# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 12:43:32 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: ~{N}-(1,3-dimethyl-2-oxidanylidene-6-pyrrolidin-1-yl-benzimidazol-5-yl)-2-methoxy-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1C(=O)Nc2cc3N(C)C(=O)N(C)c3cc2N4CCCC4
#
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
 5XF  5XF  ~{N}-(1,3-dimethyl-2-oxidanylidene-6-pyrrolidin-1-yl-benzimidazol-5-yl)-2-methoxy-benzamide  ligand  52  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_5XF
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
 5XF  CAO  C  CH2   0  -0.280   1.2870  -3.0473  -1.4031
 5XF  CAP  C  CH2   0  -0.464   0.4313  -4.2989  -1.2069
 5XF  CAQ  C  CH2   0  -0.465   0.0353  -4.2727   0.2859
 5XF  CAR  C  CH2   0  -0.306   0.6432  -2.9766   0.8243
 5XF  NAN  N  NT    0  -0.546   0.7851  -2.1514  -0.3740
 5XF  CAA  C  CR6   0   0.229   1.4100  -0.8975  -0.1899
 5XF  CAB  C  CR16  0  -0.372   2.7877  -0.7187  -0.3016
 5XF  CAC  C  CR56  0   0.338   3.2984   0.5440  -0.0846
 5XF  NAH  N  NR5   0  -0.585   4.5862   1.0337  -0.1229
 5XF  CAL  C  CH3   0  -0.536   5.7616   0.2586  -0.4223
 5XF  CAI  C  CR5   0   0.652   4.5840   2.3737   0.1833
 5XF  OAK  O  O     0  -0.506   5.5514   3.1128   0.2459
 5XF  NAJ  N  NR5   0  -0.585   3.2694   2.7165   0.4032
 5XF  CAM  C  CH3   0  -0.536   2.8146   4.0327   0.7689
 5XF  CAD  C  CR56  0   0.360   2.4646   1.6093   0.2501
 5XF  CAE  C  CR16  0  -0.413   1.0968   1.4635   0.3648
 5XF  CAF  C  CR6   0   0.312   0.5708   0.1906   0.1311
 5XF  NAG  N  NH1   0  -0.722  -0.7931  -0.1071   0.1617
 5XF  CAS  C  C     0   0.505  -1.8312   0.6248   0.6205
 5XF  OAU  O  O     0  -0.463  -1.7406   1.7572   1.0640
 5XF  CAT  C  CR6   0  -0.172  -3.1334  -0.1098   0.5617
 5XF  CAV  C  CR16  0  -0.261  -3.2659  -1.3413   1.1915
 5XF  CAW  C  CR16  0  -0.273  -4.4803  -2.0133   1.2041
 5XF  CAX  C  CR16  0  -0.238  -5.5693  -1.4440   0.5648
 5XF  CAY  C  CR16  0  -0.383  -5.4570  -0.2200  -0.0831
 5XF  CAZ  C  CR6   0   0.386  -4.2400   0.4575  -0.0877
 5XF  OBA  O  O2    0  -0.459  -4.0335   1.6271  -0.7103
 5XF  CBB  C  CH3   0  -0.439  -5.1043   2.2224  -1.4189
 5XF  H1   H  HCH2  0   0.208   2.3482  -3.2965  -1.2605
 5XF  H2   H  HCH2  0   0.246   1.1807  -2.5997  -2.3921
 5XF  H3   H  HCH2  0   0.239  -0.4558  -4.2558  -1.8388
 5XF  H4   H  HCH2  0   0.239   0.9788  -5.2002  -1.4796
 5XF  H5   H  HCH2  0   0.237  -1.0494  -4.2669   0.3963
 5XF  H6   H  HCH2  0   0.240   0.4109  -5.1375   0.8316
 5XF  H7   H  HCH2  0   0.248   0.0178  -2.4810   1.5697
 5XF  H8   H  HCH2  0   0.224   1.6209  -3.1677   1.2893
 5XF  H9   H  HCR6  0   0.274   3.4337  -1.5528  -0.5429
