# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:02:42 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: 3-nitro-N-[1-phenyl-5-(piperidin-1-ylmethyl)-1H-benzimidazol-2-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1nc2cc(CN3CCCCC3)ccc2n1c4ccccc4)c5cccc(c5)[N](=O)=O
#
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
 T20  T20  3-nitro-N-[1-phenyl-5-(piperidin-1-ylmethyl)-1H-benzimidazol-2-yl]benzamide  ligand  59  34  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T20
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
 T20  C1   C  CR16  0  -0.278  -0.8056  -2.5467   1.4767
 T20  C2   C  CR16  0  -0.249  -1.2363  -3.7924   1.9096
 T20  C3   C  CR16  0  -0.243  -0.9988  -4.9204   1.1351
 T20  C4   C  CR16  0  -0.253  -0.3366  -4.8027  -0.0799
 T20  C5   C  CR16  0  -0.260   0.0777  -3.5584  -0.5321
 T20  C6   C  CR6   0   0.231  -0.1583  -2.4354   0.2507
 T20  C7   C  CR16  0  -0.285   2.7903  -1.3993  -0.2970
 T20  C8   C  CR56  0   0.325   1.5685  -0.7535  -0.4197
 T20  C9   C  CR56  0   0.169   1.4646   0.5887  -0.8001
 T20  C10  C  CR16  0  -0.397   2.6155   1.3236  -1.0745
 T20  C11  C  CR6   0   0.072   3.8472   0.6978  -0.9676
 T20  C12  C  CR16  0  -0.298   3.9203  -0.6508  -0.5784
 T20  C13  C  CR16  0  -0.257  -4.5447  -0.7750   0.6172
 T20  C14  C  CR16  0  -0.234  -5.8762  -1.1110   0.8110
 T20  C15  C  CR16  0  -0.260  -6.8821  -0.3114   0.2978
 T20  C16  C  CR6   0   0.282  -6.5266   0.8343  -0.3996
 T20  C17  C  CR16  0  -0.288  -5.2061   1.1973  -0.5913
 T20  C18  C  CR6   0  -0.047  -4.2042   0.3752  -0.0907
 T20  N19  N  NR5   0  -0.671   0.2677  -1.1641  -0.2042
 T20  C20  C  CR5   0   0.704  -0.5198  -0.0753  -0.4751
 T20  N21  N  N     0  -0.474   0.1445   0.9798  -0.8320
 T20  N23  N  NH1   0  -0.774  -1.8863  -0.2070  -0.3660
 T20  C24  C  C     0   0.546  -2.7907   0.8159  -0.2958
 T20  O25  O  O     0  -0.415  -2.4974   1.9855  -0.3886
 T20  O27  O  O     0  -0.371  -7.2453   2.6531  -1.5880
 T20  O28  O  O     0  -0.370  -8.7233   1.3818  -0.7210
 T20  C30  C  CH2   0  -0.272   5.7007   1.9123   1.0039
 T20  C31  C  CH2   0  -0.436   6.7268   1.6750   2.1008
 T20  C32  C  CH2   0  -0.440   8.0944   2.2004   1.6858
 T20  C33  C  CH2   0  -0.438   8.4895   1.6096   0.3385
 T20  C34  C  CH2   0  -0.276   7.3992   1.8461  -0.6955
 T20  N35  N  NT    0  -0.411   6.1217   1.3150  -0.2522
 T20  H1   H  HCR6  0   0.287  -0.9615  -1.6685   2.0906
 T20  H2   H  HCR6  0   0.272  -1.7465  -3.8810   2.8594
 T20  H3   H  HCR6  0   0.269  -1.3271  -5.8917   1.4800
 T20  H4   H  HCR6  0   0.271  -0.1508  -5.6802  -0.6845
 T20  H5   H  HCR6  0   0.281   0.5769  -3.4581  -1.4875
 T20  H6   H  HCR6  0   0.267   2.8679  -2.4358   0.0045
 T20  H7   H  HCR6  0   0.250   2.5456   2.3677  -1.3559
 T20  H8   H  HCR6  0   0.246   4.8950  -1.1115  -0.4805
 T20  H9   H  HCR6  0   0.269  -3.7858  -1.4124   1.0543
 T20  H10  H  HCR6  0   0.292  -6.1314  -2.0010   1.3680
 T20  H11  H  HCR6  0   0.309  -7.9172  -0.5822   0.4447
 T20  H12  H  HCR6  0   0.306  -4.9467   2.0994  -1.1267
 T20  H13  H  HCH2  0   0.244   5.5361   1.0632  -2.2151
