# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:51:18 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N-(2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazol-5-yl)guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)Nc1ccc2[nH]c(NCCN3CCOCC3)nc2c1
#
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
 6N2  6N2  N-(2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazol-5-yl)guanidine  ligand  43  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_6N2
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
 6N2  N1   N  NH2   0  -0.847   7.9351   0.3813   0.0683
 6N2  C2   C  CR16  0  -0.393   3.8743  -1.7585  -0.3411
 6N2  N3   N  NR15  0  -0.742   0.2941  -0.7744  -0.2170
 6N2  C4   C  CR56  0   0.320   1.6678  -0.9160  -0.2306
 6N2  C5   C  CR5   0   0.672   0.0369   0.5484  -0.0307
 6N2  C6   C  CH2   0  -0.290  -2.3931   0.2648  -0.2636
 6N2  C    C  C     0   0.561   6.5965   0.7201   0.0876
 6N2  N    N  N     0  -0.702   6.1316   1.9052   0.2206
 6N2  N2   N  NH1   0  -0.754   5.7885  -0.3682  -0.1224
 6N2  C1   C  CR6   0   0.360   4.3961  -0.4639  -0.1510
 6N2  C13  C  CR16  0  -0.449   3.5346   0.6226  -0.0043
 6N2  C12  C  CR56  0   0.192   2.1630   0.3828  -0.0466
 6N2  C3   C  CR16  0  -0.302   2.5099  -2.0011  -0.3828
 6N2  N6   N  N     0  -0.544   1.1260   1.2768   0.0718
 6N2  H1   H  HNH2  0   0.389   8.5553   1.0915   0.4230
 6N2  H2   H  HNH2  0   0.387   8.1816  -0.5314   0.4194
 6N2  H3   H  HCR6  0   0.256   4.5560  -2.5932  -0.4543
 6N2  H4   H  HNR5  0   0.421  -0.3813  -1.5108  -0.3380
 6N2  H5   H  HNH1  0   0.394  -1.2792   2.0371  -0.0420
 6N2  H6   H  HCH2  0   0.236  -2.4468   0.0298  -1.3327
 6N2  H7   H  HCH2  0   0.240  -2.3552  -0.6817   0.2801
 6N2  H9   H  H     0   0.326   6.8852   2.5590   0.3996
 6N2  H10  H  HNH1  0   0.399   6.2667  -1.2341  -0.3108
 6N2  H11  H  HCR6  0   0.278   3.9232   1.6182   0.1359
 6N2  H12  H  HCR6  0   0.260   2.1356  -3.0059  -0.5293
 6N2  C7   C  CH2   0  -0.290  -3.6356   1.0484   0.1399
 6N2  N5   N  NT    0  -0.430  -4.8582   0.3418  -0.1769
 6N2  C9   C  CH2   0  -0.305  -6.0016   1.2390  -0.1819
 6N2  C10  C  CH2   0  -0.189  -7.2614   0.4822  -0.5558
 6N2  O1   O  O2    0  -0.484  -7.4969  -0.5980   0.3194
 6N2  C14  C  CH2   0  -0.186  -6.3967  -1.4790   0.3275
 6N2  C15  C  CH2   0  -0.313  -5.1135  -0.7719   0.7219
 6N2  H8   H  HCH2  0   0.209  -3.5706   1.3100   1.2087
 6N2  H13  H  HCH2  0   0.244  -3.6386   1.9903  -0.4162
 6N2  H14  H  HCH2  0   0.199  -6.1428   1.7276   0.7974
 6N2  H15  H  HCH2  0   0.244  -5.8369   2.0298  -0.9175
 6N2  H16  H  HCH2  0   0.237  -8.1261   1.1453  -0.5003
 6N2  H17  H  HCH2  0   0.200  -7.1761   0.1243  -1.5918
