# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 12:50:21 2022
#   Inital geometry file: a 152 line input string
#   Ligand name: ~{N}-(2,2-diphenylethyl)-1,5-dimethyl-~{N}-[2-(methylamino)-2-oxidanylidene-ethyl]-6-oxidanylidene-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)CN(CC(c1ccccc1)c2ccccc2)C(=O)C3=CN(C)C(=O)C(=C3)C
#
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
 VBH  VBH  ~{N}-(2,2-diphenylethyl)-1,5-dimethyl-~{N}-[2-(methylamino)-2-oxidanylidene-ethyl]-6-oxidanylidene-pyridine-3-carboxamide  ligand  58  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VBH
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
 VBH  N1   N  NT    0  -0.453  39.4665  19.4758   8.6597
 VBH  C4   C  CH1   0  -0.407  40.4037  18.8855  10.8776
 VBH  C5   C  CR6   0   0.162  40.1955  18.0570  12.1260
 VBH  C6   C  CR16  0  -0.292  40.6247  18.5742  13.3484
 VBH  C7   C  CR16  0  -0.240  40.4856  17.8489  14.5211
 VBH  C8   C  CR16  0  -0.267  39.9097  16.5838  14.4939
 VBH  C10  C  CR16  0  -0.325  39.6195  16.7895  12.1111
 VBH  C13  C  CR16  0  -0.230  43.7869  17.5086   9.7922
 VBH  C15  C  CR16  0  -0.242  43.7821  19.8808   9.4371
 VBH  C17  C  C     0   0.539  40.2313  19.3619   7.5472
 VBH  C20  C  CR6   0  -0.129  42.5610  16.6849   6.2931
 VBH  C21  C  CH3   0  -0.709  43.9895  16.4790   5.9075
 VBH  C22  C  CR6   0   0.556  41.6793  15.5428   6.1865
 VBH  C24  C  CR16  0   0.024  39.9095  16.9510   7.0156
 VBH  O2   O  O     0  -0.491  42.0313  14.4336   5.7991
 VBH  C19  C  CR16  0  -0.143  42.0824  17.8740   6.7390
 VBH  N2   N  NR6   0  -0.506  40.3554  15.7630   6.5493
 VBH  C23  C  CH3   0  -0.519  39.4353  14.6410   6.4243
 VBH  C18  C  CR6   0  -0.194  40.7332  18.0232   7.1455
 VBH  O1   O  O     0  -0.476  40.4872  20.3364   6.8529
 VBH  C2   C  CH2   0  -0.440  38.8759  20.7726   8.8900
 VBH  C1   C  C     0   0.543  37.8871  21.1319   7.7861
 VBH  O    O  O     0  -0.487  37.2502  20.2795   7.1881
 VBH  N    N  NH1   0  -0.626  37.7333  22.4443   7.5778
 VBH  C    C  CH3   0  -0.512  36.7781  22.9687   6.6303
 VBH  C3   C  CH2   0  -0.321  39.4215  18.5227   9.7511
 VBH  C11  C  CR6   0   0.152  41.8301  18.8013  10.3747
 VBH  C16  C  CR16  0  -0.312  42.4884  19.9482   9.9405
 VBH  C14  C  CR16  0  -0.267  44.4369  18.6599   9.3649
 VBH  C12  C  CR16  0  -0.285  42.4956  17.5800  10.2924
 VBH  C9   C  CR16  0  -0.238  39.4772  16.0588  13.2857
 VBH  H1   H  HCH1  0   0.277  40.2160  19.9277  11.1581
 VBH  H2   H  HCR6  0   0.249  41.0756  19.5598  13.3770
 VBH  H3   H  HCR6  0   0.253  40.8243  18.2717  15.4584
 VBH  H4   H  HCR6  0   0.253  39.7980  16.0150  15.4078
 VBH  H5   H  HCR6  0   0.254  39.2757  16.3501  11.1833
 VBH  H7   H  HCR6  0   0.252  44.2776  20.7846   9.1062
 VBH  H8   H  HCH3  0   0.243  44.5545  17.4047   6.0049
