# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 00:29:37 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 1H-benzimidazol-2-yl(4-{[3-(morpholin-4-yl)pyrazin-2-yl]oxy}phenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(c1[nH]c2ccccc2n1)c3ccc(Oc4nccnc4N5CCOCC5)cc3
#
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
 2F5  2F5  1H-benzimidazol-2-yl(4-{[3-(morpholin-4-yl)pyrazin-2-yl]oxy}phenyl)methanone  ligand  49  30  .  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_2F5
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
 2F5  O01  O  O     0  -0.381   3.4598  -2.7027  -0.6092
 2F5  C02  C  C     0   0.304   3.1352  -1.5706  -0.3069
 2F5  C03  C  CR5   0   0.354   4.2057  -0.6008   0.0129
 2F5  N04  N  NR15  0  -0.685   5.5032  -0.9313  -0.2191
 2F5  C05  C  CR56  0   0.342   6.2668   0.1102   0.2082
 2F5  C06  C  CR16  0  -0.300   7.6431   0.3315   0.2200
 2F5  C07  C  CR16  0  -0.269   8.0672   1.5345   0.7454
 2F5  C08  C  CR16  0  -0.268   7.1596   2.4904   1.2432
 2F5  C09  C  CR16  0  -0.325   5.7995   2.2678   1.2292
 2F5  C10  C  CR56  0   0.145   5.3459   1.0544   0.7010
 2F5  N11  N  N     0  -0.454   4.0726   0.5773   0.5652
 2F5  C12  C  CR6   0  -0.018   1.7133  -1.1691  -0.2284
 2F5  C13  C  CR16  0  -0.261   0.7672  -2.1736  -0.0135
 2F5  C14  C  CR16  0  -0.300  -0.5819  -1.8745   0.0338
 2F5  C15  C  CR6   0   0.377  -0.9904  -0.5632  -0.1533
 2F5  O16  O  O2    0  -0.515  -2.3258  -0.2669  -0.0388
 2F5  C17  C  CR6   0   0.438  -3.0608  -0.1262  -1.1618
 2F5  N18  N  N     0  -0.390  -2.5146  -0.3167  -2.3220
 2F5  C19  C  CR16  0  -0.130  -3.2987  -0.2482  -3.4061
 2F5  C20  C  CR16  0  -0.124  -4.6432  -0.0087  -3.2771
 2F5  N21  N  N     0  -0.405  -5.1994   0.2109  -2.0820
 2F5  C22  C  CR6   0   0.414  -4.4431   0.1812  -1.0065
 2F5  N23  N  NT    0  -0.506  -5.0086   0.3538   0.2377
 2F5  C24  C  CH2   0  -0.328  -4.4902   1.3969   1.1197
 2F5  C25  C  CH2   0  -0.185  -4.9421   1.1211   2.5400
 2F5  O26  O  O2    0  -0.484  -6.3460   1.0314   2.6308
 2F5  C27  C  CH2   0  -0.187  -6.8451   0.0287   1.7742
 2F5  C28  C  CH2   0  -0.315  -6.4571   0.2686   0.3259
 2F5  C29  C  CR16  0  -0.293  -0.0721   0.4474  -0.3868
 2F5  C30  C  CR16  0  -0.268   1.2785   0.1442  -0.4159
 2F5  H1   H  HNR5  0   0.425   5.8286  -1.7945  -0.6274
 2F5  H2   H  HCR6  0   0.273   8.3434  -0.3999  -0.1606
 2F5  H3   H  HCR6  0   0.263   9.1265   1.7525   0.7778
 2F5  H4   H  HCR6  0   0.260   7.5451   3.4179   1.6446
 2F5  H5   H  HCR6  0   0.262   5.1024   3.0027   1.6103
 2F5  H7   H  HCR6  0   0.275   1.0857  -3.1970   0.1319
 2F5  H8   H  HCR6  0   0.280  -1.3124  -2.6513   0.2179
