# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:11:28 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=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
 6NK  6NK  2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazole-6-carboxamide  ligand  40  21  .  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_6NK
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
 6NK  C1   C  CR6   0  -0.077  -4.5848  -0.3656  -0.0330
 6NK  C2   C  CR16  0  -0.296  -4.8324   1.0082  -0.1765
 6NK  C3   C  CR16  0  -0.337  -3.8063   1.9376  -0.2331
 6NK  C4   C  CR56  0   0.168  -2.4940   1.4822  -0.1411
 6NK  N5   N  NR15  0  -0.743  -0.8890  -0.0136   0.0500
 6NK  C12  C  CR56  0   0.366  -2.2601   0.0997  -0.0057
 6NK  C13  C  CR16  0  -0.341  -3.2705  -0.8339   0.0425
 6NK  O    O  O     0  -0.493  -5.4371  -2.5739  -0.1585
 6NK  C    C  C     0   0.493  -5.6738  -1.3829   0.0137
 6NK  N1   N  NH2   0  -0.823  -6.9189  -0.9339   0.2471
 6NK  C5   C  CR5   0   0.686  -0.3799   1.2449  -0.0532
 6NK  N2   N  N     0  -0.533  -1.3123   2.1690  -0.1663
 6NK  N3   N  NH1   0  -0.689   0.9408   1.4973  -0.0705
 6NK  C6   C  CH2   0  -0.287   1.9466   0.5190   0.2831
 6NK  C7   C  CH2   0  -0.290   3.3183   1.0181  -0.1503
 6NK  H1   H  HCR6  0   0.246  -5.8463   1.3737  -0.2744
 6NK  H2   H  HCR6  0   0.254  -4.0220   2.9909  -0.3532
 6NK  H3   H  HNR5  0   0.426  -0.3706  -0.8689   0.1686
 6NK  H4   H  HCR6  0   0.266  -3.0634  -1.8907   0.1438
 6NK  H5   H  HNH2  0   0.410  -7.1171   0.0093   0.5289
 6NK  H6   H  HNH2  0   0.401  -7.6758  -1.5945   0.3139
 6NK  H8   H  HNH1  0   0.399   1.1777   2.4685   0.0613
 6NK  H9   H  HCH2  0   0.241   1.9599   0.3113   1.3581
 6NK  H10  H  HCH2  0   0.239   1.7182  -0.4186  -0.2283
 6NK  H11  H  HCH2  0   0.212   3.3012   1.2503  -1.2268
 6NK  H12  H  HCH2  0   0.245   3.5246   1.9577   0.3701
 6NK  N4   N  NT    0  -0.432   4.3597   0.0761   0.1964
 6NK  C9   C  CH2   0  -0.305   5.6654   0.7055   0.2899
 6NK  C10  C  CH2   0  -0.188   6.6983  -0.3123   0.7342
 6NK  O1   O  O2    0  -0.485   6.7550  -1.4129  -0.1466
 6NK  C14  C  CH2   0  -0.185   5.4914  -2.0300  -0.2561
 6NK  C15  C  CH2   0  -0.312   4.4287  -1.0513  -0.7175
 6NK  H7   H  HCH2  0   0.200   5.9772   1.1513  -0.6700
 6NK  H13  H  HCH2  0   0.244   5.6271   1.5132   1.0250
 6NK  H14  H  HCH2  0   0.237   7.6895   0.1435   0.7543
 6NK  H15  H  HCH2  0   0.200   6.4586  -0.6486   1.7528
 6NK  H16  H  HCH2  0   0.237   5.5861  -2.8455  -0.9744
 6NK  H17  H  HCH2  0   0.201   5.1914  -2.4631   0.7090
 6NK  H18  H  HCH2  0   0.243   3.4717  -1.5765  -0.7496
 6NK  H19  H  HCH2  0   0.202   4.6514  -0.7211  -1.7470

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
 6NK  C7   C6   single    1.523  0.020  1.523
 6NK  C6   N3   single    1.447  0.020  1.447
 6NK  N3   C5   single    1.345  0.020  1.345
 6NK  C5   N2   aromatic  1.318  0.020  1.318
 6NK  C5   N5   aromatic  1.362  0.020  1.362
 6NK  N2   C4   aromatic  1.367  0.020  1.367
 6NK  N5   C12  aromatic  1.377  0.020  1.377
 6NK  C4   C12  aromatic  1.409  0.020  1.409
 6NK  C4   C3   aromatic  1.392  0.020  1.392
 6NK  C12  C13  aromatic  1.377  0.020  1.377
 6NK  C3   C2   aromatic  1.386  0.020  1.386
 6NK  C13  C1   aromatic  1.397  0.020  1.397
 6NK  C2   C1   aromatic  1.403  0.020  1.403
 6NK  C1   C    single    1.491  0.020  1.491
