# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 16:40:04 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: N-[(pyridin-2-yl)methyl]-4-[4-(pyridin-4-yl)-1H-pyrazol-1-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccccn1)c2ccc(cc2)n3cc(cn3)c4ccncc4
#
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
 6BJ  6BJ  N-[(pyridin-2-yl)methyl]-4-[4-(pyridin-4-yl)-1H-pyrazol-1-yl]benzamide  ligand  44  27  .  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_6BJ
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
 6BJ  C1   C  CR5   0  -0.128  -4.5619  -0.5739   0.1822
 6BJ  C2   C  CR15  0   0.027  -3.5290   0.3175  -0.0032
 6BJ  C3   C  CR15  0  -0.065  -3.9055  -1.7956   0.4629
 6BJ  O1   O  O     0  -0.495   3.0846   2.8437  -0.4788
 6BJ  C11  C  CR6   0  -0.041   1.5516   1.0623  -0.1628
 6BJ  C12  C  CR16  0  -0.282   1.2730  -0.2978  -0.2822
 6BJ  C13  C  CR16  0  -0.263   0.4930   1.9362   0.0690
 6BJ  C14  C  CR16  0  -0.285  -0.0210  -0.7752  -0.1742
 6BJ  C15  C  C     0   0.558   2.9235   1.6424  -0.2970
 6BJ  C16  C  CH2   0  -0.285   5.3156   1.2145  -0.3502
 6BJ  C17  C  CR6   0   0.228   6.2446   0.0298  -0.2681
 6BJ  C18  C  CR16  0  -0.328   7.6142   0.2072  -0.4445
 6BJ  C19  C  CR16  0  -0.145   8.4418  -0.8971  -0.3619
 6BJ  C20  C  CR16  0  -0.336   7.8798  -2.1425  -0.1069
 6BJ  C21  C  CR16  0  -0.057   6.5087  -2.2174   0.0553
 6BJ  N1   N  NR5   0  -0.411  -2.3806  -0.3711   0.1670
 6BJ  N2   N  N     0  -0.261  -2.6026  -1.6601   0.4469
 6BJ  C4   C  CR16  0  -0.059  -7.8818   1.0596  -0.4234
 6BJ  N3   N  N     0  -0.412  -8.7623   0.1355  -0.0528
 6BJ  C5   C  CR16  0  -0.059  -8.2729  -1.0158   0.3938
 6BJ  C6   C  CR16  0  -0.406  -6.9196  -1.2922   0.4914
 6BJ  C7   C  CR6   0   0.190  -5.9941  -0.3242   0.1009
 6BJ  C8   C  CR16  0  -0.408  -6.5101   0.8837  -0.3696
 6BJ  C9   C  CR6   0   0.390  -1.0642   0.1123   0.0651
 6BJ  C10  C  CR16  0  -0.305  -0.8033   1.4720   0.1956
 6BJ  N4   N  NH1   0  -0.680   3.9500   0.7898  -0.2068
 6BJ  N5   N  N     0  -0.458   5.7094  -1.1566  -0.0232
 6BJ  H1   H  HCR5  0   0.308  -3.5348   1.3652  -0.2536
 6BJ  H2   H  HCR5  0   0.277  -4.3450  -2.7596   0.6698
 6BJ  H3   H  HCR6  0   0.258   2.0522  -1.0191  -0.4916
 6BJ  H4   H  HCR6  0   0.268   0.6802   2.9967   0.1653
 6BJ  H5   H  HCR6  0   0.286  -0.2150  -1.8319  -0.2857
 6BJ  H6   H  HCH2  0   0.267   5.5851   1.9385   0.4258
 6BJ  H7   H  HCH2  0   0.267   5.4637   1.7228  -1.3074