 5XF  H10  H  HCH3  0   0.254   5.6826  -0.1947  -1.4104
 5XF  H11  H  HCH3  0   0.268   6.6302   0.9101  -0.4081
 5XF  H12  H  HCH3  0   0.254   5.9044  -0.5304   0.3161
 5XF  H13  H  HCH3  0   0.268   3.6420   4.7309   0.6876
 5XF  H14  H  HCH3  0   0.255   2.0189   4.3596   0.1004
 5XF  H15  H  HCH3  0   0.254   2.4417   4.0478   1.7931
 5XF  H16  H  HCR6  0   0.290   0.4621   2.3007   0.6069
 5XF  H17  H  HNH1  0   0.411  -0.9876  -1.0264  -0.2210
 5XF  H18  H  HCR6  0   0.271  -2.4137  -1.7737   1.7025
 5XF  H19  H  HCR6  0   0.260  -4.5712  -2.9648   1.7095
 5XF  H20  H  HCR6  0   0.266  -6.5248  -1.9521   0.5635
 5XF  H21  H  HCR6  0   0.286  -6.3243   0.1897  -0.5821
 5XF  H22  H  HCH3  0   0.232  -5.4658   1.5801  -2.2258
 5XF  H23  H  HCH3  0   0.232  -5.9414   2.4710  -0.7620
 5XF  H24  H  HCH3  0   0.262  -4.7128   3.1405  -1.8492

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
 5XF  CBB  OBA  single    1.415  0.020  1.415
 5XF  CAY  CAX  aromatic  1.389  0.020  1.389
 5XF  CAY  CAZ  aromatic  1.393  0.020  1.393
 5XF  CAX  CAW  aromatic  1.385  0.020  1.385
 5XF  OBA  CAZ  single    1.341  0.020  1.341
 5XF  CAZ  CAT  aromatic  1.403  0.020  1.403
 5XF  CAW  CAV  aromatic  1.388  0.020  1.388
 5XF  CAP  CAQ  single    1.545  0.020  1.545
 5XF  CAP  CAO  single    1.529  0.020  1.529
 5XF  CAQ  CAR  single    1.529  0.020  1.529
 5XF  CAV  CAT  aromatic  1.389  0.020  1.389
 5XF  CAT  CAS  single    1.496  0.020  1.496
 5XF  CAO  NAN  single    1.454  0.020  1.454
 5XF  CAR  NAN  single    1.462  0.020  1.462
 5XF  NAN  CAA  single    1.413  0.020  1.413
 5XF  CAS  NAG  single    1.351  0.020  1.351
 5XF  CAS  OAU  double    1.219  0.020  1.219
 5XF  NAG  CAF  single    1.396  0.020  1.396
 5XF  CAA  CAF  aromatic  1.411  0.020  1.411
 5XF  CAA  CAB  aromatic  1.394  0.020  1.394
 5XF  CAF  CAE  aromatic  1.397  0.020  1.397
 5XF  CAB  CAC  aromatic  1.379  0.020  1.379
 5XF  CAE  CAD  aromatic  1.380  0.020  1.380
 5XF  CAC  CAD  aromatic  1.394  0.020  1.394
 5XF  CAC  NAH  single    1.378  0.020  1.378
 5XF  CAD  NAJ  single    1.377  0.020  1.377
 5XF  NAH  CAL  single    1.439  0.020  1.439
 5XF  NAH  CAI  single    1.375  0.020  1.375
 5XF  NAJ  CAI  single    1.376  0.020  1.376
 5XF  NAJ  CAM  single    1.440  0.020  1.440
 5XF  CAI  OAK  double    1.219  0.020  1.219
 5XF  CAO  H1   single    0.970  0.020  1.090
 5XF  CAO  H2   single    0.970  0.020  1.090
 5XF  CAP  H3   single    0.970  0.020  1.090
 5XF  CAP  H4   single    0.970  0.020  1.090
 5XF  CAQ  H5   single    0.970  0.020  1.090
 5XF  CAQ  H6   single    0.970  0.020  1.090
 5XF  CAR  H7   single    0.970  0.020  1.090