 6N2  H18  H  HCH2  0   0.237  -6.6177  -2.2741   1.0409
 6N2  H19  H  HCH2  0   0.201  -6.2662  -1.9393  -0.6623
 6N2  H20  H  HCH2  0   0.245  -4.2990  -1.4964   0.6687
 6N2  H21  H  HCH2  0   0.201  -5.1807  -0.4354   1.7711
 6N2  N4   N  NH1   0  -0.691  -1.2176   1.0372   0.0726

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
 6N2  C6   N4   single    1.446  0.020  1.446
 6N2  N4   C5   single    1.350  0.020  1.350
 6N2  C5   N6   aromatic  1.314  0.020  1.314
 6N2  C5   N3   aromatic  1.360  0.020  1.360
 6N2  N6   C12  aromatic  1.374  0.020  1.374
 6N2  N3   C4   aromatic  1.381  0.020  1.381
 6N2  C12  C4   aromatic  1.402  0.020  1.402
 6N2  C12  C13  aromatic  1.393  0.020  1.393
 6N2  C4   C3   aromatic  1.382  0.020  1.382
 6N2  C13  C1   aromatic  1.394  0.020  1.394
 6N2  C3   C2   aromatic  1.386  0.020  1.386
 6N2  C1   C2   aromatic  1.409  0.020  1.409
 6N2  C1   N2   single    1.396  0.020  1.396
 6N2  N2   C    single    1.372  0.020  1.372
 6N2  C    N    double    1.280  0.020  1.280
 6N2  C    N1   single    1.381  0.020  1.381
 6N2  N1   H1   single    0.890  0.020  1.040
 6N2  N1   H2   single    0.890  0.020  1.040
 6N2  C2   H3   single    0.930  0.020  1.080
 6N2  N3   H4   single    0.860  0.020  1.020
 6N2  N4   H5   single    0.890  0.020  1.040
 6N2  C6   H6   single    0.970  0.020  1.090
 6N2  C6   H7   single    0.970  0.020  1.090
 6N2  N    H9   single    0.890  0.020  1.040
 6N2  N2   H10  single    0.860  0.020  1.020
 6N2  C13  H11  single    0.930  0.020  1.080
 6N2  C3   H12  single    0.930  0.020  1.080
 6N2  C6   C7   single    1.523  0.020  1.523
 6N2  C7   N5   single    1.447  0.020  1.447
 6N2  N5   C9   single    1.453  0.020  1.453
 6N2  C9   C10  single    1.516  0.020  1.516
 6N2  C10  O1   single    1.410  0.020  1.410
 6N2  O1   C14  single    1.410  0.020  1.410
 6N2  C14  C15  single    1.517  0.020  1.517
 6N2  C15  N5   single    1.454  0.020  1.454
 6N2  C7   H8   single    0.970  0.020  1.090
 6N2  C7   H13  single    0.970  0.020  1.090
 6N2  C9   H14  single    0.970  0.020  1.090
 6N2  C9   H15  single    0.970  0.020  1.090
 6N2  C10  H16  single    0.970  0.020  1.090
 6N2  C10  H17  single    0.970  0.020  1.090
 6N2  C14  H18  single    0.970  0.020  1.090
 6N2  C14  H19  single    0.970  0.020  1.090
 6N2  C15  H20  single    0.970  0.020  1.090
 6N2  C15  H21  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
 6N2  H2   N1   H1   111.41  3.000
 6N2  H2   N1   C    117.01  3.000
 6N2  H1   N1   C    114.77  3.000
 6N2  H3   C2   C3   118.76  3.000
 6N2  H3   C2   C1   119.27  3.000
 6N2  C3   C2   C1   121.97  3.000
 6N2  H4   N3   C5   126.94  3.000
 6N2  H4   N3   C4   126.24  3.000
