# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 02:16:17 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-(1H-benzimidazol-2-ylmethyl)-1H-benzimidazole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2[nH]c(Cc3[nH]c4ccccc4n3)nc2c1
#
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
 BAI  BAI  2-(1H-benzimidazol-2-ylmethyl)-1H-benzimidazole-5-carboximidamide  ligand  36  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BAI
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
 BAI  C1    C  CR6   0   0.029   1.9365  -0.3844   0.8097
 BAI  C2    C  CR16  0  -0.312   0.5557  -0.6472   0.9068
 BAI  C3    C  CR16  0  -0.290  -0.0228  -1.1081   2.0746
 BAI  C4    C  CR56  0   0.339   0.8225  -1.2968   3.1596
 BAI  C5    C  CR56  0   0.165   2.2035  -1.0474   3.0878
 BAI  C6    C  CR16  0  -0.372   2.7681  -0.5936   1.9011
 BAI  C7    C  C     0   0.337   2.5330   0.1116  -0.4615
 BAI  C8    C  CR5   0   0.440   1.8206  -1.7163   5.0706
 BAI  C9    C  CH2   0  -0.664   1.9666  -2.0899   6.5091
 BAI  N1    N  NH2   0  -0.824   1.6696   0.7656  -1.2951
 BAI  N2    N  N     0  -0.655   3.7638  -0.1344  -0.7040
 BAI  N3    N  NR15  0  -0.697   0.6156  -1.7199   4.4428
 BAI  N4    N  N     0  -0.456   2.7936  -1.3184   4.3003
 BAI  C1'   C  CR16  0  -0.272   3.6421   2.3965  10.0267
 BAI  C2'   C  CR16  0  -0.278   2.4475   2.9872   9.5877
 BAI  C3'   C  CR16  0  -0.308   1.6051   2.3436   8.6975
 BAI  C4'   C  CR56  0   0.341   2.0038   1.0853   8.2626
 BAI  C5'   C  CR56  0   0.134   3.1966   0.4786   8.6898
 BAI  C6'   C  CR16  0  -0.333   4.0313   1.1434   9.5872
 BAI  C8'   C  CR5   0   0.461   2.2743  -0.8978   7.3528
 BAI  N3'   N  NR15  0  -0.695   1.4411   0.1743   7.4090
 BAI  N4'   N  N     0  -0.471   3.3331  -0.7573   8.0986
 BAI  H2    H  HCR6  0   0.259  -0.0797  -0.5092   0.0420
 BAI  H3    H  HCR6  0   0.271  -1.0835  -1.3124   2.1303
 BAI  H6    H  HCR6  0   0.255   3.8293  -0.3971   1.8278
 BAI  H91   H  HCH2  0   0.309   2.7830  -2.8024   6.6188
 BAI  H92   H  HCH2  0   0.309   1.0562  -2.5763   6.8676
 BAI  HH11  H  HNH2  0   0.393   0.8907   1.2561  -0.8871
 BAI  HH12  H  HNH2  0   0.390   2.0676   1.2385  -2.0909
 BAI  HH21  H  H     0   0.321   4.0581   0.2955  -1.5768
 BAI  HN3   H  HNR5  0   0.425  -0.2624  -2.0081   4.8461
 BAI  H2'   H  HCR6  0   0.256   2.1794   3.9695   9.9538
 BAI  H3'   H  HCR6  0   0.267   0.6841   2.8004   8.3597
 BAI  H6'   H  HCR6  0   0.255   4.9534   0.6900   9.9276
 BAI  HN3'  H  HNR5  0   0.418   0.5622   0.2719   6.9253
 BAI  H1'   H  HCR6  0   0.253   4.2693   2.9355  10.7245

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
 BAI  C1   C2    aromatic  1.409  0.020  1.409
 BAI  C1   C6    aromatic  1.388  0.020  1.388
