# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:35:09 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1cc(NC(=O)C=C)ccc1C)c2cccc3ccccc23
#
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
 VBY  VBY  5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide  ligand  49  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VBY
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
 VBY  C1   C  C     0   0.490  49.5896  31.7557  -0.0294
 VBY  C10  C  CR6   0   0.078  48.0955  33.7399   0.3987
 VBY  C11  C  CR66  0   0.111  52.8977  27.9599  -2.0104
 VBY  C12  C  CR16  0  -0.332  53.7539  29.0018  -2.4357
 VBY  C13  C  CR16  0  -0.381  50.4791  34.0627   0.1108
 VBY  C14  C  CR16  0  -0.342  51.1036  27.1360  -0.5890
 VBY  C16  C  CH3   0  -0.733  46.8761  32.8696   0.4976
 VBY  C17  C  CR16  0  -0.290  47.9902  35.1171   0.5494
 VBY  C18  C  CR16  0  -0.310  52.9847  26.6709  -2.5873
 VBY  C19  C  CR6   0   0.384  50.3496  35.4462   0.2403
 VBY  C20  C  CR16  0  -0.248  51.2116  25.8986  -1.1644
 VBY  C21  C  CR16  0  -0.302  49.0806  35.9727   0.4685
 VBY  C22  C  CR16  0  -0.261  52.1625  25.6591  -2.1757
 VBY  C24  C  C     0   0.518  51.6778  37.5460   0.1332
 VBY  C25  C  C1    0  -0.310  53.0842  38.0230   0.0732
 VBY  C27  C  C2    0  -0.492  54.1338  37.3960   0.5939
 VBY  C3   C  CR6   0  -0.062  49.3781  33.2230   0.1818
 VBY  C4   C  CR16  0  -0.342  52.7103  30.4907  -0.8610
 VBY  C5   C  CR6   0   0.115  51.8558  29.5143  -0.4191
 VBY  C6   C  CH1   0  -0.144  50.8694  29.7972   0.6996
 VBY  C8   C  CR66  0   0.100  51.9386  28.2095  -0.9902
 VBY  C9   C  CR16  0  -0.242  53.6618  30.2403  -1.8693
 VBY  N2   N  NH1   0  -0.633  50.5071  31.1961   0.7782
 VBY  O7   O  O     0  -0.471  48.9764  31.1293  -0.8795
 VBY  N01  N  NH1   0  -0.752  51.5227  36.1978   0.1409
 VBY  O26  O  O     0  -0.471  50.7558  38.3442   0.1696
 VBY  C01  C  CH3   0  -0.671  51.4288  29.3549   2.0488
 VBY  H2   H  HCR6  0   0.283  51.4627  33.6419  -0.0689
 VBY  H3   H  HCR6  0   0.250  50.3633  27.2804   0.1861
 VBY  H4   H  HCH3  0   0.243  47.0308  32.0267   1.1723
 VBY  H5   H  HCH3  0   0.246  46.0299  33.4417   0.8752
 VBY  H6   H  HCH3  0   0.252  46.5943  32.4590  -0.4718
 VBY  H7   H  HCR6  0   0.256  47.0157  35.5491   0.7427
 VBY  H8   H  HCR6  0   0.256  53.7198  26.4994  -3.3648
 VBY  H9   H  HCR6  0   0.260  50.5606  25.0974  -0.8396
 VBY  H10  H  HCR6  0   0.283  48.9277  37.0325   0.5853
 VBY  H11  H  HCR6  0   0.258  52.2381  24.6765  -2.6228
 VBY  H12  H  H     0   0.283  53.2042  39.0012  -0.3775
 VBY  H13  H  H     0   0.271  55.1182  37.8410   0.5475
 VBY  H14  H  H     0   0.264  54.0671  36.4411   1.1012
 VBY  H15  H  HCR6  0   0.256  52.6608  31.4845  -0.4345
 VBY  H16  H  HCH1  0   0.257  49.9479  29.2454   0.5030
 VBY  H17  H  HCR6  0   0.256  54.3173  31.0392  -2.1907
 VBY  H18  H  HNH1  0   0.410  50.9343  31.7631   1.4942
 VBY  H19  H  HNH1  0   0.418  52.3592  35.6538  -0.0066
 VBY  H20  H  HCH3  0   0.250  50.6855  29.4841   2.8358
 VBY  H21  H  HCH3  0   0.249  51.7156  28.3050   2.0239
 VBY  H22  H  HCH3  0   0.238  52.3166  29.9334   2.3103
 VBY  H1   H  HCR6  0   0.255  54.4810  28.8030  -3.2136

