# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:34:05 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3cc(Cl)c(Cl)cc23
#
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
 RFZ  RFZ  5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole  ligand  32  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RFZ
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
 RFZ  C6    C   CR56  0   0.357   0.5733  -0.4295   0.0777
 RFZ  C5    C   CR16  0  -0.265   1.4189   0.6610   0.2202
 RFZ  C4    C   CR6   0  -0.018   2.7509   0.4562  -0.0877
 RFZ  CL2   CL  CL    0  -0.097   3.8483   1.7768   0.0707
 RFZ  C3    C   CR6   0  -0.019   3.2190  -0.7962  -0.5244
 RFZ  CL1   CL  CL    0  -0.102   4.8924  -1.0040  -0.8940
 RFZ  C2    C   CR16  0  -0.282   2.3664  -1.8734  -0.6656
 RFZ  C7    C   CR56  0   0.132   1.0227  -1.6847  -0.3595
 RFZ  N2    N   N     0  -0.461  -0.0240  -2.5695  -0.4010
 RFZ  C1    C   CR15  0   0.109  -1.0571  -1.8821  -0.0062
 RFZ  N1    N   NR5   0  -0.548  -0.7698  -0.5868   0.2953
 RFZ  C1'   C   CH1   0   0.167  -1.6656   0.4541   0.7875
 RFZ  O4'   O   O2    0  -0.494  -2.8555  -0.1263   1.2183
 RFZ  C4'   C   CH1   0   0.007  -3.9501   0.2433   0.3769
 RFZ  C5'   C   CH2   0  -0.155  -4.8296  -0.9500   0.0996
 RFZ  O5'   O   OH1   0  -0.668  -5.3975  -1.3890   1.3076
 RFZ  C3'   C   CH1   0  -0.039  -3.3031   0.8227  -0.8777
 RFZ  O3'   O   OH1   0  -0.655  -4.1625   1.7445  -1.4850
 RFZ  C2'   C   CH1   0  -0.044  -2.0254   1.4533  -0.3111
 RFZ  O2'   O   OH1   0  -0.663  -2.2981   2.6792   0.3068
 RFZ  H5    H   HCR6  0   0.304   1.0750   1.6307   0.5534
 RFZ  H2    H   HCR6  0   0.290   2.7347  -2.8334  -1.0007
 RFZ  H1    H   HCR5  0   0.302  -2.0548  -2.2812   0.0901
 RFZ  H1'   H   HCH1  0   0.287  -1.1570   0.9453   1.6234
 RFZ  H4'   H   HCH1  0   0.248  -4.5410   1.0187   0.8803
 RFZ  H5'   H   HCH2  0   0.216  -5.5926  -0.6355  -0.6242
 RFZ  H5'A  H   HCH2  0   0.199  -4.2362  -1.7362  -0.3874
 RFZ  HO5'  H   HOH1  0   0.460  -5.9764  -2.1324   1.1163
 RFZ  H3'   H   HCH1  0   0.247  -3.0343   0.0110  -1.5669
 RFZ  HO3'  H   HOH1  0   0.470  -3.8935   1.8657  -2.4014
 RFZ  H2'   H   HCH1  0   0.262  -1.2343   1.5424  -1.0665
 RFZ  HO2'  H   HOH1  0   0.453  -2.9491   3.1458  -0.2323

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
 RFZ  O3'  C3'   single    1.399  0.020  1.399
 RFZ  C3'  C4'   single    1.526  0.020  1.526
 RFZ  C3'  C2'   single    1.533  0.020  1.533
 RFZ  C4'  C5'   single    1.508  0.020  1.508
 RFZ  C4'  O4'   single    1.429  0.020  1.429
 RFZ  C5'  O5'   single    1.405  0.020  1.405
 RFZ  O2'  C2'   single    1.400  0.020  1.400
 RFZ  C2'  C1'   single    1.528  0.020  1.528
