# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 02:35:55 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2,2'-carbonylbis(1H-benzimidazole-6-carboximidamide)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2nc([nH]c2c1)C(=O)c3[nH]c4cc(ccc4n3)C(N)=N
#
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
 BAO  BAO  2,2'-carbonylbis(1H-benzimidazole-6-carboximidamide)  ligand  40  26  .  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_BAO
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
 BAO  C1    C  CR6   0  -0.014   0.5075   0.0769   5.5888
 BAO  C2    C  CR16  0  -0.287   1.7727  -0.0164   4.9631
 BAO  C3    C  CR16  0  -0.312   1.9029  -0.0969   3.5956
 BAO  C4    C  CR56  0   0.138   0.7349  -0.0952   2.8268
 BAO  C5    C  CR56  0   0.371  -0.5192  -0.0112   3.4609
 BAO  C6    C  CR16  0  -0.342  -0.6571   0.0822   4.8415
 BAO  C7    C  C     0   0.333   0.4113   0.1890   7.0730
 BAO  N1    N  N     0  -0.640  -0.4348   0.9215   7.6903
 BAO  N2    N  NH2   0  -0.802   1.3398  -0.5311   7.7626
 BAO  N3    N  N     0  -0.430   0.5736  -0.1686   1.4746
 BAO  N4    N  NR15  0  -0.693  -1.4242  -0.0477   2.4480
 BAO  C8    C  CR5   0   0.378  -0.7198  -0.1358   1.2883
 BAO  C1'   C  CR6   0   0.026   0.4728   0.1151  -5.5714
 BAO  C2'   C  CR16  0  -0.296   1.6575   0.5705  -4.9460
 BAO  C3'   C  CR16  0  -0.314   1.7628   0.6830  -3.5784
 BAO  C4'   C  CR56  0   0.137   0.6542   0.3247  -2.8058
 BAO  C5'   C  CR56  0   0.377  -0.5211  -0.1231  -3.4387
 BAO  C6'   C  CR16  0  -0.331  -0.6354  -0.2330  -4.8196
 BAO  C7'   C  C     0   0.339   0.3851   0.0160  -7.0560
 BAO  N1'   N  N     0  -0.651  -0.7589   0.1440  -7.6104
 BAO  N2'   N  NH2   0  -0.822   1.5766  -0.1577  -7.6989
 BAO  N3'   N  N     0  -0.431   0.4873   0.3299  -1.4524
 BAO  N4'   N  NR15  0  -0.693  -1.3865  -0.3797  -2.4220
 BAO  C8'   C  CR5   0   0.378  -0.7345  -0.0954  -1.2633
 BAO  C9    C  C     0   0.244  -1.4516  -0.2331   0.0143
 BAO  O9    O  O     0  -0.364  -2.6509  -0.4247   0.0188
 BAO  H2    H  HCR6  0   0.267   2.6635  -0.0022   5.5769
 BAO  H3    H  HCR6  0   0.267   2.8771  -0.1559   3.1286
 BAO  H6    H  HCR6  0   0.282  -1.6324   0.1317   5.3079
 BAO  HN1   H  H     0   0.333  -0.9770   1.4726   7.0354
 BAO  HN21  H  HNH2  0   0.385   1.2147  -0.5781   8.7614
 BAO  HN22  H  HNH2  0   0.394   1.6932  -1.3775   7.3487
 BAO  HN4   H  HNR5  0   0.430  -2.4294  -0.0134   2.5311
 BAO  H2'   H  HCR6  0   0.262   2.5023   0.8633  -5.5554
 BAO  H3'   H  HCR6  0   0.266   2.6718   1.0429  -3.1155
 BAO  H6'   H  HCR6  0   0.273  -1.5430  -0.5800  -5.2938
 BAO  H1'   H  H     0   0.325  -0.6937   0.0208  -8.6172
 BAO  H2'1  H  HNH2  0   0.392   1.5438  -0.3626  -8.6851
 BAO  H2'2  H  HNH2  0   0.396   2.3197  -0.6322  -7.2129
 BAO  HN4'  H  HNR5  0   0.429  -2.3343  -0.7170  -2.5027

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
 BAO  C1   C2    aromatic  1.415  0.020  1.415
 BAO  C1   C6    aromatic  1.384  0.020  1.384