 BAI  C1   C7    single    1.489  0.020  1.489
 BAI  C2   C3    aromatic  1.382  0.020  1.382
 BAI  C2   H2    single    0.930  0.020  1.080
 BAI  C3   C4    aromatic  1.388  0.020  1.388
 BAI  C3   H3    single    0.930  0.020  1.080
 BAI  C4   C5    aromatic  1.405  0.020  1.405
 BAI  C4   N3    aromatic  1.367  0.020  1.367
 BAI  C5   C6    aromatic  1.390  0.020  1.390
 BAI  C5   N4    aromatic  1.375  0.020  1.375
 BAI  C6   H6    single    0.930  0.020  1.080
 BAI  C7   N1    single    1.367  0.020  1.367
 BAI  C7   N2    double    1.278  0.020  1.278
 BAI  C8   C9    single    1.493  0.020  1.493
 BAI  C8   N3    aromatic  1.359  0.020  1.359
 BAI  C8   N4    aromatic  1.303  0.020  1.303
 BAI  C9   C8'   single    1.492  0.020  1.492
 BAI  C9   H91   single    0.970  0.020  1.090
 BAI  C9   H92   single    0.970  0.020  1.090
 BAI  N1   HH11  single    0.890  0.020  1.040
 BAI  N1   HH12  single    0.890  0.020  1.040
 BAI  N2   HH21  single    0.890  0.020  1.040
 BAI  N3   HN3   single    0.860  0.020  1.020
 BAI  C1'  C2'   aromatic  1.403  0.020  1.403
 BAI  C1'  C6'   aromatic  1.384  0.020  1.384
 BAI  C1'  H1'   single    0.930  0.020  1.080
 BAI  C2'  C3'   aromatic  1.384  0.020  1.384
 BAI  C2'  H2'   single    0.930  0.020  1.080
 BAI  C3'  C4'   aromatic  1.390  0.020  1.390
 BAI  C3'  H3'   single    0.930  0.020  1.080
 BAI  C4'  C5'   aromatic  1.405  0.020  1.405
 BAI  C4'  N3'   aromatic  1.369  0.020  1.369
 BAI  C5'  C6'   aromatic  1.394  0.020  1.394
 BAI  C5'  N4'   aromatic  1.377  0.020  1.377
 BAI  C6'  H6'   single    0.930  0.020  1.080
 BAI  C8'  N3'   aromatic  1.359  0.020  1.359
 BAI  C8'  N4'   aromatic  1.303  0.020  1.303
 BAI  N3'  HN3'  single    0.860  0.020  1.020

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
 BAI  C7    C1   C6    118.78  3.000
 BAI  C7    C1   C2    120.90  3.000
 BAI  C6    C1   C2    120.32  3.000
 BAI  H2    C2   C3    118.16  3.000
 BAI  H2    C2   C1    119.78  3.000
 BAI  C3    C2   C1    122.05  3.000
 BAI  H3    C3   C4    122.09  3.000
 BAI  H3    C3   C2    121.12  3.000
 BAI  C4    C3   C2    116.79  3.000
 BAI  N3    C4   C5    104.57  3.000
 BAI  N3    C4   C3    133.12  3.000
 BAI  C5    C4   C3    122.30  3.000
 BAI  N4    C5   C6    129.98  3.000
 BAI  N4    C5   C4    109.98  3.000
 BAI  C6    C5   C4    120.04  3.000
 BAI  H6    C6   C5    121.04  3.000
 BAI  H6    C6   C1    120.47  3.000
 BAI  C5    C6   C1    118.49  3.000
 BAI  N2    C7   N1    125.78  3.000
 BAI  N2    C7   C1    118.91  3.000
 BAI  N1    C7   C1    115.27  3.000
 BAI  N4    C8   N3    112.94  3.000
 BAI  N4    C8   C9    124.94  3.000
 BAI  N3    C8   C9    122.09  3.000
 BAI  H92   C9   H91   107.47  3.000
