# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 11:24:36 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 3-methyl-N-(1-methylpiperidin-4-yl)-5-[5-(propan-2-yl)-1H-benzimidazol-2-yl]-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1ccc2[nH]c(nc2c1)c3[nH]nc(C)c3C(=O)NC4CCN(C)CC4
#
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
 5BE  5BE  3-methyl-N-(1-methylpiperidin-4-yl)-5-[5-(propan-2-yl)-1H-benzimidazol-2-yl]-1H-pyrazole-4-carboxamide  ligand  56  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5BE
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
 5BE  C1    C  CH2   0  -0.277   2.0391   3.3169  -0.2924
 5BE  C2    C  CR5   0   0.405  -0.8000  -1.8986  -0.0401
 5BE  C3    C  CR5   0   0.422   0.2727  -2.8703   0.0571
 5BE  C4    C  CR5   0  -0.339   1.5970  -2.7085   0.4242
 5BE  C5    C  CR5   0   0.270   2.1329  -4.0148   0.4198
 5BE  N6    N  N     0  -0.266   1.2122  -4.8899   0.0610
 5BE  N7    N  NR15  0  -0.513   0.1058  -4.1878  -0.1494
 5BE  C8    C  CH3   0  -0.740   3.5249  -4.4345   0.7386
 5BE  C9    C  C     0   0.458   2.3175  -1.4624   0.7690
 5BE  O10   O  O     0  -0.489   3.0243  -1.3941   1.7670
 5BE  N11   N  NH1   0  -0.631   2.1521  -0.4481  -0.0915
 5BE  C12   C  CH1   0  -0.056   2.5567   0.9163   0.1810
 5BE  C13   C  CH2   0  -0.466   1.6164   1.8776  -0.5339
 5BE  N14   N  NT    0  -0.409   3.4097   3.5435  -0.7098
 5BE  C15   C  CH2   0  -0.283   4.3263   2.6732   0.0022
 5BE  C16   C  CH2   0  -0.429   3.9949   1.2077  -0.2363
 5BE  N17   N  N     0  -0.458  -0.8756  -0.8245   0.6995
 5BE  N18   N  NR15  0  -0.707  -1.8372  -2.0183  -0.9122
 5BE  C19   C  CR56  0   0.325  -2.6410  -0.9253  -0.7284
 5BE  C20   C  CR56  0   0.170  -2.0172  -0.1877   0.2883
 5BE  C21   C  CR16  0  -0.430  -2.5782   1.0123   0.7301
 5BE  C22   C  CR6   0   0.163  -3.7513   1.4578   0.1476
 5BE  C23   C  CR16  0  -0.323  -4.3531   0.6937  -0.8757
 5BE  C24   C  CR16  0  -0.294  -3.8207  -0.4976  -1.3290
 5BE  C25   C  CH1   0  -0.329  -4.3813   2.7584   0.5946
 5BE  C26   C  CH3   0  -0.643  -4.3594   3.8003  -0.5238
 5BE  C27   C  CH3   0  -0.645  -5.8010   2.5478   1.1199
 5BE  C28   C  CH3   0  -0.517   3.7780   4.9325  -0.5595
 5BE  H1    H  HCH2  0   0.239   1.3854   3.9869  -0.8559
 5BE  H1A   H  HCH2  0   0.188   1.8973   3.5644   0.7756
 5BE  HN7   H  HNR5  0   0.426  -0.7509  -4.6728  -0.3692
 5BE  H8    H  HCH3  0   0.253   3.7638  -4.2379   1.7834
 5BE  H8A   H  HCH3  0   0.251   3.6536  -5.4988   0.5518
 5BE  H8B   H  HCH3  0   0.249   4.2513  -3.8922   0.1333
 5BE  HN11  H  HNH1  0   0.398   1.5780  -0.6036  -0.9046
 5BE  H12   H  HCH1  0   0.233   2.4702   1.0802   1.2606
 5BE  H13   H  HCH2  0   0.249   0.5906   1.7301  -0.1882
 5BE  H13A  H  HCH2  0   0.227   1.6315   1.6736  -1.6099
 5BE  H15   H  HCH2  0   0.238   5.3430   2.8804  -0.3402
