# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 21:44:42 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-chloranyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)C(=O)Nc2ccc3nc(CN4CCCCC4)[nH]c3c2
#
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
 M7Z  M7Z  4-chloranyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide  ligand  47  26  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M7Z
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
 M7Z  C1   C   CR16  0  -0.197   6.8229  -0.5764  -0.7428
 M7Z  C2   C   CR16  0  -0.269   5.4617  -0.7415  -0.9311
 M7Z  N2   N   NT    0  -0.410  -5.9107  -0.3424  -0.3039
 M7Z  C3   C   CR6   0  -0.027   4.5512   0.1676  -0.3973
 M7Z  C4   C   CR16  0  -0.298   5.0314   1.2682   0.3086
 M7Z  C5   C   CR16  0  -0.194   6.3925   1.4529   0.4938
 M7Z  C6   C   C     0   0.528   3.0980  -0.0632  -0.6588
 M7Z  C7   C   CR6   0   0.363   0.8586   0.4411   0.3022
 M7Z  C8   C   CR16  0  -0.369   0.2725   1.0749   1.4188
 M7Z  C9   C   CR16  0  -0.325  -1.0946   1.1760   1.5695
 M7Z  C10  C   CR56  0   0.116  -1.9092   0.6317   0.5792
 M7Z  C11  C   CR5   0   0.440  -3.5078  -0.0445  -0.6510
 M7Z  C12  C   CH2   0  -0.369  -4.8429  -0.3063  -1.2700
 M7Z  C13  C   CH2   0  -0.279  -7.2052  -0.2282  -0.9569
 M7Z  C14  C   CH2   0  -0.441  -8.3317  -0.1579   0.0616
 M7Z  C15  C   CH2   0  -0.439  -8.3007  -1.3610   0.9950
 M7Z  C16  C   CH2   0  -0.439  -6.9156  -1.5037   1.6112
 M7Z  C17  C   CH2   0  -0.281  -5.8423  -1.5288   0.5352
 M7Z  C18  C   CR56  0   0.373  -1.3097  -0.0019  -0.5182
 M7Z  C19  C   CR16  0  -0.399   0.0639  -0.1170  -0.6929
 M7Z  O    O   O     0  -0.463   2.7310  -0.6662  -1.6539
 M7Z  C    C   CR6   0  -0.040   7.2769   0.5232  -0.0294
 M7Z  CL   CL  CL    0  -0.114   8.9762   0.7417   0.2045
 M7Z  N    N   NH1   0  -0.757   2.2607   0.4286   0.2835
 M7Z  N3   N   NR15  0  -0.709  -2.3629  -0.4276  -1.2800
 M7Z  N1   N   N     0  -0.459  -3.2790   0.5912   0.4636
 M7Z  H1   H   HCR6  0   0.287   7.5204  -1.2957  -1.1494
 M7Z  H2   H   HCR6  0   0.273   5.1088  -1.5960  -1.4923
 M7Z  H4   H   HCR6  0   0.272   4.3605   2.0197   0.7056
 M7Z  H5   H   HCR6  0   0.289   6.7545   2.3171   1.0328
 M7Z  H6   H   HCR6  0   0.267   0.9176   1.4975   2.1799
 M7Z  H7   H   HCR6  0   0.258  -1.5170   1.6682   2.4356
 M7Z  H8   H   HCH2  0   0.224  -4.7828  -1.2280  -1.8745
 M7Z  H9   H   HCH2  0   0.276  -5.0403   0.5027  -1.9817
 M7Z  H10  H   HCH2  0   0.236  -7.2056   0.6762  -1.5708
 M7Z  H11  H   HCH2  0   0.186  -7.3852  -1.0751  -1.6436
 M7Z  H12  H   HCH2  0   0.216  -8.2289   0.7623   0.6450
 M7Z  H13  H   HCH2  0   0.231  -9.2871  -0.0973  -0.4642
 M7Z  H14  H   HCH2  0   0.231  -9.0612  -1.2636   1.7727
 M7Z  H15  H   HCH2  0   0.210  -8.5442  -2.2683   0.4321
 M7Z  H16  H   HCH2  0   0.216  -6.7254  -0.6644   2.2871
 M7Z  H17  H   HCH2  0   0.231  -6.8476  -2.4153   2.2091
 M7Z  H18  H   HCH2  0   0.186  -5.9505  -2.4464  -0.0715
 M7Z  H19  H   HCH2  0   0.241  -4.8574  -1.5756   1.0033
 M7Z  H20  H   HCR6  0   0.290   0.4799  -0.6122  -1.5543