 BAI  H92   C9   C8'   109.99  3.000
 BAI  H91   C9   C8'   108.13  3.000
 BAI  H92   C9   C8    110.24  3.000
 BAI  H91   C9   C8    109.51  3.000
 BAI  C8'   C9   C8    111.40  3.000
 BAI  HH12  N1   HH11  113.39  3.000
 BAI  HH12  N1   C7    117.17  3.000
 BAI  HH11  N1   C7    118.34  3.000
 BAI  HH21  N2   C7    111.11  3.000
 BAI  HN3   N3   C8    126.03  3.000
 BAI  HN3   N3   C4    126.57  3.000
 BAI  C8    N3   C4    107.38  3.000
 BAI  C8    N4   C5    105.13  3.000
 BAI  H1'   C1'  C6'   119.53  3.000
 BAI  H1'   C1'  C2'   119.05  3.000
 BAI  C6'   C1'  C2'   121.42  3.000
 BAI  H2'   C2'  C3'   119.27  3.000
 BAI  H2'   C2'  C1'   119.16  3.000
 BAI  C3'   C2'  C1'   121.57  3.000
 BAI  H3'   C3'  C4'   121.92  3.000
 BAI  H3'   C3'  C2'   121.49  3.000
 BAI  C4'   C3'  C2'   116.59  3.000
 BAI  N3'   C4'  C5'   104.55  3.000
 BAI  N3'   C4'  C3'   132.80  3.000
 BAI  C5'   C4'  C3'   122.65  3.000
 BAI  N4'   C5'  C6'   130.18  3.000
 BAI  N4'   C5'  C4'   109.95  3.000
 BAI  C6'   C5'  C4'   119.88  3.000
 BAI  H6'   C6'  C5'   120.83  3.000
 BAI  H6'   C6'  C1'   121.27  3.000
 BAI  C5'   C6'  C1'   117.90  3.000
 BAI  N4'   C8'  N3'   112.92  3.000
 BAI  N4'   C8'  C9    125.26  3.000
 BAI  N3'   C8'  C9    121.81  3.000
 BAI  HN3'  N3'  C8'   126.24  3.000
 BAI  HN3'  N3'  C4'   126.38  3.000
 BAI  C8'   N3'  C4'   107.38  3.000
 BAI  C8'   N4'  C5'   105.20  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
 BAI  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 BAI  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 BAI  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 BAI  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 BAI  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 BAI  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 BAI  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 BAI  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 BAI  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 BAI  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 BAI  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 BAI  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 BAI  CONST_13  C8    N3   C4   C5      0.00   0.0  0
 BAI  CONST_14  N3    C8   N4   C5      0.00   0.0  0
 BAI  CONST_15  N3    C4   C5   C6    180.00   0.0  0
 BAI  CONST_16  C8    N4   C5   C6    180.00   0.0  0
 BAI  CONST_17  N4    C5   C4   N3      0.00   0.0  0
 BAI  CONST_18  C4'   C3'  C2'  C1'     0.00   0.0  0
 BAI  CONST_19  C4'   C5'  C6'  C1'     0.00   0.0  0
 BAI  CONST_20  N4'   C5'  C6'  C1'   180.00   0.0  0
 BAI  CONST_21  C5'   C6'  C1'  C2'     0.00   0.0  0
 BAI  CONST_22  C5'   C4'  C3'  C2'     0.00   0.0  0