 2F5  H9   H  HCR6  0   0.273  -2.8350  -0.4135  -4.3694
 2F5  H10  H  HCR6  0   0.269  -5.2969   0.0160  -4.1396
 2F5  H11  H  HCH2  0   0.268  -3.4042   1.4316   1.0964
 2F5  H12  H  HCH2  0   0.232  -4.8570   2.3802   0.7942
 2F5  H13  H  HCH2  0   0.207  -4.4700   0.1940   2.8940
 2F5  H14  H  HCH2  0   0.242  -4.6224   1.9344   3.1928
 2F5  H15  H  HCH2  0   0.205  -6.4802  -0.9601   2.0863
 2F5  H16  H  HCH2  0   0.242  -7.9320   0.0305   1.8679
 2F5  H17  H  HCH2  0   0.225  -6.9417   1.1795  -0.0506
 2F5  H18  H  HCH2  0   0.258  -6.8155  -0.5650  -0.2776
 2F5  H19  H  HCR6  0   0.281  -0.4044   1.4658  -0.5402
 2F5  H20  H  HCR6  0   0.276   1.9882   0.9371  -0.5947

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
 2F5  C19  C20  aromatic  1.372  0.020  1.372
 2F5  C19  N18  aromatic  1.340  0.020  1.340
 2F5  C20  N21  aromatic  1.336  0.020  1.336
 2F5  O01  C02  double    1.216  0.020  1.216
 2F5  N18  C17  aromatic  1.296  0.020  1.296
 2F5  N21  C22  aromatic  1.315  0.020  1.315
 2F5  C02  C03  single    1.479  0.020  1.479
 2F5  C02  C12  single    1.480  0.020  1.480
 2F5  C03  N11  aromatic  1.308  0.020  1.308
 2F5  C03  N04  aromatic  1.359  0.020  1.359
 2F5  C30  C12  aromatic  1.396  0.020  1.396
 2F5  C30  C29  aromatic  1.385  0.020  1.385
 2F5  N11  C10  aromatic  1.366  0.020  1.366
 2F5  N04  C05  aromatic  1.360  0.020  1.360
 2F5  C12  C13  aromatic  1.397  0.020  1.397
 2F5  C10  C05  aromatic  1.408  0.020  1.408
 2F5  C10  C09  aromatic  1.399  0.020  1.399
 2F5  C05  C06  aromatic  1.394  0.020  1.394
 2F5  C29  C15  aromatic  1.385  0.020  1.385
 2F5  C17  C22  aromatic  1.425  0.020  1.425
 2F5  C17  O16  single    1.350  0.020  1.350
 2F5  C09  C08  aromatic  1.378  0.020  1.378
 2F5  C06  C07  aromatic  1.380  0.020  1.380
 2F5  C22  N23  single    1.377  0.020  1.377
 2F5  C08  C07  aromatic  1.409  0.020  1.409
 2F5  C13  C14  aromatic  1.383  0.020  1.383
 2F5  C15  C14  aromatic  1.386  0.020  1.386
 2F5  C15  O16  single    1.373  0.020  1.373
 2F5  N23  C28  single    1.454  0.020  1.454
 2F5  N23  C24  single    1.461  0.020  1.461
 2F5  C28  C27  single    1.518  0.020  1.518
 2F5  C24  C25  single    1.516  0.020  1.516
 2F5  C27  O26  single    1.410  0.020  1.410
 2F5  C25  O26  single    1.410  0.020  1.410
 2F5  N04  H1   single    0.860  0.020  1.020
 2F5  C06  H2   single    0.930  0.020  1.080
 2F5  C07  H3   single    0.930  0.020  1.080
 2F5  C08  H4   single    0.930  0.020  1.080
 2F5  C09  H5   single    0.930  0.020  1.080
 2F5  C13  H7   single    0.930  0.020  1.080
 2F5  C14  H8   single    0.930  0.020  1.080
 2F5  C19  H9   single    0.930  0.020  1.080
