# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:58:06 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [5-amino-1-(2-methyl-1H-benzimidazol-6-yl)-1H-pyrazol-4-yl](1H-indol-2-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c2cc(ccc2n1)n3ncc(c3N)C(=O)c4[nH]c5ccccc5c4
#
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
 LWJ  LWJ  '[5-amino-1-(2-methyl-1H-benzimidazol-6-yl)-1H-pyrazol-4-yl](1H-indol-2-yl)methanone'  ligand  43  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LWJ
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
 LWJ  C1   C  CR56  0   0.144  -5.3409   0.1762   0.6543
 LWJ  C2   C  CR56  0   0.356  -4.7388  -0.6396  -0.3206
 LWJ  N3   N  NR15  0  -0.690  -5.7858  -1.2609  -0.9408
 LWJ  C4   C  CR5   0   0.423  -6.9321  -0.8231  -0.3527
 LWJ  N5   N  N     0  -0.475  -6.7061   0.0368   0.6048
 LWJ  C6   C  CR56  0   0.059   5.6048   0.1644  -0.5296
 LWJ  C7   C  CR56  0   0.345   5.0245  -0.7268   0.4010
 LWJ  C8   C  CR16  0  -0.308   5.7619  -1.7339   1.0268
 LWJ  C9   C  CR16  0  -0.277   7.0938  -1.8435   0.6883
 LWJ  C10  C  CR16  0  -0.269   7.6893  -0.9761  -0.2481
 LWJ  C11  C  CR16  0  -0.338   6.9614   0.0221  -0.8577
 LWJ  C12  C  CR5   0   0.233   3.4382   0.6947  -0.2636
 LWJ  N13  N  NR15  0  -0.743   3.7100  -0.3966   0.5260
 LWJ  C14  C  CR15  0  -0.394   4.5794   1.0655  -0.9277
 LWJ  C15  C  CR5   0   0.626  -0.3647   1.1013  -0.0008
 LWJ  C16  C  CR5   0  -0.306   0.9297   0.5606  -0.1058
 LWJ  C17  C  CR15  0  -0.083   0.7173  -0.8390   0.0087
 LWJ  N18  N  N     0  -0.280  -0.5372  -1.1358   0.1816
 LWJ  N19  N  NR5   0  -0.457  -1.1933   0.0578   0.1944
 LWJ  O21  O  O     0  -0.446   2.0584   2.5177  -0.6956
 LWJ  C22  C  CR6   0   0.285  -2.6000   0.0897   0.3333
 LWJ  C23  C  CR16  0  -0.339  -3.3678  -0.6961  -0.5116
 LWJ  C24  C  CR16  0  -0.332  -4.5449   0.9572   1.4877
 LWJ  C25  C  CR16  0  -0.311  -3.1724   0.8982   1.3262
 LWJ  N26  N  NH2   0  -0.839  -0.7657   2.3828  -0.0396
 LWJ  C27  C  CH3   0  -0.751  -8.2659  -1.3054  -0.7869
 LWJ  H1   H  HNR5  0   0.422  -5.7279  -1.9212  -1.7001
 LWJ  H4   H  HCR6  0   0.256   7.6965  -2.6143   1.1507
 LWJ  H5   H  HCR6  0   0.252   8.7372  -1.0999  -0.4880
 LWJ  H6   H  HCR6  0   0.252   7.4276   0.6872  -1.5738
 LWJ  H7   H  HNR5  0   0.416   3.0938  -0.7773   1.2257
 LWJ  H8   H  HCR5  0   0.261   4.6589   1.8697  -1.6417
 LWJ  H9   H  HCR5  0   0.273   1.4443  -1.6335  -0.0622
 LWJ  H10  H  HCR6  0   0.281  -2.9126  -1.3151  -1.2731
 LWJ  H11  H  HCR6  0   0.264  -4.9849   1.5811   2.2546