 6BJ  H8   H  HCR6  0   0.271   8.0158   1.1922  -0.6447
 6BJ  H9   H  HCR6  0   0.277   9.5103  -0.7914  -0.4944
 6BJ  H10  H  HCR6  0   0.274   8.4899  -3.0320  -0.0354
 6BJ  H11  H  HCR6  0   0.268   6.0288  -3.1678   0.2581
 6BJ  H12  H  HCR6  0   0.266  -8.2868   1.9970  -0.7881
 6BJ  H13  H  HCR6  0   0.265  -8.9957  -1.7663   0.6945
 6BJ  H14  H  HCR6  0   0.266  -6.6021  -2.2520   0.8763
 6BJ  H15  H  HCR6  0   0.260  -5.8628   1.6849  -0.7006
 6BJ  H16  H  HCR6  0   0.286  -1.5962   2.1765   0.4071
 6BJ  H17  H  HNH1  0   0.411   3.8231  -0.1881   0.0104

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
 6BJ  C21  C20  aromatic  1.383  0.020  1.383
 6BJ  C21  N5   aromatic  1.331  0.020  1.331
 6BJ  C20  C19  aromatic  1.390  0.020  1.390
 6BJ  N5   C17  aromatic  1.324  0.020  1.324
 6BJ  C19  C18  aromatic  1.383  0.020  1.383
 6BJ  C17  C18  aromatic  1.392  0.020  1.392
 6BJ  C17  C16  single    1.508  0.020  1.508
 6BJ  C16  N4   single    1.437  0.020  1.437
 6BJ  N4   C15  single    1.337  0.020  1.337
 6BJ  C15  O1   double    1.226  0.020  1.226
 6BJ  C15  C11  single    1.496  0.020  1.496
 6BJ  C12  C11  aromatic  1.393  0.020  1.393
 6BJ  C12  C14  aromatic  1.383  0.020  1.383
 6BJ  C11  C13  aromatic  1.392  0.020  1.392
 6BJ  C14  C9   aromatic  1.390  0.020  1.390
 6BJ  C13  C10  aromatic  1.383  0.020  1.383
 6BJ  C9   C10  aromatic  1.391  0.020  1.391
 6BJ  C9   N1   single    1.406  0.020  1.406
 6BJ  N2   N1   aromatic  1.338  0.020  1.338
 6BJ  N2   C3   aromatic  1.310  0.020  1.310
 6BJ  N1   C2   aromatic  1.350  0.020  1.350
 6BJ  C3   C1   aromatic  1.415  0.020  1.415
 6BJ  C2   C1   aromatic  1.377  0.020  1.377
 6BJ  C1   C7   single    1.456  0.020  1.456
 6BJ  C7   C6   aromatic  1.395  0.020  1.395
 6BJ  C7   C8   aromatic  1.395  0.020  1.395
 6BJ  C6   C5   aromatic  1.385  0.020  1.385
 6BJ  C8   C4   aromatic  1.384  0.020  1.384
 6BJ  C5   N3   aromatic  1.328  0.020  1.328
 6BJ  C4   N3   aromatic  1.329  0.020  1.329
 6BJ  C2   H1   single    0.930  0.020  1.080
 6BJ  C3   H2   single    0.930  0.020  1.080
 6BJ  C12  H3   single    0.930  0.020  1.080
 6BJ  C13  H4   single    0.930  0.020  1.080
 6BJ  C14  H5   single    0.930  0.020  1.080
 6BJ  C16  H6   single    0.970  0.020  1.090
 6BJ  C16  H7   single    0.970  0.020  1.090
 6BJ  C18  H8   single    0.930  0.020  1.080
 6BJ  C19  H9   single    0.930  0.020  1.080
 6BJ  C20  H10  single    0.930  0.020  1.080