 BAO  C1   C7    single    1.492  0.020  1.492
 BAO  C2   C3    aromatic  1.376  0.020  1.376
 BAO  C2   H2    single    0.930  0.020  1.080
 BAO  C3   C4    aromatic  1.398  0.020  1.398
 BAO  C3   H3    single    0.930  0.020  1.080
 BAO  C4   C5    aromatic  1.408  0.020  1.408
 BAO  C4   N3    aromatic  1.364  0.020  1.364
 BAO  C5   C6    aromatic  1.391  0.020  1.391
 BAO  C5   N4    aromatic  1.359  0.020  1.359
 BAO  C6   H6    single    0.930  0.020  1.080
 BAO  C7   N1    double    1.278  0.020  1.278
 BAO  C7   N2    single    1.362  0.020  1.362
 BAO  N1   HN1   single    0.890  0.020  1.040
 BAO  N2   HN21  single    0.890  0.020  1.040
 BAO  N2   HN22  single    0.890  0.020  1.040
 BAO  N3   C8    aromatic  1.307  0.020  1.307
 BAO  N4   C8    aromatic  1.360  0.020  1.360
 BAO  N4   HN4   single    0.860  0.020  1.020
 BAO  C8   C9    single    1.472  0.020  1.472
 BAO  C1'  C2'   aromatic  1.415  0.020  1.415
 BAO  C1'  C6'   aromatic  1.384  0.020  1.384
 BAO  C1'  C7'   single    1.491  0.020  1.491
 BAO  C2'  C3'   aromatic  1.376  0.020  1.376
 BAO  C2'  H2'   single    0.930  0.020  1.080
 BAO  C3'  C4'   aromatic  1.398  0.020  1.398
 BAO  C3'  H3'   single    0.930  0.020  1.080
 BAO  C4'  C5'   aromatic  1.408  0.020  1.408
 BAO  C4'  N3'   aromatic  1.364  0.020  1.364
 BAO  C5'  C6'   aromatic  1.390  0.020  1.390
 BAO  C5'  N4'   aromatic  1.360  0.020  1.360
 BAO  C6'  H6'   single    0.930  0.020  1.080
 BAO  C7'  N1'   double    1.278  0.020  1.278
 BAO  C7'  N2'   single    1.365  0.020  1.365
 BAO  N1'  H1'   single    0.890  0.020  1.040
 BAO  N2'  H2'1  single    0.890  0.020  1.040
 BAO  N2'  H2'2  single    0.890  0.020  1.040
 BAO  N3'  C8'   aromatic  1.307  0.020  1.307
 BAO  N4'  C8'   aromatic  1.360  0.020  1.360
 BAO  N4'  HN4'  single    0.860  0.020  1.020
 BAO  C8'  C9    single    1.472  0.020  1.472
 BAO  C9   O9    double    1.215  0.020  1.215

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
 BAO  C7    C1   C6    118.87  3.000
 BAO  C7    C1   C2    120.18  3.000
 BAO  C6    C1   C2    120.94  3.000
 BAO  H2    C2   C3    119.12  3.000
 BAO  H2    C2   C1    118.99  3.000
 BAO  C3    C2   C1    121.87  3.000
 BAO  H3    C3   C4    120.99  3.000
 BAO  H3    C3   C2    121.15  3.000
 BAO  C4    C3   C2    117.86  3.000
 BAO  N3    C4   C5    110.14  3.000
 BAO  N3    C4   C3    130.08  3.000
 BAO  C5    C4   C3    119.77  3.000
 BAO  N4    C5   C6    132.52  3.000
 BAO  N4    C5   C4    104.84  3.000
 BAO  C6    C5   C4    122.64  3.000
 BAO  H6    C6   C5    121.35  3.000
 BAO  H6    C6   C1    121.73  3.000
 BAO  C5    C6   C1    116.90  3.000
 BAO  N2    C7   N1    120.64  3.000
 BAO  N2    C7   C1    114.83  3.000
 BAO  N1    C7   C1    124.50  3.000
 BAO  HN1   N1   C7    110.72  3.000
 BAO  HN22  N2   HN21  114.33  3.000
 BAO  HN22  N2   C7    118.40  3.000
 BAO  HN21  N2   C7    116.22  3.000
 BAO  C8    N3   C4    104.89  3.000
 BAO  HN4   N4   C8    126.05  3.000
 BAO  HN4   N4   C5    126.95  3.000
