# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:39:13 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 5-[1-(1,3-dimethoxypropan-2-yl)-5-morpholin-4-yl-benzimidazol-2-yl]-1,3-dimethyl-pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCC(COC)n1c2ccc(cc2nc1C3=CN(C)C(=O)C(=C3)C)N4CCOCC4
#
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
 NV2  NV2  5-[1-(1,3-dimethoxypropan-2-yl)-5-morpholin-4-yl-benzimidazol-2-yl]-1,3-dimethyl-pyridin-2-one  ligand  61  31  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NV2
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
 NV2  C15  C  CH3   0  -0.404  -2.7608  -1.1385  -3.2878
 NV2  C20  C  CR5   0   0.424  -0.7812   0.6080  -0.0026
 NV2  C22  C  CR56  0   0.152   1.3497   0.6377   0.1205
 NV2  C26  C  CR16  0  -0.363   3.2409  -1.3530   0.3174
 NV2  C28  C  CR16  0  -0.306   1.9067  -1.7216   0.2613
 NV2  C01  C  CH3   0  -0.398  -2.7522  -4.2119   2.3132
 NV2  O05  O  O2    0  -0.482  -2.1979  -3.7026   1.1252
 NV2  C06  C  CH2   0  -0.119  -1.6922  -2.4065   1.2773
 NV2  C09  C  CH1   0  -0.206  -1.1849  -1.9290  -0.0791
 NV2  C11  C  CH2   0  -0.126  -2.3025  -1.8214  -1.1073
 NV2  O14  O  O2    0  -0.478  -1.7950  -1.2339  -2.2712
 NV2  N19  N  NR5   0  -0.548  -0.4086  -0.7063   0.0698
 NV2  N21  N  N     0  -0.470   0.2334   1.4316   0.0242
 NV2  C23  C  CR16  0  -0.432   2.6898   0.9994   0.2027
 NV2  C25  C  CR6   0   0.352   3.6540  -0.0032   0.2975
 NV2  C30  C  CR56  0   0.331   0.9673  -0.7079   0.1568
 NV2  N31  N  NT    0  -0.524   5.0091   0.3508   0.3952
 NV2  C32  C  CH2   0  -0.320   5.5191   1.2463  -0.6354
 NV2  C35  C  CH2   0  -0.187   6.8768   1.7864  -0.2324
 NV2  O38  O  O2    0  -0.483   7.7917   0.7482   0.0353
 NV2  C39  C  CH2   0  -0.183   7.3027  -0.0886   1.0578
 NV2  C42  C  CH2   0  -0.329   5.9608  -0.6993   0.6976
 NV2  C45  C  CR6   0  -0.165  -2.1724   1.0645  -0.0900
 NV2  C46  C  CR16  0  -0.175  -3.0896   0.9386   0.9841
 NV2  C48  C  CR6   0  -0.124  -4.3687   1.3865   0.8816
 NV2  C49  C  CH3   0  -0.711  -5.3618   1.2772   1.9924
 NV2  C53  C  CR6   0   0.560  -4.8193   2.0126  -0.3429
 NV2  O54  O  O     0  -0.498  -5.9556   2.4400  -0.5199
 NV2  N55  N  NR6   0  -0.506  -3.8723   2.1209  -1.3533
 NV2  C56  C  CH3   0  -0.524  -4.2977   2.7397  -2.6017
 NV2  C60  C  CR16  0   0.038  -2.6037   1.6730  -1.2249
 NV2  H1   H  HCH3  0   0.239  -2.3122  -0.6164  -4.1315
 NV2  H2   H  HCH3  0   0.217  -3.1000  -2.1243  -3.6259
 NV2  H3   H  HCH3  0   0.202  -3.6440  -0.5749  -2.9621
 NV2  H4   H  HCR6  0   0.270   3.9760  -2.1430   0.3700
 NV2  H5   H  HCR6  0   0.268   1.6349  -2.7693   0.2882
 NV2  H6   H  HCH3  0   0.209  -2.0122  -4.2696   3.1196
 NV2  H7   H  HCH3  0   0.210  -3.5913  -3.6015   2.6660
 NV2  H8   H  HCH3  0   0.238  -3.1184  -5.2166   2.1078
 NV2  H9   H  HCH2  0   0.203  -2.4686  -1.7248   1.6517
