# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:39:57 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 4,5,6,7-tetrabromo-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3c(Br)c(Br)c(Br)c(Br)c23
#
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
 EXX  EXX  4,5,6,7-tetrabromo-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-1H-benzimidazole  ligand  31  21  .  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_EXX
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
 EXX  BRE  BR  BR    0   0.034   1.9078   3.4183   0.4819
 EXX  CAN  C   CR6   0  -0.207   1.1951   1.7075   0.2733
 EXX  CAL  C   CR6   0  -0.106   1.9496   0.5525   0.3793
 EXX  BRC  BR  BR    0   0.040   3.7790   0.6787   0.7552
 EXX  CAM  C   CR6   0  -0.122   1.3427  -0.7103   0.2029
 EXX  BRD  BR  BR    0   0.044   2.3938  -2.2546   0.3399
 EXX  CAO  C   CR6   0  -0.143  -0.0169  -0.8308  -0.0729
 EXX  BRF  BR  BR    0   0.049  -0.7833  -2.5195  -0.3349
 EXX  CAQ  C   CR56  0   0.439  -0.7733   0.3393  -0.1622
 EXX  CAP  C   CR56  0   0.207  -0.1653   1.5978   0.0012
 EXX  NAJ  N   N     0  -0.433  -1.0781   2.5951  -0.1441
 EXX  CAG  C   CR15  0   0.123  -2.2005   1.9820  -0.3785
 EXX  NAU  N   NR5   0  -0.554  -2.0980   0.6273  -0.4030
 EXX  CAT  C   CH1   0   0.181  -3.2421  -0.2966  -0.5528
 EXX  OAK  O   O2    0  -0.496  -4.3326   0.4354  -1.0239
 EXX  CAI  C   CH2   0  -0.544  -3.6632  -0.8954   0.7829
 EXX  CAR  C   CH1   0   0.016  -4.7268   0.0901   1.2591
 EXX  OAB  O   OH1   0  -0.659  -5.6816  -0.4357   2.1355
 EXX  CAS  C   CH1   0   0.004  -5.3868   0.4753  -0.0591
 EXX  CAH  C   CH2   0  -0.157  -6.0421   1.8330  -0.0409
 EXX  OAA  O   OH1   0  -0.668  -6.6779   2.0528  -1.2755
 EXX  H1   H   HCR5  0   0.311  -3.1359   2.4876  -0.5546
 EXX  H2   H   HCH1  0   0.283  -2.9628  -1.0414  -1.2960
 EXX  H3   H   HCH2  0   0.272  -4.1189  -1.8735   0.6123
 EXX  H4   H   HCH2  0   0.281  -2.8404  -1.0189   1.4857
 EXX  H5   H   HCH1  0   0.224  -4.2384   0.9742   1.6940
 EXX  H6   H   HOH1  0   0.463  -5.2901  -0.4974   3.0120
 EXX  H7   H   HCH1  0   0.245  -6.1350  -0.2866  -0.3167
 EXX  H8   H   HCH2  0   0.216  -6.7531   1.8405   0.7952
 EXX  H9   H   HCH2  0   0.199  -5.2871   2.6010   0.1767
 EXX  H10  H   HOH1  0   0.460  -7.1159   2.9081  -1.2410

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
 EXX  BRD  CAM  single    1.873  0.020  1.873
 EXX  BRF  CAO  single    1.873  0.020  1.873
 EXX  CAM  CAO  aromatic  1.393  0.020  1.393
 EXX  CAM  CAL  aromatic  1.412  0.020  1.412
 EXX  BRC  CAL  single    1.872  0.020  1.872
 EXX  CAO  CAQ  aromatic  1.396  0.020  1.396
 EXX  CAL  CAN  aromatic  1.384  0.020  1.384
 EXX  CAQ  NAU  aromatic  1.377  0.020  1.377
