# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:33:02 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: N-(1H-benzimidazol-2-ylmethyl)-N'-(2,4-dichlorophenyl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(Nc2nc(NCc3[nH]c4ccccc4n3)nc(n2)N5CCOCC5)c(Cl)c1
#
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
 3BJ  3BJ  N-(1H-benzimidazol-2-ylmethyl)-N'-(2,4-dichlorophenyl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine  ligand  52  32  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3BJ
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
 3BJ  C1   C   CR56  0   0.338   3.8846  -1.1882  -0.2788
 3BJ  C3   C   CR16  0  -0.335   4.9952   0.9642  -0.2890
 3BJ  C4   C   CR16  0  -0.273   5.5803   0.5947  -1.4878
 3BJ  C5   C   CR16  0  -0.280   5.3202  -0.6525  -2.0750
 3BJ  C6   C   CR16  0  -0.310   4.4666  -1.5677  -1.4819
 3BJ  N7   N   NR15  0  -0.688   3.0098  -1.8133   0.5702
 3BJ  C8   C   CR5   0   0.448   2.7693  -0.9649   1.5995
 3BJ  C12  C   CR6   0   0.638  -0.2263  -1.8485   1.5943
 3BJ  C14  C   CR6   0   0.659  -2.2005  -2.3225   0.6365
 3BJ  C16  C   CR6   0   0.626  -1.2357  -0.3155   0.3298
 3BJ  C19  C   CH2   0  -0.328  -3.2426  -4.5313   0.9203
 3BJ  C10  C   CH2   0  -0.385   1.8761  -1.3310   2.7410
 3BJ  C20  C   CH2   0  -0.182  -3.3970  -5.4995  -0.2415
 3BJ  C22  C   CH2   0  -0.182  -4.4681  -3.8826  -1.5365
 3BJ  C23  C   CH2   0  -0.329  -4.3557  -2.8528  -0.4245
 3BJ  C25  C   CR6   0   0.452  -0.4545   1.9791  -0.2981
 3BJ  C26  C   CR16  0  -0.336   0.7995   2.0004   0.3177
 3BJ  C27  C   CR16  0  -0.199   1.6302   3.1032   0.2291
 3BJ  C28  C   CR6   0  -0.067   1.2253   4.2202  -0.4791
 3BJ  C30  C   CR6   0  -0.149  -0.8316   3.1317  -1.0059
 3BJ  C29  C   CR16  0  -0.168  -0.0107   4.2407  -1.1016
 3BJ  CL1  CL  CL    0  -0.126   2.2611   5.6020  -0.5971
 3BJ  N24  N   NH1   0  -0.774  -1.3284   0.9078  -0.2646
 3BJ  N17  N   N     0  -0.537  -0.1873  -0.6157   1.0805
 3BJ  N13  N   N     0  -0.540  -1.1927  -2.7387   1.4091
 3BJ  N18  N   NT    0  -0.504  -3.2169  -3.1723   0.4146
 3BJ  O21  O   O2    0  -0.484  -4.5303  -5.1957  -1.0242
 3BJ  N15  N   N     0  -0.547  -2.2666  -1.1111   0.0740
 3BJ  N11  N   NH1   0  -0.669   0.8121  -2.2216   2.3626
 3BJ  C2   C   CR56  0   0.146   4.1354   0.0556   0.3257
 3BJ  N9   N   N     0  -0.487   3.4212   0.1598   1.4974
 3BJ  H1   H   HCR6  0   0.252   5.1985   1.9284   0.1596
 3BJ  H2   H   HCR6  0   0.251   6.2540   1.2798  -1.9855
 3BJ  H3   H   HCR6  0   0.254   5.7965  -0.9045  -3.0134
 3BJ  H4   H   HCR6  0   0.265   4.2655  -2.5297  -1.9349
 3BJ  H5   H   HNR5  0   0.416   2.6046  -2.7287   0.4533
 3BJ  H6   H   HCH2  0   0.244  -4.0844  -4.6402   1.6123
 3BJ  H7   H   HCH2  0   0.275  -2.3281  -4.7440   1.4659
 3BJ  H8   H   HCH2  0   0.300   2.4643  -1.8411   3.5057