 NV2  H10  H  HCH2  0   0.228  -0.8657  -2.3802   2.0017
 NV2  H11  H  HCH1  0   0.279  -0.4763  -2.6731  -0.4513
 NV2  H12  H  HCH2  0   0.241  -2.6698  -2.8366  -1.3016
 NV2  H13  H  HCH2  0   0.212  -3.1538  -1.2519  -0.7115
 NV2  H14  H  HCR6  0   0.257   2.9645   2.0467   0.2070
 NV2  H15  H  HCH2  0   0.217   5.5945   0.7283  -1.6040
 NV2  H16  H  HCH2  0   0.256   4.8454   2.0909  -0.7717
 NV2  H17  H  HCH2  0   0.240   7.2902   2.3883  -1.0429
 NV2  H18  H  HCH2  0   0.204   6.7634   2.4341   0.6483
 NV2  H19  H  HCH2  0   0.240   8.0362  -0.8811   1.2132
 NV2  H20  H  HCH2  0   0.203   7.2044   0.4716   1.9987
 NV2  H21  H  HCH2  0   0.254   5.6136  -1.2775   1.5561
 NV2  H22  H  HCH2  0   0.214   6.0902  -1.4007  -0.1420
 NV2  H23  H  HCR6  0   0.269  -2.7559   0.4926   1.9141
 NV2  H24  H  HCH3  0   0.246  -5.7161   2.2600   2.3079
 NV2  H25  H  HCH3  0   0.246  -6.2403   0.7083   1.6834
 NV2  H26  H  HCH3  0   0.244  -4.9265   0.7811   2.8582
 NV2  H27  H  HCH3  0   0.265  -4.5977   3.7721  -2.4363
 NV2  H28  H  HCH3  0   0.261  -3.4705   2.7198  -3.3038
 NV2  H29  H  HCH3  0   0.263  -5.1364   2.1943  -3.0284
 NV2  H30  H  HCR6  0   0.311  -1.9573   1.8111  -2.0796

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
 NV2  C01  O05  single    1.406  0.020  1.406
 NV2  C06  O05  single    1.400  0.020  1.400
 NV2  C06  C09  single    1.525  0.020  1.525
 NV2  C11  C09  single    1.522  0.020  1.522
 NV2  C11  O14  single    1.399  0.020  1.399
 NV2  C15  O14  single    1.405  0.020  1.405
 NV2  C09  N19  single    1.456  0.020  1.456
 NV2  C28  C26  aromatic  1.385  0.020  1.385
 NV2  C28  C30  aromatic  1.386  0.020  1.386
 NV2  C26  C25  aromatic  1.412  0.020  1.412
 NV2  N19  C30  aromatic  1.379  0.020  1.379
 NV2  N19  C20  aromatic  1.368  0.020  1.368
 NV2  C30  C22  aromatic  1.399  0.020  1.399
 NV2  C32  C35  single    1.516  0.020  1.516
 NV2  C32  N31  single    1.458  0.020  1.458
 NV2  C35  O38  single    1.409  0.020  1.409
 NV2  C25  N31  single    1.404  0.020  1.404
 NV2  C25  C23  aromatic  1.394  0.020  1.394
 NV2  N31  C42  single    1.449  0.020  1.449
 NV2  C56  N55  single    1.457  0.020  1.457
 NV2  C20  C45  single    1.467  0.020  1.467
 NV2  C20  N21  aromatic  1.307  0.020  1.307
 NV2  C60  N55  single    1.351  0.020  1.351
 NV2  C60  C45  double    1.358  0.020  1.358
 NV2  C22  C23  aromatic  1.391  0.020  1.391
 NV2  C22  N21  aromatic  1.373  0.020  1.373
 NV2  N55  C53  single    1.389  0.020  1.389
 NV2  C45  C46  single    1.418  0.020  1.418
 NV2  O38  C39  single    1.409  0.020  1.409
 NV2  C42  C39  single    1.518  0.020  1.518
 NV2  C53  O54  double    1.227  0.020  1.227
 NV2  C53  C48  single    1.447  0.020  1.447
 NV2  C46  C48  double    1.359  0.020  1.359
 NV2  C48  C49  single    1.494  0.020  1.494
 NV2  C15  H1   single    0.970  0.020  1.090
