# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:51:57 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazole-6-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NNC(=O)c1ccc2nc(NCCN3CCOCC3)[nH]c2c1
#
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
 6N1  6N1  2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazole-6-carbohydrazide  ligand  42  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6N1
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
 6N1  C1   C  CR6   0  -0.084  -4.1729  -0.1567  -0.1182
 6N1  C2   C  CR16  0  -0.303  -4.3775   1.2246  -0.2585
 6N1  C3   C  CR16  0  -0.339  -3.3208   2.1207  -0.3054
 6N1  C4   C  CR56  0   0.168  -2.0250   1.6232  -0.2053
 6N1  N5   N  NR15  0  -0.744  -0.4693   0.0766  -0.0115
 6N1  C12  C  CR56  0   0.365  -1.8357   0.2334  -0.0771
 6N1  C13  C  CR16  0  -0.341  -2.8756  -0.6685  -0.0415
 6N1  O    O  O     0  -0.483  -5.1354  -2.3020  -0.4282
 6N1  C    C  C     0   0.517  -5.2952  -1.1399  -0.0863
 6N1  N1   N  NH1   0  -0.535  -6.4720  -0.6506   0.3556
 6N1  N    N  NH2   0  -0.638  -7.6010  -1.4481   0.4026
 6N1  C5   C  CR5   0   0.685   0.0802   1.3193  -0.1031
 6N1  N2   N  N     0  -0.533  -0.8210   2.2728  -0.2178
 6N1  N3   N  NH1   0  -0.689   1.4090   1.5284  -0.1083
 6N1  C6   C  CH2   0  -0.287   2.3772   0.5169   0.2570
 6N1  H1   H  HCR6  0   0.250  -5.3804   1.6176  -0.3669
 6N1  H2   H  HCR6  0   0.253  -3.5013   3.1808  -0.4258
 6N1  H3   H  HNR5  0   0.426   0.0206  -0.7959   0.1032
 6N1  H4   H  HCR6  0   0.265  -2.7027  -1.7325   0.0517
 6N1  H5   H  HNH1  0   0.404  -6.5137   0.2748   0.7557
 6N1  H6   H  HNH2  0   0.370  -7.9136  -1.5266   1.3618
 6N1  H7   H  HNH2  0   0.371  -8.3408  -1.0018  -0.1236
 6N1  H9   H  HNH1  0   0.399   1.6751   2.4908   0.0347
 6N1  H10  H  HCH2  0   0.241   2.3630   0.3023   1.3308
 6N1  H11  H  HCH2  0   0.239   2.1300  -0.4095  -0.2657
 6N1  C7   C  CH2   0  -0.290   3.7713   0.9770  -0.1470
 6N1  N4   N  NT    0  -0.431   4.7784   0.0019   0.2107
 6N1  C9   C  CH2   0  -0.305   6.1011   0.5934   0.3149
 6N1  C10  C  CH2   0  -0.188   7.1031  -0.4540   0.7605
 6N1  O1   O  O2    0  -0.485   7.1333  -1.5528  -0.1238
 6N1  C14  C  CH2   0  -0.184   5.8540  -2.1345  -0.2407
 6N1  C15  C  CH2   0  -0.313   4.8213  -1.1255  -0.7054
 6N1  H8   H  HCH2  0   0.212   3.7818   1.2164  -1.2222
 6N1  H12  H  HCH2  0   0.246   3.9964   1.9064   0.3839
 6N1  H13  H  HCH2  0   0.200   6.4311   1.0347  -0.6412
 6N1  H14  H  HCH2  0   0.244   6.0808   1.3985   1.0533
 6N1  H15  H  HCH2  0   0.237   8.1063  -0.0257   0.7864
 6N1  H16  H  HCH2  0   0.200   6.8500  -0.7874   1.7769