 2F5  C20  H10  single    0.930  0.020  1.080
 2F5  C24  H11  single    0.970  0.020  1.090
 2F5  C24  H12  single    0.970  0.020  1.090
 2F5  C25  H13  single    0.970  0.020  1.090
 2F5  C25  H14  single    0.970  0.020  1.090
 2F5  C27  H15  single    0.970  0.020  1.090
 2F5  C27  H16  single    0.970  0.020  1.090
 2F5  C28  H17  single    0.970  0.020  1.090
 2F5  C28  H18  single    0.970  0.020  1.090
 2F5  C29  H19  single    0.930  0.020  1.080
 2F5  C30  H20  single    0.930  0.020  1.080

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
 2F5  C12  C02  C03  120.40  3.000
 2F5  C12  C02  O01  121.49  3.000
 2F5  C03  C02  O01  118.09  3.000
 2F5  N11  C03  N04  112.85  3.000
 2F5  N04  C03  C02  119.64  3.000
 2F5  N11  C03  C02  127.45  3.000
 2F5  H1   N04  C05  126.96  3.000
 2F5  H1   N04  C03  125.82  3.000
 2F5  C05  N04  C03  107.23  3.000
 2F5  C10  C05  C06  122.44  3.000
 2F5  C06  C05  N04  132.72  3.000
 2F5  C10  C05  N04  104.85  3.000
 2F5  H2   C06  C07  121.64  3.000
 2F5  H2   C06  C05  121.93  3.000
 2F5  C07  C06  C05  116.43  3.000
 2F5  H3   C07  C08  118.91  3.000
 2F5  H3   C07  C06  119.22  3.000
 2F5  C08  C07  C06  121.88  3.000
 2F5  H4   C08  C09  119.60  3.000
 2F5  H4   C08  C07  118.90  3.000
 2F5  C09  C08  C07  121.50  3.000
 2F5  H5   C09  C10  120.87  3.000
 2F5  H5   C09  C08  121.49  3.000
 2F5  C10  C09  C08  117.64  3.000
 2F5  N11  C10  C09  129.98  3.000
 2F5  C09  C10  C05  120.11  3.000
 2F5  N11  C10  C05  109.91  3.000
 2F5  C10  N11  C03  105.17  3.000
 2F5  C30  C12  C13  119.10  3.000
 2F5  C13  C12  C02  117.65  3.000
 2F5  C30  C12  C02  123.19  3.000
 2F5  H7   C13  C14  119.17  3.000
 2F5  H7   C13  C12  120.11  3.000
 2F5  C14  C13  C12  120.71  3.000
 2F5  H8   C14  C15  120.21  3.000
 2F5  H8   C14  C13  120.61  3.000
 2F5  C15  C14  C13  119.18  3.000
 2F5  C29  C15  O16  120.10  3.000
 2F5  O16  C15  C14  118.66  3.000
 2F5  C29  C15  C14  121.17  3.000
 2F5  C17  O16  C15  118.88  3.000
 2F5  C22  C17  N18  122.56  3.000
 2F5  C22  C17  O16  117.40  3.000
 2F5  N18  C17  O16  120.00  3.000
 2F5  C19  N18  C17  118.04  3.000
 2F5  H9   C19  C20  122.04  3.000
 2F5  H9   C19  N18  117.51  3.000
 2F5  C20  C19  N18  120.43  3.000
 2F5  H10  C20  N21  117.22  3.000
 2F5  H10  C20  C19  121.39  3.000
 2F5  N21  C20  C19  121.38  3.000
 2F5  C22  N21  C20  119.23  3.000
 2F5  N23  C22  N21  119.98  3.000
 2F5  N23  C22  C17  121.59  3.000
 2F5  N21  C22  C17  118.28  3.000
 2F5  C28  N23  C24  111.02  3.000
 2F5  C24  N23  C22  119.28  3.000
 2F5  C28  N23  C22  117.16  3.000
 2F5  H12  C24  H11  107.38  3.000
 2F5  H12  C24  C25  109.93  3.000
 2F5  H11  C24  C25  108.89  3.000