 LWJ  H12  H  HCR6  0   0.279  -2.5306   1.4680   1.9853
 LWJ  H13  H  HNH2  0   0.411  -0.1059   3.0358  -0.4300
 LWJ  H14  H  HNH2  0   0.407  -1.7374   2.5878  -0.2093
 LWJ  H15  H  HCH3  0   0.266  -8.4223  -1.1187  -1.8497
 LWJ  H16  H  HCH3  0   0.268  -8.3631  -2.3797  -0.6249
 LWJ  H17  H  HCH3  0   0.266  -9.0458  -0.7990  -0.2250
 LWJ  C20  C  C     0   0.329   2.1161   1.3340  -0.3687
 LWJ  H3   H  HCR6  0   0.264   5.3055  -2.4029   1.7452

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
 LWJ  C27  C4   single    1.483  0.020  1.483
 LWJ  C4   N5   aromatic  1.307  0.020  1.307
 LWJ  C4   N3   aromatic  1.361  0.020  1.361
 LWJ  N5   C1   aromatic  1.373  0.020  1.373
 LWJ  N3   C2   aromatic  1.366  0.020  1.366
 LWJ  C1   C2   aromatic  1.407  0.020  1.407
 LWJ  C1   C24  aromatic  1.392  0.020  1.392
 LWJ  C2   C23  aromatic  1.385  0.020  1.385
 LWJ  C24  C25  aromatic  1.383  0.020  1.383
 LWJ  C23  C22  aromatic  1.386  0.020  1.386
 LWJ  C25  C22  aromatic  1.403  0.020  1.403
 LWJ  C22  N19  single    1.414  0.020  1.414
 LWJ  N19  N18  aromatic  1.362  0.020  1.362
 LWJ  N19  C15  aromatic  1.347  0.020  1.347
 LWJ  N18  C17  aromatic  1.301  0.020  1.301
 LWJ  N26  C15  single    1.343  0.020  1.343
 LWJ  C15  C16  aromatic  1.407  0.020  1.407
 LWJ  C17  C16  aromatic  1.420  0.020  1.420
 LWJ  C16  C20  single    1.440  0.020  1.440
 LWJ  C20  O21  double    1.229  0.020  1.229
 LWJ  C20  C12  single    1.472  0.020  1.472
 LWJ  C12  N13  aromatic  1.374  0.020  1.374
 LWJ  C12  C14  aromatic  1.371  0.020  1.371
 LWJ  N13  C7   aromatic  1.361  0.020  1.361
 LWJ  C14  C6   aromatic  1.422  0.020  1.422
 LWJ  C7   C8   aromatic  1.396  0.020  1.396
 LWJ  C7   C6   aromatic  1.413  0.020  1.413
 LWJ  C8   C9   aromatic  1.379  0.020  1.379
 LWJ  C6   C11  aromatic  1.403  0.020  1.403
 LWJ  C9   C10  aromatic  1.409  0.020  1.409
 LWJ  C11  C10  aromatic  1.378  0.020  1.378
 LWJ  N3   H1   single    0.860  0.020  1.020
 LWJ  C8   H3   single    0.930  0.020  1.080
 LWJ  C9   H4   single    0.930  0.020  1.080
 LWJ  C10  H5   single    0.930  0.020  1.080
 LWJ  C11  H6   single    0.930  0.020  1.080
 LWJ  N13  H7   single    0.860  0.020  1.020
 LWJ  C14  H8   single    0.930  0.020  1.080
 LWJ  C17  H9   single    0.930  0.020  1.080
 LWJ  C23  H10  single    0.930  0.020  1.080
 LWJ  C24  H11  single    0.930  0.020  1.080
 LWJ  C25  H12  single    0.930  0.020  1.080
 LWJ  N26  H13  single    0.890  0.020  1.040
 LWJ  N26  H14  single    0.890  0.020  1.040
