# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:52:39 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(4-azanyl-5-bromanyl-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(Br)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
 EKK  EKK  (2~{R},3~{R},4~{S},5~{R})-2-(4-azanyl-5-bromanyl-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)oxolane-3,4-diol  ligand  33  20  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EKK
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
 EKK  O3   O   OH1   0  -0.668   3.2827   2.8108   0.7725
 EKK  C4   C   CR15  0   0.211   1.9660  -0.8332   0.3720
 EKK  C5   C   CR15  0   0.005   0.0847   0.8161   0.1784
 EKK  C6   C   CR5   0  -0.300  -1.2743   0.7670   0.1306
 EKK  C7   C   CR56  0  -0.019  -1.6670  -0.5971   0.2684
 EKK  C8   C   CR6   0   0.448  -2.8539  -1.3621   0.3103
 EKK  N2   N   N     0  -0.475  -2.7628  -2.6861   0.4641
 EKK  C9   C   CR16  0   0.045  -1.5597  -3.2409   0.5782
 EKK  C10  C   CR56  0   0.525  -0.4778  -1.3258   0.3967
 EKK  N3   N   N     0  -0.459  -0.3851  -2.6467   0.5533
 EKK  BR   BR  BR    0  -0.050  -2.3798   2.2585  -0.0516
 EKK  N    N   NR5   0  -0.555   0.5678  -0.4603   0.3416
 EKK  C3   C   CR15  0  -0.014   2.6140  -0.9002  -1.0141
 EKK  O1   O   OH1   0  -0.652   2.3942  -2.1513  -1.5807
 EKK  C2   C   CR15  0  -0.035   4.0646  -0.5395  -0.6890
 EKK  O2   O   OH1   0  -0.667   4.6884  -1.6877  -0.1788
 EKK  O    O   O     0  -0.493   2.6750   0.1351   1.0859
 EKK  C1   C   CR15  0  -0.051   3.8503   0.5355   0.3759
 EKK  C    C   CH2   0  -0.166   3.6944   1.9180  -0.2316
 EKK  H1   H   HOH1  0   0.459   3.2087   3.6857   0.3809
 EKK  H2   H   HCR5  0   0.261   2.0128  -1.8116   0.8615
 EKK  H3   H   HCR5  0   0.319   0.7420   1.6696   0.1452
 EKK  H4   H   HNH2  0   0.406  -4.2398   0.1459   0.0790
 EKK  H5   H   HNH2  0   0.403  -4.8788  -1.4433   0.2390
 EKK  H6   H   HCR6  0   0.250  -1.5517  -4.3184   0.7055
 EKK  H7   H   HCR5  0   0.243   2.1954  -0.0998  -1.6384
 EKK  H8   H   HOH1  0   0.462   2.6584  -2.1198  -2.5053
 EKK  H9   H   HCR5  0   0.252   4.5965  -0.1424  -1.5636
 EKK  H10  H   HOH1  0   0.457   5.5876  -1.4581   0.0757
 EKK  H11  H   HCR5  0   0.260   4.6761   0.5583   1.0941
 EKK  H12  H   HCH2  0   0.200   2.9803   1.8972  -1.0669
 EKK  H13  H   HCH2  0   0.224   4.6661   2.1980  -0.6589
 EKK  N1   N   NH2   0  -0.825  -4.0778  -0.8362   0.2080

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
 EKK  O3   C    single    1.405  0.020  1.405
 EKK  BR   C6   single    1.865  0.020  1.865
 EKK  C    C1   single    1.518  0.020  1.518
 EKK  C5   C6   aromatic  1.361  0.020  1.361
 EKK  C5   N    aromatic  1.375  0.020  1.375
 EKK  C6   C7   aromatic  1.426  0.020  1.426
 EKK  C1   O    single    1.430  0.020  1.430
 EKK  C1   C2   single    1.528  0.020  1.528