 6NK  C    O    double    1.226  0.020  1.226
 6NK  C    N1   single    1.344  0.020  1.344
 6NK  C2   H1   single    0.930  0.020  1.080
 6NK  C3   H2   single    0.930  0.020  1.080
 6NK  N5   H3   single    0.860  0.020  1.020
 6NK  C13  H4   single    0.930  0.020  1.080
 6NK  N1   H5   single    0.860  0.020  1.020
 6NK  N1   H6   single    0.860  0.020  1.020
 6NK  N3   H8   single    0.890  0.020  1.040
 6NK  C6   H9   single    0.970  0.020  1.090
 6NK  C6   H10  single    0.970  0.020  1.090
 6NK  C7   H11  single    0.970  0.020  1.090
 6NK  C7   H12  single    0.970  0.020  1.090
 6NK  C7   N4   single    1.446  0.020  1.446
 6NK  N4   C9   single    1.453  0.020  1.453
 6NK  C9   C10  single    1.517  0.020  1.517
 6NK  C10  O1   single    1.411  0.020  1.411
 6NK  O1   C14  single    1.410  0.020  1.410
 6NK  C14  C15  single    1.517  0.020  1.517
 6NK  C15  N4   single    1.453  0.020  1.453
 6NK  C9   H7   single    0.970  0.020  1.090
 6NK  C9   H13  single    0.970  0.020  1.090
 6NK  C10  H14  single    0.970  0.020  1.090
 6NK  C10  H15  single    0.970  0.020  1.090
 6NK  C14  H16  single    0.970  0.020  1.090
 6NK  C14  H17  single    0.970  0.020  1.090
 6NK  C15  H18  single    0.970  0.020  1.090
 6NK  C15  H19  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
 6NK  C    C1   C13  117.17  3.000
 6NK  C    C1   C2   122.84  3.000
 6NK  C13  C1   C2   119.97  3.000
 6NK  H1   C2   C3   117.62  3.000
 6NK  H1   C2   C1   120.34  3.000
 6NK  C3   C2   C1   122.02  3.000
 6NK  H2   C3   C4   120.92  3.000
 6NK  H2   C3   C2   120.66  3.000
 6NK  C4   C3   C2   118.42  3.000
 6NK  N2   C4   C12  110.57  3.000
 6NK  C12  C4   C3   118.94  3.000
 6NK  N2   C4   C3   130.49  3.000
 6NK  H3   N5   C5   126.97  3.000
 6NK  H3   N5   C12  125.96  3.000
 6NK  C5   N5   C12  107.05  3.000
 6NK  C13  C12  N5   132.35  3.000
 6NK  C13  C12  C4   123.17  3.000
 6NK  N5   C12  C4   104.48  3.000
 6NK  H4   C13  C12  121.70  3.000
 6NK  H4   C13  C1   120.84  3.000
 6NK  C12  C13  C1   117.46  3.000
 6NK  N1   C    O    121.84  3.000
 6NK  N1   C    C1   117.01  3.000
 6NK  O    C    C1   121.15  3.000
 6NK  H6   N1   H5   116.70  3.000
 6NK  H6   N1   C    119.26  3.000
 6NK  H5   N1   C    123.04  3.000
 6NK  N3   C5   N2   124.21  3.000
 6NK  N2   C5   N5   112.97  3.000
 6NK  N3   C5   N5   122.80  3.000
 6NK  C5   N2   C4   104.94  3.000
 6NK  H8   N3   C6   117.13  3.000
 6NK  H8   N3   C5   114.19  3.000
 6NK  C6   N3   C5   123.55  3.000
 6NK  H10  C6   H9   107.43  3.000
 6NK  H10  C6   C7   109.66  3.000
 6NK  H9   C6   C7   109.30  3.000
 6NK  H10  C6   N3   108.70  3.000
 6NK  H9   C6   N3   112.13  3.000
 6NK  C7   C6   N3   109.57  3.000
 6NK  N4   C7   H12  108.04  3.000
 6NK  N4   C7   H11  112.51  3.000
 6NK  H12  C7   H11  106.67  3.000
 6NK  N4   C7   C6   111.53  3.000
 6NK  H12  C7   C6   108.42  3.000
 6NK  H11  C7   C6   109.47  3.000
 6NK  C15  N4   C9   109.51  3.000
 6NK  C15  N4   C7   112.88  3.000
 6NK  C9   N4   C7   112.36  3.000
 6NK  H13  C9   H7   107.25  3.000
 6NK  H13  C9   C10  108.83  3.000
 6NK  H7   C9   C10  109.48  3.000
 6NK  H13  C9   N4   109.40  3.000
 6NK  H7   C9   N4   111.90  3.000
 6NK  C10  C9   N4   109.90  3.000
 6NK  H15  C10  H14  107.99  3.000
 6NK  H15  C10  O1   110.40  3.000
 6NK  H14  C10  O1   107.51  3.000