 NV2  C15  H2   single    0.970  0.020  1.090
 NV2  C15  H3   single    0.970  0.020  1.090
 NV2  C26  H4   single    0.930  0.020  1.080
 NV2  C28  H5   single    0.930  0.020  1.080
 NV2  C01  H6   single    0.970  0.020  1.090
 NV2  C01  H7   single    0.970  0.020  1.090
 NV2  C01  H8   single    0.970  0.020  1.090
 NV2  C06  H9   single    0.970  0.020  1.090
 NV2  C06  H10  single    0.970  0.020  1.090
 NV2  C09  H11  single    0.970  0.020  1.090
 NV2  C11  H12  single    0.970  0.020  1.090
 NV2  C11  H13  single    0.970  0.020  1.090
 NV2  C23  H14  single    0.930  0.020  1.080
 NV2  C32  H15  single    0.970  0.020  1.090
 NV2  C32  H16  single    0.970  0.020  1.090
 NV2  C35  H17  single    0.970  0.020  1.090
 NV2  C35  H18  single    0.970  0.020  1.090
 NV2  C39  H19  single    0.970  0.020  1.090
 NV2  C39  H20  single    0.970  0.020  1.090
 NV2  C42  H21  single    0.970  0.020  1.090
 NV2  C42  H22  single    0.970  0.020  1.090
 NV2  C46  H23  single    0.930  0.020  1.080
 NV2  C49  H24  single    0.970  0.020  1.090
 NV2  C49  H25  single    0.970  0.020  1.090
 NV2  C49  H26  single    0.970  0.020  1.090
 NV2  C56  H27  single    0.970  0.020  1.090
 NV2  C56  H28  single    0.970  0.020  1.090
 NV2  C56  H29  single    0.970  0.020  1.090
 NV2  C60  H30  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
 NV2  H3   C15  H2   107.73  3.000
 NV2  H3   C15  H1   108.38  3.000
 NV2  H2   C15  H1   108.64  3.000
 NV2  H3   C15  O14  111.92  3.000
 NV2  H2   C15  O14  112.01  3.000
 NV2  H1   C15  O14  108.05  3.000
 NV2  C45  C20  N21  122.77  3.000
 NV2  N21  C20  N19  113.14  3.000
 NV2  C45  C20  N19  124.09  3.000
 NV2  C30  C22  C23  120.79  3.000
 NV2  C23  C22  N21  129.59  3.000
 NV2  C30  C22  N21  109.61  3.000
 NV2  H4   C26  C25  120.05  3.000
 NV2  H4   C26  C28  117.56  3.000
 NV2  C25  C26  C28  122.39  3.000
 NV2  H5   C28  C30  122.65  3.000
 NV2  H5   C28  C26  119.88  3.000
 NV2  C30  C28  C26  117.46  3.000
 NV2  H8   C01  H7   108.49  3.000
 NV2  H8   C01  H6   108.50  3.000
 NV2  H7   C01  H6   108.03  3.000
 NV2  H8   C01  O05  107.90  3.000
 NV2  H7   C01  O05  111.83  3.000
 NV2  H6   C01  O05  111.99  3.000
 NV2  C06  O05  C01  112.71  3.000
 NV2  H10  C06  H9   106.97  3.000
 NV2  H10  C06  C09  109.18  3.000
 NV2  H9   C06  C09  110.11  3.000
 NV2  H10  C06  O05  111.43  3.000
 NV2  H9   C06  O05  110.87  3.000
 NV2  C09  C06  O05  108.27  3.000
 NV2  H11  C09  N19  105.12  3.000
 NV2  H11  C09  C11  107.11  3.000
 NV2  N19  C09  C11  113.65  3.000
 NV2  H11  C09  C06  107.78  3.000
 NV2  N19  C09  C06  110.45  3.000
 NV2  C11  C09  C06  112.25  3.000
 NV2  H13  C11  H12  106.51  3.000
 NV2  H13  C11  O14  111.30  3.000
 NV2  H12  C11  O14  111.27  3.000
 NV2  H13  C11  C09  111.24  3.000
 NV2  H12  C11  C09  107.46  3.000
 NV2  O14  C11  C09  108.98  3.000
 NV2  C11  O14  C15  112.39  3.000