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
 VBY  C22  C18  aromatic  1.367  0.020  1.367
 VBY  C22  C20  aromatic  1.409  0.020  1.409
 VBY  C18  C11  aromatic  1.415  0.020  1.415
 VBY  C20  C14  aromatic  1.369  0.020  1.369
 VBY  C11  C12  aromatic  1.414  0.020  1.414
 VBY  C11  C8   aromatic  1.422  0.020  1.422
 VBY  C14  C8   aromatic  1.418  0.020  1.418
 VBY  C25  C27  double    1.329  0.020  1.329
 VBY  C25  C24  single    1.486  0.020  1.486
 VBY  O26  C24  double    1.220  0.020  1.220
 VBY  C12  C9   aromatic  1.365  0.020  1.365
 VBY  C8   C5   aromatic  1.427  0.020  1.427
 VBY  C24  N01  single    1.357  0.020  1.357
 VBY  O7   C1   double    1.221  0.020  1.221
 VBY  N01  C19  single    1.397  0.020  1.397
 VBY  C9   C4   aromatic  1.409  0.020  1.409
 VBY  C13  C19  aromatic  1.396  0.020  1.396
 VBY  C13  C3   aromatic  1.387  0.020  1.387
 VBY  C19  C21  aromatic  1.393  0.020  1.393
 VBY  C5   C4   aromatic  1.371  0.020  1.371
 VBY  C5   C6   single    1.518  0.020  1.518
 VBY  C1   C3   single    1.497  0.020  1.497
 VBY  C1   N2   single    1.344  0.020  1.344
 VBY  C3   C10  aromatic  1.400  0.020  1.400
 VBY  C21  C17  aromatic  1.388  0.020  1.388
 VBY  C10  C17  aromatic  1.389  0.020  1.389
 VBY  C10  C16  single    1.501  0.020  1.501
 VBY  C6   N2   single    1.447  0.020  1.447
 VBY  C6   C01  single    1.526  0.020  1.526
 VBY  C12  H1   single    0.930  0.020  1.080
 VBY  C13  H2   single    0.930  0.020  1.080
 VBY  C14  H3   single    0.930  0.020  1.080
 VBY  C16  H4   single    0.970  0.020  1.090
 VBY  C16  H5   single    0.970  0.020  1.090
 VBY  C16  H6   single    0.970  0.020  1.090
 VBY  C17  H7   single    0.930  0.020  1.080
 VBY  C18  H8   single    0.930  0.020  1.080
 VBY  C20  H9   single    0.930  0.020  1.080
 VBY  C21  H10  single    0.930  0.020  1.080
 VBY  C22  H11  single    0.930  0.020  1.080
 VBY  C25  H12  single    0.930  0.020  1.080
 VBY  C27  H13  single    0.930  0.020  1.080
 VBY  C27  H14  single    0.930  0.020  1.080
 VBY  C4   H15  single    0.930  0.020  1.080
 VBY  C6   H16  single    0.970  0.020  1.090
 VBY  C9   H17  single    0.930  0.020  1.080
 VBY  N2   H18  single    0.860  0.020  1.020
 VBY  N01  H19  single    0.860  0.020  1.020
 VBY  C01  H20  single    0.970  0.020  1.090
 VBY  C01  H21  single    0.970  0.020  1.090
 VBY  C01  H22  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
 VBY  O7   C1   N2   123.19  3.000
 VBY  N2   C1   C3   114.81  3.000
 VBY  O7   C1   C3   122.00  3.000
 VBY  C3   C10  C17  116.89  3.000
 VBY  C17  C10  C16  120.39  3.000
 VBY  C3   C10  C16  122.71  3.000
 VBY  C8   C11  C18  119.59  3.000
 VBY  C8   C11  C12  119.65  3.000
 VBY  C18  C11  C12  120.76  3.000
 VBY  H1   C12  C9   120.65  3.000
 VBY  H1   C12  C11  119.16  3.000
 VBY  C9   C12  C11  120.20  3.000
 VBY  H2   C13  C3   119.57  3.000
 VBY  H2   C13  C19  118.95  3.000
 VBY  C3   C13  C19  121.47  3.000
 VBY  H3   C14  C8   120.31  3.000
 VBY  H3   C14  C20  118.42  3.000
 VBY  C8   C14  C20  121.26  3.000
 VBY  H6   C16  H5   107.78  3.000
 VBY  H6   C16  H4   107.21  3.000
 VBY  H5   C16  H4   107.56  3.000
 VBY  H6   C16  C10  111.70  3.000
 VBY  H5   C16  C10  110.45  3.000