 3BJ  H9   H   HCH2  0   0.273   1.5012  -0.4090   3.1891
 3BJ  H10  H   HCH2  0   0.207  -2.4846  -5.4772  -0.8545
 3BJ  H11  H   HCH2  0   0.243  -3.5239  -6.5149   0.1368
 3BJ  H12  H   HCH2  0   0.243  -5.3795  -3.7132  -2.1114
 3BJ  H13  H   HCH2  0   0.208  -3.6112  -3.7736  -2.2162
 3BJ  H14  H   HCH2  0   0.277  -4.2430  -1.8582  -0.8463
 3BJ  H15  H   HCH2  0   0.245  -5.2645  -2.8603   0.1871
 3BJ  H16  H   HCR6  0   0.338   1.1364   1.1412   0.8716
 3BJ  H17  H   HCR6  0   0.276   2.5930   3.0742   0.7209
 3BJ  H18  H   HCR6  0   0.300  -0.3382   5.1073  -1.6589
 3BJ  H19  H   HNH1  0   0.402  -2.1828   1.0124  -0.7927
 3BJ  H20  H   HNH1  0   0.407   0.7588  -3.1267   2.7989
 3BJ  CL2  CL  CL    0  -0.106  -2.3717   3.1946  -1.8024

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
 3BJ  C10  N11  single    1.438  0.020  1.438
 3BJ  C10  C8   single    1.495  0.020  1.495
 3BJ  N11  C12  single    1.345  0.020  1.345
 3BJ  C12  N13  aromatic  1.327  0.020  1.327
 3BJ  C12  N17  aromatic  1.336  0.020  1.336
 3BJ  C8   N7   aromatic  1.355  0.020  1.355
 3BJ  C8   N9   aromatic  1.304  0.020  1.304
 3BJ  N13  C14  aromatic  1.336  0.020  1.336
 3BJ  N17  C16  aromatic  1.324  0.020  1.324
 3BJ  C26  C27  aromatic  1.383  0.020  1.383
 3BJ  C26  C25  aromatic  1.397  0.020  1.397
 3BJ  C23  C22  single    1.520  0.020  1.520
 3BJ  C23  N18  single    1.450  0.020  1.450
 3BJ  C27  C28  aromatic  1.383  0.020  1.383
 3BJ  N7   C1   aromatic  1.370  0.020  1.370
 3BJ  C22  O21  single    1.411  0.020  1.411
 3BJ  N9   C2   aromatic  1.376  0.020  1.376
 3BJ  C14  N18  single    1.343  0.020  1.343
 3BJ  C14  N15  aromatic  1.337  0.020  1.337
 3BJ  O21  C20  single    1.410  0.020  1.410
 3BJ  C16  N15  aromatic  1.327  0.020  1.327
 3BJ  C16  N24  single    1.363  0.020  1.363
 3BJ  N18  C19  single    1.450  0.020  1.450
 3BJ  N24  C25  single    1.383  0.020  1.383
 3BJ  C25  C30  aromatic  1.404  0.020  1.404
 3BJ  C1   C2   aromatic  1.405  0.020  1.405
 3BJ  C1   C6   aromatic  1.389  0.020  1.389
 3BJ  C28  CL1  single    1.731  0.020  1.731
 3BJ  C28  C29  aromatic  1.384  0.020  1.384
 3BJ  C2   C3   aromatic  1.394  0.020  1.394
 3BJ  C19  C20  single    1.520  0.020  1.520
 3BJ  C6   C5   aromatic  1.385  0.020  1.385
 3BJ  C30  C29  aromatic  1.383  0.020  1.383
 3BJ  C30  CL2  single    1.735  0.020  1.735
 3BJ  C3   C4   aromatic  1.384  0.020  1.384
 3BJ  C5   C4   aromatic  1.403  0.020  1.403
 3BJ  C3   H1   single    0.930  0.020  1.080
 3BJ  C4   H2   single    0.930  0.020  1.080
 3BJ  C5   H3   single    0.930  0.020  1.080
 3BJ  C6   H4   single    0.930  0.020  1.080
 3BJ  N7   H5   single    0.860  0.020  1.020
 3BJ  C19  H6   single    0.970  0.020  1.090
 3BJ  C19  H7   single    0.970  0.020  1.090
 3BJ  C10  H8   single    0.970  0.020  1.090