 BAO  C8    N4   C5    107.00  3.000
 BAO  C9    C8   N4    119.00  3.000
 BAO  C9    C8   N3    127.84  3.000
 BAO  N4    C8   N3    113.12  3.000
 BAO  C7'   C1'  C6'   118.51  3.000
 BAO  C7'   C1'  C2'   120.72  3.000
 BAO  C6'   C1'  C2'   120.76  3.000
 BAO  H2'   C2'  C3'   118.54  3.000
 BAO  H2'   C2'  C1'   119.47  3.000
 BAO  C3'   C2'  C1'   121.98  3.000
 BAO  H3'   C3'  C4'   121.01  3.000
 BAO  H3'   C3'  C2'   121.11  3.000
 BAO  C4'   C3'  C2'   117.87  3.000
 BAO  N3'   C4'  C5'   110.19  3.000
 BAO  N3'   C4'  C3'   130.13  3.000
 BAO  C5'   C4'  C3'   119.67  3.000
 BAO  N4'   C5'  C6'   132.51  3.000
 BAO  N4'   C5'  C4'   104.79  3.000
 BAO  C6'   C5'  C4'   122.71  3.000
 BAO  H6'   C6'  C5'   122.01  3.000
 BAO  H6'   C6'  C1'   120.98  3.000
 BAO  C5'   C6'  C1'   117.00  3.000
 BAO  N2'   C7'  N1'   126.16  3.000
 BAO  N2'   C7'  C1'   115.23  3.000
 BAO  N1'   C7'  C1'   118.57  3.000
 BAO  H1'   N1'  C7'   111.11  3.000
 BAO  H2'2  N2'  H2'1  113.62  3.000
 BAO  H2'2  N2'  C7'   118.48  3.000
 BAO  H2'1  N2'  C7'   117.28  3.000
 BAO  C8'   N3'  C4'   104.87  3.000
 BAO  HN4'  N4'  C8'   126.05  3.000
 BAO  HN4'  N4'  C5'   126.94  3.000
 BAO  C8'   N4'  C5'   107.01  3.000
 BAO  C9    C8'  N4'   119.12  3.000
 BAO  C9    C8'  N3'   127.69  3.000
 BAO  N4'   C8'  N3'   113.14  3.000
 BAO  O9    C9   C8'   119.95  3.000
 BAO  O9    C9   C8    119.86  3.000
 BAO  C8'   C9   C8    120.19  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
 BAO  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 BAO  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 BAO  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 BAO  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 BAO  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 BAO  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 BAO  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 BAO  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 BAO  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 BAO  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 BAO  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 BAO  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 BAO  CONST_13  C8    N3   C4   C5      0.00   0.0  0
 BAO  CONST_14  N3    C8   N4   C5      0.00   0.0  0
 BAO  CONST_15  N3    C4   C5   C6    180.00   0.0  0
 BAO  CONST_16  C8    N4   C5   C6    180.00   0.0  0
 BAO  CONST_17  N4    C5   C4   N3      0.00   0.0  0
 BAO  CONST_18  C4'   C3'  C2'  C1'     0.00   0.0  0
 BAO  CONST_19  C4'   C5'  C6'  C1'     0.00   0.0  0
 BAO  CONST_20  N4'   C5'  C6'  C1'   180.00   0.0  0
 BAO  CONST_21  C5'   C6'  C1'  C2'     0.00   0.0  0
 BAO  CONST_22  C5'   C4'  C3'  C2'     0.00   0.0  0
 BAO  CONST_23  N3'   C4'  C3'  C2'   180.00   0.0  0
 BAO  CONST_24  C6'   C1'  C2'  C3'     0.00   0.0  0
 BAO  CONST_25  C6'   C5'  C4'  C3'     0.00   0.0  0
 BAO  CONST_26  N4'   C5'  C4'  C3'   180.00   0.0  0
 BAO  CONST_27  C8'   N3'  C4'  C3'   180.00   0.0  0