 VBH  H9   H  HCH3  0   0.242  44.4661  15.7271   6.5395
 VBH  H10  H  HCH3  0   0.243  44.0830  16.1320   4.8771
 VBH  H11  H  HCR6  0   0.318  38.8566  16.9977   7.2605
 VBH  H12  H  HCR6  0   0.264  42.7506  18.7233   6.8129
 VBH  H13  H  HCH3  0   0.260  38.4469  14.9575   6.7426
 VBH  H14  H  HCH3  0   0.260  39.3829  14.3024   5.3917
 VBH  H15  H  HCH3  0   0.261  39.7579  13.8107   7.0488
 VBH  H16  H  HCH2  0   0.275  39.6325  21.5521   9.0151
 VBH  H17  H  HCH2  0   0.298  38.3147  20.7299   9.8261
 VBH  H18  H  HNH1  0   0.404  38.3204  23.0950   8.0727
 VBH  H19  H  HCH3  0   0.249  36.8150  24.0536   6.6681
 VBH  H20  H  HCH3  0   0.237  37.0046  22.6534   5.6111
 VBH  H21  H  HCH3  0   0.238  35.7623  22.6523   6.8681
 VBH  H22  H  HCH2  0   0.274  38.4022  18.4953  10.1421
 VBH  H23  H  HCH2  0   0.273  39.6451  17.5276   9.3786
 VBH  H24  H  HCR6  0   0.254  41.9868  20.9074  10.0020
 VBH  H25  H  HCR6  0   0.252  45.4458  18.6043   8.9766
 VBH  H26  H  HCR6  0   0.252  42.0047  16.6727  10.6243
 VBH  H27  H  HCR6  0   0.254  39.0268  15.0750  13.2512
 VBH  H6   H  HCR6  0   0.251  44.2876  16.5505   9.7333

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
 VBH  C23  N2   single    1.456  0.020  1.456
 VBH  O2   C22  double    1.227  0.020  1.227
 VBH  O1   C17  double    1.224  0.020  1.224
 VBH  C22  N2   single    1.390  0.020  1.390
 VBH  C22  C20  single    1.447  0.020  1.447
 VBH  N2   C24  single    1.352  0.020  1.352
 VBH  C21  C20  single    1.494  0.020  1.494
 VBH  C20  C19  double    1.357  0.020  1.357
 VBH  C24  C18  double    1.358  0.020  1.358
 VBH  C19  C18  single    1.417  0.020  1.417
 VBH  C18  C17  single    1.485  0.020  1.485
 VBH  C17  N1   single    1.355  0.020  1.355
 VBH  O    C1   double    1.220  0.020  1.220
 VBH  C    N    single    1.444  0.020  1.444
 VBH  N    C1   single    1.338  0.020  1.338
 VBH  C1   C2   single    1.525  0.020  1.525
 VBH  N1   C2   single    1.443  0.020  1.443
 VBH  N1   C3   single    1.450  0.020  1.450
 VBH  C3   C4   single    1.538  0.020  1.538
 VBH  C14  C15  aromatic  1.387  0.020  1.387
 VBH  C14  C13  aromatic  1.390  0.020  1.390
 VBH  C15  C16  aromatic  1.390  0.020  1.390
 VBH  C13  C12  aromatic  1.387  0.020  1.387
 VBH  C16  C11  aromatic  1.392  0.020  1.392
 VBH  C12  C11  aromatic  1.393  0.020  1.393
 VBH  C11  C4   single    1.515  0.020  1.515
 VBH  C4   C5   single    1.513  0.020  1.513
 VBH  C10  C5   aromatic  1.392  0.020  1.392
 VBH  C10  C9   aromatic  1.391  0.020  1.391
 VBH  C5   C6   aromatic  1.395  0.020  1.395
 VBH  C9   C8   aromatic  1.386  0.020  1.386
 VBH  C6   C7   aromatic  1.386  0.020  1.386
 VBH  C8   C7   aromatic  1.390  0.020  1.390
 VBH  C4   H1   single    0.970  0.020  1.090
 VBH  C6   H2   single    0.930  0.020  1.080
