# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:15:38 2021
#   Inital geometry file: a 43 line input string
#   Ligand name: 2,5-dichloro-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1[nH]c2ccc(Cl)cc2n1
#
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
 WBD  WBD  2,5-dichloro-1H-benzimidazole  ligand  15  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WBD
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
 WBD  C1   C   CR56  0   0.151  64.3680  32.7716  -37.4927
 WBD  C2   C   CR5   0   0.373  63.3379  34.6041  -37.3916
 WBD  C3   C   CR16  0  -0.293  65.2466  31.7291  -37.7779
 WBD  C4   C   CR6   0  -0.049  65.0166  30.5293  -37.1360
 WBD  C5   C   CR16  0  -0.236  63.9602  30.3391  -36.2358
 WBD  N1   N   NR15  0  -0.666  62.6633  33.7892  -36.5508
 WBD  C6   C   CR16  0  -0.299  63.0855  31.3706  -35.9500
 WBD  CL1  CL  CL    0  -0.132  66.0778  29.1908  -37.4526
 WBD  C    C   CR56  0   0.365  63.3086  32.5805  -36.5915
 WBD  CL   CL  CL    0  -0.064  62.8386  36.2099  -37.6230
 WBD  N    N   N     0  -0.436  64.3547  34.0594  -37.9772
 WBD  H1   H   HCR6  0   0.284  66.0665  31.8587  -38.4709
 WBD  H2   H   HCR6  0   0.282  63.8281  29.3774  -35.7596
 WBD  H3   H   HNR5  0   0.435  61.8438  34.0258  -36.0126
 WBD  H4   H   HCR6  0   0.284  62.2687  31.2301  -35.2555

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
 WBD  N    C1  aromatic  1.376  0.020  1.376
 WBD  N    C2  aromatic  1.294  0.020  1.294
 WBD  C3   C1  aromatic  1.393  0.020  1.393
 WBD  C3   C4  aromatic  1.380  0.020  1.380
 WBD  CL   C2  single    1.697  0.020  1.697
 WBD  C1   C   aromatic  1.404  0.020  1.404
 WBD  CL1  C4  single    1.737  0.020  1.737
 WBD  C2   N1  aromatic  1.351  0.020  1.351
 WBD  C4   C5  aromatic  1.401  0.020  1.401
 WBD  C    N1  aromatic  1.371  0.020  1.371
 WBD  C    C6  aromatic  1.388  0.020  1.388
 WBD  C5   C6  aromatic  1.382  0.020  1.382
 WBD  C3   H1  single    0.930  0.020  1.080
 WBD  C5   H2  single    0.930  0.020  1.080
 WBD  N1   H3  single    0.860  0.020  1.020
 WBD  C6   H4  single    0.930  0.020  1.080

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
 WBD  N    C1  C   110.25  3.000
 WBD  C    C1  C3  120.36  3.000
 WBD  N    C1  C3  129.39  3.000
 WBD  N    C2  CL  124.60  3.000
 WBD  CL   C2  N1  120.56  3.000
 WBD  N    C2  N1  114.84  3.000
 WBD  H1   C3  C4  121.92  3.000
 WBD  H1   C3  C1  121.32  3.000
 WBD  C4   C3  C1  116.77  3.000
 WBD  CL1  C4  C5  118.24  3.000
 WBD  C5   C4  C3  122.86  3.000
 WBD  CL1  C4  C3  118.90  3.000
 WBD  H2   C5  C6  119.69  3.000
 WBD  H2   C5  C4  119.73  3.000
 WBD  C6   C5  C4  120.58  3.000
 WBD  H3   N1  C   127.25  3.000
 WBD  H3   N1  C2  126.59  3.000
 WBD  C    N1  C2  106.16  3.000
 WBD  H4   C6  C   122.12  3.000
 WBD  H4   C6  C5  120.92  3.000
 WBD  C    C6  C5  116.96  3.000
 WBD  C6   C   N1  132.80  3.000
 WBD  C6   C   C1  122.47  3.000
 WBD  N1   C   C1  104.73  3.000
 WBD  C2   N   C1  104.02  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
 WBD  CONST_01  N1   C2  N   C1    0.00  0.0  0
 WBD  CONST_02  C5   C4  C3  C1    0.00  0.0  0
 WBD  CONST_03  C2   N1  C   C1    0.00  0.0  0
 WBD  CONST_04  C5   C6  C   C1    0.00  0.0  0
 WBD  CONST_05  C3   C1  N   C2  180.00  0.0  0
 WBD  CONST_06  C    C1  N   C2    0.00  0.0  0
 WBD  CONST_07  C6   C   N1  C2  180.00  0.0  0
 WBD  CONST_08  N1   C   C1  C3  180.00  0.0  0
 WBD  CONST_09  C6   C   C1  C3    0.00  0.0  0
 WBD  CONST_10  C6   C5  C4  C3    0.00  0.0  0
 WBD  CONST_11  N    C1  C3  C4  180.00  0.0  0
 WBD  CONST_12  C    C1  C3  C4    0.00  0.0  0
 WBD  CONST_13  C    C6  C5  C4    0.00  0.0  0
 WBD  CONST_14  N1   C   C6  C5  180.00  0.0  0
 WBD  CONST_15  N    C1  C   N1    0.00  0.0  0
 WBD  CONST_16  N    C1  C   C6  180.00  0.0  0
 WBD  CONST_17  N    C2  N1  C     0.00  0.0  0
 WBD  CONST_18  CL   C2  N   C1  180.00  0.0  0
 WBD  CONST_19  CL1  C4  C3  C1  180.00  0.0  0
 WBD  CONST_20  CL1  C4  C5  C6  180.00  0.0  0
 WBD  CONST_21  CL   C2  N1  C   180.00  0.0  0
 WBD  CONST_22  H3   N1  C   C1  180.00  0.0  0
 WBD  CONST_23  H4   C6  C   C1  180.00  0.0  0
 WBD  CONST_24  H2   C5  C4  C3  180.00  0.0  0
 WBD  CONST_25  H1   C3  C4  C5  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
 WBD  plan-1  C1   0.020
 WBD  plan-1  C2   0.020
 WBD  plan-1  C3   0.020
 WBD  plan-1  C4   0.020
 WBD  plan-1  C5   0.020
 WBD  plan-1  N1   0.020
 WBD  plan-1  C6   0.020
 WBD  plan-1  CL1  0.020
 WBD  plan-1  C    0.020
 WBD  plan-1  CL   0.020
 WBD  plan-1  N    0.020
 WBD  plan-1  H1   0.020
 WBD  plan-1  H2   0.020
 WBD  plan-1  H3   0.020
 WBD  plan-1  H4   0.020