 6N2  C5   N3   C4   106.81  3.000
 6N2  C3   C4   C12  121.77  3.000
 6N2  C3   C4   N3   133.45  3.000
 6N2  C12  C4   N3   104.78  3.000
 6N2  N6   C5   N4   124.29  3.000
 6N2  N6   C5   N3   113.13  3.000
 6N2  N4   C5   N3   122.56  3.000
 6N2  C7   C6   H7   110.01  3.000
 6N2  C7   C6   H6   109.19  3.000
 6N2  H7   C6   H6   107.54  3.000
 6N2  C7   C6   N4   109.07  3.000
 6N2  H7   C6   N4   108.60  3.000
 6N2  H6   C6   N4   112.40  3.000
 6N2  N2   C    N    122.45  3.000
 6N2  N    C    N1   125.50  3.000
 6N2  N2   C    N1   111.98  3.000
 6N2  H9   N    C    110.21  3.000
 6N2  H10  N2   C1   114.26  3.000
 6N2  H10  N2   C    115.54  3.000
 6N2  C1   N2   C    130.17  3.000
 6N2  C13  C1   N2   124.10  3.000
 6N2  N2   C1   C2   115.80  3.000
 6N2  C13  C1   C2   120.09  3.000
 6N2  H11  C13  C12  121.19  3.000
 6N2  H11  C13  C1   120.70  3.000
 6N2  C12  C13  C1   118.10  3.000
 6N2  N6   C12  C13  128.93  3.000
 6N2  C13  C12  C4   120.75  3.000
 6N2  N6   C12  C4   110.33  3.000
 6N2  H12  C3   C4   122.22  3.000
 6N2  H12  C3   C2   120.46  3.000
 6N2  C4   C3   C2   117.32  3.000
 6N2  C12  N6   C5   104.95  3.000
 6N2  H13  C7   H8   106.78  3.000
 6N2  H13  C7   N5   107.87  3.000
 6N2  H8   C7   N5   112.21  3.000
 6N2  H13  C7   C6   108.09  3.000
 6N2  H8   C7   C6   109.31  3.000
 6N2  N5   C7   C6   112.33  3.000
 6N2  C15  N5   C9   109.68  3.000
 6N2  C15  N5   C7   112.77  3.000
 6N2  C9   N5   C7   111.34  3.000
 6N2  H15  C9   H14  107.23  3.000
 6N2  H15  C9   C10  108.69  3.000
 6N2  H14  C9   C10  109.48  3.000
 6N2  H15  C9   N5   109.30  3.000
 6N2  H14  C9   N5   111.78  3.000
 6N2  C10  C9   N5   110.26  3.000
 6N2  H17  C10  H16  107.90  3.000
 6N2  H17  C10  O1   110.39  3.000
 6N2  H16  C10  O1   107.56  3.000
 6N2  H17  C10  C9   109.29  3.000
 6N2  H16  C10  C9   110.03  3.000
 6N2  O1   C10  C9   111.59  3.000
 6N2  C14  O1   C10  110.61  3.000
 6N2  H19  C14  H18  107.92  3.000
 6N2  H19  C14  C15  109.20  3.000
 6N2  H18  C14  C15  109.94  3.000
 6N2  H19  C14  O1   110.43  3.000
 6N2  H18  C14  O1   107.53  3.000
 6N2  C15  C14  O1   111.73  3.000
 6N2  H21  C15  H20  107.10  3.000
 6N2  H21  C15  C14  109.73  3.000
 6N2  H20  C15  C14  108.00  3.000
 6N2  H21  C15  N5   111.40  3.000
 6N2  H20  C15  N5   110.32  3.000
 6N2  C14  C15  N5   110.18  3.000
 6N2  H5   N4   C6   116.97  3.000
 6N2  H5   N4   C5   114.02  3.000
 6N2  C6   N4   C5   122.96  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
 6N2  CONST_01  N3   C4   C3   C2    180.00   0.0  0
 6N2  CONST_02  C12  C4   C3   C2      0.00   0.0  0
 6N2  CONST_03  C12  C13  C1   C2      0.00   0.0  0
 6N2  CONST_04  C12  N6   C5   N3      0.00   0.0  0