 T20  H14  H  HCH2  0   0.206   4.8634   2.5090  -1.4797
 T20  H15  H  HNH1  0   0.435  -2.2454  -1.1502  -0.4058
 T20  H16  H  HCH2  0   0.238   4.7436   1.4775   1.2977
 T20  H17  H  HCH2  0   0.181   5.5331   2.9995   0.8915
 T20  H18  H  HCH2  0   0.228   6.3874   2.1563   3.0207
 T20  H19  H  HCH2  0   0.214   6.7888   0.6020   2.3055
 T20  H20  H  HCH2  0   0.209   8.0529   3.2920   1.6034
 T20  H21  H  HCH2  0   0.230   8.8460   1.9719   2.4448
 T20  H22  H  HCH2  0   0.229   9.4245   2.0465  -0.0188
 T20  H23  H  HCH2  0   0.214   8.6587   0.5336   0.4416
 T20  H24  H  HCH2  0   0.181   7.3335   2.9284  -0.9096
 T20  H25  H  HCH2  0   0.231   7.6696   1.3584  -1.6357
 T20  C22  C  CH2   0  -0.321   5.1135   1.4521  -1.2825
 T20  N26  N  N     0   0.330  -7.5769   1.6874  -0.9439

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
 T20  C3   C4   aromatic  1.389  0.020  1.389
 T20  C3   C2   aromatic  1.389  0.020  1.389
 T20  C4   C5   aromatic  1.387  0.020  1.387
 T20  C2   C1   aromatic  1.387  0.020  1.387
 T20  O27  N26  double    1.207  0.020  1.207
 T20  O28  N26  double    1.207  0.020  1.207
 T20  C5   C6   aromatic  1.389  0.020  1.389
 T20  N26  C16  single    1.458  0.020  1.458
 T20  C1   C6   aromatic  1.391  0.020  1.391
 T20  C6   N19  single    1.416  0.020  1.416
 T20  C16  C17  aromatic  1.383  0.020  1.383
 T20  C16  C15  aromatic  1.388  0.020  1.388
 T20  C17  C18  aromatic  1.389  0.020  1.389
 T20  N19  C8   aromatic  1.381  0.020  1.381
 T20  N19  C20  aromatic  1.371  0.020  1.371
 T20  C15  C14  aromatic  1.384  0.020  1.384
 T20  C7   C8   aromatic  1.387  0.020  1.387
 T20  C7   C12  aromatic  1.384  0.020  1.384
 T20  N23  C20  single    1.377  0.020  1.377
 T20  N23  C24  single    1.367  0.020  1.367
 T20  C8   C9   aromatic  1.399  0.020  1.399
 T20  C20  N21  aromatic  1.297  0.020  1.297
 T20  C18  C24  single    1.495  0.020  1.495
 T20  C18  C13  aromatic  1.393  0.020  1.393
 T20  C12  C11  aromatic  1.406  0.020  1.406
 T20  C14  C13  aromatic  1.387  0.020  1.387
 T20  C24  O25  double    1.209  0.020  1.209
 T20  C9   N21  aromatic  1.377  0.020  1.377
 T20  C9   C10  aromatic  1.393  0.020  1.393
 T20  C11  C10  aromatic  1.386  0.020  1.386
 T20  C11  C22  single    1.507  0.020  1.507
 T20  C34  C33  single    1.521  0.020  1.521
 T20  C34  N35  single    1.453  0.020  1.453
 T20  C33  C32  single    1.523  0.020  1.523
 T20  C22  N35  single    1.448  0.020  1.448
 T20  N35  C30  single    1.453  0.020  1.453
 T20  C32  C31  single    1.523  0.020  1.523
 T20  C30  C31  single    1.521  0.020  1.521
 T20  C1   H1   single    0.930  0.020  1.080
 T20  C2   H2   single    0.930  0.020  1.080
 T20  C3   H3   single    0.930  0.020  1.080
 T20  C4   H4   single    0.930  0.020  1.080
 T20  C5   H5   single    0.930  0.020  1.080
 T20  C7   H6   single    0.930  0.020  1.080
 T20  C10  H7   single    0.930  0.020  1.080
 T20  C12  H8   single    0.930  0.020  1.080
 T20  C13  H9   single    0.930  0.020  1.080
 T20  C14  H10  single    0.930  0.020  1.080
 T20  C15  H11  single    0.930  0.020  1.080
 T20  C17  H12  single    0.930  0.020  1.080
