# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:54:54 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: N-(4-tert-butylphenyl)-N-[(1R)-2-[(3-methoxypropyl)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)NCCCOC)c1cccnc1)c2ccc(cc2)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
 VEJ  VEJ  N-(4-tert-butylphenyl)-N-[(1R)-2-[(3-methoxypropyl)amino]-2-oxo-1-(pyridin-3-yl)ethyl]propanamide  ligand  63  30  .  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_VEJ
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
 VEJ  N1   N  NH1   0  -0.615   8.4635   1.6902  22.8797
 VEJ  C4   C  C     0   0.547   8.3983   1.1414  21.6631
 VEJ  C5   C  CH2   0  -0.279   9.5071   2.6148  23.2723
 VEJ  C6   C  CH2   0  -0.477  10.8275   1.9226  23.5944
 VEJ  C7   C  CH2   0  -0.149  11.8704   2.8800  24.1312
 VEJ  C8   C  CH3   0  -0.393  13.1315   4.7749  23.5947
 VEJ  C10  C  CR16  0  -0.086   7.4584  -0.5129  19.0420
 VEJ  C13  C  CR16  0  -0.186   5.6577   0.8780  19.7127
 VEJ  C15  C  CR16  0  -0.223  10.1207  -1.5146  21.6719
 VEJ  C17  C  CR6   0   0.207  11.5354  -1.8431  23.6157
 VEJ  C20  C  CT    0  -0.172  12.8902  -2.0792  24.2728
 VEJ  C21  C  CH3   0  -0.666  14.0237  -2.1589  23.2500
 VEJ  C22  C  CH3   0  -0.631  12.8511  -3.4000  25.0531
 VEJ  O1   O  O     0  -0.465   9.1446   1.4324  20.7441
 VEJ  O2   O  O2    0  -0.486  12.1815   3.8415  23.1521
 VEJ  C3   C  CH1   0  -0.297   7.2625   0.1189  21.4880
 VEJ  C9   C  CR6   0   0.076   6.7819   0.1462  20.0615
 VEJ  C12  C  CR16  0  -0.321   5.2618   0.9246  18.3852
 VEJ  C11  C  CR16  0  -0.075   6.0110   0.2289  17.4499
 VEJ  N2   N  N     0  -0.405   7.0885  -0.4800  17.7692
 VEJ  N    N  NT    0  -0.554   7.7044  -1.2157  21.9062
 VEJ  C2   C  C     0   0.525   6.7435  -2.1897  21.9271
 VEJ  O    O  O     0  -0.466   5.5861  -1.9236  21.6524
 VEJ  C1   C  CH2   0  -0.565   7.1880  -3.6115  22.1865
 VEJ  C    C  CH3   0  -0.667   7.7580  -4.2284  20.9079
 VEJ  C14  C  CR6   0   0.211   8.9958  -1.4193  22.4726
 VEJ  C19  C  CR16  0  -0.234   9.1418  -1.5205  23.8529
 VEJ  C18  C  CR16  0  -0.314  10.3885  -1.7399  24.4085
 VEJ  C23  C  CH3   0  -0.640  13.1905  -0.9237  25.2365
 VEJ  C16  C  CR16  0  -0.338  11.3724  -1.7193  22.2397
 VEJ  H1   H  HNH1  0   0.407   7.8345   1.3645  23.5958
 VEJ  H2   H  HCH2  0   0.247   9.6406   3.3514  22.4805
 VEJ  H3   H  HCH2  0   0.247   9.1432   3.1505  24.1498
 VEJ  H4   H  HCH2  0   0.242  10.6608   1.1480  24.3465
 VEJ  H5   H  HCH2  0   0.239  11.2110   1.4130  22.7078
 VEJ  H6   H  HCH2  0   0.210  12.7724   2.3203  24.4202
 VEJ  H7   H  HCH2  0   0.196  11.4987   3.3664  25.0461