 5XF  CAR  H8   single    0.970  0.020  1.090
 5XF  CAB  H9   single    0.930  0.020  1.080
 5XF  CAL  H10  single    0.970  0.020  1.090
 5XF  CAL  H11  single    0.970  0.020  1.090
 5XF  CAL  H12  single    0.970  0.020  1.090
 5XF  CAM  H13  single    0.970  0.020  1.090
 5XF  CAM  H14  single    0.970  0.020  1.090
 5XF  CAM  H15  single    0.970  0.020  1.090
 5XF  CAE  H16  single    0.930  0.020  1.080
 5XF  NAG  H17  single    0.860  0.020  1.020
 5XF  CAV  H18  single    0.930  0.020  1.080
 5XF  CAW  H19  single    0.930  0.020  1.080
 5XF  CAX  H20  single    0.930  0.020  1.080
 5XF  CAY  H21  single    0.930  0.020  1.080
 5XF  CBB  H22  single    0.970  0.020  1.090
 5XF  CBB  H23  single    0.970  0.020  1.090
 5XF  CBB  H24  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
 5XF  H2   CAO  H1   107.74  3.000
 5XF  H2   CAO  NAN  110.81  3.000
 5XF  H1   CAO  NAN  112.40  3.000
 5XF  H2   CAO  CAP  113.44  3.000
 5XF  H1   CAO  CAP  109.76  3.000
 5XF  NAN  CAO  CAP  102.74  3.000
 5XF  H4   CAP  H3   107.26  3.000
 5XF  H4   CAP  CAQ  112.63  3.000
 5XF  H3   CAP  CAQ  110.55  3.000
 5XF  H4   CAP  CAO  111.35  3.000
 5XF  H3   CAP  CAO  110.41  3.000
 5XF  CAQ  CAP  CAO  104.69  3.000
 5XF  H6   CAQ  H5   107.25  3.000
 5XF  H6   CAQ  CAR  111.06  3.000
 5XF  H5   CAQ  CAR  110.81  3.000
 5XF  H6   CAQ  CAP  112.47  3.000
 5XF  H5   CAQ  CAP  110.67  3.000
 5XF  CAR  CAQ  CAP  104.64  3.000
 5XF  H8   CAR  H7   107.42  3.000
 5XF  H8   CAR  NAN  111.01  3.000
 5XF  H7   CAR  NAN  111.04  3.000
 5XF  H8   CAR  CAQ  110.80  3.000
 5XF  H7   CAR  CAQ  113.41  3.000
 5XF  NAN  CAR  CAQ  103.20  3.000
 5XF  CAA  NAN  CAR  115.91  3.000
 5XF  CAA  NAN  CAO  119.11  3.000
 5XF  CAR  NAN  CAO  105.42  3.000
 5XF  CAF  CAA  CAB  120.47  3.000
 5XF  CAB  CAA  NAN  122.72  3.000
 5XF  CAF  CAA  NAN  116.80  3.000
 5XF  H9   CAB  CAC  121.31  3.000
 5XF  H9   CAB  CAA  120.60  3.000
 5XF  CAC  CAB  CAA  118.09  3.000
 5XF  CAD  CAC  NAH  107.10  3.000
 5XF  NAH  CAC  CAB  131.83  3.000
 5XF  CAD  CAC  CAB  121.07  3.000
 5XF  CAI  NAH  CAL  124.94  3.000
 5XF  CAI  NAH  CAC  109.79  3.000
 5XF  CAL  NAH  CAC  125.27  3.000
 5XF  H12  CAL  H11  108.70  3.000
 5XF  H12  CAL  H10  108.82  3.000
 5XF  H11  CAL  H10  108.62  3.000
 5XF  H12  CAL  NAH  110.85  3.000
 5XF  H11  CAL  NAH  109.11  3.000
 5XF  H10  CAL  NAH  110.69  3.000
 5XF  NAJ  CAI  OAK  126.79  3.000
 5XF  OAK  CAI  NAH  126.95  3.000
 5XF  NAJ  CAI  NAH  106.26  3.000
 5XF  CAD  NAJ  CAM  125.35  3.000
 5XF  CAM  NAJ  CAI  124.75  3.000
 5XF  CAD  NAJ  CAI  109.89  3.000
 5XF  H15  CAM  H14  108.82  3.000
 5XF  H15  CAM  H13  108.79  3.000
 5XF  H14  CAM  H13  108.52  3.000
