# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 01:43:02 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 3-(1H-benzimidazol-2-yl)-1H-indazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1nc(c2[nH]c3ccccc3n2)c4ccccc14
#
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
 IDZ  IDZ  3-(1H-benzimidazol-2-yl)-1H-indazole  ligand  28  18  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IDZ
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
 IDZ  C1   C  CR16  0  -0.300  -4.4223  -0.1111   0.0090
 IDZ  C2   C  CR16  0  -0.264  -4.5740   1.2565  -0.0030
 IDZ  C3   C  CR16  0  -0.264  -3.4640   2.1273  -0.0163
 IDZ  C4   C  CR16  0  -0.336  -2.1751   1.6450  -0.0175
 IDZ  C5   C  CR56  0  -0.097  -1.9924   0.2557  -0.0056
 IDZ  C6   C  CR5   0   0.159  -0.8841  -0.6389  -0.0029
 IDZ  C7   C  CR5   0   0.445   0.5275  -0.3269  -0.0109
 IDZ  N8   N  NR15  0  -0.708   1.4803  -1.2965  -0.0092
 IDZ  C9   C  CR56  0   0.337   2.6955  -0.6701  -0.0181
 IDZ  C10  C  CR16  0  -0.313   4.0018  -1.1452  -0.0205
 IDZ  C11  C  CR16  0  -0.278   5.0083  -0.1947  -0.0307
 IDZ  C12  C  CR16  0  -0.271   4.7212   1.1794  -0.0390
 IDZ  C13  C  CR16  0  -0.343   3.4186   1.6444  -0.0369
 IDZ  C14  C  CR56  0   0.151   2.3893   0.7030  -0.0261
 IDZ  N16  N  NR15  0  -0.533  -2.6184  -1.8592   0.0155
 IDZ  C17  C  CR56  0   0.424  -3.1105  -0.5955   0.0060
 IDZ  NAL  N  N     0  -0.488   1.0280   0.8809  -0.0212
 IDZ  NAI  N  N     0  -0.253  -1.2951  -1.8884   0.0096
 IDZ  H1   H  HCR6  0   0.275  -5.2739  -0.7780   0.0187
 IDZ  H2   H  HCR6  0   0.264  -5.5712   1.6771  -0.0027
 IDZ  H3   H  HCR6  0   0.259  -3.6361   3.1953  -0.0256
 IDZ  H4   H  HCR6  0   0.258  -1.3261   2.3137  -0.0267
 IDZ  H8   H  HNR5  0   0.420   1.3098  -2.2900   0.0028
 IDZ  H10  H  HCR6  0   0.266   4.2240  -2.2041  -0.0146
 IDZ  H11  H  HCR6  0   0.256   6.0412  -0.5176  -0.0326
 IDZ  H12  H  HCR6  0   0.254   5.5390   1.8877  -0.0468
 IDZ  H13  H  HCR6  0   0.254   3.2009   2.7048  -0.0427
 IDZ  H16  H  HNR5  0   0.425  -3.1349  -2.7244   0.0194

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
 IDZ  C1   C2   aromatic  1.376  0.020  1.376
 IDZ  C1   C17  aromatic  1.398  0.020  1.398
 IDZ  C1   H1   single    0.930  0.020  1.080
 IDZ  C2   C3   aromatic  1.411  0.020  1.411
 IDZ  C2   H2   single    0.930  0.020  1.080
 IDZ  C3   C4   aromatic  1.376  0.020  1.376
 IDZ  C3   H3   single    0.930  0.020  1.080
 IDZ  C4   C5   aromatic  1.401  0.020  1.401
 IDZ  C4   H4   single    0.930  0.020  1.080
 IDZ  C5   C6   aromatic  1.424  0.020  1.424
 IDZ  C5   C17  aromatic  1.405  0.020  1.405
 IDZ  C6   C7   single    1.446  0.020  1.446
 IDZ  C6   NAI  aromatic  1.315  0.020  1.315
 IDZ  C7   N8   aromatic  1.359  0.020  1.359
 IDZ  C7   NAL  aromatic  1.307  0.020  1.307
 IDZ  N8   C9   aromatic  1.367  0.020  1.367
 IDZ  N8   H8   single    0.860  0.020  1.020
 IDZ  C9   C10  aromatic  1.390  0.020  1.390