 6NK  H15  C10  C9   109.16  3.000
 6NK  H14  C10  C9   110.11  3.000
 6NK  O1   C10  C9   111.59  3.000
 6NK  C14  O1   C10  110.72  3.000
 6NK  H17  C14  H16  107.89  3.000
 6NK  H17  C14  C15  109.27  3.000
 6NK  H16  C14  C15  110.05  3.000
 6NK  H17  C14  O1   110.41  3.000
 6NK  H16  C14  O1   107.49  3.000
 6NK  C15  C14  O1   111.65  3.000
 6NK  H19  C15  H18  107.05  3.000
 6NK  H19  C15  C14  109.60  3.000
 6NK  H18  C15  C14  108.21  3.000
 6NK  H19  C15  N4   111.35  3.000
 6NK  H18  C15  N4   110.49  3.000
 6NK  C14  C15  N4   110.04  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
 6NK  CONST_01  N5   C12  C13  C1    180.00   0.0  0
 6NK  CONST_02  C4   C12  C13  C1      0.00   0.0  0
 6NK  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 6NK  CONST_04  N2   C4   C3   C2    180.00   0.0  0
 6NK  CONST_05  C12  C4   C3   C2      0.00   0.0  0
 6NK  CONST_06  C12  C13  C1   C2      0.00   0.0  0
 6NK  CONST_07  C5   N2   C4   C3    180.00   0.0  0
 6NK  CONST_08  N5   C12  C4   C3    180.00   0.0  0
 6NK  CONST_09  C13  C12  C4   C3      0.00   0.0  0
 6NK  CONST_10  C13  C1   C2   C3      0.00   0.0  0
 6NK  CONST_11  N5   C5   N2   C4      0.00   0.0  0
 6NK  CONST_12  C5   N5   C12  C4      0.00   0.0  0
 6NK  CONST_13  N2   C4   C12  N5      0.00   0.0  0
 6NK  CONST_14  N2   C5   N5   C12     0.00   0.0  0
 6NK  CONST_15  C5   N2   C4   C12     0.00   0.0  0
 6NK  CONST_16  C5   N5   C12  C13   180.00   0.0  0
 6NK  CONST_17  N2   C4   C12  C13   180.00   0.0  0
 6NK  CONST_18  C    C1   C2   C3    180.00   0.0  0
 6NK  CONST_19  N3   C5   N2   C4    180.00   0.0  0
 6NK  CONST_20  N3   C5   N5   C12   180.00   0.0  0
 6NK  CONST_21  C    C1   C13  C12   180.00   0.0  0
 6NK  CONST_22  H2   C3   C2   C1    180.00   0.0  0
 6NK  CONST_23  H4   C13  C1   C2    180.00   0.0  0
 6NK  CONST_24  H3   N5   C12  C4    180.00   0.0  0
 6NK  CONST_25  H1   C2   C3   C4    180.00   0.0  0
 6NK  CONST_26  C6   N3   C5   N5      0.00   0.0  0
 6NK  CONST_27  C6   N3   C5   N2    180.00   0.0  0
 6NK  CONST_28  H8   N3   C5   N5    180.00   0.0  0
 6NK  CONST_29  H5   N1   C    C1      0.00   0.0  0
 6NK  CONST_30  H6   N1   C    C1    180.00   0.0  0
 6NK  Var_01    O1   C10  C9   N4     57.68  30.0  1
 6NK  Var_02    O1   C14  C15  N4    -57.26  30.0  1
 6NK  Var_03    C14  C15  N4   C9     56.84  30.0  1
 6NK  Var_04    C15  N4   C9   C10   -57.02  30.0  1
 6NK  Var_05    C15  C14  O1   C10    57.10  30.0  1
 6NK  Var_06    O    C    C1   C2    163.62  30.0  2
 6NK  Var_07    C9   N4   C7   C6   -157.35  30.0  3
 6NK  Var_08    C7   C6   N3   C5    166.90  30.0  1
 6NK  Var_09    N4   C7   C6   N3    179.40  30.0  1

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
 6NK  plan-1  C1   0.020
 6NK  plan-1  C2   0.020
 6NK  plan-1  C3   0.020
 6NK  plan-1  C4   0.020
 6NK  plan-1  N5   0.020
 6NK  plan-1  C12  0.020
 6NK  plan-1  C13  0.020
 6NK  plan-1  C    0.020
 6NK  plan-1  C5   0.020
 6NK  plan-1  N2   0.020
 6NK  plan-1  N3   0.020
 6NK  plan-1  H1   0.020
 6NK  plan-1  H2   0.020
 6NK  plan-1  H3   0.020
 6NK  plan-1  H4   0.020
 6NK  plan-2  C5   0.020
 6NK  plan-2  N3   0.020
 6NK  plan-2  C6   0.020
 6NK  plan-2  H8   0.020
 6NK  plan-3  C1   0.020
 6NK  plan-3  O    0.020
 6NK  plan-3  C    0.020
 6NK  plan-3  N1   0.020
 6NK  plan-3  H5   0.020
 6NK  plan-3  H6   0.020