 6N1  H17  H  HCH2  0   0.237   5.9297  -2.9496  -0.9617
 6N1  H18  H  HCH2  0   0.201   5.5363  -2.5622   0.7212
 6N1  H19  H  HCH2  0   0.244   3.8499  -1.6234  -0.7433
 6N1  H20  H  HCH2  0   0.202   5.0587  -0.7992  -1.7326

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
 6N1  C6   N3   single    1.447  0.020  1.447
 6N1  N3   C5   single    1.345  0.020  1.345
 6N1  C5   N2   aromatic  1.317  0.020  1.317
 6N1  C5   N5   aromatic  1.362  0.020  1.362
 6N1  N2   C4   aromatic  1.368  0.020  1.368
 6N1  N5   C12  aromatic  1.377  0.020  1.377
 6N1  C4   C12  aromatic  1.409  0.020  1.409
 6N1  C4   C3   aromatic  1.392  0.020  1.392
 6N1  C12  C13  aromatic  1.377  0.020  1.377
 6N1  C3   C2   aromatic  1.386  0.020  1.386
 6N1  C13  C1   aromatic  1.397  0.020  1.397
 6N1  C2   C1   aromatic  1.403  0.020  1.403
 6N1  C1   C    single    1.492  0.020  1.492
 6N1  C    O    double    1.222  0.020  1.222
 6N1  C    N1   single    1.349  0.020  1.349
 6N1  N1   N    single    1.383  0.020  1.383
 6N1  C2   H1   single    0.930  0.020  1.080
 6N1  C3   H2   single    0.930  0.020  1.080
 6N1  N5   H3   single    0.860  0.020  1.020
 6N1  C13  H4   single    0.930  0.020  1.080
 6N1  N1   H5   single    0.860  0.020  1.020
 6N1  N    H6   single    0.890  0.020  1.040
 6N1  N    H7   single    0.890  0.020  1.040
 6N1  N3   H9   single    0.890  0.020  1.040
 6N1  C6   H10  single    0.970  0.020  1.090
 6N1  C6   H11  single    0.970  0.020  1.090
 6N1  C6   C7   single    1.523  0.020  1.523
 6N1  C7   N4   single    1.447  0.020  1.447
 6N1  N4   C9   single    1.453  0.020  1.453
 6N1  C9   C10  single    1.516  0.020  1.516
 6N1  C10  O1   single    1.411  0.020  1.411
 6N1  O1   C14  single    1.410  0.020  1.410
 6N1  C14  C15  single    1.517  0.020  1.517
 6N1  C15  N4   single    1.453  0.020  1.453
 6N1  C7   H8   single    0.970  0.020  1.090
 6N1  C7   H12  single    0.970  0.020  1.090
 6N1  C9   H13  single    0.970  0.020  1.090
 6N1  C9   H14  single    0.970  0.020  1.090
 6N1  C10  H15  single    0.970  0.020  1.090
 6N1  C10  H16  single    0.970  0.020  1.090
 6N1  C14  H17  single    0.970  0.020  1.090
 6N1  C14  H18  single    0.970  0.020  1.090
 6N1  C15  H19  single    0.970  0.020  1.090
 6N1  C15  H20  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
 6N1  C    C1   C13  117.12  3.000
 6N1  C    C1   C2   122.75  3.000
 6N1  C13  C1   C2   120.10  3.000
 6N1  H1   C2   C3   117.91  3.000
 6N1  H1   C2   C1   120.16  3.000
 6N1  C3   C2   C1   121.91  3.000
 6N1  H2   C3   C4   120.90  3.000
 6N1  H2   C3   C2   120.66  3.000
 6N1  C4   C3   C2   118.44  3.000