 IDZ  C9   C14  aromatic  1.407  0.020  1.407
 IDZ  C10  C11  aromatic  1.384  0.020  1.384
 IDZ  C10  H10  single    0.930  0.020  1.080
 IDZ  C11  C12  aromatic  1.404  0.020  1.404
 IDZ  C11  H11  single    0.930  0.020  1.080
 IDZ  C12  C13  aromatic  1.383  0.020  1.383
 IDZ  C12  H12  single    0.930  0.020  1.080
 IDZ  C13  C14  aromatic  1.395  0.020  1.395
 IDZ  C13  H13  single    0.930  0.020  1.080
 IDZ  C14  NAL  aromatic  1.373  0.020  1.373
 IDZ  N16  C17  aromatic  1.356  0.020  1.356
 IDZ  N16  NAI  aromatic  1.324  0.020  1.324
 IDZ  N16  H16  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
 IDZ  H1   C1   C17  121.67  3.000
 IDZ  H1   C1   C2   121.74  3.000
 IDZ  C17  C1   C2   116.59  3.000
 IDZ  H2   C2   C3   119.02  3.000
 IDZ  H2   C2   C1   119.20  3.000
 IDZ  C3   C2   C1   121.79  3.000
 IDZ  H3   C3   C4   119.67  3.000
 IDZ  H3   C3   C2   118.96  3.000
 IDZ  C4   C3   C2   121.37  3.000
 IDZ  H4   C4   C5   120.73  3.000
 IDZ  H4   C4   C3   121.26  3.000
 IDZ  C5   C4   C3   118.00  3.000
 IDZ  C17  C5   C6   103.81  3.000
 IDZ  C17  C5   C4   119.79  3.000
 IDZ  C6   C5   C4   136.40  3.000
 IDZ  NAI  C6   C7   120.67  3.000
 IDZ  NAI  C6   C5   110.70  3.000
 IDZ  C7   C6   C5   128.63  3.000
 IDZ  NAL  C7   N8   112.99  3.000
 IDZ  NAL  C7   C6   124.97  3.000
 IDZ  N8   C7   C6   122.04  3.000
 IDZ  H8   N8   C9   127.01  3.000
 IDZ  H8   N8   C7   125.76  3.000
 IDZ  C9   N8   C7   107.23  3.000
 IDZ  C14  C9   C10  122.56  3.000
 IDZ  C14  C9   N8   104.70  3.000
 IDZ  C10  C9   N8   132.74  3.000
 IDZ  H10  C10  C11  121.51  3.000
 IDZ  H10  C10  C9   121.83  3.000
 IDZ  C11  C10  C9   116.65  3.000
 IDZ  H11  C11  C12  119.16  3.000
 IDZ  H11  C11  C10  119.28  3.000
 IDZ  C12  C11  C10  121.56  3.000
 IDZ  H12  C12  C13  119.46  3.000
 IDZ  H12  C12  C11  119.10  3.000
 IDZ  C13  C12  C11  121.45  3.000
 IDZ  H13  C13  C14  120.84  3.000
 IDZ  H13  C13  C12  121.25  3.000
 IDZ  C14  C13  C12  117.91  3.000
 IDZ  NAL  C14  C13  130.11  3.000
 IDZ  NAL  C14  C9   110.02  3.000
 IDZ  C13  C14  C9   119.87  3.000
 IDZ  H16  N16  NAI  119.57  3.000
 IDZ  H16  N16  C17  127.89  3.000
 IDZ  NAI  N16  C17  112.54  3.000
 IDZ  N16  C17  C5   106.01  3.000
 IDZ  N16  C17  C1   131.54  3.000
 IDZ  C5   C17  C1   122.45  3.000
 IDZ  C14  NAL  C7   105.06  3.000
 IDZ  N16  NAI  C6   106.95  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
 IDZ  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 IDZ  CONST_02  C4   C5   C17  C1     0.00  0.0  0
 IDZ  CONST_03  C6   C5   C17  C1   180.00  0.0  0
 IDZ  CONST_04  NAI  N16  C17  C1   180.00  0.0  0
 IDZ  CONST_05  C5   C17  C1   C2     0.00  0.0  0
 IDZ  CONST_06  N16  C17  C1   C2   180.00  0.0  0
 IDZ  CONST_07  C5   C4   C3   C2     0.00  0.0  0
 IDZ  CONST_08  C17  C1   C2   C3     0.00  0.0  0
 IDZ  CONST_09  C6   C5   C4   C3   180.00  0.0  0
 IDZ  CONST_10  C17  C5   C4   C3     0.00  0.0  0
 IDZ  CONST_11  C7   C6   C5   C4     0.00  0.0  0