 3BJ  C10  H9   single    0.970  0.020  1.090
 3BJ  C20  H10  single    0.970  0.020  1.090
 3BJ  C20  H11  single    0.970  0.020  1.090
 3BJ  C22  H12  single    0.970  0.020  1.090
 3BJ  C22  H13  single    0.970  0.020  1.090
 3BJ  C23  H14  single    0.970  0.020  1.090
 3BJ  C23  H15  single    0.970  0.020  1.090
 3BJ  C26  H16  single    0.930  0.020  1.080
 3BJ  C27  H17  single    0.930  0.020  1.080
 3BJ  C29  H18  single    0.930  0.020  1.080
 3BJ  N24  H19  single    0.860  0.020  1.020
 3BJ  N11  H20  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
 3BJ  C2   C1   N7   104.55  3.000
 3BJ  C2   C1   C6   122.64  3.000
 3BJ  N7   C1   C6   132.80  3.000
 3BJ  H1   C3   C2   120.90  3.000
 3BJ  H1   C3   C4   121.15  3.000
 3BJ  C2   C3   C4   117.95  3.000
 3BJ  H2   C4   C5   119.06  3.000
 3BJ  H2   C4   C3   119.51  3.000
 3BJ  C5   C4   C3   121.43  3.000
 3BJ  H3   C5   C6   119.26  3.000
 3BJ  H3   C5   C4   119.24  3.000
 3BJ  C6   C5   C4   121.50  3.000
 3BJ  H4   C6   C5   121.51  3.000
 3BJ  H4   C6   C1   121.84  3.000
 3BJ  C5   C6   C1   116.65  3.000
 3BJ  H5   N7   C8   125.83  3.000
 3BJ  H5   N7   C1   126.81  3.000
 3BJ  C8   N7   C1   107.35  3.000
 3BJ  N9   C8   C10  124.73  3.000
 3BJ  N9   C8   N7   113.06  3.000
 3BJ  C10  C8   N7   122.18  3.000
 3BJ  N11  C12  N13  117.14  3.000
 3BJ  N13  C12  N17  125.92  3.000
 3BJ  N11  C12  N17  116.95  3.000
 3BJ  N15  C14  N18  117.79  3.000
 3BJ  N15  C14  N13  124.23  3.000
 3BJ  N18  C14  N13  117.98  3.000
 3BJ  N15  C16  N17  126.05  3.000
 3BJ  N15  C16  N24  113.65  3.000
 3BJ  N17  C16  N24  120.30  3.000
 3BJ  H7   C19  H6   108.08  3.000
 3BJ  H7   C19  N18  110.11  3.000
 3BJ  H6   C19  N18  109.10  3.000
 3BJ  H7   C19  C20  110.17  3.000
 3BJ  H6   C19  C20  109.97  3.000
 3BJ  N18  C19  C20  109.40  3.000
 3BJ  H9   C10  H8   107.00  3.000
 3BJ  H9   C10  N11  112.14  3.000
 3BJ  H8   C10  N11  107.08  3.000
 3BJ  H9   C10  C8   108.17  3.000
 3BJ  H8   C10  C8   109.12  3.000
 3BJ  N11  C10  C8   113.12  3.000
 3BJ  H11  C20  H10  107.98  3.000
 3BJ  H11  C20  O21  107.43  3.000
 3BJ  H10  C20  O21  110.68  3.000
 3BJ  H11  C20  C19  109.85  3.000
 3BJ  H10  C20  C19  109.20  3.000
 3BJ  O21  C20  C19  111.63  3.000
 3BJ  H13  C22  H12  108.06  3.000
 3BJ  H13  C22  O21  110.57  3.000
 3BJ  H12  C22  O21  107.40  3.000
 3BJ  H13  C22  C23  109.12  3.000
 3BJ  H12  C22  C23  110.01  3.000
 3BJ  O21  C22  C23  111.61  3.000
 3BJ  H15  C23  H14  108.01  3.000
 3BJ  H15  C23  N18  109.08  3.000
 3BJ  H14  C23  N18  110.18  3.000
 3BJ  H15  C23  C22  110.03  3.000
 3BJ  H14  C23  C22  110.12  3.000
 3BJ  N18  C23  C22  109.40  3.000
 3BJ  N24  C25  C30  118.58  3.000
 3BJ  C30  C25  C26  116.79  3.000
 3BJ  N24  C25  C26  124.63  3.000
 3BJ  H16  C26  C27  118.77  3.000