 6BJ  C21  H11  single    0.930  0.020  1.080
 6BJ  C4   H12  single    0.930  0.020  1.080
 6BJ  C5   H13  single    0.930  0.020  1.080
 6BJ  C6   H14  single    0.930  0.020  1.080
 6BJ  C8   H15  single    0.930  0.020  1.080
 6BJ  C10  H16  single    0.930  0.020  1.080
 6BJ  N4   H17  single    0.860  0.020  1.020

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
 6BJ  C7   C1   C3   127.98  3.000
 6BJ  C7   C1   C2   128.27  3.000
 6BJ  C3   C1   C2   103.75  3.000
 6BJ  H1   C2   N1   122.01  3.000
 6BJ  H1   C2   C1   131.06  3.000
 6BJ  N1   C2   C1   106.92  3.000
 6BJ  H2   C3   N2   119.98  3.000
 6BJ  H2   C3   C1   128.33  3.000
 6BJ  N2   C3   C1   111.69  3.000
 6BJ  C15  C11  C13  117.97  3.000
 6BJ  C13  C11  C12  118.35  3.000
 6BJ  C15  C11  C12  123.67  3.000
 6BJ  H3   C12  C14  117.29  3.000
 6BJ  H3   C12  C11  121.54  3.000
 6BJ  C14  C12  C11  121.14  3.000
 6BJ  H4   C13  C10  118.92  3.000
 6BJ  H4   C13  C11  119.92  3.000
 6BJ  C10  C13  C11  121.16  3.000
 6BJ  H5   C14  C9   120.50  3.000
 6BJ  H5   C14  C12  119.84  3.000
 6BJ  C9   C14  C12  119.66  3.000
 6BJ  N4   C15  C11  116.79  3.000
 6BJ  C11  C15  O1   120.94  3.000
 6BJ  N4   C15  O1   122.28  3.000
 6BJ  H7   C16  H6   106.24  3.000
 6BJ  H7   C16  N4   110.69  3.000
 6BJ  H6   C16  N4   111.02  3.000
 6BJ  H7   C16  C17  109.22  3.000
 6BJ  H6   C16  C17  109.23  3.000
 6BJ  N4   C16  C17  110.35  3.000
 6BJ  N5   C17  C18  122.35  3.000
 6BJ  C18  C17  C16  119.94  3.000
 6BJ  N5   C17  C16  117.71  3.000
 6BJ  H8   C18  C19  121.05  3.000
 6BJ  H8   C18  C17  120.30  3.000
 6BJ  C19  C18  C17  118.65  3.000
 6BJ  H9   C19  C20  120.62  3.000
 6BJ  H9   C19  C18  120.39  3.000
 6BJ  C20  C19  C18  118.99  3.000
 6BJ  H10  C20  C21  120.49  3.000
 6BJ  H10  C20  C19  121.41  3.000
 6BJ  C21  C20  C19  118.10  3.000
 6BJ  H11  C21  N5   116.37  3.000
 6BJ  H11  C21  C20  120.57  3.000
 6BJ  N5   C21  C20  123.06  3.000
 6BJ  C9   N1   N2   120.13  3.000
 6BJ  N2   N1   C2   112.13  3.000
 6BJ  C9   N1   C2   127.73  3.000
 6BJ  N1   N2   C3   105.51  3.000
 6BJ  H12  C4   C8   119.55  3.000
 6BJ  H12  C4   N3   116.58  3.000
 6BJ  C8   C4   N3   123.88  3.000
 6BJ  C5   N3   C4   116.89  3.000
 6BJ  H13  C5   C6   119.58  3.000
 6BJ  H13  C5   N3   116.58  3.000
 6BJ  C6   C5   N3   123.84  3.000
 6BJ  H14  C6   C7   121.37  3.000
 6BJ  H14  C6   C5   119.28  3.000
 6BJ  C7   C6   C5   119.35  3.000
 6BJ  C8   C7   C6   116.73  3.000