 VBH  C7   H3   single    0.930  0.020  1.080
 VBH  C8   H4   single    0.930  0.020  1.080
 VBH  C10  H5   single    0.930  0.020  1.080
 VBH  C13  H6   single    0.930  0.020  1.080
 VBH  C15  H7   single    0.930  0.020  1.080
 VBH  C21  H8   single    0.970  0.020  1.090
 VBH  C21  H9   single    0.970  0.020  1.090
 VBH  C21  H10  single    0.970  0.020  1.090
 VBH  C24  H11  single    0.930  0.020  1.080
 VBH  C19  H12  single    0.930  0.020  1.080
 VBH  C23  H13  single    0.970  0.020  1.090
 VBH  C23  H14  single    0.970  0.020  1.090
 VBH  C23  H15  single    0.970  0.020  1.090
 VBH  C2   H16  single    0.970  0.020  1.090
 VBH  C2   H17  single    0.970  0.020  1.090
 VBH  N    H18  single    0.860  0.020  1.020
 VBH  C    H19  single    0.970  0.020  1.090
 VBH  C    H20  single    0.970  0.020  1.090
 VBH  C    H21  single    0.970  0.020  1.090
 VBH  C3   H22  single    0.970  0.020  1.090
 VBH  C3   H23  single    0.970  0.020  1.090
 VBH  C16  H24  single    0.930  0.020  1.080
 VBH  C14  H25  single    0.930  0.020  1.080
 VBH  C12  H26  single    0.930  0.020  1.080
 VBH  C9   H27  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
 VBH  C3   N1   C2   117.25  3.000
 VBH  C3   N1   C17  125.48  3.000
 VBH  C2   N1   C17  115.94  3.000
 VBH  H1   C4   C11  107.41  3.000
 VBH  H1   C4   C3   107.61  3.000
 VBH  C11  C4   C3   110.19  3.000
 VBH  H1   C4   C5   106.63  3.000
 VBH  C11  C4   C5   111.91  3.000
 VBH  C3   C4   C5   112.79  3.000
 VBH  C10  C5   C6   118.31  3.000
 VBH  C6   C5   C4   118.54  3.000
 VBH  C10  C5   C4   123.14  3.000
 VBH  H2   C6   C7   119.68  3.000
 VBH  H2   C6   C5   119.22  3.000
 VBH  C7   C6   C5   121.10  3.000
 VBH  H3   C7   C8   120.13  3.000
 VBH  H3   C7   C6   119.79  3.000
 VBH  C8   C7   C6   120.08  3.000
 VBH  H4   C8   C9   120.31  3.000
 VBH  H4   C8   C7   120.29  3.000
 VBH  C9   C8   C7   119.40  3.000
 VBH  H5   C10  C9   118.56  3.000
 VBH  H5   C10  C5   120.66  3.000
 VBH  C9   C10  C5   120.77  3.000
 VBH  H6   C13  C12  119.73  3.000
 VBH  H6   C13  C14  120.01  3.000
 VBH  C12  C13  C14  120.26  3.000
 VBH  H7   C15  C14  120.18  3.000
 VBH  H7   C15  C16  119.76  3.000
 VBH  C14  C15  C16  120.06  3.000
 VBH  O1   C17  C18  119.59  3.000
 VBH  C18  C17  N1   119.26  3.000
 VBH  O1   C17  N1   121.13  3.000
 VBH  C19  C20  C22  120.07  3.000
 VBH  C19  C20  C21  122.87  3.000
 VBH  C22  C20  C21  117.06  3.000
 VBH  H10  C21  H9   106.87  3.000
 VBH  H10  C21  H8   108.08  3.000
 VBH  H9   C21  H8   107.89  3.000
 VBH  H10  C21  C20  111.68  3.000
 VBH  H9   C21  C20  111.28  3.000
 VBH  H8   C21  C20  110.85  3.000
 VBH  N2   C22  O2   119.93  3.000
 VBH  N2   C22  C20  115.85  3.000
 VBH  O2   C22  C20  124.21  3.000
 VBH  H11  C24  C18  122.30  3.000
 VBH  H11  C24  N2   115.91  3.000
