# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 06:10:23 2021
#   Inital geometry file: a 152 line input string
#   Ligand name: N-(4-tert-butylphenyl)-N-[(1R)-2-[(oxan-4-yl)amino]-2-oxo-1-(pyridin-3-yl)ethyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N([C@@H](C(=O)NC1CCOCC1)c2cccnc2)c3ccc(cc3)C(C)(C)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
 VEP  VEP  N-(4-tert-butylphenyl)-N-[(1R)-2-[(oxan-4-yl)amino]-2-oxo-1-(pyridin-3-yl)ethyl]propanamide  ligand  64  31  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VEP
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
 VEP  N1   N  NH1   0  -0.625   7.9194   1.9928  22.5488
 VEP  C4   C  C     0   0.550   8.0771   1.3759  21.3713
 VEP  C5   C  CH1   0  -0.078   8.8476   2.9783  23.0647
 VEP  C6   C  CH2   0  -0.466   8.1155   4.0106  23.9146
 VEP  C7   C  CH2   0  -0.185   9.1178   4.9882  24.5101
 VEP  C8   C  CH2   0  -0.185  10.8544   3.4207  24.4800
 VEP  C10  C  CR6   0   0.072   6.6772   0.3245  19.6187
 VEP  C13  C  CR16  0  -0.321   5.2799   1.0733  17.8266
 VEP  C15  C  CR6   0   0.199   8.7787  -1.1315  22.2008
 VEP  C17  C  CR16  0  -0.340  11.1760  -1.3414  22.1808
 VEP  C20  C  CR16  0  -0.229   8.8119  -1.1251  23.5904
 VEP  C22  C  CH3   0  -0.632  12.7099  -0.1445  25.1736
 VEP  C24  C  CH3   0  -0.632  12.4921  -2.6348  25.2978
 VEP  O1   O  O     0  -0.463   8.9478   1.6497  20.5642
 VEP  C9   C  CH2   0  -0.447   9.9659   2.3397  23.8855
 VEP  O2   O  O2    0  -0.483  10.1169   4.3356  25.2614
 VEP  C3   C  CH1   0  -0.293   7.0294   0.2877  21.0823
 VEP  C14  C  CR16  0  -0.186   5.5515   1.0067  19.1843
 VEP  C12  C  CR16  0  -0.075   6.1510   0.4476  16.9492
 VEP  N2   N  N     0  -0.405   7.2317  -0.2128  17.3509
 VEP  C11  C  CR16  0  -0.089   7.4827  -0.2656  18.6519
 VEP  N    N  NT    0  -0.559   7.5350  -1.0189  21.5128
 VEP  C2   C  C     0   0.560   6.6591  -2.0665  21.4429
 VEP  O    O  O     0  -0.471   5.5283  -1.9029  21.0216
 VEP  C1   C  CH2   0  -0.582   7.1692  -3.4190  21.8918
 VEP  C    C  CH3   0  -0.656   6.2497  -4.5586  21.4880
 VEP  C19  C  CR16  0  -0.309  10.0176  -1.2346  24.2593
 VEP  C18  C  CR6   0   0.202  11.2290  -1.3398  23.5721
 VEP  C23  C  CH3   0  -0.665  13.7501  -1.5828  23.4346
 VEP  C16  C  CR16  0  -0.217   9.9689  -1.2403  21.5014
 VEP  H1   H  HNH1  0   0.403   7.2064   1.6549  23.1771
 VEP  H2   H  HCH1  0   0.250   9.2884   3.4882  22.2043
 VEP  H3   H  HCH2  0   0.250   7.3899   4.5611  23.3114
 VEP  H4   H  HCH2  0   0.232   7.5633   3.5113  24.7181
 VEP  H5   H  HCH2  0   0.201   9.5733   5.5773  23.7000
 VEP  H6   H  HCH2  0   0.241   8.6163   5.6875  25.1808
 VEP  H7   H  HCH2  0   0.236  11.6105   2.9808  25.1327
 VEP  H8   H  HCH2  0   0.200  11.3845   3.9472  23.6720
 VEP  H9   H  HCR6  0   0.271   4.4073   1.5923  17.4549
 VEP  H10  H  HCR6  0   0.256  12.0806  -1.4255  21.5945
 VEP  H11  H  HCR6  0   0.264   7.8919  -1.0338  24.1551
 VEP  H12  H  HCH3  0   0.228  11.9039  -0.0116  25.8971