 VEJ  H8   H  HCH3  0   0.232  13.3186   5.4787  22.7842
 VEJ  H9   H  HCH3  0   0.202  12.7808   5.3387  24.4678
 VEJ  H10  H  HCH3  0   0.202  14.0820   4.2983  23.8644
 VEJ  H11  H  HCR6  0   0.255   8.3369  -1.1086  19.2643
 VEJ  H12  H  HCR6  0   0.267   5.0918   1.4056  20.4713
 VEJ  H13  H  HCR6  0   0.269  10.0306  -1.4382  20.5964
 VEJ  H14  H  HCH3  0   0.239  14.9692  -2.3365  23.7641
 VEJ  H15  H  HCH3  0   0.231  13.8772  -2.9750  22.5403
 VEJ  H16  H  HCH3  0   0.230  14.1298  -1.2313  22.6847
 VEJ  H17  H  HCH3  0   0.229  12.0858  -3.3966  25.8303
 VEJ  H18  H  HCH3  0   0.229  12.6516  -4.2433  24.3892
 VEJ  H19  H  HCH3  0   0.228  13.8123  -3.5788  25.5399
 VEJ  H20  H  HCH1  0   0.292   6.4284   0.4261  22.1287
 VEJ  H21  H  HCR6  0   0.271   4.3860   1.4811  18.0811
 VEJ  H22  H  HCR6  0   0.263   5.7296   0.2411  16.4027
 VEJ  H23  H  HCH2  0   0.264   6.3087  -4.1708  22.5064
 VEJ  H24  H  HCH2  0   0.264   7.9222  -3.6808  22.9878
 VEJ  H25  H  HCH3  0   0.248   8.0097  -5.2746  21.0764
 VEJ  H26  H  HCH3  0   0.235   7.0368  -4.1852  20.0917
 VEJ  H27  H  HCH3  0   0.234   8.6642  -3.7175  20.5846
 VEJ  H28  H  HCR6  0   0.266   8.2722  -1.4417  24.4942
 VEJ  H29  H  HCR6  0   0.252  10.4640  -1.8211  25.4857
 VEJ  H30  H  HCH3  0   0.230  12.4402  -0.8360  26.0236
 VEJ  H31  H  HCH3  0   0.230  14.1588  -1.0735  25.7182
 VEJ  H32  H  HCH3  0   0.233  13.2290   0.0284  24.7038
 VEJ  H33  H  HCR6  0   0.255  12.2220  -1.7863  21.5747

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
 VEJ  C11  N2   aromatic  1.329  0.020  1.329
 VEJ  C11  C12  aromatic  1.386  0.020  1.386
 VEJ  N2   C10  aromatic  1.326  0.020  1.326
 VEJ  C12  C13  aromatic  1.386  0.020  1.386
 VEJ  C10  C9   aromatic  1.390  0.020  1.390
 VEJ  C13  C9   aromatic  1.386  0.020  1.386
 VEJ  C9   C3   single    1.506  0.020  1.506
 VEJ  C    C1   single    1.530  0.020  1.530
 VEJ  O1   C4   double    1.219  0.020  1.219
 VEJ  O    C2   double    1.219  0.020  1.219
 VEJ  C2   C1   single    1.512  0.020  1.512
 VEJ  C2   N    single    1.368  0.020  1.368
 VEJ  C3   N    single    1.467  0.020  1.467
 VEJ  C3   C4   single    1.538  0.020  1.538
 VEJ  C15  C16  aromatic  1.390  0.020  1.390
 VEJ  C15  C14  aromatic  1.384  0.020  1.384
 VEJ  N    C14  single    1.425  0.020  1.425
 VEJ  C4   N1   single    1.336  0.020  1.336
 VEJ  C16  C17  aromatic  1.391  0.020  1.391
 VEJ  C14  C19  aromatic  1.392  0.020  1.392
 VEJ  O2   C8   single    1.403  0.020  1.403
 VEJ  O2   C7   single    1.407  0.020  1.407
 VEJ  N1   C5   single    1.448  0.020  1.448