 RFZ  O4'  C1'   single    1.392  0.020  1.392
 RFZ  C1'  N1    single    1.459  0.020  1.459
 RFZ  N1   C1    aromatic  1.361  0.020  1.361
 RFZ  N1   C6    aromatic  1.370  0.020  1.370
 RFZ  C1   N2    aromatic  1.302  0.020  1.302
 RFZ  C5   C6    aromatic  1.387  0.020  1.387
 RFZ  C5   C4    aromatic  1.382  0.020  1.382
 RFZ  C6   C7    aromatic  1.403  0.020  1.403
 RFZ  CL2  C4    single    1.724  0.020  1.724
 RFZ  C4   C3    aromatic  1.406  0.020  1.406
 RFZ  N2   C7    aromatic  1.371  0.020  1.371
 RFZ  C7   C2    aromatic  1.391  0.020  1.391
 RFZ  C3   C2    aromatic  1.381  0.020  1.381
 RFZ  C3   CL1   single    1.726  0.020  1.726
 RFZ  C5   H5    single    0.930  0.020  1.080
 RFZ  C2   H2    single    0.930  0.020  1.080
 RFZ  C1   H1    single    0.930  0.020  1.080
 RFZ  C1'  H1'   single    0.970  0.020  1.090
 RFZ  C4'  H4'   single    0.970  0.020  1.090
 RFZ  C5'  H5'   single    0.970  0.020  1.090
 RFZ  C5'  H5'A  single    0.970  0.020  1.090
 RFZ  O5'  HO5'  single    0.850  0.020  0.980
 RFZ  C3'  H3'   single    0.970  0.020  1.090
 RFZ  O3'  HO3'  single    0.850  0.020  0.980
 RFZ  C2'  H2'   single    0.970  0.020  1.090
 RFZ  O2'  HO2'  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
 RFZ  N1    C6   C7   105.12  3.000
 RFZ  C7    C6   C5   122.68  3.000
 RFZ  N1    C6   C5   132.19  3.000
 RFZ  H5    C5   C4   120.52  3.000
 RFZ  H5    C5   C6   122.87  3.000
 RFZ  C4    C5   C6   116.61  3.000
 RFZ  C3    C4   CL2  119.91  3.000
 RFZ  C3    C4   C5   121.45  3.000
 RFZ  CL2   C4   C5   118.64  3.000
 RFZ  C2    C3   CL1  118.86  3.000
 RFZ  CL1   C3   C4   119.76  3.000
 RFZ  C2    C3   C4   121.39  3.000
 RFZ  H2    C2   C7   121.17  3.000
 RFZ  H2    C2   C3   120.92  3.000
 RFZ  C7    C2   C3   117.91  3.000
 RFZ  N2    C7   C2   130.03  3.000
 RFZ  C2    C7   C6   119.96  3.000
 RFZ  N2    C7   C6   110.01  3.000
 RFZ  C1    N2   C7   104.82  3.000
 RFZ  H1    C1   N1   121.85  3.000
 RFZ  H1    C1   N2   124.43  3.000
 RFZ  N1    C1   N2   113.72  3.000
 RFZ  C1'   N1   C1   128.64  3.000
 RFZ  C1    N1   C6   106.33  3.000
 RFZ  C1'   N1   C6   125.02  3.000
 RFZ  H1'   C1'  C2'  111.40  3.000
 RFZ  H1'   C1'  O4'  110.35  3.000
 RFZ  C2'   C1'  O4'  107.09  3.000
 RFZ  H1'   C1'  N1   107.00  3.000
 RFZ  O4'   C1'  N1   109.37  3.000
 RFZ  C2'   C1'  N1   111.63  3.000
 RFZ  C4'   O4'  C1'  111.38  3.000
 RFZ  H4'   C4'  C3'  109.71  3.000
 RFZ  H4'   C4'  C5'  109.23  3.000
 RFZ  C3'   C4'  C5'  113.36  3.000
 RFZ  H4'   C4'  O4'  108.98  3.000
 RFZ  C5'   C4'  O4'  110.50  3.000
 RFZ  C3'   C4'  O4'  104.92  3.000
 RFZ  H5'A  C5'  H5'  106.74  3.000
 RFZ  H5'A  C5'  O5'  112.07  3.000
