# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 22:43:27 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2R)-2-(3-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-5-bromo-4-oxidophenyl)butanedioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3cc(cc(Br)c3[O-])[C@@H](CC([O-])=O)C([O-])=O
#
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
 847  847  (2R)-2-(3-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-5-bromo-4-oxidophenyl)butanedioate  ligand  41  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_847
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
 847  C1    C   CR6    0  -0.002   5.9752  -0.6721  -0.0101
 847  C2    C   CR16   0  -0.297   6.0724   0.7207  -0.1863
 847  C3    C   CR16   0  -0.305   4.9423   1.5051  -0.3167
 847  C4    C   CR56   0   0.359   3.7130   0.8619  -0.2565
 847  C5    C   CR56   0   0.171   3.5947  -0.5343  -0.0700
 847  C6    C   CR16   0  -0.378   4.7378  -1.3117   0.0482
 847  C7    C   C      0   0.581   7.1990  -1.4685   0.1115
 847  N1    N   NH2    0  -0.769   7.2337  -2.6843  -0.3843
 847  N2    N   NC2    1  -0.771   8.2494  -0.9606   0.7144
 847  N3    N   NR15   0  -0.730   2.4335   1.3021  -0.3421
 847  N4    N   N      0  -0.504   2.2791  -0.8984  -0.0403
 847  C8    C   CR5    0   0.496   1.6072   0.2235  -0.2108
 847  C1'   C   CR6    0  -0.222   0.1685   0.3614  -0.2707
 847  C2'   C   CR16   0  -0.387  -0.6255  -0.7807  -0.1032
 847  C3'   C   CR6    0   0.134  -2.0032  -0.7493  -0.1604
 847  CVX   C   CH1    0  -0.406  -2.8428  -1.9901   0.0302
 847  CWX   C   C      0   0.420  -3.6280  -2.2644  -1.2690
 847  OXX   O   O      0  -0.624  -3.0296  -2.8945  -2.1648
 847  OYX   O   OC    -1  -0.617  -4.7817  -1.7921  -1.3479
 847  C6X   C   CH2    0  -0.548  -3.7516  -1.8750   1.2474
 847  C7X   C   C      0   0.408  -4.6576  -3.0915   1.4804
 847  O8X   O   O      0  -0.615  -4.2772  -4.1888   1.0230
 847  O9X   O   OC    -1  -0.636  -5.6959  -2.8981   2.1505
 847  C4'   C   CR16   0  -0.265  -2.6016   0.4970  -0.4098
 847  C5'   C   CR6    0  -0.263  -1.8391   1.6284  -0.5691
 847  C6'   C   CR6    0   0.364  -0.4082   1.6553  -0.5096
 847  O6'   O   OC    -1  -0.582   0.2600   2.7183  -0.6597
 847  BR5'  BR  BR     0  -0.115  -2.6929   3.2903  -0.9000
 847  HC2   H   HCR6   0   0.271   7.0435   1.1930  -0.2577
 847  HC3   H   HCR6   0   0.275   5.0232   2.5730  -0.4670
 847  HC6   H   HCR6   0   0.272   4.6545  -2.3786   0.2118
 847  HH11  H   HNH2   0   0.434   8.0295  -3.2911  -0.2605
 847  HH12  H   HNH2   0   0.444   6.4892  -3.0232  -0.9711
 847  HH21  H   HNC2   0   0.443   8.1843  -0.0912   1.2175
 847  HH22  H   HNC2   0   0.435   9.1309  -1.4490   0.7586
 847  HN3   H   HNR5   0   0.421   2.0371   2.2303  -0.4923
 847  HC2'  H   HCR6   0   0.231  -0.1254  -1.7245   0.0846
 847  H31B  H   HCH1   0   0.204  -2.1544  -2.8248   0.1864
 847  H42A  H   HCH2   0   0.214  -3.1283  -1.7453   2.1421
 847  H42B  H   HCH2   0   0.204  -4.3667  -0.9749   1.1856
 847  HC4'  H   HCR6   0   0.252  -3.6810   0.5566  -0.4855

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
 847  C1   C2    aromatic  1.407  0.020  1.407
 847  C1   C6    aromatic  1.394  0.020  1.394
 847  C1   C7    single    1.465  0.020  1.465
 847  C2   C3    aromatic  1.382  0.020  1.382
 847  C2   HC2   single    0.930  0.020  1.080
 847  C3   C4    aromatic  1.389  0.020  1.389
 847  C3   HC3   single    0.930  0.020  1.080
 847  C4   C5    aromatic  1.414  0.020  1.414
 847  C4   N3    aromatic  1.356  0.020  1.356
 847  C5   C6    aromatic  1.387  0.020  1.387
 847  C5   N4    aromatic  1.365  0.020  1.365
 847  C6   HC6   single    0.930  0.020  1.080
 847  C7   N1    single    1.313  0.020  1.313
 847  C7   N2    double    1.313  0.020  1.313
 847  N1   HH11  single    0.860  0.020  1.020
 847  N1   HH12  single    0.860  0.020  1.020
 847  N2   HH21  single    0.860  0.020  1.020
 847  N2   HH22  single    0.860  0.020  1.020
 847  N3   C8    aromatic  1.365  0.020  1.365