 2F5  H12  C24  N23  109.97  3.000
 2F5  H11  C24  N23  111.37  3.000
 2F5  C25  C24  N23  109.26  3.000
 2F5  H14  C25  H13  108.08  3.000
 2F5  H14  C25  O26  107.50  3.000
 2F5  H13  C25  O26  110.69  3.000
 2F5  H14  C25  C24  109.74  3.000
 2F5  H13  C25  C24  109.10  3.000
 2F5  O26  C25  C24  111.65  3.000
 2F5  C27  O26  C25  111.01  3.000
 2F5  H16  C27  H15  107.93  3.000
 2F5  H16  C27  C28  109.65  3.000
 2F5  H15  C27  C28  109.15  3.000
 2F5  H16  C27  O26  107.41  3.000
 2F5  H15  C27  O26  110.47  3.000
 2F5  C28  C27  O26  112.13  3.000
 2F5  H18  C28  H17  107.42  3.000
 2F5  H18  C28  C27  108.86  3.000
 2F5  H17  C28  C27  110.20  3.000
 2F5  H18  C28  N23  109.81  3.000
 2F5  H17  C28  N23  111.73  3.000
 2F5  C27  C28  N23  108.77  3.000
 2F5  H19  C29  C30  120.18  3.000
 2F5  H19  C29  C15  120.45  3.000
 2F5  C30  C29  C15  119.37  3.000
 2F5  H20  C30  C29  118.96  3.000
 2F5  H20  C30  C12  120.58  3.000
 2F5  C29  C30  C12  120.46  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
 2F5  CONST_01  C05  C10  N11  C03     0.00   0.0  0
 2F5  CONST_02  C09  C10  N11  C03   180.00   0.0  0
 2F5  CONST_03  C10  C05  N04  C03     0.00   0.0  0
 2F5  CONST_04  C06  C05  N04  C03   180.00   0.0  0
 2F5  CONST_05  C10  N11  C03  N04     0.00   0.0  0
 2F5  CONST_06  N11  C10  C05  N04     0.00   0.0  0
 2F5  CONST_07  C09  C10  C05  N04   180.00   0.0  0
 2F5  CONST_08  C07  C06  C05  N04   180.00   0.0  0
 2F5  CONST_09  N11  C03  N04  C05     0.00   0.0  0
 2F5  CONST_10  C08  C09  C10  C05     0.00   0.0  0
 2F5  CONST_11  C08  C07  C06  C05     0.00   0.0  0
 2F5  CONST_12  N11  C10  C05  C06   180.00   0.0  0
 2F5  CONST_13  C09  C10  C05  C06     0.00   0.0  0
 2F5  CONST_14  C09  C08  C07  C06     0.00   0.0  0
 2F5  CONST_15  C10  C05  C06  C07     0.00   0.0  0
 2F5  CONST_16  C10  C09  C08  C07     0.00   0.0  0
 2F5  CONST_17  N11  C10  C09  C08   180.00   0.0  0
 2F5  CONST_18  C15  C29  C30  C12     0.00   0.0  0
 2F5  CONST_19  C15  C14  C13  C12     0.00   0.0  0
 2F5  CONST_20  C29  C30  C12  C13     0.00   0.0  0
 2F5  CONST_21  C29  C15  C14  C13     0.00   0.0  0
 2F5  CONST_22  C30  C12  C13  C14     0.00   0.0  0
 2F5  CONST_23  C30  C29  C15  C14     0.00   0.0  0
 2F5  CONST_24  C20  C19  N18  C17     0.00   0.0  0
 2F5  CONST_25  C20  N21  C22  C17     0.00   0.0  0
 2F5  CONST_26  N21  C20  C19  N18     0.00   0.0  0
 2F5  CONST_27  N21  C22  C17  N18     0.00   0.0  0
 2F5  CONST_28  C22  N21  C20  C19     0.00   0.0  0
 2F5  CONST_29  C22  C17  N18  C19     0.00   0.0  0
 2F5  CONST_30  N23  C22  C17  N18   180.00   0.0  0
 2F5  CONST_31  N23  C22  N21  C20   180.00   0.0  0