 T20  C22  H13  single    0.970  0.020  1.090
 T20  C22  H14  single    0.970  0.020  1.090
 T20  N23  H15  single    0.860  0.020  1.020
 T20  C30  H16  single    0.970  0.020  1.090
 T20  C30  H17  single    0.970  0.020  1.090
 T20  C31  H18  single    0.970  0.020  1.090
 T20  C31  H19  single    0.970  0.020  1.090
 T20  C32  H20  single    0.970  0.020  1.090
 T20  C32  H21  single    0.970  0.020  1.090
 T20  C33  H22  single    0.970  0.020  1.090
 T20  C33  H23  single    0.970  0.020  1.090
 T20  C34  H24  single    0.970  0.020  1.090
 T20  C34  H25  single    0.970  0.020  1.090

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
 T20  H1   C1   C6   120.13  3.000
 T20  H1   C1   C2   120.44  3.000
 T20  C6   C1   C2   119.43  3.000
 T20  H2   C2   C3   120.25  3.000
 T20  H2   C2   C1   119.60  3.000
 T20  C3   C2   C1   120.15  3.000
 T20  H3   C3   C4   119.98  3.000
 T20  H3   C3   C2   119.98  3.000
 T20  C4   C3   C2   120.04  3.000
 T20  H4   C4   C5   119.61  3.000
 T20  H4   C4   C3   120.15  3.000
 T20  C5   C4   C3   120.24  3.000
 T20  H5   C5   C6   120.05  3.000
 T20  H5   C5   C4   120.56  3.000
 T20  C6   C5   C4   119.38  3.000
 T20  N19  C6   C5   119.58  3.000
 T20  N19  C6   C1   119.68  3.000
 T20  C5   C6   C1   120.74  3.000
 T20  H6   C7   C12  121.06  3.000
 T20  H6   C7   C8   122.25  3.000
 T20  C12  C7   C8   116.69  3.000
 T20  N19  C8   C9   104.94  3.000
 T20  C9   C8   C7   122.42  3.000
 T20  N19  C8   C7   132.63  3.000
 T20  N21  C9   C10  129.62  3.000
 T20  C10  C9   C8   119.89  3.000
 T20  N21  C9   C8   110.48  3.000
 T20  H7   C10  C11  120.83  3.000
 T20  H7   C10  C9   120.41  3.000
 T20  C11  C10  C9   118.75  3.000
 T20  C22  C11  C12  119.63  3.000
 T20  C22  C11  C10  120.31  3.000
 T20  C12  C11  C10  120.06  3.000
 T20  H8   C12  C11  118.70  3.000
 T20  H8   C12  C7   119.11  3.000
 T20  C11  C12  C7   122.18  3.000
 T20  H9   C13  C18  121.31  3.000
 T20  H9   C13  C14  118.27  3.000
 T20  C18  C13  C14  120.39  3.000
 T20  H10  C14  C15  119.70  3.000
 T20  H10  C14  C13  119.89  3.000
 T20  C15  C14  C13  120.40  3.000
 T20  H11  C15  C16  121.40  3.000
 T20  H11  C15  C14  120.09  3.000
 T20  C16  C15  C14  118.51  3.000
 T20  N26  C16  C17  118.84  3.000
 T20  C17  C16  C15  122.08  3.000
 T20  N26  C16  C15  119.08  3.000
 T20  H12  C17  C18  119.96  3.000
 T20  H12  C17  C16  121.14  3.000
 T20  C18  C17  C16  118.90  3.000
 T20  C24  C18  C17  117.26  3.000
 T20  C24  C18  C13  122.98  3.000
 T20  C17  C18  C13  119.70  3.000
 T20  C20  N19  C8   105.91  3.000
 T20  C20  N19  C6   127.14  3.000
 T20  C8   N19  C6   126.91  3.000
 T20  N23  C20  N21  127.44  3.000
 T20  N21  C20  N19  113.97  3.000
 T20  N23  C20  N19  118.58  3.000
 T20  C20  N21  C9   104.70  3.000
 T20  H15  N23  C24  117.75  3.000
 T20  H15  N23  C20  116.04  3.000
 T20  C24  N23  C20  126.08  3.000
 T20  O25  C24  N23  124.00  3.000
 T20  O25  C24  C18  121.67  3.000
 T20  N23  C24  C18  114.33  3.000
 T20  H17  C30  H16  106.63  3.000
 T20  H17  C30  N35  111.11  3.000
 T20  H16  C30  N35  108.84  3.000
 T20  H17  C30  C31  109.21  3.000