 6N1  N2   C4   C12  110.55  3.000
 6N1  C12  C4   C3   118.97  3.000
 6N1  N2   C4   C3   130.47  3.000
 6N1  H3   N5   C5   127.00  3.000
 6N1  H3   N5   C12  125.93  3.000
 6N1  C5   N5   C12  107.05  3.000
 6N1  C13  C12  N5   132.34  3.000
 6N1  C13  C12  C4   123.17  3.000
 6N1  N5   C12  C4   104.48  3.000
 6N1  H4   C13  C12  121.71  3.000
 6N1  H4   C13  C1   120.90  3.000
 6N1  C12  C13  C1   117.39  3.000
 6N1  N1   C    O    123.42  3.000
 6N1  N1   C    C1   115.10  3.000
 6N1  O    C    C1   121.48  3.000
 6N1  H5   N1   N    118.79  3.000
 6N1  H5   N1   C    119.90  3.000
 6N1  N    N1   C    120.94  3.000
 6N1  H7   N    H6   107.54  3.000
 6N1  H7   N    N1   108.96  3.000
 6N1  H6   N    N1   109.22  3.000
 6N1  N3   C5   N2   124.27  3.000
 6N1  N2   C5   N5   112.98  3.000
 6N1  N3   C5   N5   122.73  3.000
 6N1  C5   N2   C4   104.93  3.000
 6N1  H9   N3   C6   117.04  3.000
 6N1  H9   N3   C5   114.10  3.000
 6N1  C6   N3   C5   123.46  3.000
 6N1  C7   C6   H11  109.67  3.000
 6N1  C7   C6   H10  109.34  3.000
 6N1  H11  C6   H10  107.47  3.000
 6N1  C7   C6   N3   109.53  3.000
 6N1  H11  C6   N3   108.70  3.000
 6N1  H10  C6   N3   112.08  3.000
 6N1  H12  C7   H8   106.69  3.000
 6N1  H12  C7   N4   108.02  3.000
 6N1  H8   C7   N4   112.40  3.000
 6N1  H12  C7   C6   108.45  3.000
 6N1  H8   C7   C6   109.47  3.000
 6N1  N4   C7   C6   111.60  3.000
 6N1  C15  N4   C9   109.52  3.000
 6N1  C15  N4   C7   112.80  3.000
 6N1  C9   N4   C7   112.15  3.000
 6N1  H14  C9   H13  107.24  3.000
 6N1  H14  C9   C10  108.82  3.000
 6N1  H13  C9   C10  109.46  3.000
 6N1  H14  C9   N4   109.36  3.000
 6N1  H13  C9   N4   111.90  3.000
 6N1  C10  C9   N4   109.97  3.000
 6N1  H16  C10  H15  107.99  3.000
 6N1  H16  C10  O1   110.38  3.000
 6N1  H15  C10  O1   107.52  3.000
 6N1  H16  C10  C9   109.21  3.000
 6N1  H15  C10  C9   110.08  3.000
 6N1  O1   C10  C9   111.58  3.000
 6N1  C14  O1   C10  110.72  3.000
 6N1  H18  C14  H17  107.92  3.000
 6N1  H18  C14  C15  109.27  3.000
 6N1  H17  C14  C15  109.99  3.000
 6N1  H18  C14  O1   110.49  3.000
 6N1  H17  C14  O1   107.46  3.000
 6N1  C15  C14  O1   111.63  3.000
 6N1  H20  C15  H19  107.08  3.000
 6N1  H20  C15  C14  109.60  3.000
 6N1  H19  C15  C14  108.23  3.000
 6N1  H20  C15  N4   111.33  3.000
 6N1  H19  C15  N4   110.44  3.000
 6N1  C14  C15  N4   110.07  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
 6N1  CONST_01  N5   C12  C13  C1    180.00   0.0  0
 6N1  CONST_02  C4   C12  C13  C1      0.00   0.0  0
 6N1  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 6N1  CONST_04  N2   C4   C3   C2    180.00   0.0  0