 BAO  CONST_28  C8'   N4'  C5'  C4'     0.00   0.0  0
 BAO  CONST_29  N4'   C8'  N3'  C4'     0.00   0.0  0
 BAO  CONST_30  C8'   N3'  C4'  C5'     0.00   0.0  0
 BAO  CONST_31  N3'   C8'  N4'  C5'     0.00   0.0  0
 BAO  CONST_32  N3'   C4'  C5'  C6'   180.00   0.0  0
 BAO  CONST_33  C8'   N4'  C5'  C6'   180.00   0.0  0
 BAO  CONST_34  N4'   C5'  C4'  N3'     0.00   0.0  0
 BAO  CONST_35  C7    C1   C2   C3    180.00   0.0  0
 BAO  CONST_36  C9    C8   N3   C4    180.00   0.0  0
 BAO  CONST_37  C7    C1   C6   C5    180.00   0.0  0
 BAO  CONST_38  C9    C8   N4   C5    180.00   0.0  0
 BAO  CONST_39  C7'   C1'  C2'  C3'   180.00   0.0  0
 BAO  CONST_40  C9    C8'  N3'  C4'   180.00   0.0  0
 BAO  CONST_41  C7'   C1'  C6'  C5'   180.00   0.0  0
 BAO  CONST_42  C9    C8'  N4'  C5'   180.00   0.0  0
 BAO  CONST_43  H3    C3   C2   C1    180.00   0.0  0
 BAO  CONST_44  H6    C6   C1   C2    180.00   0.0  0
 BAO  CONST_45  H2    C2   C3   C4    180.00   0.0  0
 BAO  CONST_46  HN4   N4   C5   C4    180.00   0.0  0
 BAO  CONST_47  H3'   C3'  C2'  C1'   180.00   0.0  0
 BAO  CONST_48  H6'   C6'  C1'  C2'   180.00   0.0  0
 BAO  CONST_49  H2'   C2'  C3'  C4'   180.00   0.0  0
 BAO  CONST_50  HN4'  N4'  C5'  C4'   180.00   0.0  0
 BAO  CONST_51  HN1   N1   C7   C1      0.00   0.0  0
 BAO  CONST_52  HN21  N2   C7   C1    180.00   0.0  0
 BAO  CONST_54  H1'   N1'  C7'  C1'   180.00   0.0  0
 BAO  CONST_55  H2'1  N2'  C7'  C1'   180.00   0.0  0
 BAO  Var_01    C8'   C9   C8   N3    -13.23  30.0  2
 BAO  Var_02    N3'   C8'  C9   C8    -12.34  30.0  2
 BAO  Var_03    N1    C7   C1   C2    141.66  30.0  2
 BAO  Var_04    N1'   C7'  C1'  C2'  -151.72  30.0  2

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
 BAO  plan-1  C1    0.020
 BAO  plan-1  C2    0.020
 BAO  plan-1  C3    0.020
 BAO  plan-1  C4    0.020
 BAO  plan-1  C5    0.020
 BAO  plan-1  C6    0.020
 BAO  plan-1  C7    0.020
 BAO  plan-1  N3    0.020
 BAO  plan-1  N4    0.020
 BAO  plan-1  C8    0.020
 BAO  plan-1  C9    0.020
 BAO  plan-1  H2    0.020
 BAO  plan-1  H3    0.020
 BAO  plan-1  H6    0.020
 BAO  plan-1  HN4   0.020
 BAO  plan-2  C1'   0.020
 BAO  plan-2  C2'   0.020
 BAO  plan-2  C3'   0.020
 BAO  plan-2  C4'   0.020
 BAO  plan-2  C5'   0.020
 BAO  plan-2  C6'   0.020
 BAO  plan-2  C7'   0.020
 BAO  plan-2  N3'   0.020
 BAO  plan-2  N4'   0.020
 BAO  plan-2  C8'   0.020
 BAO  plan-2  C9    0.020
 BAO  plan-2  H2'   0.020
 BAO  plan-2  H3'   0.020
 BAO  plan-2  H6'   0.020
 BAO  plan-2  HN4'  0.020
 BAO  plan-3  C8    0.020
 BAO  plan-3  C8'   0.020
 BAO  plan-3  C9    0.020
 BAO  plan-3  O9    0.020
 BAO  plan-4  C1    0.020
 BAO  plan-4  C7    0.020
 BAO  plan-4  N1    0.020
 BAO  plan-4  N2    0.020
 BAO  plan-4  HN1   0.020
 BAO  plan-4  HN21  0.020
 BAO  plan-4  HN22  0.020
 BAO  plan-5  C1'   0.020
 BAO  plan-5  C7'   0.020
 BAO  plan-5  N1'   0.020
 BAO  plan-5  N2'   0.020
 BAO  plan-5  H1'   0.020
 BAO  plan-5  H2'1  0.020
 BAO  plan-5  H2'2  0.020