 LWJ  C27  H15  single    0.970  0.020  1.090
 LWJ  C27  H16  single    0.970  0.020  1.090
 LWJ  C27  H17  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
 LWJ  C24  C1   N5   130.32  3.000
 LWJ  C24  C1   C2   119.71  3.000
 LWJ  N5   C1   C2   109.98  3.000
 LWJ  C23  C2   N3   132.63  3.000
 LWJ  C23  C2   C1   122.87  3.000
 LWJ  N3   C2   C1   104.50  3.000
 LWJ  H1   N3   C4   125.79  3.000
 LWJ  H1   N3   C2   126.57  3.000
 LWJ  C4   N3   C2   107.64  3.000
 LWJ  C27  C4   N5   125.73  3.000
 LWJ  N5   C4   N3   112.50  3.000
 LWJ  C27  C4   N3   121.76  3.000
 LWJ  C4   N5   C1   105.38  3.000
 LWJ  C14  C6   C11  134.11  3.000
 LWJ  C11  C6   C7   119.15  3.000
 LWJ  C14  C6   C7   106.73  3.000
 LWJ  N13  C7   C8   130.08  3.000
 LWJ  C8   C7   C6   122.22  3.000
 LWJ  N13  C7   C6   107.70  3.000
 LWJ  H3   C8   C9   121.41  3.000
 LWJ  H3   C8   C7   121.37  3.000
 LWJ  C9   C8   C7   117.22  3.000
 LWJ  H4   C9   C10  119.16  3.000
 LWJ  H4   C9   C8   119.33  3.000
 LWJ  C10  C9   C8   121.52  3.000
 LWJ  H5   C10  C11  119.77  3.000
 LWJ  H5   C10  C9   119.10  3.000
 LWJ  C11  C10  C9   121.13  3.000
 LWJ  H6   C11  C10  120.68  3.000
 LWJ  H6   C11  C6   120.57  3.000
 LWJ  C10  C11  C6   118.75  3.000
 LWJ  C20  C12  C14  126.53  3.000
 LWJ  C14  C12  N13  109.17  3.000
 LWJ  C20  C12  N13  124.29  3.000
 LWJ  H7   N13  C12  125.34  3.000
 LWJ  H7   N13  C7   124.26  3.000
 LWJ  C12  N13  C7   109.32  3.000
 LWJ  H8   C14  C12  125.71  3.000
 LWJ  H8   C14  C6   127.22  3.000
 LWJ  C12  C14  C6   107.04  3.000
 LWJ  N26  C15  N19  124.03  3.000
 LWJ  N26  C15  C16  129.73  3.000
 LWJ  N19  C15  C16  106.21  3.000
 LWJ  C20  C16  C17  131.83  3.000
 LWJ  C20  C16  C15  124.41  3.000
 LWJ  C17  C16  C15  103.60  3.000
 LWJ  H9   C17  N18  119.37  3.000
 LWJ  H9   C17  C16  128.27  3.000
 LWJ  N18  C17  C16  112.32  3.000
 LWJ  N19  N18  C17  105.42  3.000
 LWJ  C22  N19  N18  119.99  3.000
 LWJ  N18  N19  C15  112.41  3.000
 LWJ  C22  N19  C15  127.51  3.000
 LWJ  C25  C22  C23  122.16  3.000
 LWJ  C25  C22  N19  119.25  3.000
 LWJ  C23  C22  N19  118.59  3.000
 LWJ  H10  C23  C22  121.36  3.000
 LWJ  H10  C23  C2   122.47  3.000
 LWJ  C22  C23  C2   116.17  3.000
 LWJ  H11  C24  C25  120.72  3.000
 LWJ  H11  C24  C1   121.01  3.000
 LWJ  C25  C24  C1   118.26  3.000
 LWJ  H12  C25  C24  119.66  3.000
 LWJ  H12  C25  C22  119.51  3.000
 LWJ  C24  C25  C22  120.81  3.000
 LWJ  H14  N26  H13  115.76  3.000
 LWJ  H14  N26  C15  119.14  3.000