 VEJ  C5   C6   single    1.525  0.020  1.525
 VEJ  C6   C7   single    1.514  0.020  1.514
 VEJ  C21  C20  single    1.529  0.020  1.529
 VEJ  C17  C18  aromatic  1.398  0.020  1.398
 VEJ  C17  C20  single    1.524  0.020  1.524
 VEJ  C19  C18  aromatic  1.382  0.020  1.382
 VEJ  C20  C23  single    1.534  0.020  1.534
 VEJ  C20  C22  single    1.535  0.020  1.535
 VEJ  N1   H1   single    0.860  0.020  1.020
 VEJ  C5   H2   single    0.970  0.020  1.090
 VEJ  C5   H3   single    0.970  0.020  1.090
 VEJ  C6   H4   single    0.970  0.020  1.090
 VEJ  C6   H5   single    0.970  0.020  1.090
 VEJ  C7   H6   single    0.970  0.020  1.090
 VEJ  C7   H7   single    0.970  0.020  1.090
 VEJ  C8   H8   single    0.970  0.020  1.090
 VEJ  C8   H9   single    0.970  0.020  1.090
 VEJ  C8   H10  single    0.970  0.020  1.090
 VEJ  C10  H11  single    0.930  0.020  1.080
 VEJ  C13  H12  single    0.930  0.020  1.080
 VEJ  C15  H13  single    0.930  0.020  1.080
 VEJ  C21  H14  single    0.970  0.020  1.090
 VEJ  C21  H15  single    0.970  0.020  1.090
 VEJ  C21  H16  single    0.970  0.020  1.090
 VEJ  C22  H17  single    0.970  0.020  1.090
 VEJ  C22  H18  single    0.970  0.020  1.090
 VEJ  C22  H19  single    0.970  0.020  1.090
 VEJ  C3   H20  single    0.970  0.020  1.090
 VEJ  C12  H21  single    0.930  0.020  1.080
 VEJ  C11  H22  single    0.930  0.020  1.080
 VEJ  C1   H23  single    0.970  0.020  1.090
 VEJ  C1   H24  single    0.970  0.020  1.090
 VEJ  C    H25  single    0.970  0.020  1.090
 VEJ  C    H26  single    0.970  0.020  1.090
 VEJ  C    H27  single    0.970  0.020  1.090
 VEJ  C19  H28  single    0.930  0.020  1.080
 VEJ  C18  H29  single    0.930  0.020  1.080
 VEJ  C23  H30  single    0.970  0.020  1.090
 VEJ  C23  H31  single    0.970  0.020  1.090
 VEJ  C23  H32  single    0.970  0.020  1.090
 VEJ  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
 VEJ  H1   N1   C5   117.62  3.000
 VEJ  H1   N1   C4   118.95  3.000
 VEJ  C5   N1   C4   122.96  3.000
 VEJ  C3   C4   O1   121.66  3.000
 VEJ  C3   C4   N1   114.37  3.000
 VEJ  O1   C4   N1   123.95  3.000
 VEJ  H3   C5   H2   107.07  3.000
 VEJ  H3   C5   C6   109.99  3.000
 VEJ  H2   C5   C6   110.74  3.000
 VEJ  H3   C5   N1   106.93  3.000
 VEJ  H2   C5   N1   108.84  3.000
 VEJ  C6   C5   N1   113.03  3.000
 VEJ  H5   C6   H4   106.36  3.000
 VEJ  H5   C6   C7   109.94  3.000
 VEJ  H4   C6   C7   108.02  3.000
 VEJ  H5   C6   C5   110.14  3.000
 VEJ  H4   C6   C5   109.58  3.000
 VEJ  C7   C6   C5   112.60  3.000
 VEJ  H7   C7   H6   106.46  3.000
 VEJ  H7   C7   O2   110.55  3.000
 VEJ  H6   C7   O2   110.44  3.000