 3BJ  H16  C26  C25  119.71  3.000
 3BJ  C27  C26  C25  121.52  3.000
 3BJ  H17  C27  C28  121.00  3.000
 3BJ  H17  C27  C26  118.95  3.000
 3BJ  C28  C27  C26  120.05  3.000
 3BJ  CL1  C28  C29  119.47  3.000
 3BJ  C29  C28  C27  120.24  3.000
 3BJ  CL1  C28  C27  120.29  3.000
 3BJ  C29  C30  CL2  117.77  3.000
 3BJ  CL2  C30  C25  119.97  3.000
 3BJ  C29  C30  C25  122.26  3.000
 3BJ  H18  C29  C30  119.91  3.000
 3BJ  H18  C29  C28  120.94  3.000
 3BJ  C30  C29  C28  119.15  3.000
 3BJ  H19  N24  C25  116.21  3.000
 3BJ  H19  N24  C16  112.24  3.000
 3BJ  C25  N24  C16  131.51  3.000
 3BJ  C16  N17  C12  113.83  3.000
 3BJ  C14  N13  C12  114.90  3.000
 3BJ  C23  N18  C19  113.22  3.000
 3BJ  C19  N18  C14  123.27  3.000
 3BJ  C23  N18  C14  123.39  3.000
 3BJ  C22  O21  C20  111.50  3.000
 3BJ  C16  N15  C14  115.07  3.000
 3BJ  H20  N11  C10  118.82  3.000
 3BJ  H20  N11  C12  117.16  3.000
 3BJ  C10  N11  C12  123.36  3.000
 3BJ  N9   C2   C3   130.26  3.000
 3BJ  C3   C2   C1   119.82  3.000
 3BJ  N9   C2   C1   109.91  3.000
 3BJ  C2   N9   C8   105.12  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
 3BJ  CONST_01  N9   C8   N7   C1      0.00   0.0  0
 3BJ  CONST_02  C8   N9   C2   C1      0.00   0.0  0
 3BJ  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 3BJ  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 3BJ  CONST_05  C8   N9   C2   C3    180.00   0.0  0
 3BJ  CONST_06  N7   C1   C2   C3    180.00   0.0  0
 3BJ  CONST_07  C6   C1   C2   C3      0.00   0.0  0
 3BJ  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 3BJ  CONST_09  N9   C2   C3   C4    180.00   0.0  0
 3BJ  CONST_10  N7   C1   C6   C5    180.00   0.0  0
 3BJ  CONST_11  C2   C1   C6   C5      0.00   0.0  0
 3BJ  CONST_12  C2   C3   C4   C5      0.00   0.0  0
 3BJ  CONST_13  C8   N7   C1   C6    180.00   0.0  0
 3BJ  CONST_14  N9   C2   C1   C6    180.00   0.0  0
 3BJ  CONST_15  C2   N9   C8   N7      0.00   0.0  0
 3BJ  CONST_16  N9   C2   C1   N7      0.00   0.0  0
 3BJ  CONST_17  C2   C1   N7   C8      0.00   0.0  0
 3BJ  CONST_18  N15  C14  N13  C12     0.00   0.0  0
 3BJ  CONST_19  N15  C16  N17  C12     0.00   0.0  0
 3BJ  CONST_20  N17  C12  N13  C14     0.00   0.0  0
 3BJ  CONST_21  N17  C16  N15  C14     0.00   0.0  0
 3BJ  CONST_22  N13  C12  N17  C16     0.00   0.0  0
 3BJ  CONST_23  N13  C14  N15  C16     0.00   0.0  0
 3BJ  CONST_24  C28  C27  C26  C25     0.00   0.0  0
 3BJ  CONST_25  C28  C29  C30  C25     0.00   0.0  0
 3BJ  CONST_26  C29  C28  C27  C26     0.00   0.0  0
 3BJ  CONST_27  C29  C30  C25  C26     0.00   0.0  0
 3BJ  CONST_28  C30  C25  C26  C27     0.00   0.0  0
 3BJ  CONST_29  C30  C29  C28  C27     0.00   0.0  0
 3BJ  CONST_30  N18  C14  N13  C12   180.00   0.0  0
 3BJ  CONST_31  N18  C14  N15  C16   180.00   0.0  0
 3BJ  CONST_32  C10  C8   N7   C1    180.00   0.0  0