 VEP  H13  H  HCH3  0   0.230  13.6493  -0.1730  25.7299
 VEP  H14  H  HCH3  0   0.230  12.7294   0.7366  24.5296
 VEP  H15  H  HCH3  0   0.230  11.6712  -2.5631  26.0112
 VEP  H16  H  HCH3  0   0.229  12.3774  -3.5678  24.7435
 VEP  H17  H  HCH3  0   0.228  13.4208  -2.6964  25.8688
 VEP  H18  H  HCH2  0   0.226   9.5313   1.7352  24.6865
 VEP  H19  H  HCH2  0   0.248  10.5643   1.6660  23.2678
 VEP  H20  H  HCH1  0   0.287   6.1229   0.5208  21.6515
 VEP  H21  H  HCR6  0   0.267   4.8882   1.4805  19.8984
 VEP  H22  H  HCR6  0   0.263   5.9684   0.4774  15.8807
 VEP  H23  H  HCR6  0   0.262   8.3677  -0.8201  18.9438
 VEP  H24  H  HCH2  0   0.275   7.2854  -3.4021  22.9796
 VEP  H25  H  HCH2  0   0.267   8.1749  -3.5812  21.4969
 VEP  H26  H  HCH3  0   0.234   6.6492  -5.5012  21.8602
 VEP  H27  H  HCH3  0   0.229   5.2483  -4.4375  21.8983
 VEP  H28  H  HCH3  0   0.228   6.1617  -4.6407  20.4050
 VEP  H29  H  HCR6  0   0.252  10.0048  -1.2209  25.3420
 VEP  H30  H  HCH3  0   0.238  14.6576  -1.6388  24.0378
 VEP  H31  H  HCH3  0   0.231  13.6988  -2.4952  22.8375
 VEP  H32  H  HCH3  0   0.231  13.8643  -0.7379  22.7534
 VEP  H33  H  HCR6  0   0.266   9.9625  -1.2538  20.4195
 VEP  C21  C  CT    0  -0.174  12.5365  -1.4280  24.3506

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
 VEP  C12  N2   aromatic  1.329  0.020  1.329
 VEP  C12  C13  aromatic  1.386  0.020  1.386
 VEP  N2   C11  aromatic  1.326  0.020  1.326
 VEP  C13  C14  aromatic  1.386  0.020  1.386
 VEP  C11  C10  aromatic  1.390  0.020  1.390
 VEP  C    C1   single    1.519  0.020  1.519
 VEP  C14  C10  aromatic  1.386  0.020  1.386
 VEP  C10  C3   single    1.506  0.020  1.506
 VEP  O1   C4   double    1.218  0.020  1.218
 VEP  O    C2   double    1.218  0.020  1.218
 VEP  C1   C2   single    1.514  0.020  1.514
 VEP  C3   C4   single    1.538  0.020  1.538
 VEP  C3   N    single    1.466  0.020  1.466
 VEP  C2   N    single    1.367  0.020  1.367
 VEP  C4   N1   single    1.339  0.020  1.339
 VEP  N    C15  single    1.426  0.020  1.426
 VEP  C16  C15  aromatic  1.385  0.020  1.385
 VEP  C16  C17  aromatic  1.389  0.020  1.389
 VEP  C15  C20  aromatic  1.390  0.020  1.390
 VEP  C17  C18  aromatic  1.392  0.020  1.392
 VEP  N1   C5   single    1.449  0.020  1.449
 VEP  C5   C6   single    1.524  0.020  1.524
 VEP  C5   C9   single    1.527  0.020  1.527
 VEP  C6   C7   single    1.522  0.020  1.522
 VEP  C7   O2   single    1.410  0.020  1.410
 VEP  C23  C21  single    1.528  0.020  1.528
 VEP  C20  C19  aromatic  1.383  0.020  1.383
 VEP  C18  C19  aromatic  1.397  0.020  1.397
 VEP  C18  C21  single    1.524  0.020  1.524
 VEP  C9   C8   single    1.520  0.020  1.520
 VEP  C8   O2   single    1.411  0.020  1.411
 VEP  C21  C24  single    1.535  0.020  1.535
 VEP  C21  C22  single    1.534  0.020  1.534
 VEP  N1   H1   single    0.860  0.020  1.020
 VEP  C5   H2   single    0.970  0.020  1.090
 VEP  C6   H3   single    0.970  0.020  1.090