 VEJ  H7   C7   C6   109.97  3.000
 VEJ  H6   C7   C6   109.64  3.000
 VEJ  O2   C7   C6   109.73  3.000
 VEJ  H10  C8   H9   107.74  3.000
 VEJ  H10  C8   H8   108.34  3.000
 VEJ  H9   C8   H8   108.36  3.000
 VEJ  H10  C8   O2   112.04  3.000
 VEJ  H9   C8   O2   112.11  3.000
 VEJ  H8   C8   O2   108.13  3.000
 VEJ  H11  C10  N2   115.88  3.000
 VEJ  H11  C10  C9   120.29  3.000
 VEJ  N2   C10  C9   123.82  3.000
 VEJ  H12  C13  C12  120.33  3.000
 VEJ  H12  C13  C9   120.30  3.000
 VEJ  C12  C13  C9   119.37  3.000
 VEJ  H13  C15  C16  119.44  3.000
 VEJ  H13  C15  C14  120.17  3.000
 VEJ  C16  C15  C14  120.39  3.000
 VEJ  C16  C17  C18  117.27  3.000
 VEJ  C18  C17  C20  119.75  3.000
 VEJ  C16  C17  C20  122.98  3.000
 VEJ  C23  C20  C22  109.50  3.000
 VEJ  C22  C20  C21  108.32  3.000
 VEJ  C23  C20  C21  108.32  3.000
 VEJ  C22  C20  C17  109.26  3.000
 VEJ  C23  C20  C17  109.15  3.000
 VEJ  C21  C20  C17  112.25  3.000
 VEJ  H16  C21  H15  108.16  3.000
 VEJ  H16  C21  H14  107.35  3.000
 VEJ  H15  C21  H14  107.52  3.000
 VEJ  H16  C21  C20  111.98  3.000
 VEJ  H15  C21  C20  111.99  3.000
 VEJ  H14  C21  C20  109.63  3.000
 VEJ  H19  C22  H18  107.78  3.000
 VEJ  H19  C22  H17  107.48  3.000
 VEJ  H18  C22  H17  107.92  3.000
 VEJ  H19  C22  C20  110.19  3.000
 VEJ  H18  C22  C20  111.12  3.000
 VEJ  H17  C22  C20  112.18  3.000
 VEJ  C8   O2   C7   112.62  3.000
 VEJ  H20  C3   N    108.53  3.000
 VEJ  H20  C3   C9   107.81  3.000
 VEJ  N    C3   C9   112.51  3.000
 VEJ  H20  C3   C4   108.01  3.000
 VEJ  N    C3   C4   110.49  3.000
 VEJ  C9   C3   C4   109.36  3.000
 VEJ  C3   C9   C13  120.46  3.000
 VEJ  C3   C9   C10  122.08  3.000
 VEJ  C13  C9   C10  117.43  3.000
 VEJ  H21  C12  C11  120.43  3.000
 VEJ  H21  C12  C13  121.20  3.000
 VEJ  C11  C12  C13  118.37  3.000
 VEJ  H22  C11  N2   116.65  3.000
 VEJ  H22  C11  C12  120.39  3.000
 VEJ  N2   C11  C12  122.96  3.000
 VEJ  C11  N2   C10  118.05  3.000
 VEJ  C14  N    C2   121.91  3.000
 VEJ  C14  N    C3   121.09  3.000
 VEJ  C2   N    C3   116.14  3.000
 VEJ  C1   C2   O    121.54  3.000
 VEJ  C1   C2   N    117.75  3.000
 VEJ  O    C2   N    120.52  3.000
 VEJ  H24  C1   H23  107.18  3.000
 VEJ  H24  C1   C    109.76  3.000
 VEJ  H23  C1   C    109.81  3.000
 VEJ  H24  C1   C2   112.59  3.000
 VEJ  H23  C1   C2   107.20  3.000
 VEJ  C    C1   C2   110.20  3.000
 VEJ  H27  C    H26  108.03  3.000
 VEJ  H27  C    H25  107.71  3.000
 VEJ  H26  C    H25  107.87  3.000
 VEJ  H27  C    C1   111.64  3.000
 VEJ  H26  C    C1   111.30  3.000
 VEJ  H25  C    C1   110.13  3.000
 VEJ  C19  C14  N    119.99  3.000