 T20  H16  C30  C31  109.60  3.000
 T20  N35  C30  C31  111.34  3.000
 T20  H19  C31  H18  106.99  3.000
 T20  H19  C31  C32  109.78  3.000
 T20  H18  C31  C32  110.89  3.000
 T20  H19  C31  C30  109.04  3.000
 T20  H18  C31  C30  109.21  3.000
 T20  C32  C31  C30  110.83  3.000
 T20  H21  C32  H20  106.66  3.000
 T20  H21  C32  C33  110.79  3.000
 T20  H20  C32  C33  109.26  3.000
 T20  H21  C32  C31  110.88  3.000
 T20  H20  C32  C31  109.29  3.000
 T20  C33  C32  C31  109.89  3.000
 T20  H23  C33  H22  106.97  3.000
 T20  H23  C33  C34  109.13  3.000
 T20  H22  C33  C34  109.21  3.000
 T20  H23  C33  C32  109.77  3.000
 T20  H22  C33  C32  110.87  3.000
 T20  C34  C33  C32  110.80  3.000
 T20  H25  C34  H24  106.55  3.000
 T20  H25  C34  N35  108.48  3.000
 T20  H24  C34  N35  111.39  3.000
 T20  H25  C34  C33  109.76  3.000
 T20  H24  C34  C33  109.06  3.000
 T20  N35  C34  C33  111.47  3.000
 T20  C34  N35  C30  111.61  3.000
 T20  C30  N35  C22  111.99  3.000
 T20  C34  N35  C22  111.13  3.000
 T20  H14  C22  H13  105.98  3.000
 T20  H14  C22  N35  112.05  3.000
 T20  H13  C22  N35  107.68  3.000
 T20  H14  C22  C11  109.04  3.000
 T20  H13  C22  C11  108.93  3.000
 T20  N35  C22  C11  112.89  3.000
 T20  O28  N26  O27  124.18  3.000
 T20  O28  N26  C16  117.83  3.000
 T20  O27  N26  C16  117.99  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
 T20  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 T20  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 T20  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 T20  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 T20  CONST_07  N19  C6   C1   C2   180.00   0.0  0
 T20  CONST_08  C6   C5   C4   C3     0.00   0.0  0
 T20  CONST_09  C6   C1   C2   C3     0.00   0.0  0
 T20  CONST_10  N19  C6   C5   C4   180.00   0.0  0
 T20  CONST_13  C7   C8   N19  C6     0.00   0.0  0
 T20  CONST_14  C9   C8   N19  C6   180.00   0.0  0
 T20  CONST_15  N21  C20  N19  C6   180.00   0.0  0
 T20  CONST_16  C20  N19  C8   C7   180.00   0.0  0
 T20  CONST_17  N21  C9   C8   C7   180.00   0.0  0
 T20  CONST_18  C10  C9   C8   C7     0.00   0.0  0
 T20  CONST_19  C10  C11  C12  C7     0.00   0.0  0
 T20  CONST_20  N21  C20  N19  C8     0.00   0.0  0
 T20  CONST_21  C11  C12  C7   C8     0.00   0.0  0
 T20  CONST_22  C20  N21  C9   C8     0.00   0.0  0
 T20  CONST_23  C11  C10  C9   C8     0.00   0.0  0
 T20  CONST_24  C20  N19  C8   C9     0.00   0.0  0
 T20  CONST_25  C12  C7   C8   C9     0.00   0.0  0
 T20  CONST_26  N19  C20  N21  C9     0.00   0.0  0
 T20  CONST_27  C12  C11  C10  C9     0.00   0.0  0
 T20  CONST_28  N19  C8   C9   C10  180.00   0.0  0
 T20  CONST_29  C20  N21  C9   C10  180.00   0.0  0
 T20  CONST_30  N21  C9   C10  C11  180.00   0.0  0
 T20  CONST_31  N19  C8   C7   C12  180.00   0.0  0
 T20  CONST_32  C16  C17  C18  C13    0.00   0.0  0
 T20  CONST_33  C16  C15  C14  C13    0.00   0.0  0
 T20  CONST_34  C17  C16  C15  C14    0.00   0.0  0
 T20  CONST_35  C17  C18  C13  C14    0.00   0.0  0
 T20  CONST_36  C18  C17  C16  C15    0.00   0.0  0
 T20  CONST_37  C18  C13  C14  C15    0.00   0.0  0