 EXX  CAQ  CAP  aromatic  1.407  0.020  1.407
 EXX  OAB  CAR  single    1.399  0.020  1.399
 EXX  CAT  NAU  single    1.478  0.020  1.478
 EXX  CAT  OAK  single    1.395  0.020  1.395
 EXX  CAT  CAI  single    1.523  0.020  1.523
 EXX  CAN  CAP  aromatic  1.392  0.020  1.392
 EXX  CAN  BRE  single    1.865  0.020  1.865
 EXX  NAU  CAG  aromatic  1.359  0.020  1.359
 EXX  OAK  CAS  single    1.430  0.020  1.430
 EXX  CAP  NAJ  aromatic  1.360  0.020  1.360
 EXX  CAI  CAR  single    1.526  0.020  1.526
 EXX  CAR  CAS  single    1.524  0.020  1.524
 EXX  CAS  CAH  single    1.508  0.020  1.508
 EXX  CAG  NAJ  aromatic  1.300  0.020  1.300
 EXX  CAH  OAA  single    1.406  0.020  1.406
 EXX  CAG  H1   single    0.930  0.020  1.080
 EXX  CAT  H2   single    0.970  0.020  1.090
 EXX  CAI  H3   single    0.970  0.020  1.090
 EXX  CAI  H4   single    0.970  0.020  1.090
 EXX  CAR  H5   single    0.970  0.020  1.090
 EXX  OAB  H6   single    0.850  0.020  0.980
 EXX  CAS  H7   single    0.970  0.020  1.090
 EXX  CAH  H8   single    0.970  0.020  1.090
 EXX  CAH  H9   single    0.970  0.020  1.090
 EXX  OAA  H10  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
 EXX  CAP  CAN  CAL  118.83  3.000
 EXX  CAP  CAN  BRE  117.89  3.000
 EXX  CAL  CAN  BRE  123.29  3.000
 EXX  CAM  CAL  BRC  120.35  3.000
 EXX  BRC  CAL  CAN  119.47  3.000
 EXX  CAM  CAL  CAN  120.17  3.000
 EXX  CAO  CAM  BRD  119.41  3.000
 EXX  CAO  CAM  CAL  121.45  3.000
 EXX  BRD  CAM  CAL  119.14  3.000
 EXX  CAQ  CAO  BRF  121.67  3.000
 EXX  CAQ  CAO  CAM  117.98  3.000
 EXX  BRF  CAO  CAM  120.35  3.000
 EXX  NAU  CAQ  CAP  104.41  3.000
 EXX  CAP  CAQ  CAO  120.53  3.000
 EXX  NAU  CAQ  CAO  135.05  3.000
 EXX  NAJ  CAP  CAQ  110.70  3.000
 EXX  NAJ  CAP  CAN  128.26  3.000
 EXX  CAQ  CAP  CAN  121.04  3.000
 EXX  CAG  NAJ  CAP  104.65  3.000
 EXX  H1   CAG  NAU  122.02  3.000
 EXX  H1   CAG  NAJ  123.88  3.000
 EXX  NAU  CAG  NAJ  114.10  3.000
 EXX  CAT  NAU  CAG  124.51  3.000
 EXX  CAG  NAU  CAQ  106.14  3.000
 EXX  CAT  NAU  CAQ  129.17  3.000
 EXX  H2   CAT  CAI  113.62  3.000
 EXX  H2   CAT  OAK  109.21  3.000
 EXX  CAI  CAT  OAK  106.64  3.000
 EXX  H2   CAT  NAU  107.35  3.000
 EXX  CAI  CAT  NAU  111.76  3.000
 EXX  OAK  CAT  NAU  108.13  3.000
 EXX  CAS  OAK  CAT  111.29  3.000
 EXX  H4   CAI  H3   108.33  3.000
 EXX  H4   CAI  CAR  113.48  3.000
 EXX  H3   CAI  CAR  109.64  3.000
 EXX  H4   CAI  CAT  113.68  3.000
 EXX  H3   CAI  CAT  109.29  3.000
 EXX  CAR  CAI  CAT  102.26  3.000
 EXX  H5   CAR  CAS  109.35  3.000
 EXX  H5   CAR  OAB  110.96  3.000
 EXX  CAS  CAR  OAB  109.97  3.000
 EXX  H5   CAR  CAI  109.45  3.000
 EXX  CAS  CAR  CAI  101.25  3.000
 EXX  OAB  CAR  CAI  115.37  3.000