 IDZ  CONST_12  NAI  C6   C5   C4   180.00  0.0  0
 IDZ  CONST_13  N16  C17  C5   C4   180.00  0.0  0
 IDZ  CONST_14  N8   C7   C6   C5   180.00  0.0  0
 IDZ  CONST_15  NAL  C7   C6   C5     0.00  0.0  0
 IDZ  CONST_16  N16  NAI  C6   C5     0.00  0.0  0
 IDZ  CONST_17  NAI  N16  C17  C5     0.00  0.0  0
 IDZ  CONST_18  N16  C17  C5   C6     0.00  0.0  0
 IDZ  CONST_19  C9   N8   C7   C6   180.00  0.0  0
 IDZ  CONST_20  C14  NAL  C7   C6   180.00  0.0  0
 IDZ  CONST_21  C17  N16  NAI  C6     0.00  0.0  0
 IDZ  CONST_22  C17  C5   C6   C7   180.00  0.0  0
 IDZ  CONST_23  N16  NAI  C6   C7   180.00  0.0  0
 IDZ  CONST_24  C10  C9   N8   C7   180.00  0.0  0
 IDZ  CONST_25  C14  C9   N8   C7     0.00  0.0  0
 IDZ  CONST_26  C9   C14  NAL  C7     0.00  0.0  0
 IDZ  CONST_27  C13  C14  NAL  C7   180.00  0.0  0
 IDZ  CONST_28  NAI  C6   C7   N8     0.00  0.0  0
 IDZ  CONST_29  C14  NAL  C7   N8     0.00  0.0  0
 IDZ  CONST_30  C11  C10  C9   N8   180.00  0.0  0
 IDZ  CONST_31  C13  C14  C9   N8   180.00  0.0  0
 IDZ  CONST_32  NAL  C14  C9   N8     0.00  0.0  0
 IDZ  CONST_33  NAL  C7   N8   C9     0.00  0.0  0
 IDZ  CONST_34  C12  C11  C10  C9     0.00  0.0  0
 IDZ  CONST_35  C12  C13  C14  C9     0.00  0.0  0
 IDZ  CONST_36  C13  C14  C9   C10    0.00  0.0  0
 IDZ  CONST_37  NAL  C14  C9   C10  180.00  0.0  0
 IDZ  CONST_38  C13  C12  C11  C10    0.00  0.0  0
 IDZ  CONST_39  C14  C9   C10  C11    0.00  0.0  0
 IDZ  CONST_40  C14  C13  C12  C11    0.00  0.0  0
 IDZ  CONST_41  NAL  C14  C13  C12  180.00  0.0  0
 IDZ  CONST_42  NAI  C6   C5   C17    0.00  0.0  0
 IDZ  CONST_43  NAI  C6   C7   NAL  180.00  0.0  0
 IDZ  CONST_44  H3   C3   C2   C1   180.00  0.0  0
 IDZ  CONST_45  H16  N16  C17  C1     0.00  0.0  0
 IDZ  CONST_46  H4   C4   C3   C2   180.00  0.0  0
 IDZ  CONST_47  H1   C1   C2   C3   180.00  0.0  0
 IDZ  CONST_48  H2   C2   C3   C4   180.00  0.0  0
 IDZ  CONST_49  H8   N8   C7   C6     0.00  0.0  0
 IDZ  CONST_50  H10  C10  C9   N8     0.00  0.0  0
 IDZ  CONST_51  H11  C11  C10  C9   180.00  0.0  0
 IDZ  CONST_52  H13  C13  C14  C9   180.00  0.0  0
 IDZ  CONST_53  H12  C12  C11  C10  180.00  0.0  0

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
 IDZ  plan-1  C1   0.020
 IDZ  plan-1  C2   0.020
 IDZ  plan-1  C3   0.020
 IDZ  plan-1  C4   0.020
 IDZ  plan-1  C5   0.020
 IDZ  plan-1  C6   0.020
 IDZ  plan-1  C7   0.020
 IDZ  plan-1  N16  0.020
 IDZ  plan-1  C17  0.020
 IDZ  plan-1  NAI  0.020
 IDZ  plan-1  H1   0.020
 IDZ  plan-1  H2   0.020
 IDZ  plan-1  H3   0.020
 IDZ  plan-1  H4   0.020
 IDZ  plan-1  H16  0.020
 IDZ  plan-2  C6   0.020
 IDZ  plan-2  C7   0.020
 IDZ  plan-2  N8   0.020
 IDZ  plan-2  C9   0.020
 IDZ  plan-2  C10  0.020
 IDZ  plan-2  C11  0.020
 IDZ  plan-2  C12  0.020
 IDZ  plan-2  C13  0.020
 IDZ  plan-2  C14  0.020
 IDZ  plan-2  NAL  0.020
 IDZ  plan-2  H8   0.020
 IDZ  plan-2  H10  0.020
 IDZ  plan-2  H11  0.020
 IDZ  plan-2  H12  0.020
 IDZ  plan-2  H13  0.020

