6K  H9   C8   O1   109.36  3.000
 U6K  C19  C8   O1   106.34  3.000
 U6K  C9   C8   O1   108.76  3.000
 U6K  H12  C11  C10  118.89  3.000
 U6K  H12  C11  C12  120.72  3.000
 U6K  C10  C11  C12  120.39  3.000
 U6K  H13  C12  C13  119.12  3.000
 U6K  H13  C12  C11  120.15  3.000
 U6K  C13  C12  C11  120.73  3.000
 U6K  C17  C13  C14  118.06  3.000
 U6K  C17  C13  C12  118.86  3.000
 U6K  C14  C13  C12  123.09  3.000
 U6K  H14  C14  C15  121.15  3.000
 U6K  H14  C14  C13  119.63  3.000
 U6K  C15  C14  C13  119.22  3.000
 U6K  H15  C15  C16  120.01  3.000
 U6K  H15  C15  C14  121.70  3.000
 U6K  C16  C15  C14  118.29  3.000
 U6K  H16  C16  N5   116.43  3.000
 U6K  H16  C16  C15  119.29  3.000
 U6K  N5   C16  C15  124.28  3.000
 U6K  C18  C17  N5   118.30  3.000
 U6K  C18  C17  C13  119.78  3.000
 U6K  N5   C17  C13  121.92  3.000
 U6K  H20  C20  O4   111.26  3.000
 U6K  H20  C20  C19  109.01  3.000
 U6K  O4   C20  C19  114.33  3.000
 U6K  H20  C20  C7   110.20  3.000
 U6K  O4   C20  C7   109.87  3.000
 U6K  C19  C20  C7   101.75  3.000
 U6K  H2   N1   H23  105.75  3.000
 U6K  H2   N1   C1   109.13  3.000
 U6K  H23  N1   C1   109.35  3.000
 U6K  C2   N2   C1   117.00  3.000
 U6K  H24  N3   C3   117.53  3.000
 U6K  H24  N3   C2   116.60  3.000
 U6K  C3   N3   C2   121.09  3.000
 U6K  C7   N4   C6   121.39  3.000
 U6K  C7   N4   C3   118.50  3.000
 U6K  C6   N4   C3   105.32  3.000
 U6K  H8   C7   O1   109.67  3.000
 U6K  H8   C7   N4   106.83  3.000
 U6K  O1   C7   N4   112.39  3.000
 U6K  H8   C7   C20  108.57  3.000
 U6K  N4   C7   C20  114.47  3.000
 U6K  O1   C7   C20  104.84  3.000
 U6K  C7   O1   C8   111.04  3.000
 U6K  H10  C9   H11  107.72  3.000
 U6K  H10  C9   O2   110.73  3.000
 U6K  H11  C9   O2   110.76  3.000
 U6K  H10  C9   C8   111.34  3.000
 U6K  H11  C9   C8   109.75  3.000
 U6K  O2   C9   C8   106.56  3.000
 U6K  C10  O2   C9   119.39  3.000
 U6K  C18  C10  O2   125.03  3.000
 U6K  O2   C10  C11  114.59  3.000
 U6K  C18  C10  C11  120.37  3.000
 U6K  C17  N5   C16  118.24  3.000
 U6K  H17  C18  C10  122.44  3.000
 U6K  H17  C18  C17  117.69  3.000
 U6K  C10  C18  C17  119.87  3.000
 U6K  H18  C19  O3   111.41  3.000
 U6K  H18  C19  C20  112.03  3.000
 U6K  O3   C19  C20  110.98  3.000
 U6K  H18  C19  C8   112.12  3.000
 U6K  O3   C19  C8   108.48  3.000
 U6K  C20  C19  C8   101.37  3.000
 U6K  H19  O3   C19  107.68  3.000
 U6K  H21  O4   C20  108.87  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
 U6K  CONST_01  C14  C13  C12  C11   180.00   0.0  0
 U6K  CONST_02  C17  C13  C12  C11     0.00   0.0  0
 U6K  CONST_03  C17  C18  C10  C11     0.00   0.0  0
 U6K  CONST_04  C15  C14  C13  C12   180.00   0.0  0
 U6K  CONST_05  N5   C17  C13  C12   180.00   0.0  0
 U6K  CONST_06  C18  C17  C13  C12     0.00   0.0  0
 U6K  CONST_07  C18  C10  C11  C12     0.00   0.0  0
 U6K  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 U6K  CONST_09  C16  N5   C17  C13     0.00   0.0  0
 U6K  CONST_10  C10  C18  C17  C13     0.00   0.0  0
 U6K  CONST_11  C10  C11  C12  C13     0.00   0.0  0
 U6K  CONST_12  N5   C16  C15  C14     0.00   0.0  0
 U6K  CONST_13  N5   C17  C13  C14     0.00   0.0  0
 U6K  CONST_14  C18  C17  C13  C14   180.00   0.0  0