 EXX  H6   OAB  CAR  108.50  3.000
 EXX  H7   CAS  CAH  109.36  3.000
 EXX  H7   CAS  CAR  108.82  3.000
 EXX  CAH  CAS  CAR  113.92  3.000
 EXX  H7   CAS  OAK  108.94  3.000
 EXX  CAH  CAS  OAK  110.72  3.000
 EXX  CAR  CAS  OAK  104.92  3.000
 EXX  H9   CAH  H8   106.83  3.000
 EXX  H9   CAH  OAA  112.05  3.000
 EXX  H8   CAH  OAA  112.01  3.000
 EXX  H9   CAH  CAS  109.46  3.000
 EXX  H8   CAH  CAS  107.27  3.000
 EXX  OAA  CAH  CAS  109.07  3.000
 EXX  H10  OAA  CAH  108.28  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
 EXX  CONST_01  CAO  CAM  CAL  CAN    0.00  0.0  0
 EXX  CONST_02  CAO  CAQ  CAP  CAN    0.00  0.0  0
 EXX  CONST_03  NAU  CAQ  CAP  CAN  180.00  0.0  0
 EXX  CONST_04  CAG  NAJ  CAP  CAN  180.00  0.0  0
 EXX  CONST_05  CAQ  CAO  CAM  CAL    0.00  0.0  0
 EXX  CONST_06  CAQ  CAP  CAN  CAL    0.00  0.0  0
 EXX  CONST_07  NAJ  CAP  CAN  CAL  180.00  0.0  0
 EXX  CONST_08  NAU  CAQ  CAO  CAM  180.00  0.0  0
 EXX  CONST_09  CAP  CAQ  CAO  CAM    0.00  0.0  0
 EXX  CONST_10  CAP  CAN  CAL  CAM    0.00  0.0  0
 EXX  CONST_11  CAG  NAU  CAQ  CAO  180.00  0.0  0
 EXX  CONST_12  NAJ  CAP  CAQ  CAO  180.00  0.0  0
 EXX  CONST_13  NAJ  CAG  NAU  CAQ    0.00  0.0  0
 EXX  CONST_14  CAG  NAJ  CAP  CAQ    0.00  0.0  0
 EXX  CONST_15  CAG  NAU  CAQ  CAP    0.00  0.0  0
 EXX  CONST_16  NAU  CAG  NAJ  CAP    0.00  0.0  0
 EXX  CONST_17  NAU  CAQ  CAP  NAJ    0.00  0.0  0
 EXX  CONST_18  CAT  NAU  CAQ  CAO    0.00  0.0  0
 EXX  CONST_19  CAT  NAU  CAQ  CAP  180.00  0.0  0
 EXX  CONST_20  CAT  NAU  CAG  NAJ  180.00  0.0  0
 EXX  CONST_21  CAM  CAL  CAN  BRE  180.00  0.0  0
 EXX  CONST_22  CAQ  CAP  CAN  BRE  180.00  0.0  0
 EXX  CONST_23  NAJ  CAP  CAN  BRE    0.00  0.0  0
 EXX  CONST_24  BRD  CAM  CAL  CAN  180.00  0.0  0
 EXX  CONST_25  BRF  CAO  CAM  CAL  180.00  0.0  0
 EXX  CONST_26  CAO  CAM  CAL  BRC  180.00  0.0  0
 EXX  CONST_27  CAP  CAN  CAL  BRC  180.00  0.0  0
 EXX  CONST_28  CAQ  CAO  CAM  BRD  180.00  0.0  0
 EXX  CONST_29  NAU  CAQ  CAO  BRF    0.00  0.0  0
 EXX  CONST_30  CAP  CAQ  CAO  BRF  180.00  0.0  0
 EXX  CONST_31  H1   CAG  NAU  CAQ  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
 EXX  chir_01  CAT  NAU  OAK  CAI  positiv
 EXX  chir_02  CAR  OAB  CAS  CAI  positiv
 EXX  chir_03  CAS  OAK  CAR  CAH  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
 EXX  plan-1  BRE  0.020
 EXX  plan-1  CAN  0.020
 EXX  plan-1  CAL  0.020
 EXX  plan-1  BRC  0.020
 EXX  plan-1  CAM  0.020
 EXX  plan-1  BRD  0.020
 EXX  plan-1  CAO  0.020
 EXX  plan-1  BRF  0.020
 EXX  plan-1  CAQ  0.020
 EXX  plan-1  CAP  0.020
 EXX  plan-1  NAJ  0.020
 EXX  plan-1  CAG  0.020
 EXX  plan-1  NAU  0.020
 EXX  plan-1  CAT  0.020
 EXX  plan-1  H1   0.020