 6BJ  C8   C7   C1   122.08  3.000
 6BJ  C6   C7   C1   121.20  3.000
 6BJ  H15  C8   C7   121.53  3.000
 6BJ  H15  C8   C4   119.15  3.000
 6BJ  C7   C8   C4   119.32  3.000
 6BJ  C10  C9   N1   120.33  3.000
 6BJ  N1   C9   C14  119.70  3.000
 6BJ  C10  C9   C14  119.97  3.000
 6BJ  H16  C10  C9   121.18  3.000
 6BJ  H16  C10  C13  119.11  3.000
 6BJ  C9   C10  C13  119.71  3.000
 6BJ  H17  N4   C16  115.28  3.000
 6BJ  H17  N4   C15  122.38  3.000
 6BJ  C16  N4   C15  122.28  3.000
 6BJ  C21  N5   C17  118.84  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
 6BJ  CONST_01  N1   N2   C3   C1      0.00   0.0  0
 6BJ  CONST_02  C9   N1   C2   C1    180.00   0.0  0
 6BJ  CONST_03  N2   N1   C2   C1      0.00   0.0  0
 6BJ  CONST_04  C5   C6   C7   C1    180.00   0.0  0
 6BJ  CONST_05  C4   C8   C7   C1    180.00   0.0  0
 6BJ  CONST_08  C3   N2   N1   C2      0.00   0.0  0
 6BJ  CONST_09  N2   C3   C1   C2      0.00   0.0  0
 6BJ  CONST_10  C6   C7   C1   C2    180.00   0.0  0
 6BJ  CONST_11  C8   C7   C1   C2      0.00   0.0  0
 6BJ  CONST_12  C9   N1   N2   C3    180.00   0.0  0
 6BJ  CONST_13  N1   C2   C1   C3      0.00   0.0  0
 6BJ  CONST_14  C6   C7   C1   C3      0.00   0.0  0
 6BJ  CONST_15  C8   C7   C1   C3    180.00   0.0  0
 6BJ  CONST_16  C9   C14  C12  C11     0.00   0.0  0
 6BJ  CONST_17  C9   C10  C13  C11     0.00   0.0  0
 6BJ  CONST_18  C10  C13  C11  C12     0.00   0.0  0
 6BJ  CONST_19  C10  C9   C14  C12     0.00   0.0  0
 6BJ  CONST_20  N1   C9   C14  C12   180.00   0.0  0
 6BJ  CONST_21  C14  C12  C11  C13     0.00   0.0  0
 6BJ  CONST_22  C14  C9   C10  C13     0.00   0.0  0
 6BJ  CONST_23  N1   C9   C10  C13   180.00   0.0  0
 6BJ  CONST_25  C20  C21  N5   C17     0.00   0.0  0
 6BJ  CONST_26  C20  C19  C18  C17     0.00   0.0  0
 6BJ  CONST_27  C21  C20  C19  C18     0.00   0.0  0
 6BJ  CONST_28  C21  N5   C17  C18     0.00   0.0  0
 6BJ  CONST_29  N5   C21  C20  C19     0.00   0.0  0
 6BJ  CONST_30  N5   C17  C18  C19     0.00   0.0  0
 6BJ  CONST_31  C7   C1   C2   N1    180.00   0.0  0
 6BJ  CONST_33  C7   C1   C3   N2    180.00   0.0  0
 6BJ  CONST_34  C6   C7   C8   C4      0.00   0.0  0
 6BJ  CONST_35  C6   C5   N3   C4      0.00   0.0  0
 6BJ  CONST_36  C7   C6   C5   N3      0.00   0.0  0
 6BJ  CONST_37  C7   C8   C4   N3      0.00   0.0  0
 6BJ  CONST_38  C8   C7   C6   C5      0.00   0.0  0
 6BJ  CONST_39  C8   C4   N3   C5      0.00   0.0  0
 6BJ  CONST_40  C15  C11  C12  C14   180.00   0.0  0