 RFZ  H5'   C5'  O5'  112.05  3.000
 RFZ  H5'A  C5'  C4'  109.43  3.000
 RFZ  H5'   C5'  C4'  107.45  3.000
 RFZ  O5'   C5'  C4'  108.96  3.000
 RFZ  HO5'  O5'  C5'  108.29  3.000
 RFZ  H3'   C3'  C2'  109.39  3.000
 RFZ  H3'   C3'  O3'  111.40  3.000
 RFZ  C2'   C3'  O3'  113.66  3.000
 RFZ  H3'   C3'  C4'  109.82  3.000
 RFZ  C2'   C3'  C4'  101.87  3.000
 RFZ  O3'   C3'  C4'  110.28  3.000
 RFZ  HO3'  O3'  C3'  108.94  3.000
 RFZ  H2'   C2'  O2'  111.91  3.000
 RFZ  H2'   C2'  C3'  112.32  3.000
 RFZ  O2'   C2'  C3'  111.16  3.000
 RFZ  H2'   C2'  C1'  112.22  3.000
 RFZ  O2'   C2'  C1'  107.53  3.000
 RFZ  C3'   C2'  C1'  101.13  3.000
 RFZ  HO2'  O2'  C2'  107.95  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
 RFZ  CONST_01  N2   C1  N1  C6     0.00  0.0  0
 RFZ  CONST_02  C3   C4  C5  C6     0.00  0.0  0
 RFZ  CONST_03  C1   N2  C7  C6     0.00  0.0  0
 RFZ  CONST_04  C3   C2  C7  C6     0.00  0.0  0
 RFZ  CONST_05  C1   N1  C6  C5   180.00  0.0  0
 RFZ  CONST_06  N2   C7  C6  C5   180.00  0.0  0
 RFZ  CONST_07  C2   C7  C6  C5     0.00  0.0  0
 RFZ  CONST_08  C2   C3  C4  C5     0.00  0.0  0
 RFZ  CONST_09  N1   C6  C5  C4   180.00  0.0  0
 RFZ  CONST_10  C7   C6  C5  C4     0.00  0.0  0
 RFZ  CONST_11  C7   C2  C3  C4     0.00  0.0  0
 RFZ  CONST_12  N2   C7  C2  C3   180.00  0.0  0
 RFZ  CONST_13  N1   C6  C7  C2   180.00  0.0  0
 RFZ  CONST_14  C1   N2  C7  C2   180.00  0.0  0
 RFZ  CONST_15  C1   N1  C6  C7     0.00  0.0  0
 RFZ  CONST_16  N1   C1  N2  C7     0.00  0.0  0
 RFZ  CONST_17  N1   C6  C7  N2     0.00  0.0  0
 RFZ  CONST_18  C1'  N1  C6  C5     0.00  0.0  0
 RFZ  CONST_19  C1'  N1  C6  C7   180.00  0.0  0
 RFZ  CONST_20  C1'  N1  C1  N2   180.00  0.0  0
 RFZ  CONST_21  CL2  C4  C5  C6   180.00  0.0  0
 RFZ  CONST_22  CL1  C3  C4  C5   180.00  0.0  0
 RFZ  CONST_23  C2   C3  C4  CL2  180.00  0.0  0
 RFZ  CONST_24  C7   C2  C3  CL1  180.00  0.0  0
 RFZ  CONST_25  H1   C1  N1  C6   180.00  0.0  0
 RFZ  CONST_26  H2   C2  C7  C6   180.00  0.0  0
 RFZ  CONST_27  H5   C5  C4  C3   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
 RFZ  chir_01  C1'  C2'  O4'  N1   negativ
 RFZ  chir_02  C4'  O4'  C5'  C3'  positiv
 RFZ  chir_03  C3'  O3'  C4'  C2'  positiv
 RFZ  chir_04  C2'  O2'  C3'  C1'  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
 RFZ  plan-1  C6   0.020
 RFZ  plan-1  C5   0.020
 RFZ  plan-1  C4   0.020
 RFZ  plan-1  CL2  0.020
 RFZ  plan-1  C3   0.020
 RFZ  plan-1  CL1  0.020
 RFZ  plan-1  C2   0.020
 RFZ  plan-1  C7   0.020
 RFZ  plan-1  N2   0.020
 RFZ  plan-1  C1   0.020
 RFZ  plan-1  N1   0.020
 RFZ  plan-1  C1'  0.020
 RFZ  plan-1  H5   0.020
 RFZ  plan-1  H2   0.020
 RFZ  plan-1  H1   0.020