 EKK  O    C4   single    1.396  0.020  1.396
 EKK  N    C4   single    1.447  0.020  1.447
 EKK  N    C10  aromatic  1.358  0.020  1.358
 EKK  C2   O2   single    1.403  0.020  1.403
 EKK  C2   C3   single    1.530  0.020  1.530
 EKK  C7   C8   aromatic  1.413  0.020  1.413
 EKK  C7   C10  aromatic  1.400  0.020  1.400
 EKK  N1   C8   single    1.336  0.020  1.336
 EKK  C4   C3   single    1.532  0.020  1.532
 EKK  C8   N2   aromatic  1.336  0.020  1.336
 EKK  C10  N3   aromatic  1.333  0.020  1.333
 EKK  C3   O1   single    1.391  0.020  1.391
 EKK  N2   C9   aromatic  1.330  0.020  1.330
 EKK  N3   C9   aromatic  1.317  0.020  1.317
 EKK  O3   H1   single    0.850  0.020  0.980
 EKK  C4   H2   single    0.970  0.020  1.090
 EKK  C5   H3   single    0.930  0.020  1.080
 EKK  N1   H4   single    0.860  0.020  1.020
 EKK  N1   H5   single    0.860  0.020  1.020
 EKK  C9   H6   single    0.930  0.020  1.080
 EKK  C3   H7   single    0.970  0.020  1.090
 EKK  O1   H8   single    0.850  0.020  0.980
 EKK  C2   H9   single    0.970  0.020  1.090
 EKK  O2   H10  single    0.850  0.020  0.980
 EKK  C1   H11  single    0.970  0.020  1.090
 EKK  C    H12  single    0.970  0.020  1.090
 EKK  C    H13  single    0.970  0.020  1.090

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
 EKK  H1   O3   C    108.03  3.000
 EKK  H2   C4   O    111.68  3.000
 EKK  H2   C4   C3   110.33  3.000
 EKK  O    C4   C3   106.15  3.000
 EKK  H2   C4   N    106.32  3.000
 EKK  C3   C4   N    113.64  3.000
 EKK  O    C4   N    108.82  3.000
 EKK  H3   C5   N    121.65  3.000
 EKK  H3   C5   C6   129.53  3.000
 EKK  N    C5   C6   108.77  3.000
 EKK  BR   C6   C7   127.66  3.000
 EKK  C7   C6   C5   107.82  3.000
 EKK  BR   C6   C5   124.50  3.000
 EKK  C10  C7   C8   115.40  3.000
 EKK  C10  C7   C6   105.83  3.000
 EKK  C8   C7   C6   138.77  3.000
 EKK  N2   C8   C7   118.87  3.000
 EKK  N2   C8   N1   117.48  3.000
 EKK  C7   C8   N1   123.66  3.000
 EKK  C9   N2   C8   119.01  3.000
 EKK  H6   C9   N3   116.35  3.000
 EKK  H6   C9   N2   115.53  3.000
 EKK  N3   C9   N2   128.12  3.000
 EKK  N    C10  N3   125.61  3.000
 EKK  N3   C10  C7   125.82  3.000
 EKK  N    C10  C7   108.57  3.000
 EKK  C10  N3   C9   112.78  3.000
 EKK  C10  N    C5   109.02  3.000
 EKK  C10  N    C4   125.35  3.000
 EKK  C5   N    C4   125.54  3.000
 EKK  H7   C3   C2   108.08  3.000
 EKK  H7   C3   O1   111.33  3.000
 EKK  C2   C3   O1   116.65  3.000
 EKK  H7   C3   C4   108.75  3.000
 EKK  O1   C3   C4   109.95  3.000
 EKK  C2   C3   C4   101.46  3.000
 EKK  H8   O1   C3   108.58  3.000
 EKK  H9   C2   C1   111.63  3.000
 EKK  H9   C2   O2   111.74  3.000
 EKK  C1   C2   O2   112.63  3.000
 EKK  H9   C2   C3   112.05  3.000
 EKK  O2   C2   C3   107.81  3.000
 EKK  C1   C2   C3   100.42  3.000
 EKK  H10  O2   C2   108.44  3.000