 2F5  CONST_32  C10  N11  C03  C02   180.00   0.0  0
 2F5  CONST_33  C05  N04  C03  C02   180.00   0.0  0
 2F5  CONST_34  C29  C30  C12  C02   180.00   0.0  0
 2F5  CONST_35  C14  C13  C12  C02   180.00   0.0  0
 2F5  CONST_36  O16  C15  C14  C13   180.00   0.0  0
 2F5  CONST_37  C19  N18  C17  O16   180.00   0.0  0
 2F5  CONST_38  N21  C22  C17  O16   180.00   0.0  0
 2F5  CONST_39  N23  C22  C17  O16     0.00   0.0  0
 2F5  CONST_40  C30  C29  C15  O16   180.00   0.0  0
 2F5  CONST_41  H2   C06  C05  N04     0.00   0.0  0
 2F5  CONST_42  H5   C09  C10  C05   180.00   0.0  0
 2F5  CONST_43  H3   C07  C06  C05   180.00   0.0  0
 2F5  CONST_44  H1   N04  C05  C06     0.00   0.0  0
 2F5  CONST_45  H4   C08  C07  C06   180.00   0.0  0
 2F5  CONST_46  H19  C29  C30  C12   180.00   0.0  0
 2F5  CONST_47  H8   C14  C13  C12   180.00   0.0  0
 2F5  CONST_48  H20  C30  C12  C13   180.00   0.0  0
 2F5  CONST_49  H7   C13  C14  C15   180.00   0.0  0
 2F5  CONST_50  H9   C19  N18  C17   180.00   0.0  0
 2F5  CONST_51  H10  C20  C19  N18   180.00   0.0  0
 2F5  Var_01    C28  N23  C22  C17  -162.23  30.0  2
 2F5  Var_02    C27  C28  N23  C22   161.68  30.0  1
 2F5  Var_03    C25  C24  N23  C22  -162.33  30.0  1
 2F5  Var_04    O26  C27  C28  N23    56.93  30.0  1
 2F5  Var_05    O26  C25  C24  N23   -56.71  30.0  1
 2F5  Var_06    C28  C27  O26  C25   -57.78  30.0  1
 2F5  Var_07    C30  C12  C02  C03    27.67  30.0  2
 2F5  Var_08    C12  C02  C03  N04  -172.02  30.0  2
 2F5  Var_09    N18  C17  O16  C15     2.41  30.0  2
 2F5  Var_10    C29  C15  O16  C17    82.60  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
 2F5  plan-1  O16  0.020
 2F5  plan-1  C17  0.020
 2F5  plan-1  N18  0.020
 2F5  plan-1  C19  0.020
 2F5  plan-1  C20  0.020
 2F5  plan-1  N21  0.020
 2F5  plan-1  C22  0.020
 2F5  plan-1  N23  0.020
 2F5  plan-1  H9   0.020
 2F5  plan-1  H10  0.020
 2F5  plan-2  C02  0.020
 2F5  plan-2  C12  0.020
 2F5  plan-2  C13  0.020
 2F5  plan-2  C14  0.020
 2F5  plan-2  C15  0.020
 2F5  plan-2  O16  0.020
 2F5  plan-2  C29  0.020
 2F5  plan-2  C30  0.020
 2F5  plan-2  H7   0.020
 2F5  plan-2  H8   0.020
 2F5  plan-2  H19  0.020
 2F5  plan-2  H20  0.020
 2F5  plan-3  C02  0.020
 2F5  plan-3  C03  0.020
 2F5  plan-3  N04  0.020
 2F5  plan-3  C05  0.020
 2F5  plan-3  C06  0.020
 2F5  plan-3  C07  0.020
 2F5  plan-3  C08  0.020
 2F5  plan-3  C09  0.020
 2F5  plan-3  C10  0.020
 2F5  plan-3  N11  0.020
 2F5  plan-3  H1   0.020
 2F5  plan-3  H2   0.020
 2F5  plan-3  H3   0.020
 2F5  plan-3  H4   0.020
 2F5  plan-3  H5   0.020
 2F5  plan-4  O01  0.020
 2F5  plan-4  C02  0.020
 2F5  plan-4  C03  0.020
 2F5  plan-4  C12  0.020