 VEP  C6   H4   single    0.970  0.020  1.090
 VEP  C7   H5   single    0.970  0.020  1.090
 VEP  C7   H6   single    0.970  0.020  1.090
 VEP  C8   H7   single    0.970  0.020  1.090
 VEP  C8   H8   single    0.970  0.020  1.090
 VEP  C13  H9   single    0.930  0.020  1.080
 VEP  C17  H10  single    0.930  0.020  1.080
 VEP  C20  H11  single    0.930  0.020  1.080
 VEP  C22  H12  single    0.970  0.020  1.090
 VEP  C22  H13  single    0.970  0.020  1.090
 VEP  C22  H14  single    0.970  0.020  1.090
 VEP  C24  H15  single    0.970  0.020  1.090
 VEP  C24  H16  single    0.970  0.020  1.090
 VEP  C24  H17  single    0.970  0.020  1.090
 VEP  C9   H18  single    0.970  0.020  1.090
 VEP  C9   H19  single    0.970  0.020  1.090
 VEP  C3   H20  single    0.970  0.020  1.090
 VEP  C14  H21  single    0.930  0.020  1.080
 VEP  C12  H22  single    0.930  0.020  1.080
 VEP  C11  H23  single    0.930  0.020  1.080
 VEP  C1   H24  single    0.970  0.020  1.090
 VEP  C1   H25  single    0.970  0.020  1.090
 VEP  C    H26  single    0.970  0.020  1.090
 VEP  C    H27  single    0.970  0.020  1.090
 VEP  C    H28  single    0.970  0.020  1.090
 VEP  C19  H29  single    0.930  0.020  1.080
 VEP  C23  H30  single    0.970  0.020  1.090
 VEP  C23  H31  single    0.970  0.020  1.090
 VEP  C23  H32  single    0.970  0.020  1.090
 VEP  C16  H33  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
 VEP  H1   N1   C5   117.31  3.000
 VEP  H1   N1   C4   118.49  3.000
 VEP  C5   N1   C4   123.45  3.000
 VEP  C3   C4   O1   121.42  3.000
 VEP  C3   C4   N1   114.27  3.000
 VEP  O1   C4   N1   124.29  3.000
 VEP  H2   C5   C9   108.84  3.000
 VEP  H2   C5   C6   108.46  3.000
 VEP  C9   C5   C6   109.59  3.000
 VEP  H2   C5   N1   107.18  3.000
 VEP  C9   C5   N1   112.09  3.000
 VEP  C6   C5   N1   110.57  3.000
 VEP  H4   C6   H3   107.45  3.000
 VEP  H4   C6   C7   109.75  3.000
 VEP  H3   C6   C7   109.26  3.000
 VEP  H4   C6   C5   110.02  3.000
 VEP  H3   C6   C5   110.64  3.000
 VEP  C7   C6   C5   109.69  3.000
 VEP  H6   C7   H5   107.45  3.000
 VEP  H6   C7   O2   107.14  3.000
 VEP  H5   C7   O2   110.29  3.000
 VEP  H6   C7   C6   110.47  3.000
 VEP  H5   C7   C6   109.18  3.000
 VEP  O2   C7   C6   112.20  3.000
 VEP  H8   C8   H7   107.35  3.000
 VEP  H8   C8   O2   110.37  3.000
 VEP  H7   C8   O2   106.99  3.000
 VEP  H8   C8   C9   109.55  3.000
 VEP  H7   C8   C9   110.61  3.000
 VEP  O2   C8   C9   111.84  3.000
 VEP  C11  C10  C14  117.49  3.000
 VEP  C14  C10  C3   120.43  3.000
 VEP  C11  C10  C3   122.02  3.000
 VEP  H9   C13  C12  120.43  3.000
 VEP  H9   C13  C14  121.19  3.000
 VEP  C12  C13  C14  118.39  3.000
 VEP  C16  C15  N    120.82  3.000
 VEP  C16  C15  C20  118.99  3.000
 VEP  N    C15  C20  120.19  3.000
 VEP  H10  C17  C16  117.88  3.000
 VEP  H10  C17  C18  120.67  3.000
 VEP  C16  C17  C18  121.45  3.000
 VEP  H11  C20  C19  119.66  3.000
 VEP  H11  C20  C15  120.08  3.000
 VEP  C19  C20  C15  120.26  3.000