 5XF  H15  CAM  NAJ  111.06  3.000
 5XF  H14  CAM  NAJ  110.43  3.000
 5XF  H13  CAM  NAJ  109.15  3.000
 5XF  CAE  CAD  NAJ  130.90  3.000
 5XF  NAJ  CAD  CAC  106.96  3.000
 5XF  CAE  CAD  CAC  122.14  3.000
 5XF  H16  CAE  CAF  121.57  3.000
 5XF  H16  CAE  CAD  121.33  3.000
 5XF  CAF  CAE  CAD  117.09  3.000
 5XF  NAG  CAF  CAE  123.94  3.000
 5XF  CAE  CAF  CAA  121.12  3.000
 5XF  NAG  CAF  CAA  114.93  3.000
 5XF  H17  NAG  CAS  118.16  3.000
 5XF  H17  NAG  CAF  111.85  3.000
 5XF  CAS  NAG  CAF  129.99  3.000
 5XF  CAT  CAS  OAU  122.33  3.000
 5XF  OAU  CAS  NAG  124.73  3.000
 5XF  CAT  CAS  NAG  112.93  3.000
 5XF  CAZ  CAT  CAV  119.54  3.000
 5XF  CAV  CAT  CAS  120.02  3.000
 5XF  CAZ  CAT  CAS  120.41  3.000
 5XF  H18  CAV  CAW  119.38  3.000
 5XF  H18  CAV  CAT  119.50  3.000
 5XF  CAW  CAV  CAT  121.11  3.000
 5XF  H19  CAW  CAX  120.75  3.000
 5XF  H19  CAW  CAV  120.26  3.000
 5XF  CAX  CAW  CAV  118.99  3.000
 5XF  H20  CAX  CAY  118.97  3.000
 5XF  H20  CAX  CAW  120.11  3.000
 5XF  CAY  CAX  CAW  120.92  3.000
 5XF  H21  CAY  CAZ  121.00  3.000
 5XF  H21  CAY  CAX  118.96  3.000
 5XF  CAZ  CAY  CAX  120.04  3.000
 5XF  OBA  CAZ  CAY  124.08  3.000
 5XF  OBA  CAZ  CAT  116.50  3.000
 5XF  CAY  CAZ  CAT  119.41  3.000
 5XF  CBB  OBA  CAZ  118.87  3.000
 5XF  H24  CBB  H23  108.77  3.000
 5XF  H24  CBB  H22  108.87  3.000
 5XF  H23  CBB  H22  108.91  3.000
 5XF  H24  CBB  OBA  106.32  3.000
 5XF  H23  CBB  OBA  111.97  3.000
 5XF  H22  CBB  OBA  111.89  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
 5XF  CONST_01  CAD  CAE  CAF  CAA     0.00   0.0  0
 5XF  CONST_02  CAD  CAC  CAB  CAA     0.00   0.0  0
 5XF  CONST_03  CAE  CAF  CAA  CAB     0.00   0.0  0
 5XF  CONST_04  CAE  CAD  CAC  CAB     0.00   0.0  0
 5XF  CONST_05  CAF  CAA  CAB  CAC     0.00   0.0  0
 5XF  CONST_06  CAF  CAE  CAD  CAC     0.00   0.0  0
 5XF  CONST_07  CAX  CAY  CAZ  CAT     0.00   0.0  0
 5XF  CONST_08  CAX  CAW  CAV  CAT     0.00   0.0  0
 5XF  CONST_09  CAY  CAX  CAW  CAV     0.00   0.0  0
 5XF  CONST_10  CAY  CAZ  CAT  CAV     0.00   0.0  0
 5XF  CONST_11  CAZ  CAY  CAX  CAW     0.00   0.0  0
 5XF  CONST_12  CAZ  CAT  CAV  CAW     0.00   0.0  0
 5XF  CONST_13  CAE  CAF  CAA  NAN   180.00   0.0  0
 5XF  CONST_14  CAC  CAB  CAA  NAN   180.00   0.0  0
 5XF  CONST_15  CAI  NAJ  CAD  CAC     0.00   0.0  0
 5XF  CONST_16  NAJ  CAI  NAH  CAC     0.00   0.0  0
 5XF  CONST_17  NAJ  CAD  CAC  NAH     0.00   0.0  0
 5XF  CONST_18  CAD  NAJ  CAI  NAH     0.00   0.0  0
 5XF  CONST_19  CAD  CAC  NAH  CAI     0.00   0.0  0
 5XF  CONST_20  NAG  CAF  CAA  NAN     0.00   0.0  0
 5XF  CONST_21  NAG  CAF  CAA  CAB   180.00   0.0  0