 M7Z  H21  H   HNH1  0   0.422   2.6883   0.8165   1.1100
 M7Z  H22  H   HNR5  0   0.417  -2.3083  -0.9400  -2.1464

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
 M7Z  CL   C    single    1.729  0.020  1.729
 M7Z  C5   C    aromatic  1.386  0.020  1.386
 M7Z  C5   C4   aromatic  1.386  0.020  1.386
 M7Z  C    C1   aromatic  1.387  0.020  1.387
 M7Z  C4   C3   aromatic  1.393  0.020  1.393
 M7Z  C1   C2   aromatic  1.384  0.020  1.384
 M7Z  O    C6   double    1.220  0.020  1.220
 M7Z  C3   C2   aromatic  1.393  0.020  1.393
 M7Z  C3   C6   single    1.494  0.020  1.494
 M7Z  C6   N    single    1.353  0.020  1.353
 M7Z  N    C7   single    1.402  0.020  1.402
 M7Z  C19  C7   aromatic  1.390  0.020  1.390
 M7Z  C19  C18  aromatic  1.389  0.020  1.389
 M7Z  C7   C8   aromatic  1.411  0.020  1.411
 M7Z  N3   C18  aromatic  1.368  0.020  1.368
 M7Z  N3   C11  aromatic  1.361  0.020  1.361
 M7Z  C18  C10  aromatic  1.402  0.020  1.402
 M7Z  C8   C9   aromatic  1.379  0.020  1.379
 M7Z  C11  C12  single    1.495  0.020  1.495
 M7Z  C11  N1   aromatic  1.303  0.020  1.303
 M7Z  C10  C9   aromatic  1.393  0.020  1.393
 M7Z  C10  N1   aromatic  1.375  0.020  1.375
 M7Z  C12  N2   single    1.440  0.020  1.440
 M7Z  C17  N2   single    1.455  0.020  1.455
 M7Z  C17  C16  single    1.520  0.020  1.520
 M7Z  N2   C13  single    1.454  0.020  1.454
 M7Z  C16  C15  single    1.523  0.020  1.523
 M7Z  C13  C14  single    1.520  0.020  1.520
 M7Z  C15  C14  single    1.523  0.020  1.523
 M7Z  C1   H1   single    0.930  0.020  1.080
 M7Z  C2   H2   single    0.930  0.020  1.080
 M7Z  C4   H4   single    0.930  0.020  1.080
 M7Z  C5   H5   single    0.930  0.020  1.080
 M7Z  C8   H6   single    0.930  0.020  1.080
 M7Z  C9   H7   single    0.930  0.020  1.080
 M7Z  C12  H8   single    0.970  0.020  1.090
 M7Z  C12  H9   single    0.970  0.020  1.090
 M7Z  C13  H10  single    0.970  0.020  1.090
 M7Z  C13  H11  single    0.970  0.020  1.090
 M7Z  C14  H12  single    0.970  0.020  1.090
 M7Z  C14  H13  single    0.970  0.020  1.090
 M7Z  C15  H14  single    0.970  0.020  1.090
 M7Z  C15  H15  single    0.970  0.020  1.090
 M7Z  C16  H16  single    0.970  0.020  1.090
 M7Z  C16  H17  single    0.970  0.020  1.090
 M7Z  C17  H18  single    0.970  0.020  1.090
 M7Z  C17  H19  single    0.970  0.020  1.090
 M7Z  C19  H20  single    0.930  0.020  1.080
 M7Z  N    H21  single    0.860  0.020  1.020
 M7Z  N3   H22  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
 M7Z  H1   C1   C    120.64  3.000
 M7Z  H1   C1   C2   120.26  3.000
 M7Z  C    C1   C2   119.10  3.000
 M7Z  H2   C2   C3   120.08  3.000
 M7Z  H2   C2   C1   119.06  3.000
 M7Z  C3   C2   C1   120.86  3.000
 M7Z  C17  N2   C13  111.40  3.000
 M7Z  C13  N2   C12  110.90  3.000
 M7Z  C17  N2   C12  111.86  3.000
 M7Z  C6   C3   C4   123.09  3.000
 M7Z  C6   C3   C2   117.89  3.000
 M7Z  C4   C3   C2   118.98  3.000
 M7Z  H4   C4   C5   117.84  3.000
 M7Z  H4   C4   C3   121.37  3.000
 M7Z  C5   C4   C3   120.77  3.000
 M7Z  H5   C5   C    120.72  3.000