 VEP  H14  C22  H13  107.83  3.000
 VEP  H14  C22  H12  107.82  3.000
 VEP  H13  C22  H12  107.50  3.000
 VEP  H14  C22  C21  111.15  3.000
 VEP  H13  C22  C21  110.39  3.000
 VEP  H12  C22  C21  111.96  3.000
 VEP  H17  C24  H16  107.87  3.000
 VEP  H17  C24  H15  107.57  3.000
 VEP  H16  C24  H15  108.03  3.000
 VEP  H17  C24  C21  110.03  3.000
 VEP  H16  C24  C21  111.21  3.000
 VEP  H15  C24  C21  111.97  3.000
 VEP  H19  C9   H18  106.91  3.000
 VEP  H19  C9   C8   109.84  3.000
 VEP  H18  C9   C8   109.81  3.000
 VEP  H19  C9   C5   110.80  3.000
 VEP  H18  C9   C5   109.50  3.000
 VEP  C8   C9   C5   109.92  3.000
 VEP  C8   O2   C7   112.04  3.000
 VEP  H20  C3   N    108.82  3.000
 VEP  H20  C3   C10  107.84  3.000
 VEP  N    C3   C10  112.82  3.000
 VEP  H20  C3   C4   108.39  3.000
 VEP  N    C3   C4   109.91  3.000
 VEP  C10  C3   C4   108.95  3.000
 VEP  H21  C14  C13  120.30  3.000
 VEP  H21  C14  C10  120.38  3.000
 VEP  C13  C14  C10  119.32  3.000
 VEP  H22  C12  N2   116.65  3.000
 VEP  H22  C12  C13  120.38  3.000
 VEP  N2   C12  C13  122.97  3.000
 VEP  C11  N2   C12  118.06  3.000
 VEP  H23  C11  N2   116.03  3.000
 VEP  H23  C11  C10  120.19  3.000
 VEP  N2   C11  C10  123.77  3.000
 VEP  C2   N    C3   116.56  3.000
 VEP  C2   N    C15  121.53  3.000
 VEP  C3   N    C15  120.87  3.000
 VEP  C1   C2   O    122.38  3.000
 VEP  C1   C2   N    116.98  3.000
 VEP  O    C2   N    120.63  3.000
 VEP  H25  C1   H24  105.29  3.000
 VEP  H25  C1   C    110.47  3.000
 VEP  H24  C1   C    109.88  3.000
 VEP  H25  C1   C2   109.62  3.000
 VEP  H24  C1   C2   108.48  3.000
 VEP  C    C1   C2   112.81  3.000
 VEP  H28  C    H27  107.98  3.000
 VEP  H28  C    H26  107.70  3.000
 VEP  H27  C    H26  107.74  3.000
 VEP  H28  C    C1   111.69  3.000
 VEP  H27  C    C1   111.91  3.000
 VEP  H26  C    C1   109.65  3.000
 VEP  H29  C19  C18  120.21  3.000
 VEP  H29  C19  C20  118.18  3.000
 VEP  C18  C19  C20  121.60  3.000
 VEP  C19  C18  C21  119.80  3.000
 VEP  C21  C18  C17  122.89  3.000
 VEP  C19  C18  C17  117.31  3.000
 VEP  H32  C23  H31  108.09  3.000
 VEP  H32  C23  H30  107.32  3.000
 VEP  H31  C23  H30  107.38  3.000
 VEP  H32  C23  C21  112.26  3.000
 VEP  H31  C23  C21  112.03  3.000
 VEP  H30  C23  C21  109.53  3.000
 VEP  H33  C16  C17  119.57  3.000
 VEP  H33  C16  C15  120.05  3.000
 VEP  C17  C16  C15  120.38  3.000
 VEP  C23  C21  C18  112.39  3.000
 VEP  C18  C21  C24  109.62  3.000
 VEP  C23  C21  C24  108.25  3.000
 VEP  C24  C21  C22  109.27  3.000
 VEP  C18  C21  C22  108.81  3.000
 VEP  C23  C21  C22  108.45  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
 VEP  CONST_01  C12  N2   C11  C10     0.00   0.0  0
 VEP  CONST_02  C12  C13  C14  C10     0.00   0.0  0
 VEP  CONST_03  C11  N2   C12  C13     0.00   0.0  0
 VEP  CONST_04  C11  C10  C14  C13     0.00   0.0  0
 VEP  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 VEP  CONST_06  C18  C19  C20  C15     0.00   0.0  0