 U6K  CONST_15  C17  N5   C16  C15     0.00   0.0  0
 U6K  CONST_16  C17  C13  C14  C15     0.00   0.0  0
 U6K  CONST_17  C18  C17  N5   C16   180.00   0.0  0
 U6K  CONST_18  N5   C17  C18  C10   180.00   0.0  0
 U6K  CONST_19  N3   C2   N2   C1      0.00   0.0  0
 U6K  CONST_20  N2   C2   N3   C3      0.00   0.0  0
 U6K  CONST_21  O2   C10  C11  C12   180.00   0.0  0
 U6K  CONST_22  O2   C10  C18  C17   180.00   0.0  0
 U6K  CONST_23  H17  C18  C10  C11   180.00   0.0  0
 U6K  CONST_24  H14  C14  C13  C12     0.00   0.0  0
 U6K  CONST_25  H15  C15  C14  C13   180.00   0.0  0
 U6K  CONST_26  H17  C18  C17  C13   180.00   0.0  0
 U6K  CONST_27  H12  C11  C12  C13   180.00   0.0  0
 U6K  CONST_28  H16  C16  C15  C14   180.00   0.0  0
 U6K  CONST_29  H13  C12  C13  C14     0.00   0.0  0
 U6K  CONST_30  H14  C14  C15  C16   180.00   0.0  0
 U6K  CONST_31  H16  C16  N5   C17   180.00   0.0  0
 U6K  CONST_32  H14  C14  C13  C17   180.00   0.0  0
 U6K  CONST_33  H13  C12  C13  C17   180.00   0.0  0
 U6K  CONST_34  H13  C12  C11  C10   180.00   0.0  0
 U6K  CONST_35  H15  C15  C16  N5    180.00   0.0  0
 U6K  CONST_36  H17  C18  C17  N5      0.00   0.0  0
 U6K  CONST_37  H12  C11  C10  C18   180.00   0.0  0
 U6K  CONST_38  H3   C2   N2   C1    180.00   0.0  0
 U6K  CONST_39  H3   C2   N3   C3    180.00   0.0  0
 U6K  CONST_40  H24  N3   C2   N2    180.00   0.0  0
 U6K  CONST_41  H24  N3   C2   H3      0.00   0.0  0
 U6K  Var_01    C5   C6   N4   C3    -18.13  30.0  1
 U6K  Var_02    N4   C6   C5   C4     -2.32  30.0  1
 U6K  Var_03    C7   N4   C6   C5   -156.43  30.0  1
 U6K  Var_04    H7   C6   N4   C3    163.98  30.0  1
 U6K  Var_05    H7   C6   C5   C4    175.39  30.0  1
 U6K  Var_06    H6   C5   C6   N4   -174.60  30.0  1
 U6K  Var_07    H7   C6   N4   C7     25.68  30.0  1
 U6K  Var_08    C10  O2   C9   C8    177.04  30.0  1
 U6K  Var_09    C9   O2   C10  C11  -177.44  30.0  2
 U6K  Var_10    C18  C10  O2   C9      2.59  30.0  2
 U6K  Var_11    H11  C9   O2   C10   -63.63  30.0  3
 U6K  Var_12    H10  C9   O2   C10    55.81  30.0  3

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
 U6K  chir_01  C1   C4  N1   N2   positiv
 U6K  chir_02  C3   N3  N4   C4   negativ
 U6K  chir_03  C4   C5  C3   C1   positiv
 U6K  chir_04  C8   O1  C9   C19  positiv
 U6K  chir_05  C20  O4  C19  C7   positiv
 U6K  chir_06  C7   O1  N4   C20  negativ
 U6K  chir_07  C19  O3  C20  C8   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
 U6K  plan-1  C1   0.020
 U6K  plan-1  C2   0.020
 U6K  plan-1  C3   0.020
 U6K  plan-1  N2   0.020
 U6K  plan-1  N3   0.020
 U6K  plan-1  H3   0.020
 U6K  plan-1  H24  0.020
 U6K  plan-2  C11  0.020
 U6K  plan-2  C12  0.020
 U6K  plan-2  C13  0.020
 U6K  plan-2  C14  0.020
 U6K  plan-2  C15  0.020
 U6K  plan-2  C16  0.020
 U6K  plan-2  C17  0.020
 U6K  plan-2  O2   0.020
 U6K  plan-2  C10  0.020
 U6K  plan-2  N5   0.020
 U6K  plan-2  C18  0.020
 U6K  plan-2  H13  0.020
 U6K  plan-2  H14  0.020
 U6K  plan-2  H15  0.020
 U6K  plan-2  H16  0.020
 U6K  plan-2  H17  0.020
 U6K  plan-2  H12  0.020
 U6K  plan-3  C3   0.020
 U6K  plan-3  C6   0.020
 U6K  plan-3  N4   0.020
 U6K  plan-3  C7   0.020