 5BE  H15A  H  HCH2  0   0.186   4.3139   2.8778   1.0890
 5BE  H16   H  HCH2  0   0.240   4.6876   0.5800   0.3268
 5BE  H16A  H  HCH2  0   0.219   4.1203   0.9684  -1.2966
 5BE  HN18  H  HNR5  0   0.424  -1.9506  -2.7276  -1.6197
 5BE  H21   H  HCR6  0   0.249  -2.0966   1.5837   1.5152
 5BE  H23   H  HCR6  0   0.249  -5.2708   1.0477  -1.3302
 5BE  H24   H  HCR6  0   0.266  -4.3029  -1.0664  -2.1130
 5BE  H25   H  HCH1  0   0.240  -3.7747   3.1453   1.4193
 5BE  H26   H  HCH3  0   0.230  -3.3425   3.9922  -0.8683
 5BE  H26A  H  HCH3  0   0.219  -4.9471   3.4741  -1.3842
 5BE  H26B  H  HCH3  0   0.229  -4.7799   4.7462  -0.1786
 5BE  H27   H  HCH3  0   0.231  -5.8197   1.8293   1.9402
 5BE  H27A  H  HCH3  0   0.230  -6.2187   3.4862   1.4880
 5BE  H27B  H  HCH3  0   0.218  -6.4658   2.1782   0.3364
 5BE  H28   H  HCH3  0   0.190   3.7232   5.2856   0.4827
 5BE  H28A  H  HCH3  0   0.232   4.7996   5.0896  -0.9087
 5BE  H28B  H  HCH3  0   0.231   3.1199   5.5633  -1.1591

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
 5BE  C1   C13   single    1.519  0.020  1.519
 5BE  C1   N14   single    1.451  0.020  1.451
 5BE  C2   C3    single    1.451  0.020  1.451
 5BE  C2   N17   aromatic  1.306  0.020  1.306
 5BE  C2   N18   aromatic  1.360  0.020  1.360
 5BE  C3   C4    aromatic  1.384  0.020  1.384
 5BE  C3   N7    aromatic  1.344  0.020  1.344
 5BE  C4   C5    aromatic  1.412  0.020  1.412
 5BE  C4   C9    single    1.480  0.020  1.480
 5BE  C5   N6    aromatic  1.320  0.020  1.320
 5BE  C5   C8    single    1.488  0.020  1.488
 5BE  N6   N7    aromatic  1.327  0.020  1.327
 5BE  C9   O10   double    1.225  0.020  1.225
 5BE  C9   N11   single    1.340  0.020  1.340
 5BE  N11  C12   single    1.449  0.020  1.449
 5BE  C12  C13   single    1.523  0.020  1.523
 5BE  C12  C16   single    1.526  0.020  1.526
 5BE  N14  C15   single    1.451  0.020  1.451
 5BE  N14  C28   single    1.445  0.020  1.445
 5BE  C15  C16   single    1.521  0.020  1.521
 5BE  N17  C20   aromatic  1.370  0.020  1.370
 5BE  N18  C19   aromatic  1.369  0.020  1.369
 5BE  C19  C20   aromatic  1.402  0.020  1.402
 5BE  C19  C24   aromatic  1.391  0.020  1.391
 5BE  C20  C21   aromatic  1.396  0.020  1.396
 5BE  C21  C22   aromatic  1.383  0.020  1.383
 5BE  C22  C23   aromatic  1.412  0.020  1.412
 5BE  C22  C25   single    1.513  0.020  1.513
 5BE  C23  C24   aromatic  1.381  0.020  1.381
 5BE  C25  C26   single    1.529  0.020  1.529
 5BE  C25  C27   single    1.528  0.020  1.528
 5BE  C1   H1    single    0.970  0.020  1.090
 5BE  C1   H1A   single    0.970  0.020  1.090
 5BE  N7   HN7   single    0.860  0.020  1.020
 5BE  C8   H8    single    0.970  0.020  1.090
 5BE  C8   H8A   single    0.970  0.020  1.090
 5BE  C8   H8B   single    0.970  0.020  1.090
 5BE  N11  HN11  single    0.860  0.020  1.020
 5BE  C12  H12   single    0.970  0.020  1.090