 6N2  CONST_05  N6   C12  C4   N3      0.00   0.0  0
 6N2  CONST_06  C13  C12  C4   N3    180.00   0.0  0
 6N2  CONST_07  N6   C5   N3   C4      0.00   0.0  0
 6N2  CONST_08  C5   N6   C12  C4      0.00   0.0  0
 6N2  CONST_09  C1   C13  C12  C4      0.00   0.0  0
 6N2  CONST_10  C1   C2   C3   C4      0.00   0.0  0
 6N2  CONST_11  C13  C12  N6   C5    180.00   0.0  0
 6N2  CONST_12  C12  C4   N3   C5      0.00   0.0  0
 6N2  CONST_13  C3   C4   N3   C5    180.00   0.0  0
 6N2  CONST_14  N6   C12  C13  C1    180.00   0.0  0
 6N2  CONST_15  C3   C4   C12  C13     0.00   0.0  0
 6N2  CONST_16  C3   C2   C1   C13     0.00   0.0  0
 6N2  CONST_17  N6   C12  C4   C3    180.00   0.0  0
 6N2  CONST_18  N4   C5   N3   C4    180.00   0.0  0
 6N2  CONST_19  C12  N6   C5   N4    180.00   0.0  0
 6N2  CONST_20  C12  C13  C1   N2    180.00   0.0  0
 6N2  CONST_21  C3   C2   C1   N2    180.00   0.0  0
 6N2  CONST_22  H11  C13  C1   C2    180.00   0.0  0
 6N2  CONST_23  H12  C3   C4   N3      0.00   0.0  0
 6N2  CONST_24  H3   C2   C3   C4    180.00   0.0  0
 6N2  CONST_25  H4   N3   C4   C12   180.00   0.0  0
 6N2  CONST_26  C    N2   C1   C2    180.00   0.0  0
 6N2  CONST_27  C6   N4   C5   N3      0.00   0.0  0
 6N2  CONST_28  N6   C5   N4   C6    180.00   0.0  0
 6N2  CONST_29  C13  C1   N2   C       0.00   0.0  0
 6N2  CONST_30  H10  N2   C1   C2      0.00   0.0  0
 6N2  CONST_32  C1   N2   C    N1    180.00   0.0  0
 6N2  CONST_33  C1   N2   C    N       0.00   0.0  0
 6N2  CONST_34  H9   N    C    N1      0.00   0.0  0
 6N2  Var_01    O1   C10  C9   N5     57.31  30.0  1
 6N2  Var_02    O1   C14  C15  N5    -57.15  30.0  1
 6N2  Var_03    C14  C15  N5   C9     55.97  30.0  1
 6N2  Var_04    C15  N5   C9   C10   -56.12  30.0  1
 6N2  Var_05    C15  C14  O1   C10    57.49  30.0  1
 6N2  Var_06    C9   N5   C7   C6   -162.13  30.0  3
 6N2  Var_07    N5   C7   C6   N4    179.49  30.0  3
 6N2  Var_08    C7   C6   N4   C5    172.64  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
 6N2  plan-1  C2   0.020
 6N2  plan-1  N3   0.020
 6N2  plan-1  C4   0.020
 6N2  plan-1  C5   0.020
 6N2  plan-1  N2   0.020
 6N2  plan-1  C1   0.020
 6N2  plan-1  C13  0.020
 6N2  plan-1  C12  0.020
 6N2  plan-1  C3   0.020
 6N2  plan-1  N6   0.020
 6N2  plan-1  H3   0.020
 6N2  plan-1  H4   0.020
 6N2  plan-1  H11  0.020
 6N2  plan-1  H12  0.020
 6N2  plan-1  N4   0.020
 6N2  plan-2  N1   0.020
 6N2  plan-2  C    0.020
 6N2  plan-2  N    0.020
 6N2  plan-2  N2   0.020
 6N2  plan-2  C1   0.020
 6N2  plan-2  H1   0.020
 6N2  plan-2  H2   0.020
 6N2  plan-2  H9   0.020
 6N2  plan-2  H10  0.020
 6N2  plan-3  C5   0.020
 6N2  plan-3  C6   0.020
 6N2  plan-3  H5   0.020
 6N2  plan-3  N4   0.020