 M7Z  H5   C5   C4   120.14  3.000
 M7Z  C    C5   C4   119.14  3.000
 M7Z  N    C6   O    124.16  3.000
 M7Z  N    C6   C3   115.07  3.000
 M7Z  O    C6   C3   120.77  3.000
 M7Z  N    C7   C19  123.94  3.000
 M7Z  C19  C7   C8   120.60  3.000
 M7Z  N    C7   C8   115.45  3.000
 M7Z  H6   C8   C9   119.00  3.000
 M7Z  H6   C8   C7   118.92  3.000
 M7Z  C9   C8   C7   122.08  3.000
 M7Z  H7   C9   C10  121.23  3.000
 M7Z  H7   C9   C8   120.52  3.000
 M7Z  C10  C9   C8   118.25  3.000
 M7Z  N1   C10  C18  110.30  3.000
 M7Z  N1   C10  C9   130.82  3.000
 M7Z  C18  C10  C9   118.88  3.000
 M7Z  N1   C11  N3   112.62  3.000
 M7Z  N1   C11  C12  126.61  3.000
 M7Z  N3   C11  C12  120.70  3.000
 M7Z  H9   C12  H8   105.70  3.000
 M7Z  H9   C12  C11  107.50  3.000
 M7Z  H8   C12  C11  108.93  3.000
 M7Z  H9   C12  N2   108.71  3.000
 M7Z  H8   C12  N2   112.76  3.000
 M7Z  C11  C12  N2   112.88  3.000
 M7Z  H11  C13  H10  106.56  3.000
 M7Z  H11  C13  C14  109.33  3.000
 M7Z  H10  C13  C14  109.74  3.000
 M7Z  H11  C13  N2   111.33  3.000
 M7Z  H10  C13  N2   108.52  3.000
 M7Z  C14  C13  N2   111.24  3.000
 M7Z  H13  C14  H12  106.99  3.000
 M7Z  H13  C14  C15  110.89  3.000
 M7Z  H12  C14  C15  109.61  3.000
 M7Z  H13  C14  C13  109.16  3.000
 M7Z  H12  C14  C13  109.06  3.000
 M7Z  C15  C14  C13  111.04  3.000
 M7Z  H15  C15  H14  106.56  3.000
 M7Z  H15  C15  C16  109.43  3.000
 M7Z  H14  C15  C16  110.71  3.000
 M7Z  H15  C15  C14  109.57  3.000
 M7Z  H14  C15  C14  110.60  3.000
 M7Z  C16  C15  C14  109.91  3.000
 M7Z  H17  C16  H16  106.93  3.000
 M7Z  H17  C16  C17  109.25  3.000
 M7Z  H16  C16  C17  109.10  3.000
 M7Z  H17  C16  C15  110.88  3.000
 M7Z  H16  C16  C15  109.64  3.000
 M7Z  C17  C16  C15  110.94  3.000
 M7Z  H19  C17  H18  106.75  3.000
 M7Z  H19  C17  C16  109.53  3.000
 M7Z  H18  C17  C16  109.46  3.000
 M7Z  H19  C17  N2   108.95  3.000
 M7Z  H18  C17  N2   110.84  3.000
 M7Z  C16  C17  N2   111.20  3.000
 M7Z  N3   C18  C19  131.71  3.000
 M7Z  N3   C18  C10  104.32  3.000
 M7Z  C19  C18  C10  123.96  3.000
 M7Z  H20  C19  C18  121.36  3.000
 M7Z  H20  C19  C7   122.42  3.000
 M7Z  C18  C19  C7   116.22  3.000
 M7Z  CL   C    C5   119.43  3.000
 M7Z  C5   C    C1   121.14  3.000
 M7Z  CL   C    C1   119.43  3.000
 M7Z  H21  N    C7   114.19  3.000
 M7Z  H21  N    C6   116.64  3.000
 M7Z  C7   N    C6   129.14  3.000
 M7Z  H22  N3   C18  126.53  3.000
 M7Z  H22  N3   C11  125.85  3.000
 M7Z  C18  N3   C11  107.62  3.000
 M7Z  C11  N1   C10  105.14  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
 M7Z  CONST_01  C4   C5   C    C1     0.00   0.0  0
 M7Z  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 M7Z  CONST_03  C5   C    C1   C2     0.00   0.0  0
 M7Z  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 M7Z  CONST_05  C    C5   C4   C3     0.00   0.0  0
 M7Z  CONST_06  C    C1   C2   C3     0.00   0.0  0
 M7Z  CONST_07  N3   C18  C19  C7   180.00   0.0  0
 M7Z  CONST_08  C10  C18  C19  C7     0.00   0.0  0
 M7Z  CONST_09  C10  C9   C8   C7     0.00   0.0  0
 M7Z  CONST_10  C18  C19  C7   C8     0.00   0.0  0