 NV2  C30  N19  C09  122.52  3.000
 NV2  C30  N19  C20  106.04  3.000
 NV2  C09  N19  C20  131.01  3.000
 NV2  C22  N21  C20  105.55  3.000
 NV2  H14  C23  C25  121.32  3.000
 NV2  H14  C23  C22  119.76  3.000
 NV2  C25  C23  C22  118.91  3.000
 NV2  N31  C25  C23  119.40  3.000
 NV2  C23  C25  C26  119.09  3.000
 NV2  N31  C25  C26  121.50  3.000
 NV2  N19  C30  C28  133.00  3.000
 NV2  N19  C30  C22  105.66  3.000
 NV2  C28  C30  C22  121.34  3.000
 NV2  C42  N31  C32  111.28  3.000
 NV2  C42  N31  C25  117.76  3.000
 NV2  C32  N31  C25  116.32  3.000
 NV2  H16  C32  H15  107.29  3.000
 NV2  H16  C32  C35  108.13  3.000
 NV2  H15  C32  C35  109.89  3.000
 NV2  H16  C32  N31  110.40  3.000
 NV2  H15  C32  N31  110.91  3.000
 NV2  C35  C32  N31  110.14  3.000
 NV2  H18  C35  H17  108.02  3.000
 NV2  H18  C35  O38  110.42  3.000
 NV2  H17  C35  O38  107.56  3.000
 NV2  H18  C35  C32  109.30  3.000
 NV2  H17  C35  C32  109.78  3.000
 NV2  O38  C35  C32  111.68  3.000
 NV2  C39  O38  C35  110.49  3.000
 NV2  H20  C39  H19  107.96  3.000
 NV2  H20  C39  C42  109.21  3.000
 NV2  H19  C39  C42  109.63  3.000
 NV2  H20  C39  O38  110.46  3.000
 NV2  H19  C39  O38  107.55  3.000
 NV2  C42  C39  O38  111.94  3.000
 NV2  H22  C42  H21  107.42  3.000
 NV2  H22  C42  C39  109.47  3.000
 NV2  H21  C42  C39  107.92  3.000
 NV2  H22  C42  N31  112.30  3.000
 NV2  H21  C42  N31  109.82  3.000
 NV2  C39  C42  N31  109.79  3.000
 NV2  C60  C45  C46  117.87  3.000
 NV2  C46  C45  C20  122.73  3.000
 NV2  C60  C45  C20  119.37  3.000
 NV2  H23  C46  C48  119.34  3.000
 NV2  H23  C46  C45  119.16  3.000
 NV2  C48  C46  C45  121.49  3.000
 NV2  C53  C48  C49  116.99  3.000
 NV2  C49  C48  C46  123.05  3.000
 NV2  C53  C48  C46  119.96  3.000
 NV2  H26  C49  H25  108.03  3.000
 NV2  H26  C49  H24  108.08  3.000
 NV2  H25  C49  H24  106.85  3.000
 NV2  H26  C49  C48  111.03  3.000
 NV2  H25  C49  C48  111.27  3.000
 NV2  H24  C49  C48  111.40  3.000
 NV2  N55  C53  O54  119.95  3.000
 NV2  O54  C53  C48  124.14  3.000
 NV2  N55  C53  C48  115.91  3.000
 NV2  C60  N55  C56  119.76  3.000
 NV2  C60  N55  C53  123.02  3.000
 NV2  C56  N55  C53  117.22  3.000
 NV2  H29  C56  H28  108.96  3.000
 NV2  H29  C56  H27  108.84  3.000
 NV2  H28  C56  H27  109.03  3.000
 NV2  H29  C56  N55  110.39  3.000
 NV2  H28  C56  N55  108.91  3.000
 NV2  H27  C56  N55  110.69  3.000
 NV2  H30  C60  N55  116.36  3.000
 NV2  H30  C60  C45  121.90  3.000
 NV2  N55  C60  C45  121.74  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
 NV2  CONST_01  C28  C30  N19  C20   180.00   0.0  0
 NV2  CONST_02  C22  C30  N19  C20     0.00   0.0  0
 NV2  CONST_03  C30  C22  N21  C20     0.00   0.0  0
 NV2  CONST_04  C23  C22  N21  C20   180.00   0.0  0
 NV2  CONST_05  C26  C28  C30  C22     0.00   0.0  0
 NV2  CONST_06  C26  C25  C23  C22     0.00   0.0  0