 5XF  CONST_22  NAG  CAF  CAE  CAD   180.00   0.0  0
 5XF  CONST_23  CAY  CAZ  CAT  CAS   180.00   0.0  0
 5XF  CONST_24  CAW  CAV  CAT  CAS   180.00   0.0  0
 5XF  CONST_25  OBA  CAZ  CAT  CAV   180.00   0.0  0
 5XF  CONST_26  OBA  CAZ  CAY  CAX   180.00   0.0  0
 5XF  CONST_27  CAM  NAJ  CAD  CAC   180.00   0.0  0
 5XF  CONST_28  OAK  CAI  NAH  CAC   180.00   0.0  0
 5XF  CONST_29  CAM  NAJ  CAI  NAH   180.00   0.0  0
 5XF  CONST_30  CAD  CAC  NAH  CAL   180.00   0.0  0
 5XF  CONST_31  NAJ  CAI  NAH  CAL   180.00   0.0  0
 5XF  CONST_32  CAD  NAJ  CAI  OAK   180.00   0.0  0
 5XF  CONST_33  H9   CAB  CAA  NAN     0.00   0.0  0
 5XF  CONST_34  H16  CAE  CAF  CAA   180.00   0.0  0
 5XF  CONST_35  H21  CAY  CAZ  CAT   180.00   0.0  0
 5XF  CONST_36  H19  CAW  CAV  CAT   180.00   0.0  0
 5XF  CONST_37  H20  CAX  CAW  CAV   180.00   0.0  0
 5XF  CONST_38  H18  CAV  CAW  CAX   180.00   0.0  0
 5XF  CONST_39  CAT  CAS  NAG  CAF   180.00   0.0  0
 5XF  CONST_40  CAS  NAG  CAF  CAA   180.00   0.0  0
 5XF  CONST_41  CAS  NAG  CAF  CAE     0.00   0.0  0
 5XF  CONST_42  OAK  CAI  NAH  CAL     0.00   0.0  0
 5XF  CONST_43  CAM  NAJ  CAI  OAK     0.00   0.0  0
 5XF  CONST_44  H17  NAG  CAF  CAA     0.00   0.0  0
 5XF  CONST_45  OAU  CAS  NAG  CAF     0.00   0.0  0
 5XF  Var_01    CAR  CAQ  CAP  CAO     2.32  30.0  1
 5XF  Var_02    CAQ  CAR  NAN  CAO   -42.23  30.0  1
 5XF  Var_03    CAF  CAA  NAN  CAO   142.92  30.0  2
 5XF  Var_04    NAN  CAR  CAQ  CAP    23.29  30.0  1
 5XF  Var_05    CAR  NAN  CAO  CAP    43.66  30.0  1
 5XF  Var_06    NAN  CAO  CAP  CAQ   -27.23  30.0  1
 5XF  Var_07    CAZ  CAT  CAS  NAG  -126.37  30.0  2
 5XF  Var_08    H10  CAL  NAH  CAC    58.93  30.0  3
 5XF  Var_09    H13  CAM  NAJ  CAI     8.90  30.0  3
 5XF  Var_10    H22  CBB  OBA  CAZ   -60.45  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
 5XF  plan-1  CAS  0.020
 5XF  plan-1  CAT  0.020
 5XF  plan-1  CAV  0.020
 5XF  plan-1  CAW  0.020
 5XF  plan-1  CAX  0.020
 5XF  plan-1  CAY  0.020
 5XF  plan-1  CAZ  0.020
 5XF  plan-1  OBA  0.020
 5XF  plan-1  H18  0.020
 5XF  plan-1  H19  0.020
 5XF  plan-1  H20  0.020
 5XF  plan-1  H21  0.020
 5XF  plan-2  NAN  0.020
 5XF  plan-2  CAA  0.020
 5XF  plan-2  CAB  0.020
 5XF  plan-2  CAC  0.020
 5XF  plan-2  NAH  0.020
 5XF  plan-2  CAL  0.020
 5XF  plan-2  CAI  0.020
 5XF  plan-2  OAK  0.020
 5XF  plan-2  NAJ  0.020
 5XF  plan-2  CAM  0.020
 5XF  plan-2  CAD  0.020
 5XF  plan-2  CAE  0.020
 5XF  plan-2  CAF  0.020
 5XF  plan-2  NAG  0.020
 5XF  plan-2  H9   0.020
 5XF  plan-2  H16  0.020
 5XF  plan-3  CAF  0.020
 5XF  plan-3  NAG  0.020
 5XF  plan-3  CAS  0.020
 5XF  plan-3  OAU  0.020
 5XF  plan-3  CAT  0.020
 5XF  plan-3  H17  0.020