 5BE  C13  H13   single    0.970  0.020  1.090
 5BE  C13  H13A  single    0.970  0.020  1.090
 5BE  C15  H15   single    0.970  0.020  1.090
 5BE  C15  H15A  single    0.970  0.020  1.090
 5BE  C16  H16   single    0.970  0.020  1.090
 5BE  C16  H16A  single    0.970  0.020  1.090
 5BE  N18  HN18  single    0.860  0.020  1.020
 5BE  C21  H21   single    0.930  0.020  1.080
 5BE  C23  H23   single    0.930  0.020  1.080
 5BE  C24  H24   single    0.930  0.020  1.080
 5BE  C25  H25   single    0.970  0.020  1.090
 5BE  C26  H26   single    0.970  0.020  1.090
 5BE  C26  H26A  single    0.970  0.020  1.090
 5BE  C26  H26B  single    0.970  0.020  1.090
 5BE  C27  H27   single    0.970  0.020  1.090
 5BE  C27  H27A  single    0.970  0.020  1.090
 5BE  C27  H27B  single    0.970  0.020  1.090
 5BE  C28  H28   single    0.970  0.020  1.090
 5BE  C28  H28A  single    0.970  0.020  1.090
 5BE  C28  H28B  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
 5BE  H1A   C1   H1    106.51  3.000
 5BE  H1A   C1   N14   111.36  3.000
 5BE  H1    C1   N14   108.73  3.000
 5BE  H1A   C1   C13   109.26  3.000
 5BE  H1    C1   C13   109.42  3.000
 5BE  N14   C1   C13   111.41  3.000
 5BE  N18   C2   N17   113.03  3.000
 5BE  N18   C2   C3    123.22  3.000
 5BE  N17   C2   C3    123.76  3.000
 5BE  N7    C3   C4    105.92  3.000
 5BE  N7    C3   C2    123.68  3.000
 5BE  C4    C3   C2    130.33  3.000
 5BE  C9    C4   C5    126.50  3.000
 5BE  C9    C4   C3    128.76  3.000
 5BE  C5    C4   C3    104.73  3.000
 5BE  C8    C5   N6    121.57  3.000
 5BE  C8    C5   C4    127.96  3.000
 5BE  N6    C5   C4    110.46  3.000
 5BE  N7    N6   C5    105.90  3.000
 5BE  HN7   N7   N6    119.22  3.000
 5BE  HN7   N7   C3    127.61  3.000
 5BE  N6    N7   C3    113.00  3.000
 5BE  H8B   C8   H8A   108.21  3.000
 5BE  H8B   C8   H8    107.25  3.000
 5BE  H8A   C8   H8    108.37  3.000
 5BE  H8B   C8   C5    111.35  3.000
 5BE  H8A   C8   C5    110.47  3.000
 5BE  H8    C8   C5    111.07  3.000
 5BE  N11   C9   O10   123.51  3.000
 5BE  N11   C9   C4    115.30  3.000
 5BE  O10   C9   C4    121.18  3.000
 5BE  HN11  N11  C12   117.15  3.000
 5BE  HN11  N11  C9    118.14  3.000
 5BE  C12   N11  C9    123.87  3.000
 5BE  H12   C12  C16   108.39  3.000
 5BE  H12   C12  C13   108.63  3.000
 5BE  C16   C12  C13   109.45  3.000
 5BE  H12   C12  N11   107.71  3.000
 5BE  C16   C12  N11   113.06  3.000
 5BE  C13   C12  N11   109.49  3.000
 5BE  H13A  C13  H13   107.38  3.000
 5BE  H13A  C13  C12   109.58  3.000
 5BE  H13   C13  C12   110.24  3.000
 5BE  H13A  C13  C1    109.19  3.000
 5BE  H13   C13  C1    109.80  3.000
 5BE  C12   C13  C1    110.59  3.000
 5BE  C28   N14  C15   111.38  3.000
 5BE  C28   N14  C1    111.17  3.000
 5BE  C15   N14  C1    111.22  3.000
 5BE  H15A  C15  H15   106.46  3.000
 5BE  H15A  C15  C16   109.26  3.000
