# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:26:15 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(4-azanyl-5-chloranyl-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cc(Cl)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
 EKH  EKH  (2~{R},3~{R},4~{S},5~{R})-2-(4-azanyl-5-chloranyl-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)oxolane-3,4-diol  ligand  33  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EKH
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
 EKH  CL   CL  CL    0  -0.150   2.3737  -2.6970  -0.8815
 EKH  C10  C   CR5   0  -0.258   1.5737  -1.2594  -0.3950
 EKH  C2   C   CR56  0   0.018   2.1897  -0.0631   0.0706
 EKH  C    C   CR6   0   0.463   3.4914   0.4284   0.3032
 EKH  N3   N   NH2   0  -0.823   4.5937  -0.2943   0.0855
 EKH  C4   C   CR15  0   0.048   0.2282  -1.0697  -0.3795
 EKH  N2   N   NR5   0  -0.560  -0.0325   0.2032   0.0776
 EKH  C3   C   CR56  0   0.516   1.1461   0.8217   0.3558
 EKH  N1   N   N     0  -0.464   1.2873   2.0619   0.8250
 EKH  C1   C   CR16  0   0.050   2.5480   2.3997   1.0044
 EKH  N    N   N     0  -0.475   3.6362   1.6704   0.7729
 EKH  C5   C   CH1   0   0.202  -1.3381   0.7930   0.2206
 EKH  O3   O   O2    0  -0.493  -2.1431  -0.0386   1.0094
 EKH  C8   C   CH1   0  -0.045  -3.4614  -0.1335   0.4628
 EKH  C9   C   CH2   0  -0.154  -3.7326  -1.5299  -0.0591
 EKH  O    O   OH1   0  -0.667  -3.5932  -2.4376   1.0047
 EKH  C7   C   CH1   0  -0.040  -3.5383   0.9353  -0.6300
 EKH  O1   O   OH1   0  -0.668  -3.8546   2.2031  -0.1197
 EKH  C6   C   CH1   0  -0.017  -2.0857   0.9671  -1.1014
 EKH  O2   O   OH1   0  -0.653  -1.6551   2.1296  -1.7329
 EKH  H1   H   HNH2  0   0.401   4.5602  -1.2070  -0.3327
 EKH  H2   H   HNH2  0   0.403   5.4959   0.1298   0.2171
 EKH  H3   H   HCR5  0   0.316  -0.5604  -1.7543  -0.6469
 EKH  H4   H   HCR6  0   0.251   2.7277   3.3980   1.3892
 EKH  H5   H   HCH1  0   0.261  -1.1801   1.7684   0.6927
 EKH  H6   H   HCH1  0   0.256  -4.1790   0.0808   1.2624
 EKH  H7   H   HCH2  0   0.212  -4.7481  -1.5388  -0.4765
 EKH  H8   H   HCH2  0   0.197  -3.0497  -1.7671  -0.8863
 EKH  H9   H   HOH1  0   0.458  -3.7323  -3.3248   0.6620
 EKH  H10  H   HCH1  0   0.252  -4.2253   0.6398  -1.4340
 EKH  H11  H   HOH1  0   0.457  -4.7468   2.1712   0.2401
 EKH  H12  H   HCH1  0   0.243  -1.9195   0.0833  -1.7335
 EKH  H13  H   HOH1  0   0.463  -2.0019   2.1406  -2.6302

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
 EKH  O    C9   single    1.405  0.020  1.405
 EKH  CL   C10  single    1.716  0.020  1.716
 EKH  C9   C8   single    1.515  0.020  1.515
 EKH  C4   C10  aromatic  1.359  0.020  1.359
 EKH  C4   N2   aromatic  1.377  0.020  1.377
 EKH  C10  C2   aromatic  1.424  0.020  1.424
 EKH  C8   O3   single    1.430  0.020  1.430