 847  N3   HN3   single    0.860  0.020  1.020
 847  N4   C8    aromatic  1.319  0.020  1.319
 847  C8   C1'   single    1.447  0.020  1.447
 847  C1'  C2'   aromatic  1.401  0.020  1.401
 847  C1'  C6'   aromatic  1.437  0.020  1.437
 847  C2'  C3'   aromatic  1.379  0.020  1.379
 847  C2'  HC2'  single    0.930  0.020  1.080
 847  C3'  CVX   single    1.510  0.020  1.510
 847  C3'  C4'   aromatic  1.405  0.020  1.405
 847  CVX  CWX   single    1.543  0.020  1.543
 847  CVX  C6X   single    1.523  0.020  1.523
 847  CVX  H31B  single    0.970  0.020  1.090
 847  CWX  OXX   deloc     1.248  0.020  1.248
 847  CWX  OYX   deloc     1.249  0.020  1.249
 847  C6X  C7X   single    1.535  0.020  1.535
 847  C6X  H42A  single    0.970  0.020  1.090
 847  C6X  H42B  single    0.970  0.020  1.090
 847  C7X  O8X   deloc     1.248  0.020  1.248
 847  C7X  O9X   deloc     1.251  0.020  1.251
 847  C4'  C5'   aromatic  1.374  0.020  1.374
 847  C4'  HC4'  single    0.930  0.020  1.080
 847  C5'  C6'   aromatic  1.432  0.020  1.432
 847  C5'  BR5'  single    1.897  0.020  1.897
 847  C6'  O6'   single    1.264  0.020  1.264

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
 847  C7    C1   C6    119.24  3.000
 847  C7    C1   C2    119.38  3.000
 847  C6    C1   C2    121.37  3.000
 847  HC2   C2   C3    118.68  3.000
 847  HC2   C2   C1    120.14  3.000
 847  C3    C2   C1    121.14  3.000
 847  HC3   C3   C4    121.98  3.000
 847  HC3   C3   C2    120.83  3.000
 847  C4    C3   C2    117.19  3.000
 847  N3    C4   C5    104.48  3.000
 847  N3    C4   C3    133.02  3.000
 847  C5    C4   C3    122.50  3.000
 847  N4    C5   C6    129.98  3.000
 847  N4    C5   C4    110.30  3.000
 847  C6    C5   C4    119.72  3.000
 847  HC6   C6   C5    120.11  3.000
 847  HC6   C6   C1    121.79  3.000
 847  C5    C6   C1    118.08  3.000
 847  N2    C7   N1    120.67  3.000
 847  N2    C7   C1    119.73  3.000
 847  N1    C7   C1    119.59  3.000
 847  HH12  N1   HH11  116.91  3.000
 847  HH12  N1   C7    120.81  3.000
 847  HH11  N1   C7    122.11  3.000
 847  HH22  N2   HH21  116.92  3.000
 847  HH22  N2   C7    122.13  3.000
 847  HH21  N2   C7    120.78  3.000
 847  HN3   N3   C8    119.85  3.000
 847  HN3   N3   C4    132.17  3.000
 847  C8    N3   C4    107.98  3.000
 847  C8    N4   C5    105.14  3.000
 847  C1'   C8   N4    126.38  3.000
 847  C1'   C8   N3    121.51  3.000
 847  N4    C8   N3    112.10  3.000
 847  C6'   C1'  C2'   121.78  3.000
 847  C6'   C1'  C8    119.47  3.000
 847  C2'   C1'  C8    118.75  3.000
 847  HC2'  C2'  C3'   119.18  3.000
 847  HC2'  C2'  C1'   117.96  3.000
 847  C3'   C2'  C1'   122.86  3.000
 847  C4'   C3'  CVX   120.97  3.000
 847  C4'   C3'  C2'   116.94  3.000
 847  CVX   C3'  C2'   122.10  3.000
 847  H31B  CVX  C6X   108.61  3.000
 847  H31B  CVX  CWX   107.76  3.000
 847  C6X   CVX  CWX   112.50  3.000
 847  H31B  CVX  C3'   107.18  3.000
 847  C6X   CVX  C3'   111.74  3.000
 847  CWX   CVX  C3'   108.83  3.000
 847  OYX   CWX  OXX   126.04  3.000
 847  OYX   CWX  CVX   117.13  3.000
 847  OXX   CWX  CVX   116.76  3.000
 847  H42B  C6X  H42A  105.57  3.000
 847  H42B  C6X  C7X   109.24  3.000
 847  H42A  C6X  C7X   107.75  3.000
 847  H42B  C6X  CVX   110.68  3.000
 847  H42A  C6X  CVX   108.74  3.000
 847  C7X   C6X  CVX   114.44  3.000
 847  O9X   C7X  O8X   125.82  3.000
 847  O9X   C7X  C6X   116.67  3.000
 847  O8X   C7X  C6X   117.47  3.000
 847  HC4'  C4'  C5'   119.97  3.000
 847  HC4'  C4'  C3'   119.04  3.000
 847  C5'   C4'  C3'   120.99  3.000
 847  BR5'  C5'  C6'   116.12  3.000
 847  BR5'  C5'  C4'   119.47  3.000
 847  C6'   C5'  C4'   124.41  3.000
 847  O6'   C6'  C5'   122.60  3.000
 847  O6'   C6'  C1'   124.39  3.000
 847  C5'   C6'  C1'   113.02  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