 VBH  C18  C24  N2   121.78  3.000
 VBH  H12  C19  C18  119.03  3.000
 VBH  H12  C19  C20  119.47  3.000
 VBH  C18  C19  C20  121.49  3.000
 VBH  C23  N2   C24  119.88  3.000
 VBH  C24  N2   C22  122.91  3.000
 VBH  C23  N2   C22  117.21  3.000
 VBH  H15  C23  H14  108.76  3.000
 VBH  H15  C23  H13  108.92  3.000
 VBH  H14  C23  H13  108.98  3.000
 VBH  H15  C23  N2   110.57  3.000
 VBH  H14  C23  N2   110.59  3.000
 VBH  H13  C23  N2   108.99  3.000
 VBH  C19  C18  C24  117.83  3.000
 VBH  C19  C18  C17  119.63  3.000
 VBH  C24  C18  C17  122.17  3.000
 VBH  H17  C2   H16  106.58  3.000
 VBH  H17  C2   C1   107.24  3.000
 VBH  H16  C2   C1   111.32  3.000
 VBH  H17  C2   N1   108.17  3.000
 VBH  H16  C2   N1   112.06  3.000
 VBH  C1   C2   N1   111.19  3.000
 VBH  N    C1   O    123.29  3.000
 VBH  N    C1   C2   114.73  3.000
 VBH  O    C1   C2   121.90  3.000
 VBH  H18  N    C    118.28  3.000
 VBH  H18  N    C1   119.38  3.000
 VBH  C    N    C1   122.31  3.000
 VBH  H21  C    H20  108.27  3.000
 VBH  H21  C    H19  108.30  3.000
 VBH  H20  C    H19  108.31  3.000
 VBH  H21  C    N    111.58  3.000
 VBH  H20  C    N    111.76  3.000
 VBH  H19  C    N    108.51  3.000
 VBH  H23  C3   H22  106.98  3.000
 VBH  H23  C3   C4   109.63  3.000
 VBH  H22  C3   C4   109.86  3.000
 VBH  H23  C3   N1   109.75  3.000
 VBH  H22  C3   N1   108.36  3.000
 VBH  C4   C3   N1   112.12  3.000
 VBH  C12  C11  C16  118.55  3.000
 VBH  C12  C11  C4   121.21  3.000
 VBH  C16  C11  C4   120.21  3.000
 VBH  H24  C16  C11  119.50  3.000
 VBH  H24  C16  C15  119.61  3.000
 VBH  C11  C16  C15  120.88  3.000
 VBH  H25  C14  C15  120.25  3.000
 VBH  H25  C14  C13  120.25  3.000
 VBH  C15  C14  C13  119.50  3.000
 VBH  H26  C12  C11  119.96  3.000
 VBH  H26  C12  C13  119.29  3.000
 VBH  C11  C12  C13  120.75  3.000
 VBH  H27  C9   C10  119.55  3.000
 VBH  H27  C9   C8   120.11  3.000
 VBH  C10  C9   C8   120.34  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
 VBH  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 VBH  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 VBH  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 VBH  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 VBH  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 VBH  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 VBH  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 VBH  CONST_08  C16  C11  C12  C13     0.00   0.0  0
 VBH  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 VBH  CONST_10  C12  C11  C16  C15     0.00   0.0  0
 VBH  CONST_11  C14  C15  C16  C11     0.00   0.0  0
 VBH  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 VBH  CONST_13  C24  N2   C22  C20     0.00   0.0  0
 VBH  CONST_14  C15  C16  C11  C4    180.00   0.0  0
 VBH  CONST_15  C13  C12  C11  C4    180.00   0.0  0