 EKH  C8   C7   single    1.530  0.020  1.530
 EKH  O3   C5   single    1.401  0.020  1.401
 EKH  C7   O1   single    1.403  0.020  1.403
 EKH  C7   C6   single    1.528  0.020  1.528
 EKH  N2   C5   single    1.440  0.020  1.440
 EKH  N2   C3   aromatic  1.360  0.020  1.360
 EKH  C2   C3   aromatic  1.398  0.020  1.398
 EKH  C2   C    aromatic  1.411  0.020  1.411
 EKH  N3   C    single    1.336  0.020  1.336
 EKH  C5   C6   single    1.529  0.020  1.529
 EKH  C3   N1   aromatic  1.333  0.020  1.333
 EKH  C    N    aromatic  1.336  0.020  1.336
 EKH  C6   O2   single    1.391  0.020  1.391
 EKH  N1   C1   aromatic  1.317  0.020  1.317
 EKH  N    C1   aromatic  1.330  0.020  1.330
 EKH  N3   H1   single    0.860  0.020  1.020
 EKH  N3   H2   single    0.860  0.020  1.020
 EKH  C4   H3   single    0.930  0.020  1.080
 EKH  C1   H4   single    0.930  0.020  1.080
 EKH  C5   H5   single    0.970  0.020  1.090
 EKH  C8   H6   single    0.970  0.020  1.090
 EKH  C9   H7   single    0.970  0.020  1.090
 EKH  C9   H8   single    0.970  0.020  1.090
 EKH  O    H9   single    0.850  0.020  0.980
 EKH  C7   H10  single    0.970  0.020  1.090
 EKH  O1   H11  single    0.850  0.020  0.980
 EKH  C6   H12  single    0.970  0.020  1.090
 EKH  O2   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
 EKH  C4   C10  C2   107.90  3.000
 EKH  C2   C10  CL   126.51  3.000
 EKH  C4   C10  CL   125.59  3.000
 EKH  C3   C2   C    115.77  3.000
 EKH  C    C2   C10  138.23  3.000
 EKH  C3   C2   C10  106.00  3.000
 EKH  N    C    N3   118.09  3.000
 EKH  N    C    C2   118.82  3.000
 EKH  N3   C    C2   123.10  3.000
 EKH  H2   N3   H1   117.88  3.000
 EKH  H2   N3   C    119.40  3.000
 EKH  H1   N3   C    122.13  3.000
 EKH  H3   C4   N2   122.06  3.000
 EKH  H3   C4   C10  129.26  3.000
 EKH  N2   C4   C10  108.67  3.000
 EKH  C5   N2   C3   125.40  3.000
 EKH  C3   N2   C4   108.92  3.000
 EKH  C5   N2   C4   125.67  3.000
 EKH  N1   C3   N2   125.93  3.000
 EKH  N1   C3   C2   125.56  3.000
 EKH  N2   C3   C2   108.51  3.000
 EKH  C1   N1   C3   112.81  3.000
 EKH  H4   C1   N    115.51  3.000
 EKH  H4   C1   N1   116.28  3.000
 EKH  N    C1   N1   128.21  3.000
 EKH  C1   N    C    118.83  3.000
 EKH  H5   C5   C6   109.99  3.000
 EKH  H5   C5   O3   111.65  3.000
 EKH  C6   C5   O3   105.88  3.000
 EKH  H5   C5   N2   106.08  3.000
 EKH  C6   C5   N2   113.84  3.000
 EKH  O3   C5   N2   109.51  3.000
 EKH  C8   O3   C5   110.72  3.000
 EKH  H6   C8   C7   110.58  3.000
 EKH  H6   C8   C9   108.32  3.000
 EKH  C7   C8   C9   112.87  3.000
 EKH  H6   C8   O3   108.17  3.000
 EKH  C7   C8   O3   105.84  3.000
 EKH  C9   C8   O3   110.96  3.000
 EKH  H8   C9   H7   106.68  3.000
 EKH  H8   C9   O    111.65  3.000
 EKH  H7   C9   O    111.98  3.000
 EKH  H8   C9   C8   110.31  3.000
 EKH  H7   C9   C8   107.70  3.000