 VBY  H4   C16  C10  111.93  3.000
 VBY  H7   C17  C21  118.11  3.000
 VBY  H7   C17  C10  118.87  3.000
 VBY  C21  C17  C10  123.02  3.000
 VBY  H8   C18  C22  120.46  3.000
 VBY  H8   C18  C11  118.58  3.000
 VBY  C22  C18  C11  120.97  3.000
 VBY  N01  C19  C21  125.00  3.000
 VBY  C21  C19  C13  118.32  3.000
 VBY  N01  C19  C13  116.67  3.000
 VBY  H9   C20  C22  119.71  3.000
 VBY  H9   C20  C14  119.71  3.000
 VBY  C22  C20  C14  120.58  3.000
 VBY  H10  C21  C19  121.26  3.000
 VBY  H10  C21  C17  119.25  3.000
 VBY  C19  C21  C17  119.49  3.000
 VBY  H11  C22  C20  119.88  3.000
 VBY  H11  C22  C18  120.37  3.000
 VBY  C20  C22  C18  119.75  3.000
 VBY  O26  C24  N01  124.30  3.000
 VBY  N01  C24  C25  115.29  3.000
 VBY  O26  C24  C25  120.41  3.000
 VBY  H12  C25  C27  120.09  3.000
 VBY  H12  C25  C24  114.28  3.000
 VBY  C27  C25  C24  125.46  3.000
 VBY  H14  C27  H13  116.03  3.000
 VBY  H14  C27  C25  123.42  3.000
 VBY  H13  C27  C25  120.53  3.000
 VBY  C13  C3   C10  120.79  3.000
 VBY  C10  C3   C1   120.88  3.000
 VBY  C13  C3   C1   118.30  3.000
 VBY  H15  C4   C9   118.42  3.000
 VBY  H15  C4   C5   119.89  3.000
 VBY  C9   C4   C5   121.69  3.000
 VBY  C8   C5   C6   120.20  3.000
 VBY  C6   C5   C4   120.66  3.000
 VBY  C8   C5   C4   119.09  3.000
 VBY  H16  C6   C01  108.79  3.000
 VBY  H16  C6   N2   106.67  3.000
 VBY  C01  C6   N2   108.90  3.000
 VBY  H16  C6   C5   108.76  3.000
 VBY  C01  C6   C5   111.06  3.000
 VBY  N2   C6   C5   112.51  3.000
 VBY  C5   C8   C14  123.02  3.000
 VBY  C5   C8   C11  119.13  3.000
 VBY  C14  C8   C11  117.85  3.000
 VBY  H17  C9   C4   119.37  3.000
 VBY  H17  C9   C12  120.38  3.000
 VBY  C4   C9   C12  120.25  3.000
 VBY  H18  N2   C6   118.43  3.000
 VBY  H18  N2   C1   118.80  3.000
 VBY  C6   N2   C1   122.73  3.000
 VBY  H19  N01  C24  116.11  3.000
 VBY  H19  N01  C19  114.63  3.000
 VBY  C24  N01  C19  129.12  3.000
 VBY  H22  C01  H21  107.60  3.000
 VBY  H22  C01  H20  108.59  3.000
 VBY  H21  C01  H20  108.08  3.000
 VBY  H22  C01  C6   110.88  3.000
 VBY  H21  C01  C6   110.84  3.000
 VBY  H20  C01  C6   110.73  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
 VBY  CONST_01  C19  C13  C3   C10     0.00   0.0  0
 VBY  CONST_02  C19  C21  C17  C10     0.00   0.0  0
 VBY  CONST_03  C20  C22  C18  C11     0.00   0.0  0
 VBY  CONST_04  C4   C9   C12  C11     0.00   0.0  0
 VBY  CONST_05  C20  C14  C8   C11     0.00   0.0  0
 VBY  CONST_06  C4   C5   C8   C11     0.00   0.0  0
 VBY  CONST_07  C22  C18  C11  C12   180.00   0.0  0
 VBY  CONST_08  C14  C8   C11  C12   180.00   0.0  0
 VBY  CONST_09  C5   C8   C11  C12     0.00   0.0  0
 VBY  CONST_10  C5   C4   C9   C12     0.00   0.0  0
 VBY  CONST_11  C17  C21  C19  C13     0.00   0.0  0
 VBY  CONST_12  C17  C10  C3   C13     0.00   0.0  0
 VBY  CONST_13  C18  C22  C20  C14     0.00   0.0  0
 VBY  CONST_14  C18  C11  C8   C14     0.00   0.0  0
 VBY  CONST_15  C4   C5   C8   C14   180.00   0.0  0
 VBY  CONST_16  C9   C12  C11  C18   180.00   0.0  0
 VBY  CONST_17  C5   C8   C11  C18   180.00   0.0  0
 VBY  CONST_18  C5   C8   C14  C20   180.00   0.0  0
 VBY  CONST_19  C3   C13  C19  C21     0.00   0.0  0
 VBY  CONST_20  C3   C10  C17  C21     0.00   0.0  0
