# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:59:58 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N-[(5,6-dichloro-1H-benzimidazol-2-yl)carbonyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)c1[nH]c2cc(Cl)c(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
 42Z  42Z  N-[(5,6-dichloro-1H-benzimidazol-2-yl)carbonyl]glycine  ligand  24  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_42Z
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
 42Z  C1    C   CR16   0  -0.295  -1.6619   1.3186   0.0079
 42Z  C2    C   CR56   0   0.162  -0.6944   0.3162   0.0103
 42Z  C3    C   CR56   0   0.355  -1.0792  -1.0358   0.0143
 42Z  C4    C   CR16   0  -0.265  -2.4097  -1.4323   0.0151
 42Z  C5    C   CR6    0  -0.020  -3.3548  -0.4264   0.0126
 42Z  C6    C   CR6    0  -0.011  -2.9858   0.9341   0.0091
 42Z  N13   N   NR15   0  -0.689   0.0914  -1.7318   0.0179
 42Z  C14   C   CR5    0   0.355   1.0925  -0.8205   0.0155
 42Z  N15   N   N      0  -0.465   0.6698   0.4140   0.0108
 42Z  C24   C   C      0   0.490   2.5148  -1.2624   0.0205
 42Z  N26   N   NH1    0  -0.632   3.3914  -0.2686   0.0108
 42Z  C28   C   C      0   0.402   5.5335   0.9241  -0.0079
 42Z  O30   O   OC    -1  -0.606   6.7741   0.8736   0.0001
 42Z  O32   O   O      0  -0.597   4.8093   1.9372  -0.0325
 42Z  O34   O   O      0  -0.491   2.7831  -2.4582   0.0333
 42Z  C43   C   CH2    0  -0.415   4.8203  -0.4448   0.0140
 42Z  H1    H   HCR6   0   0.291  -1.3852   2.3641   0.0051
 42Z  H4    H   HCR6   0   0.301  -2.7018  -2.4733   0.0191
 42Z  HN26  H   HNH1   0   0.397   3.0713   0.6924  -0.0026
 42Z  H43   H   HCH2   0   0.249   5.1414  -1.0007   0.9000
 42Z  H43A  H   HCH2   0   0.249   5.1410  -1.0282  -0.8543
 42Z  HN13  H   HNR5   0   0.429   0.2093  -2.7341   0.0189
 42Z  CL3   CL  CL     0  -0.100  -4.2094   2.1516   0.0074
 42Z  CL4   CL  CL     0  -0.095  -5.0236  -0.8598   0.0141

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
 42Z  C2   C1    aromatic  1.393  0.020  1.393
 42Z  C1   C6    aromatic  1.379  0.020  1.379
 42Z  C1   H1    single    0.930  0.020  1.080
 42Z  C3   C2    aromatic  1.406  0.020  1.406
 42Z  N15  C2    aromatic  1.368  0.020  1.368
 42Z  N13  C3    aromatic  1.362  0.020  1.362
 42Z  C3   C4    aromatic  1.388  0.020  1.388
 42Z  C6   CL3   single    1.726  0.020  1.726
 42Z  C4   C5    aromatic  1.380  0.020  1.380
 42Z  C4   H4    single    0.930  0.020  1.080
 42Z  C5   CL4   single    1.724  0.020  1.724
 42Z  C5   C6    aromatic  1.410  0.020  1.410
 42Z  N13  C14   aromatic  1.354  0.020  1.354
 42Z  C24  C14   single    1.489  0.020  1.489
 42Z  C14  N15   aromatic  1.305  0.020  1.305
 42Z  N26  C24   single    1.325  0.020  1.325
 42Z  C24  O34   double    1.226  0.020  1.226
 42Z  C43  N26   single    1.440  0.020  1.440
 42Z  N26  HN26  single    0.860  0.020  1.020
 42Z  O32  C28   deloc     1.246  0.020  1.246
 42Z  O30  C28   deloc     1.242  0.020  1.242
 42Z  C28  C43   single    1.544  0.020  1.544
 42Z  C43  H43   single    0.970  0.020  1.090
 42Z  C43  H43A  single    0.970  0.020  1.090
 42Z  N13  HN13  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
 42Z  H1    C1   C6   121.02  3.000
 42Z  H1    C1   C2   121.19  3.000
 42Z  C6    C1   C2   117.79  3.000
 42Z  N15   C2   C3   109.99  3.000
 42Z  N15   C2   C1   129.88  3.000
 42Z  C3    C2   C1   120.13  3.000
 42Z  N13   C3   C4   132.67  3.000
 42Z  C4    C3   C2   122.48  3.000
 42Z  N13   C3   C2   104.85  3.000
 42Z  H4    C4   C5   121.11  3.000