 VEP  CONST_07  C20  C15  C16  C17     0.00   0.0  0
 VEP  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 VEP  CONST_09  N2   C12  C13  C14     0.00   0.0  0
 VEP  CONST_10  N2   C11  C10  C14     0.00   0.0  0
 VEP  CONST_11  C16  C15  C20  C19     0.00   0.0  0
 VEP  CONST_12  C16  C17  C18  C19     0.00   0.0  0
 VEP  CONST_13  C3   C10  C14  C13   180.00   0.0  0
 VEP  CONST_14  N    C15  C16  C17   180.00   0.0  0
 VEP  CONST_15  C21  C18  C19  C20   180.00   0.0  0
 VEP  CONST_16  C16  C17  C18  C21   180.00   0.0  0
 VEP  CONST_17  N2   C11  C10  C3    180.00   0.0  0
 VEP  CONST_18  C19  C20  C15  N     180.00   0.0  0
 VEP  CONST_19  H9   C13  C14  C10   180.00   0.0  0
 VEP  CONST_20  H10  C17  C16  C15   180.00   0.0  0
 VEP  CONST_21  H29  C19  C20  C15   180.00   0.0  0
 VEP  CONST_22  H33  C16  C15  C20   180.00   0.0  0
 VEP  CONST_23  H22  C12  C13  C14   180.00   0.0  0
 VEP  CONST_24  H23  C11  C10  C14   180.00   0.0  0
 VEP  CONST_25  H21  C14  C13  C12   180.00   0.0  0
 VEP  CONST_26  H11  C20  C19  C18   180.00   0.0  0
 VEP  CONST_31  O1   C4   N1   C5      0.00   0.0  0
 VEP  CONST_32  C3   C4   N1   C5    180.00   0.0  0
 VEP  CONST_33  O    C2   N    C15   180.00   0.0  0
 VEP  CONST_34  C1   C2   N    C15     0.00   0.0  0
 VEP  CONST_35  O    C2   N    C3      0.00   0.0  0
 VEP  CONST_36  C1   C2   N    C3    180.00   0.0  0
 VEP  CONST_37  H1   N1   C4   O1    180.00   0.0  0
 VEP  Var_01    O2   C7   C6   C5    -56.27  30.0  1
 VEP  Var_02    O2   C8   C9   C5     56.40  30.0  1
 VEP  Var_03    C9   C8   O2   C7    -59.79  30.0  1
 VEP  Var_04    C23  C21  C18  C17    -2.71  30.0  2
 VEP  Var_05    H30  C23  C21  C18   179.87  30.0  3
 VEP  Var_06    H15  C24  C21  C18   -59.67  30.0  3
 VEP  Var_07    H12  C22  C21  C18    61.23  30.0  3
 VEP  Var_08    C    C1   C2   N    -166.97  30.0  1
 VEP  Var_09    H26  C    C1   C2   -178.37  30.0  3

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
 VEP  chir_01  C5  N1  C6  C9   negativ
 VEP  chir_02  C3  N   C4  C10  negativ

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
 VEP  plan-1  C10  0.020
 VEP  plan-1  C13  0.020
 VEP  plan-1  C3   0.020
 VEP  plan-1  C14  0.020
 VEP  plan-1  C12  0.020
 VEP  plan-1  N2   0.020
 VEP  plan-1  C11  0.020
 VEP  plan-1  H9   0.020
 VEP  plan-1  H21  0.020
 VEP  plan-1  H22  0.020
 VEP  plan-1  H23  0.020
 VEP  plan-2  C15  0.020
 VEP  plan-2  C17  0.020
 VEP  plan-2  C20  0.020
 VEP  plan-2  N    0.020
 VEP  plan-2  C19  0.020
 VEP  plan-2  C18  0.020
 VEP  plan-2  C16  0.020
 VEP  plan-2  H10  0.020
 VEP  plan-2  H11  0.020
 VEP  plan-2  H29  0.020
 VEP  plan-2  H33  0.020
 VEP  plan-2  C21  0.020
 VEP  plan-3  C15  0.020
 VEP  plan-3  C3   0.020
 VEP  plan-3  N    0.020
 VEP  plan-3  C2   0.020
 VEP  plan-3  O    0.020
 VEP  plan-3  C1   0.020
 VEP  plan-4  N1   0.020
 VEP  plan-4  C4   0.020
 VEP  plan-4  C5   0.020
 VEP  plan-4  O1   0.020
 VEP  plan-4  C3   0.020
 VEP  plan-4  H1   0.020