 LWJ  H13  N26  C15  115.74  3.000
 LWJ  H17  C27  H16  108.56  3.000
 LWJ  H17  C27  H15  108.75  3.000
 LWJ  H16  C27  H15  107.49  3.000
 LWJ  H17  C27  C4   110.03  3.000
 LWJ  H16  C27  C4   110.91  3.000
 LWJ  H15  C27  C4   111.02  3.000
 LWJ  O21  C20  C16  121.79  3.000
 LWJ  O21  C20  C12  118.63  3.000
 LWJ  C16  C20  C12  119.57  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
 LWJ  CONST_01  N3   C4   N5   C1     0.00   0.0  0
 LWJ  CONST_02  C4   N3   C2   C1     0.00   0.0  0
 LWJ  CONST_03  C22  C23  C2   C1     0.00   0.0  0
 LWJ  CONST_04  C22  C25  C24  C1     0.00   0.0  0
 LWJ  CONST_05  N5   C4   N3   C2     0.00   0.0  0
 LWJ  CONST_06  C4   N5   C1   C2     0.00   0.0  0
 LWJ  CONST_07  C25  C24  C1   C2     0.00   0.0  0
 LWJ  CONST_08  C25  C22  C23  C2     0.00   0.0  0
 LWJ  CONST_09  N19  C22  C23  C2   180.00   0.0  0
 LWJ  CONST_10  N5   C1   C2   N3     0.00   0.0  0
 LWJ  CONST_11  C24  C1   C2   N3   180.00   0.0  0
 LWJ  CONST_12  C22  C23  C2   N3   180.00   0.0  0
 LWJ  CONST_13  C24  C1   N5   C4   180.00   0.0  0
 LWJ  CONST_14  C23  C2   N3   C4   180.00   0.0  0
 LWJ  CONST_15  C23  C2   C1   N5   180.00   0.0  0
 LWJ  CONST_16  C25  C24  C1   N5   180.00   0.0  0
 LWJ  CONST_17  N13  C12  C14  C6     0.00   0.0  0
 LWJ  CONST_18  C12  N13  C7   C6     0.00   0.0  0
 LWJ  CONST_19  C9   C8   C7   C6     0.00   0.0  0
 LWJ  CONST_20  C9   C10  C11  C6     0.00   0.0  0
 LWJ  CONST_21  C14  C12  N13  C7     0.00   0.0  0
 LWJ  CONST_22  C10  C9   C8   C7     0.00   0.0  0
 LWJ  CONST_23  C12  C14  C6   C7     0.00   0.0  0
 LWJ  CONST_24  C10  C11  C6   C7     0.00   0.0  0
 LWJ  CONST_25  C12  N13  C7   C8   180.00   0.0  0
 LWJ  CONST_26  C14  C6   C7   C8   180.00   0.0  0
 LWJ  CONST_27  C11  C6   C7   C8     0.00   0.0  0
 LWJ  CONST_28  C11  C10  C9   C8     0.00   0.0  0
 LWJ  CONST_29  N13  C7   C8   C9   180.00   0.0  0
 LWJ  CONST_30  C14  C6   C11  C10  180.00   0.0  0
 LWJ  CONST_31  C12  C14  C6   C11  180.00   0.0  0
 LWJ  CONST_32  N13  C7   C6   C11  180.00   0.0  0
 LWJ  CONST_33  C14  C6   C7   N13    0.00   0.0  0
 LWJ  CONST_36  C17  N18  N19  C15    0.00   0.0  0
 LWJ  CONST_37  N18  C17  C16  C15    0.00   0.0  0
 LWJ  CONST_38  C22  N19  C15  C16  180.00   0.0  0
 LWJ  CONST_39  N18  N19  C15  C16    0.00   0.0  0
 LWJ  CONST_40  N19  N18  C17  C16    0.00   0.0  0
 LWJ  CONST_41  C22  N19  N18  C17  180.00   0.0  0
 LWJ  CONST_42  N19  C15  C16  C17    0.00   0.0  0
 LWJ  CONST_45  C24  C25  C22  N19  180.00   0.0  0