 EKK  C1   O    C4   110.95  3.000
 EKK  H11  C1   C    108.73  3.000
 EKK  H11  C1   O    107.46  3.000
 EKK  C    C1   O    111.67  3.000
 EKK  H11  C1   C2   111.47  3.000
 EKK  O    C1   C2   105.32  3.000
 EKK  C    C1   C2   112.10  3.000
 EKK  H13  C    H12  106.50  3.000
 EKK  H13  C    C1   107.28  3.000
 EKK  H12  C    C1   110.71  3.000
 EKK  H13  C    O3   112.05  3.000
 EKK  H12  C    O3   111.39  3.000
 EKK  C1   C    O3   108.83  3.000
 EKK  H5   N1   H4   117.78  3.000
 EKK  H5   N1   C8   119.32  3.000
 EKK  H4   N1   C8   122.88  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
 EKK  CONST_01  C8   C7   C6   C5   180.00  0.0  0
 EKK  CONST_02  C10  C7   C6   C5     0.00  0.0  0
 EKK  CONST_03  C7   C10  N    C5     0.00  0.0  0
 EKK  CONST_04  N3   C10  N    C5   180.00  0.0  0
 EKK  CONST_05  C10  N    C5   C6     0.00  0.0  0
 EKK  CONST_06  N2   C8   C7   C6   180.00  0.0  0
 EKK  CONST_07  N    C10  C7   C6     0.00  0.0  0
 EKK  CONST_08  N3   C10  C7   C6   180.00  0.0  0
 EKK  CONST_09  N    C5   C6   C7     0.00  0.0  0
 EKK  CONST_10  C9   N2   C8   C7     0.00  0.0  0
 EKK  CONST_11  C9   N3   C10  C7     0.00  0.0  0
 EKK  CONST_12  N    C10  C7   C8   180.00  0.0  0
 EKK  CONST_13  N3   C10  C7   C8     0.00  0.0  0
 EKK  CONST_14  N3   C9   N2   C8     0.00  0.0  0
 EKK  CONST_15  C10  C7   C8   N2     0.00  0.0  0
 EKK  CONST_16  C10  N3   C9   N2     0.00  0.0  0
 EKK  CONST_17  N    C10  N3   C9   180.00  0.0  0
 EKK  CONST_18  C6   C5   N    C4   180.00  0.0  0
 EKK  CONST_19  C7   C10  N    C4   180.00  0.0  0
 EKK  CONST_20  N3   C10  N    C4     0.00  0.0  0
 EKK  CONST_21  N1   C8   C7   C6     0.00  0.0  0
 EKK  CONST_22  C10  C7   C8   N1   180.00  0.0  0
 EKK  CONST_23  C9   N2   C8   N1   180.00  0.0  0
 EKK  CONST_24  BR   C6   C7   C8     0.00  0.0  0
 EKK  CONST_25  BR   C6   C7   C10  180.00  0.0  0
 EKK  CONST_26  N    C5   C6   BR   180.00  0.0  0
 EKK  CONST_27  H3   C5   N    C4     0.00  0.0  0
 EKK  CONST_28  H6   C9   N2   C8   180.00  0.0  0
 EKK  CONST_29  H4   N1   C8   C7     0.00  0.0  0
 EKK  CONST_30  H5   N1   C8   C7   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
 EKK  chir_01  C4  O   N   C3  negativ
 EKK  chir_02  C3  O1  C4  C2  negativ
 EKK  chir_03  C2  O2  C1  C3  positiv
 EKK  chir_04  C1  O   C2  C   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
 EKK  plan-1  C4   0.020
 EKK  plan-1  C5   0.020
 EKK  plan-1  C6   0.020
 EKK  plan-1  C7   0.020
 EKK  plan-1  C8   0.020
 EKK  plan-1  N2   0.020
 EKK  plan-1  C9   0.020
 EKK  plan-1  C10  0.020
 EKK  plan-1  N3   0.020
 EKK  plan-1  BR   0.020
 EKK  plan-1  N    0.020
 EKK  plan-1  H3   0.020
 EKK  plan-1  H6   0.020
 EKK  plan-1  N1   0.020
 EKK  plan-2  C8   0.020
 EKK  plan-2  H4   0.020
 EKK  plan-2  H5   0.020
 EKK  plan-2  N1   0.020