 42Z  H4    C4   C3   122.27  3.000
 42Z  C5    C4   C3   116.62  3.000
 42Z  C6    C5   CL4  119.74  3.000
 42Z  C6    C5   C4   121.61  3.000
 42Z  CL4   C5   C4   118.66  3.000
 42Z  C5    C6   CL3  119.68  3.000
 42Z  C5    C6   C1   121.37  3.000
 42Z  CL3   C6   C1   118.95  3.000
 42Z  HN13  N13  C14  125.60  3.000
 42Z  HN13  N13  C3   127.44  3.000
 42Z  C14   N13  C3   106.95  3.000
 42Z  C24   C14  N15  126.16  3.000
 42Z  N15   C14  N13  113.41  3.000
 42Z  C24   C14  N13  120.43  3.000
 42Z  C14   N15  C2   104.80  3.000
 42Z  O34   C24  N26  125.94  3.000
 42Z  O34   C24  C14  119.90  3.000
 42Z  N26   C24  C14  114.15  3.000
 42Z  HN26  N26  C43  115.45  3.000
 42Z  HN26  N26  C24  120.17  3.000
 42Z  C43   N26  C24  124.38  3.000
 42Z  C43   C28  O32  116.93  3.000
 42Z  C43   C28  O30  115.18  3.000
 42Z  O32   C28  O30  127.88  3.000
 42Z  H43A  C43  H43  106.60  3.000
 42Z  H43A  C43  C28  109.03  3.000
 42Z  H43   C43  C28  109.06  3.000
 42Z  H43A  C43  N26  110.75  3.000
 42Z  H43   C43  N26  110.81  3.000
 42Z  C28   C43  N26  110.49  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
 42Z  CONST_01  N13   C3   C2   C1   180.00   0.0  0
 42Z  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 42Z  CONST_03  C14   N15  C2   C1   180.00   0.0  0
 42Z  CONST_04  C4    C5   C6   C1     0.00   0.0  0
 42Z  CONST_05  C5    C6   C1   C2     0.00   0.0  0
 42Z  CONST_06  C14   N13  C3   C2     0.00   0.0  0
 42Z  CONST_07  C5    C4   C3   C2     0.00   0.0  0
 42Z  CONST_08  N13   C14  N15  C2     0.00   0.0  0
 42Z  CONST_09  C6    C1   C2   C3     0.00   0.0  0
 42Z  CONST_10  C14   N15  C2   C3     0.00   0.0  0
 42Z  CONST_11  N15   C14  N13  C3     0.00   0.0  0
 42Z  CONST_12  C6    C5   C4   C3     0.00   0.0  0
 42Z  CONST_13  N15   C2   C3   C4   180.00   0.0  0
 42Z  CONST_14  C14   N13  C3   C4   180.00   0.0  0
 42Z  CONST_15  N13   C3   C4   C5   180.00   0.0  0
 42Z  CONST_16  N15   C2   C1   C6   180.00   0.0  0
 42Z  CONST_17  N15   C2   C3   N13    0.00   0.0  0
 42Z  CONST_18  CL4   C5   C6   C1   180.00   0.0  0
 42Z  CONST_19  CL3   C6   C1   C2   180.00   0.0  0
 42Z  CONST_20  C24   C14  N15  C2   180.00   0.0  0
 42Z  CONST_21  C24   C14  N13  C3   180.00   0.0  0
 42Z  CONST_22  CL4   C5   C4   C3   180.00   0.0  0
 42Z  CONST_23  C4    C5   C6   CL3  180.00   0.0  0
 42Z  CONST_24  HN13  N13  C3   C2   180.00   0.0  0
 42Z  CONST_25  H4    C4   C3   C2   180.00   0.0  0
 42Z  CONST_26  H1    C1   C2   C3   180.00   0.0  0
 42Z  CONST_27  C43   N26  C24  C14  180.00   0.0  0
 42Z  CONST_28  HN26  N26  C24  C14    0.00   0.0  0
 42Z  CONST_29  C43   N26  C24  O34    0.00   0.0  0
 42Z  Var_01    N26   C24  C14  N13  179.68  30.0  2
 42Z  Var_02    C28   C43  N26  C24  179.68  30.0  2
 42Z  Var_03    O32   C28  C43  N26   -0.41  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
 42Z  plan-1  C1    0.020
 42Z  plan-1  C2    0.020
 42Z  plan-1  C3    0.020
 42Z  plan-1  C4    0.020
 42Z  plan-1  C5    0.020
 42Z  plan-1  C6    0.020
 42Z  plan-1  N13   0.020
 42Z  plan-1  C14   0.020
 42Z  plan-1  N15   0.020
 42Z  plan-1  C24   0.020
 42Z  plan-1  H1    0.020
 42Z  plan-1  H4    0.020
 42Z  plan-1  HN13  0.020
 42Z  plan-1  CL3   0.020
 42Z  plan-1  CL4   0.020
 42Z  plan-2  C14   0.020
 42Z  plan-2  C24   0.020
 42Z  plan-2  N26   0.020
 42Z  plan-2  O34   0.020
 42Z  plan-2  C43   0.020
 42Z  plan-2  HN26  0.020
 42Z  plan-3  C28   0.020
 42Z  plan-3  O30   0.020
 42Z  plan-3  O32   0.020
 42Z  plan-3  C43   0.020