 3BJ  CONST_33  N24  C16  N17  C12   180.00   0.0  0
 3BJ  CONST_34  N11  C12  N13  C14   180.00   0.0  0
 3BJ  CONST_35  N24  C16  N15  C14   180.00   0.0  0
 3BJ  CONST_36  N11  C12  N17  C16   180.00   0.0  0
 3BJ  CONST_37  C2   N9   C8   C10   180.00   0.0  0
 3BJ  CONST_38  CL1  C28  C27  C26   180.00   0.0  0
 3BJ  CONST_39  CL2  C30  C25  C26   180.00   0.0  0
 3BJ  CONST_40  N24  C25  C26  C27   180.00   0.0  0
 3BJ  CONST_41  CL2  C30  C29  C28   180.00   0.0  0
 3BJ  CONST_42  CL1  C28  C29  C30   180.00   0.0  0
 3BJ  CONST_43  N24  C25  C30  C29   180.00   0.0  0
 3BJ  CONST_44  H1   C3   C2   C1    180.00   0.0  0
 3BJ  CONST_45  H3   C5   C6   C1    180.00   0.0  0
 3BJ  CONST_46  H4   C6   C5   C4    180.00   0.0  0
 3BJ  CONST_47  H5   N7   C1   C6      0.00   0.0  0
 3BJ  CONST_48  H2   C4   C5   C6    180.00   0.0  0
 3BJ  CONST_49  H17  C27  C26  C25   180.00   0.0  0
 3BJ  CONST_50  H18  C29  C30  C25   180.00   0.0  0
 3BJ  CONST_51  H16  C26  C27  C28   180.00   0.0  0
 3BJ  CONST_52  N13  C12  N11  C10   180.00   0.0  0
 3BJ  CONST_53  N17  C12  N11  C10     0.00   0.0  0
 3BJ  CONST_54  H20  N11  C12  N17   180.00   0.0  0
 3BJ  Var_01    C22  C23  N18  C14   122.46  30.0  1
 3BJ  Var_02    C20  C19  N18  C14  -122.51  30.0  1
 3BJ  Var_03    N13  C14  N18  C19    -2.89  30.0  2
 3BJ  Var_04    C23  C22  O21  C20   -58.31  30.0  1
 3BJ  Var_05    O21  C22  C23  N18    55.01  30.0  1
 3BJ  Var_06    O21  C20  C19  N18   -54.96  30.0  1
 3BJ  Var_07    C26  C25  N24  C16     0.58  30.0  2
 3BJ  Var_08    N17  C16  N24  C25     3.40  30.0  2
 3BJ  Var_09    H10  C20  O21  C22   -63.57  30.0  1
 3BJ  Var_10    N11  C10  C8   N7    -31.27  30.0  2
 3BJ  Var_11    C12  N11  C10  C8    -70.31  30.0  3

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
 3BJ  plan-1  C12  0.020
 3BJ  plan-1  C14  0.020
 3BJ  plan-1  C16  0.020
 3BJ  plan-1  N24  0.020
 3BJ  plan-1  N17  0.020
 3BJ  plan-1  N13  0.020
 3BJ  plan-1  N18  0.020
 3BJ  plan-1  N15  0.020
 3BJ  plan-1  N11  0.020
 3BJ  plan-2  C25  0.020
 3BJ  plan-2  C26  0.020
 3BJ  plan-2  C27  0.020
 3BJ  plan-2  C28  0.020
 3BJ  plan-2  C30  0.020
 3BJ  plan-2  C29  0.020
 3BJ  plan-2  CL1  0.020
 3BJ  plan-2  N24  0.020
 3BJ  plan-2  H16  0.020
 3BJ  plan-2  H17  0.020
 3BJ  plan-2  H18  0.020
 3BJ  plan-2  CL2  0.020
 3BJ  plan-3  C1   0.020
 3BJ  plan-3  C3   0.020
 3BJ  plan-3  C4   0.020
 3BJ  plan-3  C5   0.020
 3BJ  plan-3  C6   0.020
 3BJ  plan-3  N7   0.020
 3BJ  plan-3  C8   0.020
 3BJ  plan-3  C10  0.020
 3BJ  plan-3  C2   0.020
 3BJ  plan-3  N9   0.020
 3BJ  plan-3  H1   0.020
 3BJ  plan-3  H2   0.020
 3BJ  plan-3  H3   0.020
 3BJ  plan-3  H4   0.020
 3BJ  plan-3  H5   0.020
 3BJ  plan-4  C12  0.020
 3BJ  plan-4  C10  0.020
 3BJ  plan-4  N11  0.020
 3BJ  plan-4  H20  0.020