 6N1  CONST_05  C12  C4   C3   C2      0.00   0.0  0
 6N1  CONST_06  C12  C13  C1   C2      0.00   0.0  0
 6N1  CONST_07  C5   N2   C4   C3    180.00   0.0  0
 6N1  CONST_08  N5   C12  C4   C3    180.00   0.0  0
 6N1  CONST_09  C13  C12  C4   C3      0.00   0.0  0
 6N1  CONST_10  C13  C1   C2   C3      0.00   0.0  0
 6N1  CONST_11  N5   C5   N2   C4      0.00   0.0  0
 6N1  CONST_12  C5   N5   C12  C4      0.00   0.0  0
 6N1  CONST_13  N2   C4   C12  N5      0.00   0.0  0
 6N1  CONST_14  N2   C5   N5   C12     0.00   0.0  0
 6N1  CONST_15  C5   N2   C4   C12     0.00   0.0  0
 6N1  CONST_16  C5   N5   C12  C13   180.00   0.0  0
 6N1  CONST_17  N2   C4   C12  C13   180.00   0.0  0
 6N1  CONST_18  C    C1   C2   C3    180.00   0.0  0
 6N1  CONST_19  N3   C5   N2   C4    180.00   0.0  0
 6N1  CONST_20  N3   C5   N5   C12   180.00   0.0  0
 6N1  CONST_21  C    C1   C13  C12   180.00   0.0  0
 6N1  CONST_22  H2   C3   C2   C1    180.00   0.0  0
 6N1  CONST_23  H4   C13  C1   C2    180.00   0.0  0
 6N1  CONST_24  H3   N5   C12  C4    180.00   0.0  0
 6N1  CONST_25  H1   C2   C3   C4    180.00   0.0  0
 6N1  CONST_26  C6   N3   C5   N5      0.00   0.0  0
 6N1  CONST_27  C6   N3   C5   N2    180.00   0.0  0
 6N1  CONST_28  H9   N3   C5   N5    180.00   0.0  0
 6N1  CONST_29  N    N1   C    C1    180.00   0.0  0
 6N1  CONST_30  H5   N1   C    C1      0.00   0.0  0
 6N1  CONST_31  N    N1   C    O       0.00   0.0  0
 6N1  Var_01    O1   C10  C9   N4     57.60  30.0  1
 6N1  Var_02    O1   C14  C15  N4    -57.29  30.0  1
 6N1  Var_03    C14  C15  N4   C9     56.73  30.0  1
 6N1  Var_04    C15  N4   C9   C10   -56.87  30.0  1
 6N1  Var_05    C15  C14  O1   C10    57.19  30.0  1
 6N1  Var_06    O    C    C1   C2    154.01  30.0  2
 6N1  Var_07    C9   N4   C7   C6   -158.08  30.0  3
 6N1  Var_08    C7   C6   N3   C5    167.66  30.0  2
 6N1  Var_09    N4   C7   C6   N3    179.43  30.0  3
 6N1  Var_10    H6   N    N1   C     118.20  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
 6N1  plan-1  C1   0.020
 6N1  plan-1  C2   0.020
 6N1  plan-1  C3   0.020
 6N1  plan-1  C4   0.020
 6N1  plan-1  N5   0.020
 6N1  plan-1  C12  0.020
 6N1  plan-1  C13  0.020
 6N1  plan-1  C    0.020
 6N1  plan-1  C5   0.020
 6N1  plan-1  N2   0.020
 6N1  plan-1  N3   0.020
 6N1  plan-1  H1   0.020
 6N1  plan-1  H2   0.020
 6N1  plan-1  H3   0.020
 6N1  plan-1  H4   0.020
 6N1  plan-2  C5   0.020
 6N1  plan-2  N3   0.020
 6N1  plan-2  C6   0.020
 6N1  plan-2  H9   0.020
 6N1  plan-3  C1   0.020
 6N1  plan-3  O    0.020
 6N1  plan-3  C    0.020
 6N1  plan-3  N1   0.020
 6N1  plan-3  N    0.020
 6N1  plan-3  H5   0.020