 5BE  H15   C15  C16   109.65  3.000
 5BE  H15A  C15  N14   111.36  3.000
 5BE  H15   C15  N14   108.68  3.000
 5BE  C16   C15  N14   111.31  3.000
 5BE  H16A  C16  H16   107.55  3.000
 5BE  H16A  C16  C15   109.74  3.000
 5BE  H16   C16  C15   109.57  3.000
 5BE  H16A  C16  C12   109.35  3.000
 5BE  H16   C16  C12   110.32  3.000
 5BE  C15   C16  C12   110.27  3.000
 5BE  C20   N17  C2    105.09  3.000
 5BE  HN18  N18  C19   126.14  3.000
 5BE  HN18  N18  C2    126.69  3.000
 5BE  C19   N18  C2    106.94  3.000
 5BE  C24   C19  C20   121.90  3.000
 5BE  C24   C19  N18   133.26  3.000
 5BE  C20   C19  N18   104.83  3.000
 5BE  C21   C20  C19   120.17  3.000
 5BE  C21   C20  N17   129.72  3.000
 5BE  C19   C20  N17   110.11  3.000
 5BE  H21   C21  C22   120.80  3.000
 5BE  H21   C21  C20   120.24  3.000
 5BE  C22   C21  C20   118.96  3.000
 5BE  C25   C22  C23   120.13  3.000
 5BE  C25   C22  C21   120.37  3.000
 5BE  C23   C22  C21   119.50  3.000
 5BE  H23   C23  C24   118.07  3.000
 5BE  H23   C23  C22   119.23  3.000
 5BE  C24   C23  C22   122.70  3.000
 5BE  H24   C24  C23   121.29  3.000
 5BE  H24   C24  C19   121.95  3.000
 5BE  C23   C24  C19   116.76  3.000
 5BE  H25   C25  C27   107.74  3.000
 5BE  H25   C25  C26   107.60  3.000
 5BE  C27   C25  C26   111.02  3.000
 5BE  H25   C25  C22   107.20  3.000
 5BE  C27   C25  C22   111.71  3.000
 5BE  C26   C25  C22   111.33  3.000
 5BE  H26B  C26  H26A  107.51  3.000
 5BE  H26B  C26  H26   107.86  3.000
 5BE  H26A  C26  H26   107.79  3.000
 5BE  H26B  C26  C25   110.72  3.000
 5BE  H26A  C26  C25   111.41  3.000
 5BE  H26   C26  C25   111.37  3.000
 5BE  H27B  C27  H27A  107.46  3.000
 5BE  H27B  C27  H27   107.83  3.000
 5BE  H27A  C27  H27   107.83  3.000
 5BE  H27B  C27  C25   111.44  3.000
 5BE  H27A  C27  C25   110.67  3.000
 5BE  H27   C27  C25   111.42  3.000
 5BE  H28B  C28  H28A  107.80  3.000
 5BE  H28B  C28  H28   107.73  3.000
 5BE  H28A  C28  H28   107.65  3.000
 5BE  H28B  C28  N14   110.17  3.000
 5BE  H28A  C28  N14   110.11  3.000
 5BE  H28   C28  N14   113.19  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
 5BE  CONST_01  C5    C4   C3   C2   180.00   0.0  0
 5BE  CONST_02  N6    N7   C3   C2   180.00   0.0  0
 5BE  CONST_03  C19   C20  N17  C2     0.00   0.0  0
 5BE  CONST_04  C21   C20  N17  C2   180.00   0.0  0
 5BE  CONST_05  C20   C19  N18  C2     0.00   0.0  0
 5BE  CONST_06  C24   C19  N18  C2   180.00   0.0  0
 5BE  CONST_07  C20   N17  C2   C3   180.00   0.0  0
 5BE  CONST_08  C19   N18  C2   C3   180.00   0.0  0
 5BE  CONST_09  N6    C5   C4   C3     0.00   0.0  0
 5BE  CONST_10  C5    N6   N7   C3     0.00   0.0  0
 5BE  CONST_13  N6    N7   C3   C4     0.00   0.0  0
 5BE  CONST_14  N7    N6   C5   C4     0.00   0.0  0
 5BE  CONST_15  N7    C3   C4   C5     0.00   0.0  0
 5BE  CONST_18  C19   N18  C2   N17    0.00   0.0  0