 847  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 847  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 847  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 847  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 847  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 847  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 847  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 847  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 847  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 847  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 847  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 847  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 847  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 847  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 847  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 847  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 847  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 847  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 847  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 847  CONST_20  C2'   C1'  C8   N3    180.00   0.0  0
 847  CONST_21  C6'   C1'  C8   N3      0.00   0.0  0
 847  CONST_22  C2'   C1'  C8   N4      0.00   0.0  0
 847  CONST_23  C6'   C1'  C8   N4    180.00   0.0  0
 847  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 847  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 847  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 847  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 847  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 847  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 847  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 847  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 847  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 847  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 847  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 847  CONST_35  CVX   C3'  C2'  C1'   180.00   0.0  0
 847  CONST_36  BR5'  C5'  C6'  C1'   180.00   0.0  0
 847  CONST_37  O6'   C6'  C1'  C2'   180.00   0.0  0
 847  CONST_38  BR5'  C5'  C4'  C3'   180.00   0.0  0
 847  CONST_39  C5'   C4'  C3'  CVX   180.00   0.0  0
 847  CONST_40  O6'   C6'  C5'  C4'   180.00   0.0  0
 847  CONST_41  HC3   C3   C2   C1    180.00   0.0  0
 847  CONST_42  HC6   C6   C1   C2    180.00   0.0  0
 847  CONST_43  HN3   N3   C4   C3      0.00   0.0  0
 847  CONST_44  HC2   C2   C3   C4    180.00   0.0  0
 847  CONST_45  HC2'  C2'  C1'  C8      0.00   0.0  0
 847  CONST_46  HC4'  C4'  C3'  C2'   180.00   0.0  0
 847  CONST_47  HH11  N1   C7   C1    180.00   0.0  0
 847  CONST_48  HH12  N1   C7   C1      0.00   0.0  0
 847  CONST_49  HH21  N2   C7   C1      0.00   0.0  0
 847  CONST_50  HH22  N2   C7   C1    180.00   0.0  0
 847  Var_01    N1    C7   C1   C2   -145.54  30.0  2
 847  Var_02    O8X   C7X  C6X  CVX    25.04  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
 847  chir_01  CVX  C3'  CWX  C6X  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
 847  plan-1  C8    0.020
 847  plan-1  C1'   0.020
 847  plan-1  C2'   0.020
 847  plan-1  C3'   0.020
 847  plan-1  CVX   0.020
 847  plan-1  C4'   0.020
 847  plan-1  C5'   0.020
 847  plan-1  C6'   0.020
 847  plan-1  O6'   0.020
 847  plan-1  BR5'  0.020
 847  plan-1  HC2'  0.020
 847  plan-1  HC4'  0.020
 847  plan-2  C1    0.020
 847  plan-2  C2    0.020
 847  plan-2  C3    0.020
 847  plan-2  C4    0.020
 847  plan-2  C5    0.020
 847  plan-2  C6    0.020
 847  plan-2  C7    0.020
 847  plan-2  N3    0.020
 847  plan-2  N4    0.020
 847  plan-2  C8    0.020
 847  plan-2  C1'   0.020
 847  plan-2  HC2   0.020
 847  plan-2  HC3   0.020
 847  plan-2  HC6   0.020
 847  plan-2  HN3   0.020
 847  plan-3  C1    0.020
 847  plan-3  C7    0.020
 847  plan-3  N1    0.020
 847  plan-3  N2    0.020
 847  plan-3  HH11  0.020
 847  plan-3  HH12  0.020
 847  plan-3  HH21  0.020
 847  plan-3  HH22  0.020
 847  plan-4  CVX   0.020
 847  plan-4  CWX   0.020
 847  plan-4  OXX   0.020
 847  plan-4  OYX   0.020
 847  plan-5  C6X   0.020
 847  plan-5  C7X   0.020
 847  plan-5  O8X   0.020
 847  plan-5  O9X   0.020