 LWJ  CONST_46  C24  C1   C2   C23    0.00   0.0  0
 LWJ  CONST_47  C24  C25  C22  C23    0.00   0.0  0
 LWJ  CONST_48  C27  C4   N5   C1   180.00   0.0  0
 LWJ  CONST_49  C27  C4   N3   C2   180.00   0.0  0
 LWJ  CONST_50  C20  C12  C14  C6   180.00   0.0  0
 LWJ  CONST_51  C20  C12  N13  C7   180.00   0.0  0
 LWJ  CONST_52  N26  C15  C16  C17  180.00   0.0  0
 LWJ  CONST_53  N26  C15  N19  N18  180.00   0.0  0
 LWJ  CONST_54  C20  C16  C17  N18  180.00   0.0  0
 LWJ  CONST_55  C20  C16  C15  N19  180.00   0.0  0
 LWJ  CONST_56  N26  C15  N19  C22    0.00   0.0  0
 LWJ  CONST_57  H1   N3   C2   C1   180.00   0.0  0
 LWJ  CONST_58  H10  C23  C2   C1   180.00   0.0  0
 LWJ  CONST_59  H12  C25  C24  C1   180.00   0.0  0
 LWJ  CONST_60  H11  C24  C1   C2   180.00   0.0  0
 LWJ  CONST_61  H7   N13  C7   C6   180.00   0.0  0
 LWJ  CONST_62  H3   C8   C7   C6   180.00   0.0  0
 LWJ  CONST_63  H5   C10  C11  C6   180.00   0.0  0
 LWJ  CONST_64  H4   C9   C8   C7   180.00   0.0  0
 LWJ  CONST_65  H8   C14  C6   C7   180.00   0.0  0
 LWJ  CONST_66  H6   C11  C6   C7   180.00   0.0  0
 LWJ  CONST_67  H9   C17  C16  C15  180.00   0.0  0
 LWJ  Var_01    C15  C16  C20  C12  171.14  30.0  1
 LWJ  Var_02    C16  C20  C12  N13  -25.90  30.0  2
 LWJ  Var_03    H15  C27  C4   N3   -56.84  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
 LWJ  plan-1  C15  0.020
 LWJ  plan-1  C16  0.020
 LWJ  plan-1  C17  0.020
 LWJ  plan-1  N18  0.020
 LWJ  plan-1  N19  0.020
 LWJ  plan-1  C22  0.020
 LWJ  plan-1  N26  0.020
 LWJ  plan-1  H9   0.020
 LWJ  plan-1  C20  0.020
 LWJ  plan-2  C1   0.020
 LWJ  plan-2  C2   0.020
 LWJ  plan-2  N3   0.020
 LWJ  plan-2  C4   0.020
 LWJ  plan-2  N5   0.020
 LWJ  plan-2  N19  0.020
 LWJ  plan-2  C22  0.020
 LWJ  plan-2  C23  0.020
 LWJ  plan-2  C24  0.020
 LWJ  plan-2  C25  0.020
 LWJ  plan-2  C27  0.020
 LWJ  plan-2  H1   0.020
 LWJ  plan-2  H10  0.020
 LWJ  plan-2  H11  0.020
 LWJ  plan-2  H12  0.020
 LWJ  plan-3  C6   0.020
 LWJ  plan-3  C7   0.020
 LWJ  plan-3  C8   0.020
 LWJ  plan-3  C9   0.020
 LWJ  plan-3  C10  0.020
 LWJ  plan-3  C11  0.020
 LWJ  plan-3  C12  0.020
 LWJ  plan-3  N13  0.020
 LWJ  plan-3  C14  0.020
 LWJ  plan-3  H4   0.020
 LWJ  plan-3  H5   0.020
 LWJ  plan-3  H6   0.020
 LWJ  plan-3  H7   0.020
 LWJ  plan-3  H8   0.020
 LWJ  plan-3  C20  0.020
 LWJ  plan-3  H3   0.020
 LWJ  plan-4  C15  0.020
 LWJ  plan-4  N26  0.020
 LWJ  plan-4  H13  0.020
 LWJ  plan-4  H14  0.020
 LWJ  plan-5  C12  0.020
 LWJ  plan-5  C16  0.020
 LWJ  plan-5  O21  0.020
 LWJ  plan-5  C20  0.020