 EKH  O    C9   C8   108.47  3.000
 EKH  H9   O    C9   108.18  3.000
 EKH  H10  C7   C6   111.99  3.000
 EKH  H10  C7   O1   111.62  3.000
 EKH  C6   C7   O1   107.93  3.000
 EKH  H10  C7   C8   111.49  3.000
 EKH  C6   C7   C8   100.78  3.000
 EKH  O1   C7   C8   112.51  3.000
 EKH  H11  O1   C7   108.36  3.000
 EKH  H12  C6   O2   111.35  3.000
 EKH  H12  C6   C7   107.73  3.000
 EKH  O2   C6   C7   116.86  3.000
 EKH  H12  C6   C5   109.37  3.000
 EKH  O2   C6   C5   109.65  3.000
 EKH  C7   C6   C5   101.29  3.000
 EKH  H13  O2   C6   108.74  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
 EKH  CONST_01  C3  N2   C4   C10    0.00  0.0  0
 EKH  CONST_02  N2  C3   C2   C10    0.00  0.0  0
 EKH  CONST_03  N1  C3   C2   C10  180.00  0.0  0
 EKH  CONST_04  N   C    C2   C10  180.00  0.0  0
 EKH  CONST_05  N2  C4   C10  C2     0.00  0.0  0
 EKH  CONST_06  C4  N2   C3   C2     0.00  0.0  0
 EKH  CONST_07  C1  N1   C3   C2     0.00  0.0  0
 EKH  CONST_08  C1  N    C    C2     0.00  0.0  0
 EKH  CONST_09  C4  C10  C2   C    180.00  0.0  0
 EKH  CONST_10  N2  C3   C2   C    180.00  0.0  0
 EKH  CONST_11  N1  C3   C2   C      0.00  0.0  0
 EKH  CONST_12  N1  C1   N    C      0.00  0.0  0
 EKH  CONST_13  C3  C2   C10  C4     0.00  0.0  0
 EKH  CONST_14  N1  C3   N2   C4   180.00  0.0  0
 EKH  CONST_15  C1  N1   C3   N2   180.00  0.0  0
 EKH  CONST_16  N   C    C2   C3     0.00  0.0  0
 EKH  CONST_17  N   C1   N1   C3     0.00  0.0  0
 EKH  CONST_18  C5  N2   C4   C10  180.00  0.0  0
 EKH  CONST_19  C5  N2   C3   C2   180.00  0.0  0
 EKH  CONST_20  C5  N2   C3   N1     0.00  0.0  0
 EKH  CONST_21  N2  C4   C10  CL   180.00  0.0  0
 EKH  CONST_22  C3  C2   C10  CL   180.00  0.0  0
 EKH  CONST_23  C   C2   C10  CL     0.00  0.0  0
 EKH  CONST_24  N3  C    C2   C10    0.00  0.0  0
 EKH  CONST_25  C3  C2   C    N3   180.00  0.0  0
 EKH  CONST_26  C1  N    C    N3   180.00  0.0  0
 EKH  CONST_27  H3  C4   C10  C2   180.00  0.0  0
 EKH  CONST_28  H4  C1   N    C    180.00  0.0  0
 EKH  CONST_29  H1  N3   C    C2     0.00  0.0  0
 EKH  CONST_30  H2  N3   C    C2   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
 EKH  chir_01  C5  O3  N2  C6  negativ
 EKH  chir_02  C8  O3  C9  C7  positiv
 EKH  chir_03  C7  O1  C8  C6  positiv
 EKH  chir_04  C6  O2  C7  C5  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
 EKH  plan-1  CL   0.020
 EKH  plan-1  C10  0.020
 EKH  plan-1  C2   0.020
 EKH  plan-1  C    0.020
 EKH  plan-1  N3   0.020
 EKH  plan-1  C4   0.020
 EKH  plan-1  N2   0.020
 EKH  plan-1  C3   0.020
 EKH  plan-1  N1   0.020
 EKH  plan-1  C1   0.020
 EKH  plan-1  N    0.020
 EKH  plan-1  C5   0.020
 EKH  plan-1  H3   0.020
 EKH  plan-1  H4   0.020
 EKH  plan-2  C    0.020
 EKH  plan-2  N3   0.020
 EKH  plan-2  H1   0.020
 EKH  plan-2  H2   0.020