 T20  CONST_38  N21  C9   C8   N19    0.00   0.0  0
 T20  CONST_39  N23  C20  N19  C6     0.00   0.0  0
 T20  CONST_40  C22  C11  C12  C7   180.00   0.0  0
 T20  CONST_41  N23  C20  N19  C8   180.00   0.0  0
 T20  CONST_42  N23  C20  N21  C9   180.00   0.0  0
 T20  CONST_43  C22  C11  C10  C9   180.00   0.0  0
 T20  CONST_44  N26  C16  C15  C14  180.00   0.0  0
 T20  CONST_45  C24  C18  C13  C14  180.00   0.0  0
 T20  CONST_46  C24  C18  C17  C16  180.00   0.0  0
 T20  CONST_47  N26  C16  C17  C18  180.00   0.0  0
 T20  CONST_48  H3   C3   C2   C1   180.00   0.0  0
 T20  CONST_49  H5   C5   C6   C1   180.00   0.0  0
 T20  CONST_50  H4   C4   C3   C2   180.00   0.0  0
 T20  CONST_51  H1   C1   C2   C3   180.00   0.0  0
 T20  CONST_52  H2   C2   C3   C4   180.00   0.0  0
 T20  CONST_53  H8   C12  C7   C8   180.00   0.0  0
 T20  CONST_54  H7   C10  C9   C8   180.00   0.0  0
 T20  CONST_55  H6   C7   C8   C9   180.00   0.0  0
 T20  CONST_56  H12  C17  C18  C13  180.00   0.0  0
 T20  CONST_57  H11  C15  C14  C13  180.00   0.0  0
 T20  CONST_58  H9   C13  C14  C15  180.00   0.0  0
 T20  CONST_59  H10  C14  C15  C16  180.00   0.0  0
 T20  CONST_60  C20  N23  C24  C18  180.00   0.0  0
 T20  CONST_61  O27  N26  C16  C15  180.00   0.0  0
 T20  CONST_62  O28  N26  C16  C15    0.00   0.0  0
 T20  CONST_63  O27  N26  C16  C17    0.00   0.0  0
 T20  CONST_64  O28  N26  C16  C17  180.00   0.0  0
 T20  CONST_68  O25  C24  N23  C20    0.00   0.0  0
 T20  Var_01    C33  C34  N35  C30   58.60  30.0  1
 T20  Var_02    C33  C32  C31  C30  -53.45  30.0  1
 T20  Var_03    C34  C33  C32  C31   53.28  30.0  1
 T20  Var_04    C34  N35  C30  C31  -58.67  30.0  1
 T20  Var_05    N35  C34  C33  C32  -56.03  30.0  1
 T20  Var_06    N35  C30  C31  C32   56.27  30.0  1
 T20  Var_07    N35  C22  C11  C10  130.85  30.0  2
 T20  Var_08    N23  C24  C18  C13   31.12  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
 T20  plan-1  C1   0.020
 T20  plan-1  C2   0.020
 T20  plan-1  C3   0.020
 T20  plan-1  C4   0.020
 T20  plan-1  C5   0.020
 T20  plan-1  C6   0.020
 T20  plan-1  N19  0.020
 T20  plan-1  H1   0.020
 T20  plan-1  H2   0.020
 T20  plan-1  H3   0.020
 T20  plan-1  H4   0.020
 T20  plan-1  H5   0.020
 T20  plan-2  C13  0.020
 T20  plan-2  C14  0.020
 T20  plan-2  C15  0.020
 T20  plan-2  C16  0.020
 T20  plan-2  C17  0.020
 T20  plan-2  C18  0.020
 T20  plan-2  C24  0.020
 T20  plan-2  H9   0.020
 T20  plan-2  H10  0.020
 T20  plan-2  H11  0.020
 T20  plan-2  H12  0.020
 T20  plan-2  N26  0.020
 T20  plan-3  C6   0.020
 T20  plan-3  C7   0.020
 T20  plan-3  C8   0.020
 T20  plan-3  C9   0.020
 T20  plan-3  C10  0.020
 T20  plan-3  C11  0.020
 T20  plan-3  C12  0.020
 T20  plan-3  N19  0.020
 T20  plan-3  C20  0.020
 T20  plan-3  N21  0.020
 T20  plan-3  N23  0.020
 T20  plan-3  H6   0.020
 T20  plan-3  H7   0.020
 T20  plan-3  H8   0.020
 T20  plan-3  C22  0.020
 T20  plan-4  C16  0.020
 T20  plan-4  O27  0.020
 T20  plan-4  O28  0.020
 T20  plan-4  N26  0.020
 T20  plan-5  C18  0.020
 T20  plan-5  C20  0.020
 T20  plan-5  N23  0.020
 T20  plan-5  C24  0.020
 T20  plan-5  O25  0.020
 T20  plan-5  H15  0.020