 5BE  CONST_19  N18   C19  C20  N17    0.00   0.0  0
 5BE  CONST_20  C24   C19  C20  N17  180.00   0.0  0
 5BE  CONST_21  C22   C21  C20  N17  180.00   0.0  0
 5BE  CONST_22  C20   N17  C2   N18    0.00   0.0  0
 5BE  CONST_23  C21   C20  C19  N18  180.00   0.0  0
 5BE  CONST_24  C23   C24  C19  N18  180.00   0.0  0
 5BE  CONST_25  C22   C21  C20  C19    0.00   0.0  0
 5BE  CONST_26  C22   C23  C24  C19    0.00   0.0  0
 5BE  CONST_27  C23   C24  C19  C20    0.00   0.0  0
 5BE  CONST_28  C23   C22  C21  C20    0.00   0.0  0
 5BE  CONST_29  C24   C19  C20  C21    0.00   0.0  0
 5BE  CONST_30  C24   C23  C22  C21    0.00   0.0  0
 5BE  CONST_31  C9    C4   C3   C2     0.00   0.0  0
 5BE  CONST_32  C8    C5   C4   C3   180.00   0.0  0
 5BE  CONST_33  C9    C4   C5   N6   180.00   0.0  0
 5BE  CONST_34  C9    C4   C3   N7   180.00   0.0  0
 5BE  CONST_35  C8    C5   N6   N7   180.00   0.0  0
 5BE  CONST_36  C25   C22  C21  C20  180.00   0.0  0
 5BE  CONST_37  C25   C22  C23  C24  180.00   0.0  0
 5BE  CONST_38  HN7   N7   C3   C2     0.00   0.0  0
 5BE  CONST_39  HN18  N18  C2   C3     0.00   0.0  0
 5BE  CONST_40  H21   C21  C20  N17    0.00   0.0  0
 5BE  CONST_41  H24   C24  C19  N18    0.00   0.0  0
 5BE  CONST_42  H23   C23  C24  C19  180.00   0.0  0
 5BE  CONST_43  C12   N11  C9   C4   180.00   0.0  0
 5BE  CONST_44  C12   N11  C9   O10    0.00   0.0  0
 5BE  CONST_45  HN11  N11  C9   C4     0.00   0.0  0
 5BE  Var_01    C16   C15  N14  C1    59.35  30.0  1
 5BE  Var_02    N14   C1   C13  C12   56.73  30.0  1
 5BE  Var_03    N14   C15  C16  C12  -57.26  30.0  1
 5BE  Var_04    C15   N14  C1   C13  -59.02  30.0  1
 5BE  Var_05    O10   C9   C4   C3   132.51  30.0  2
 5BE  Var_06    C26   C25  C22  C21  114.35  30.0  2
 5BE  Var_07    H28   C28  N14  C1    61.32  30.0  3
 5BE  Var_08    H8    C8   C5   C4    65.26  30.0  2
 5BE  Var_09    H26   C26  C25  C22  -57.74  30.0  3
 5BE  Var_10    H27   C27  C25  C22   56.92  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5BE  chir_01  C12  N11  C13  C16  positiv

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
 5BE  plan-1  C2    0.020
 5BE  plan-1  C3    0.020
 5BE  plan-1  C4    0.020
 5BE  plan-1  C5    0.020
 5BE  plan-1  N6    0.020
 5BE  plan-1  N7    0.020
 5BE  plan-1  C8    0.020
 5BE  plan-1  C9    0.020
 5BE  plan-1  HN7   0.020
 5BE  plan-2  C2    0.020
 5BE  plan-2  C3    0.020
 5BE  plan-2  N17   0.020
 5BE  plan-2  N18   0.020
 5BE  plan-2  C19   0.020
 5BE  plan-2  C20   0.020
 5BE  plan-2  C21   0.020
 5BE  plan-2  C22   0.020
 5BE  plan-2  C23   0.020
 5BE  plan-2  C24   0.020
 5BE  plan-2  C25   0.020
 5BE  plan-2  HN18  0.020
 5BE  plan-2  H21   0.020
 5BE  plan-2  H23   0.020
 5BE  plan-2  H24   0.020
 5BE  plan-3  C4    0.020
 5BE  plan-3  C9    0.020
 5BE  plan-3  O10   0.020
 5BE  plan-3  N11   0.020
 5BE  plan-3  C12   0.020
 5BE  plan-3  HN11  0.020