 6BJ  CONST_41  C10  C13  C11  C15   180.00   0.0  0
 6BJ  CONST_42  C21  N5   C17  C16   180.00   0.0  0
 6BJ  CONST_43  C19  C18  C17  C16   180.00   0.0  0
 6BJ  CONST_44  H14  C6   C7   C1      0.00   0.0  0
 6BJ  CONST_45  H15  C8   C7   C1      0.00   0.0  0
 6BJ  CONST_46  H2   C3   C1   C2    180.00   0.0  0
 6BJ  CONST_47  H1   C2   C1   C3    180.00   0.0  0
 6BJ  CONST_48  H5   C14  C12  C11   180.00   0.0  0
 6BJ  CONST_49  H16  C10  C13  C11   180.00   0.0  0
 6BJ  CONST_50  H4   C13  C11  C12   180.00   0.0  0
 6BJ  CONST_51  H3   C12  C11  C13   180.00   0.0  0
 6BJ  CONST_52  H11  C21  N5   C17   180.00   0.0  0
 6BJ  CONST_53  H9   C19  C18  C17   180.00   0.0  0
 6BJ  CONST_54  H10  C20  C19  C18   180.00   0.0  0
 6BJ  CONST_55  H8   C18  C19  C20   180.00   0.0  0
 6BJ  CONST_56  H13  C5   N3   C4    180.00   0.0  0
 6BJ  CONST_57  H12  C4   N3   C5    180.00   0.0  0
 6BJ  CONST_58  C16  N4   C15  C11   180.00   0.0  0
 6BJ  CONST_59  H17  N4   C15  C11     0.00   0.0  0
 6BJ  CONST_60  C16  N4   C15  O1      0.00   0.0  0
 6BJ  Var_01    C12  C11  C15  O1    163.73  30.0  2
 6BJ  Var_02    N4   C16  C17  C18   177.04  30.0  2
 6BJ  Var_03    C17  C16  N4   C15  -177.23  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
 6BJ  plan-1  C1   0.020
 6BJ  plan-1  C2   0.020
 6BJ  plan-1  C3   0.020
 6BJ  plan-1  N1   0.020
 6BJ  plan-1  N2   0.020
 6BJ  plan-1  C7   0.020
 6BJ  plan-1  C9   0.020
 6BJ  plan-1  H1   0.020
 6BJ  plan-1  H2   0.020
 6BJ  plan-2  C11  0.020
 6BJ  plan-2  C12  0.020
 6BJ  plan-2  C13  0.020
 6BJ  plan-2  C14  0.020
 6BJ  plan-2  C15  0.020
 6BJ  plan-2  N1   0.020
 6BJ  plan-2  C9   0.020
 6BJ  plan-2  C10  0.020
 6BJ  plan-2  H3   0.020
 6BJ  plan-2  H4   0.020
 6BJ  plan-2  H5   0.020
 6BJ  plan-2  H16  0.020
 6BJ  plan-3  C16  0.020
 6BJ  plan-3  C17  0.020
 6BJ  plan-3  C18  0.020
 6BJ  plan-3  C19  0.020
 6BJ  plan-3  C20  0.020
 6BJ  plan-3  C21  0.020
 6BJ  plan-3  N5   0.020
 6BJ  plan-3  H8   0.020
 6BJ  plan-3  H9   0.020
 6BJ  plan-3  H10  0.020
 6BJ  plan-3  H11  0.020
 6BJ  plan-4  C1   0.020
 6BJ  plan-4  C4   0.020
 6BJ  plan-4  N3   0.020
 6BJ  plan-4  C5   0.020
 6BJ  plan-4  C6   0.020
 6BJ  plan-4  C7   0.020
 6BJ  plan-4  C8   0.020
 6BJ  plan-4  H12  0.020
 6BJ  plan-4  H13  0.020
 6BJ  plan-4  H14  0.020
 6BJ  plan-4  H15  0.020
 6BJ  plan-5  O1   0.020
 6BJ  plan-5  C11  0.020
 6BJ  plan-5  C15  0.020
 6BJ  plan-5  C16  0.020
 6BJ  plan-5  N4   0.020
 6BJ  plan-5  H17  0.020