 BAI  CONST_23  N3'   C4'  C3'  C2'   180.00   0.0  0
 BAI  CONST_24  C6'   C1'  C2'  C3'     0.00   0.0  0
 BAI  CONST_25  C6'   C5'  C4'  C3'     0.00   0.0  0
 BAI  CONST_26  N4'   C5'  C4'  C3'   180.00   0.0  0
 BAI  CONST_27  C8'   N3'  C4'  C3'   180.00   0.0  0
 BAI  CONST_28  C8'   N4'  C5'  C4'     0.00   0.0  0
 BAI  CONST_29  N4'   C8'  N3'  C4'     0.00   0.0  0
 BAI  CONST_30  C8'   N3'  C4'  C5'     0.00   0.0  0
 BAI  CONST_31  N3'   C8'  N4'  C5'     0.00   0.0  0
 BAI  CONST_32  N3'   C4'  C5'  C6'   180.00   0.0  0
 BAI  CONST_33  C8'   N4'  C5'  C6'   180.00   0.0  0
 BAI  CONST_34  N4'   C5'  C4'  N3'     0.00   0.0  0
 BAI  CONST_35  C7    C1   C2   C3    180.00   0.0  0
 BAI  CONST_36  C9    C8   N3   C4    180.00   0.0  0
 BAI  CONST_37  C7    C1   C6   C5    180.00   0.0  0
 BAI  CONST_38  C9    C8   N4   C5    180.00   0.0  0
 BAI  CONST_39  C4'   N3'  C8'  C9    180.00   0.0  0
 BAI  CONST_40  C5'   N4'  C8'  C9    180.00   0.0  0
 BAI  CONST_41  H3    C3   C2   C1    180.00   0.0  0
 BAI  CONST_42  H6    C6   C1   C2    180.00   0.0  0
 BAI  CONST_43  HN3   N3   C4   C3      0.00   0.0  0
 BAI  CONST_44  H2    C2   C3   C4    180.00   0.0  0
 BAI  CONST_45  H3'   C3'  C2'  C1'   180.00   0.0  0
 BAI  CONST_46  H6'   C6'  C1'  C2'   180.00   0.0  0
 BAI  CONST_47  H1'   C1'  C2'  C3'   180.00   0.0  0
 BAI  CONST_48  HN3'  N3'  C4'  C3'     0.00   0.0  0
 BAI  CONST_49  H2'   C2'  C3'  C4'   180.00   0.0  0
 BAI  CONST_51  HH12  N1   C7   C1    180.00   0.0  0
 BAI  CONST_52  HH21  N2   C7   C1    180.00   0.0  0
 BAI  Var_01    N3'   C8'  C9   C8     58.81  30.0  2
 BAI  Var_02    C8'   C9   C8   N3   -108.65  30.0  2
 BAI  Var_03    N1    C7   C1   C2     24.32  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
 BAI  plan-1  C1    0.020
 BAI  plan-1  C2    0.020
 BAI  plan-1  C3    0.020
 BAI  plan-1  C4    0.020
 BAI  plan-1  C5    0.020
 BAI  plan-1  C6    0.020
 BAI  plan-1  C7    0.020
 BAI  plan-1  C8    0.020
 BAI  plan-1  C9    0.020
 BAI  plan-1  N3    0.020
 BAI  plan-1  N4    0.020
 BAI  plan-1  H2    0.020
 BAI  plan-1  H3    0.020
 BAI  plan-1  H6    0.020
 BAI  plan-1  HN3   0.020
 BAI  plan-2  C9    0.020
 BAI  plan-2  C1'   0.020
 BAI  plan-2  C2'   0.020
 BAI  plan-2  C3'   0.020
 BAI  plan-2  C4'   0.020
 BAI  plan-2  C5'   0.020
 BAI  plan-2  C6'   0.020
 BAI  plan-2  C8'   0.020
 BAI  plan-2  N3'   0.020
 BAI  plan-2  N4'   0.020
 BAI  plan-2  H2'   0.020
 BAI  plan-2  H3'   0.020
 BAI  plan-2  H6'   0.020
 BAI  plan-2  HN3'  0.020
 BAI  plan-2  H1'   0.020
 BAI  plan-3  C1    0.020
 BAI  plan-3  C7    0.020
 BAI  plan-3  N1    0.020
 BAI  plan-3  N2    0.020
 BAI  plan-3  HH11  0.020
 BAI  plan-3  HH12  0.020
 BAI  plan-3  HH21  0.020