 M7Z  CONST_11  C18  C10  C9   C8     0.00   0.0  0
 M7Z  CONST_12  N1   C10  C9   C8   180.00   0.0  0
 M7Z  CONST_13  C19  C7   C8   C9     0.00   0.0  0
 M7Z  CONST_14  C19  C18  C10  C9     0.00   0.0  0
 M7Z  CONST_15  N3   C18  C10  C9   180.00   0.0  0
 M7Z  CONST_16  C11  N1   C10  C9   180.00   0.0  0
 M7Z  CONST_17  C11  N3   C18  C10    0.00   0.0  0
 M7Z  CONST_18  N3   C11  N1   C10    0.00   0.0  0
 M7Z  CONST_19  C19  C18  N3   C11  180.00   0.0  0
 M7Z  CONST_20  C18  C10  N1   C11    0.00   0.0  0
 M7Z  CONST_21  N1   C11  N3   C18    0.00   0.0  0
 M7Z  CONST_22  N1   C10  C18  C19  180.00   0.0  0
 M7Z  CONST_23  N1   C10  C18  N3     0.00   0.0  0
 M7Z  CONST_24  C6   C3   C2   C1   180.00   0.0  0
 M7Z  CONST_25  CL   C    C1   C2   180.00   0.0  0
 M7Z  CONST_26  CL   C    C5   C4   180.00   0.0  0
 M7Z  CONST_27  C6   C3   C4   C5   180.00   0.0  0
 M7Z  CONST_28  N    C7   C8   C9   180.00   0.0  0
 M7Z  CONST_29  C12  C11  N1   C10  180.00   0.0  0
 M7Z  CONST_30  C18  N3   C11  C12  180.00   0.0  0
 M7Z  CONST_31  N    C7   C19  C18  180.00   0.0  0
 M7Z  CONST_32  H5   C5   C    C1   180.00   0.0  0
 M7Z  CONST_33  H4   C4   C3   C2   180.00   0.0  0
 M7Z  CONST_34  H1   C1   C2   C3   180.00   0.0  0
 M7Z  CONST_35  H2   C2   C3   C4   180.00   0.0  0
 M7Z  CONST_36  H7   C9   C8   C7   180.00   0.0  0
 M7Z  CONST_37  H20  C19  C7   C8   180.00   0.0  0
 M7Z  CONST_38  H22  N3   C18  C10  180.00   0.0  0
 M7Z  CONST_39  H6   C8   C9   C10  180.00   0.0  0
 M7Z  CONST_40  C7   N    C6   C3   180.00   0.0  0
 M7Z  CONST_41  C19  C7   N    C6     0.00   0.0  0
 M7Z  CONST_42  C8   C7   N    C6   180.00   0.0  0
 M7Z  CONST_43  H21  N    C7   C8     0.00   0.0  0
 M7Z  CONST_44  O    C6   N    C7     0.00   0.0  0
 M7Z  Var_01    C15  C16  C17  N2    56.40  30.0  1
 M7Z  Var_02    C15  C14  C13  N2   -56.09  30.0  1
 M7Z  Var_03    C16  C17  N2   C13  -59.24  30.0  1
 M7Z  Var_04    C16  C15  C14  C13   52.89  30.0  1
 M7Z  Var_05    C17  N2   C13  C14   59.07  30.0  1
 M7Z  Var_06    C17  C16  C15  C14  -53.03  30.0  1
 M7Z  Var_07    N3   C11  C12  N2   156.74  30.0  1
 M7Z  Var_08    O    C6   C3   C2   -26.81  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
 M7Z  plan-1  C1   0.020
 M7Z  plan-1  C2   0.020
 M7Z  plan-1  C3   0.020
 M7Z  plan-1  C4   0.020
 M7Z  plan-1  C5   0.020
 M7Z  plan-1  C6   0.020
 M7Z  plan-1  C    0.020
 M7Z  plan-1  CL   0.020
 M7Z  plan-1  H1   0.020
 M7Z  plan-1  H2   0.020
 M7Z  plan-1  H4   0.020
 M7Z  plan-1  H5   0.020
 M7Z  plan-2  C7   0.020
 M7Z  plan-2  C8   0.020
 M7Z  plan-2  C9   0.020
 M7Z  plan-2  C10  0.020
 M7Z  plan-2  C11  0.020
 M7Z  plan-2  C12  0.020
 M7Z  plan-2  C18  0.020
 M7Z  plan-2  C19  0.020
 M7Z  plan-2  N    0.020
 M7Z  plan-2  N3   0.020
 M7Z  plan-2  N1   0.020
 M7Z  plan-2  H6   0.020
 M7Z  plan-2  H7   0.020
 M7Z  plan-2  H20  0.020
 M7Z  plan-2  H22  0.020
 M7Z  plan-3  C3   0.020
 M7Z  plan-3  C6   0.020
 M7Z  plan-3  C7   0.020
 M7Z  plan-3  O    0.020
 M7Z  plan-3  N    0.020
 M7Z  plan-3  H21  0.020