 VBH  CONST_16  C9   C10  C5   C4    180.00   0.0  0
 VBH  CONST_17  C7   C6   C5   C4    180.00   0.0  0
 VBH  CONST_18  C23  N2   C22  C20   180.00   0.0  0
 VBH  CONST_19  O2   C22  N2   C24   180.00   0.0  0
 VBH  CONST_20  H27  C9   C10  C5    180.00   0.0  0
 VBH  CONST_21  H3   C7   C6   C5    180.00   0.0  0
 VBH  CONST_22  H5   C10  C5   C6    180.00   0.0  0
 VBH  CONST_23  H4   C8   C7   C6    180.00   0.0  0
 VBH  CONST_24  H2   C6   C7   C8    180.00   0.0  0
 VBH  CONST_25  H7   C15  C14  C13   180.00   0.0  0
 VBH  CONST_26  H6   C13  C14  C15   180.00   0.0  0
 VBH  CONST_27  H25  C14  C15  C16   180.00   0.0  0
 VBH  CONST_28  H26  C12  C11  C16   180.00   0.0  0
 VBH  CONST_29  H24  C16  C15  C14   180.00   0.0  0
 VBH  CONST_30  C23  N2   C22  O2      0.00   0.0  0
 VBH  CONST_31  C2   N1   C17  C18   180.00   0.0  0
 VBH  CONST_33  C2   N1   C17  O1      0.00   0.0  0
 VBH  CONST_35  C    N    C1   C2    180.00   0.0  0
 VBH  CONST_36  C    N    C1   O       0.00   0.0  0
 VBH  CONST_37  H18  N    C1   C2      0.00   0.0  0
 VBH  Var_01    C16  C11  C4   C5   -136.97  30.0  2
 VBH  Var_02    C11  C4   C5   C6     78.93  30.0  2
 VBH  Var_03    C24  C18  C17  N1     51.70  30.0  2
 VBH  Var_04    H13  C23  N2   C22   179.87  30.0  3
 VBH  Var_05    H8   C21  C20  C22   178.75  30.0  3
 VBH  Var_06    O    C1   C2   N1     30.34  30.0  1
 VBH  Var_07    C17  N1   C3   C4     93.20  30.0  1
 VBH  Var_08    C1   C2   N1   C17    64.07  30.0  3
 VBH  Var_09    H19  C    N    C1    177.94  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
 VBH  plan-1  C4   0.020
 VBH  plan-1  C5   0.020
 VBH  plan-1  C6   0.020
 VBH  plan-1  C7   0.020
 VBH  plan-1  C8   0.020
 VBH  plan-1  C10  0.020
 VBH  plan-1  C9   0.020
 VBH  plan-1  H2   0.020
 VBH  plan-1  H3   0.020
 VBH  plan-1  H4   0.020
 VBH  plan-1  H5   0.020
 VBH  plan-1  H27  0.020
 VBH  plan-2  C17  0.020
 VBH  plan-2  C20  0.020
 VBH  plan-2  C21  0.020
 VBH  plan-2  C22  0.020
 VBH  plan-2  C24  0.020
 VBH  plan-2  O2   0.020
 VBH  plan-2  C19  0.020
 VBH  plan-2  N2   0.020
 VBH  plan-2  C23  0.020
 VBH  plan-2  C18  0.020
 VBH  plan-2  H11  0.020
 VBH  plan-2  H12  0.020
 VBH  plan-3  C4   0.020
 VBH  plan-3  C13  0.020
 VBH  plan-3  C15  0.020
 VBH  plan-3  C11  0.020
 VBH  plan-3  C16  0.020
 VBH  plan-3  C14  0.020
 VBH  plan-3  C12  0.020
 VBH  plan-3  H7   0.020
 VBH  plan-3  H24  0.020
 VBH  plan-3  H25  0.020
 VBH  plan-3  H26  0.020
 VBH  plan-3  H6   0.020
 VBH  plan-4  N1   0.020
 VBH  plan-4  C17  0.020
 VBH  plan-4  C18  0.020
 VBH  plan-4  O1   0.020
 VBH  plan-4  C2   0.020
 VBH  plan-4  C3   0.020
 VBH  plan-5  C2   0.020
 VBH  plan-5  C1   0.020
 VBH  plan-5  O    0.020
 VBH  plan-5  N    0.020
 VBH  plan-5  C    0.020
 VBH  plan-5  H18  0.020