 VBY  CONST_21  C8   C11  C18  C22     0.00   0.0  0
 VBY  CONST_22  C8   C14  C20  C22     0.00   0.0  0
 VBY  CONST_23  C9   C12  C11  C8      0.00   0.0  0
 VBY  CONST_24  C9   C4   C5   C8      0.00   0.0  0
 VBY  CONST_25  C19  C13  C3   C1    180.00   0.0  0
 VBY  CONST_26  C17  C10  C3   C1    180.00   0.0  0
 VBY  CONST_27  C6   C5   C8   C11   180.00   0.0  0
 VBY  CONST_28  C16  C10  C3   C13   180.00   0.0  0
 VBY  CONST_29  C6   C5   C8   C14     0.00   0.0  0
 VBY  CONST_30  C21  C17  C10  C16   180.00   0.0  0
 VBY  CONST_31  N01  C19  C21  C17   180.00   0.0  0
 VBY  CONST_32  N01  C19  C13  C3    180.00   0.0  0
 VBY  CONST_33  C9   C4   C5   C6    180.00   0.0  0
 VBY  CONST_34  H2   C13  C3   C10   180.00   0.0  0
 VBY  CONST_35  H10  C21  C17  C10   180.00   0.0  0
 VBY  CONST_36  H11  C22  C18  C11   180.00   0.0  0
 VBY  CONST_37  H17  C9   C12  C11   180.00   0.0  0
 VBY  CONST_38  H3   C14  C8   C11   180.00   0.0  0
 VBY  CONST_39  H8   C18  C11  C12     0.00   0.0  0
 VBY  CONST_40  H15  C4   C9   C12   180.00   0.0  0
 VBY  CONST_41  H9   C20  C22  C18   180.00   0.0  0
 VBY  CONST_42  H1   C12  C11  C18     0.00   0.0  0
 VBY  CONST_43  H7   C17  C21  C19   180.00   0.0  0
 VBY  CONST_44  C24  N01  C19  C13   180.00   0.0  0
 VBY  CONST_45  C24  N01  C19  C21     0.00   0.0  0
 VBY  CONST_46  H19  N01  C19  C13     0.00   0.0  0
 VBY  CONST_47  C25  C24  N01  C19   180.00   0.0  0
 VBY  CONST_48  O26  C24  N01  C19     0.00   0.0  0
 VBY  CONST_49  C6   N2   C1   C3    180.00   0.0  0
 VBY  CONST_50  H18  N2   C1   C3      0.00   0.0  0
 VBY  CONST_51  O7   C1   N2   C6      0.00   0.0  0
 VBY  Var_01    O7   C1   C3   C10    53.33  30.0  2
 VBY  Var_02    H4   C16  C10  C17  -130.60  30.0  2
 VBY  Var_03    O26  C24  C25  C27   148.69  30.0  2
 VBY  Var_04    H13  C27  C25  C24  -176.85   0.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 VBY  chir_01  C6  C5  N2  C01  positiv

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
 VBY  plan-1  C1   0.020
 VBY  plan-1  C10  0.020
 VBY  plan-1  C13  0.020
 VBY  plan-1  C16  0.020
 VBY  plan-1  C17  0.020
 VBY  plan-1  C19  0.020
 VBY  plan-1  C21  0.020
 VBY  plan-1  C3   0.020
 VBY  plan-1  N01  0.020
 VBY  plan-1  H2   0.020
 VBY  plan-1  H7   0.020
 VBY  plan-1  H10  0.020
 VBY  plan-2  C11  0.020
 VBY  plan-2  C12  0.020
 VBY  plan-2  C14  0.020
 VBY  plan-2  C18  0.020
 VBY  plan-2  C20  0.020
 VBY  plan-2  C22  0.020
 VBY  plan-2  C4   0.020
 VBY  plan-2  C5   0.020
 VBY  plan-2  C6   0.020
 VBY  plan-2  C8   0.020
 VBY  plan-2  C9   0.020
 VBY  plan-2  H3   0.020
 VBY  plan-2  H8   0.020
 VBY  plan-2  H9   0.020
 VBY  plan-2  H11  0.020
 VBY  plan-2  H15  0.020
 VBY  plan-2  H17  0.020
 VBY  plan-2  H1   0.020
 VBY  plan-3  C1   0.020
 VBY  plan-3  C3   0.020
 VBY  plan-3  C6   0.020
 VBY  plan-3  N2   0.020
 VBY  plan-3  O7   0.020
 VBY  plan-3  H18  0.020
 VBY  plan-4  C19  0.020
 VBY  plan-4  C24  0.020
 VBY  plan-4  C25  0.020
 VBY  plan-4  N01  0.020
 VBY  plan-4  O26  0.020
 VBY  plan-4  H19  0.020
 VBY  plan-5  C24  0.020
 VBY  plan-5  C25  0.020
 VBY  plan-5  C27  0.020
 VBY  plan-5  H12  0.020
 VBY  plan-5  H13  0.020
 VBY  plan-5  H14  0.020