 NV2  CONST_07  N19  C20  N21  C22     0.00   0.0  0
 NV2  CONST_08  N19  C30  C28  C26   180.00   0.0  0
 NV2  CONST_09  C23  C25  C26  C28     0.00   0.0  0
 NV2  CONST_10  C23  C22  C30  C28     0.00   0.0  0
 NV2  CONST_11  N21  C22  C30  C28   180.00   0.0  0
 NV2  CONST_12  C23  C22  C30  N19   180.00   0.0  0
 NV2  CONST_13  N21  C22  C30  N19     0.00   0.0  0
 NV2  CONST_14  C30  N19  C20  N21     0.00   0.0  0
 NV2  CONST_15  C25  C23  C22  N21   180.00   0.0  0
 NV2  CONST_16  C30  C28  C26  C25     0.00   0.0  0
 NV2  CONST_17  C30  C22  C23  C25     0.00   0.0  0
 NV2  CONST_18  N31  C25  C23  C22   180.00   0.0  0
 NV2  CONST_19  C45  C20  N21  C22   180.00   0.0  0
 NV2  CONST_20  N31  C25  C26  C28   180.00   0.0  0
 NV2  CONST_21  C45  C20  N19  C30   180.00   0.0  0
 NV2  CONST_22  C60  N55  C53  C48     0.00   0.0  0
 NV2  CONST_23  C09  N19  C30  C22   180.00   0.0  0
 NV2  CONST_24  C09  N19  C30  C28     0.00   0.0  0
 NV2  CONST_25  C45  C20  N19  C09     0.00   0.0  0
 NV2  CONST_26  N21  C20  N19  C09   180.00   0.0  0
 NV2  CONST_27  C56  N55  C53  C48   180.00   0.0  0
 NV2  CONST_28  C60  N55  C53  O54   180.00   0.0  0
 NV2  CONST_29  H5   C28  C30  C22   180.00   0.0  0
 NV2  CONST_30  H14  C23  C25  C26   180.00   0.0  0
 NV2  CONST_31  H4   C26  C25  C23   180.00   0.0  0
 NV2  CONST_32  C56  N55  C53  O54     0.00   0.0  0
 NV2  Var_01    C32  N31  C25  C26   127.78  30.0  2
 NV2  Var_02    C60  C45  C20  N19  -113.37  30.0  2
 NV2  Var_03    C35  C32  N31  C25   167.08  30.0  1
 NV2  Var_04    C39  C42  N31  C25  -167.74  30.0  1
 NV2  Var_05    O38  C35  C32  N31    56.06  30.0  1
 NV2  Var_06    O38  C39  C42  N31   -56.60  30.0  1
 NV2  Var_07    C42  C39  O38  C35    58.54  30.0  1
 NV2  Var_08    C06  C09  N19  C20   -92.27  30.0  2
 NV2  Var_09    H24  C49  C48  C46   119.27  30.0  3
 NV2  Var_10    H27  C56  N55  C53    62.34  30.0  3
 NV2  Var_11    N19  C09  C06  O05  -168.52  30.0  3
 NV2  Var_12    C09  C11  O14  C15   178.10  30.0  2
 NV2  Var_13    C09  C06  O05  C01  -177.12  30.0  1
 NV2  Var_14    H6   C01  O05  C06   -60.62  30.0  3
 NV2  Var_15    H1   C15  O14  C11   176.39  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
 NV2  plan-1  C20  0.020
 NV2  plan-1  C45  0.020
 NV2  plan-1  C46  0.020
 NV2  plan-1  C48  0.020
 NV2  plan-1  C49  0.020
 NV2  plan-1  C53  0.020
 NV2  plan-1  O54  0.020
 NV2  plan-1  N55  0.020
 NV2  plan-1  C56  0.020
 NV2  plan-1  C60  0.020
 NV2  plan-1  H23  0.020
 NV2  plan-1  H30  0.020
 NV2  plan-2  C20  0.020
 NV2  plan-2  C22  0.020
 NV2  plan-2  C26  0.020
 NV2  plan-2  C28  0.020
 NV2  plan-2  C09  0.020
 NV2  plan-2  N19  0.020
 NV2  plan-2  N21  0.020
 NV2  plan-2  C23  0.020
 NV2  plan-2  C25  0.020
 NV2  plan-2  C30  0.020
 NV2  plan-2  N31  0.020
 NV2  plan-2  C45  0.020
 NV2  plan-2  H4   0.020
 NV2  plan-2  H5   0.020
 NV2  plan-2  H14  0.020