 VEJ  C19  C14  C15  118.91  3.000
 VEJ  N    C14  C15  121.10  3.000
 VEJ  H28  C19  C18  119.84  3.000
 VEJ  H28  C19  C14  119.84  3.000
 VEJ  C18  C19  C14  120.32  3.000
 VEJ  H29  C18  C19  118.33  3.000
 VEJ  H29  C18  C17  120.09  3.000
 VEJ  C19  C18  C17  121.58  3.000
 VEJ  H32  C23  H31  107.68  3.000
 VEJ  H32  C23  H30  107.83  3.000
 VEJ  H31  C23  H30  107.62  3.000
 VEJ  H32  C23  C20  110.93  3.000
 VEJ  H31  C23  C20  110.32  3.000
 VEJ  H30  C23  C20  112.27  3.000
 VEJ  H33  C16  C17  120.73  3.000
 VEJ  H33  C16  C15  117.75  3.000
 VEJ  C17  C16  C15  121.52  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
 VEJ  CONST_01  C12  C11  N2   C10     0.00   0.0  0
 VEJ  CONST_02  C12  C13  C9   C10     0.00   0.0  0
 VEJ  CONST_03  N2   C11  C12  C13     0.00   0.0  0
 VEJ  CONST_04  N2   C10  C9   C13     0.00   0.0  0
 VEJ  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 VEJ  CONST_06  C18  C19  C14  C15     0.00   0.0  0
 VEJ  CONST_07  C14  C15  C16  C17     0.00   0.0  0
 VEJ  CONST_08  C14  C19  C18  C17     0.00   0.0  0
 VEJ  CONST_09  C11  N2   C10  C9      0.00   0.0  0
 VEJ  CONST_10  C11  C12  C13  C9      0.00   0.0  0
 VEJ  CONST_11  C16  C15  C14  C19     0.00   0.0  0
 VEJ  CONST_12  C16  C17  C18  C19     0.00   0.0  0
 VEJ  CONST_13  C20  C17  C16  C15   180.00   0.0  0
 VEJ  CONST_14  C19  C18  C17  C20   180.00   0.0  0
 VEJ  CONST_15  N2   C10  C9   C3    180.00   0.0  0
 VEJ  CONST_16  C12  C13  C9   C3    180.00   0.0  0
 VEJ  CONST_17  C16  C15  C14  N     180.00   0.0  0
 VEJ  CONST_18  C18  C19  C14  N     180.00   0.0  0
 VEJ  CONST_19  H22  C11  N2   C10   180.00   0.0  0
 VEJ  CONST_20  H12  C13  C9   C10   180.00   0.0  0
 VEJ  CONST_21  H11  C10  C9   C13   180.00   0.0  0
 VEJ  CONST_22  H28  C19  C14  C15   180.00   0.0  0
 VEJ  CONST_23  H13  C15  C16  C17   180.00   0.0  0
 VEJ  CONST_24  H21  C12  C13  C9    180.00   0.0  0
 VEJ  CONST_25  H33  C16  C15  C14   180.00   0.0  0
 VEJ  CONST_26  H29  C18  C19  C14   180.00   0.0  0
 VEJ  CONST_31  C14  N    C2   O     180.00   0.0  0
 VEJ  CONST_33  O1   C4   N1   C5      0.00   0.0  0
 VEJ  CONST_34  C3   C4   N1   C5    180.00   0.0  0
 VEJ  CONST_35  O    C2   N    C3      0.00   0.0  0
 VEJ  CONST_36  C1   C2   N    C3    180.00   0.0  0
 VEJ  CONST_37  H1   N1   C4   O1    180.00   0.0  0
 VEJ  Var_01    C16  C17  C20  C21     0.09  30.0  3
 VEJ  Var_02    H14  C21  C20  C17  -179.53  30.0  3
 VEJ  Var_03    H30  C23  C20  C17    59.99  30.0  3
 VEJ  Var_04    H17  C22  C20  C17   -59.67  30.0  3
 VEJ  Var_05    C7   C6   C5   N1   -174.45  30.0  3
 VEJ  Var_06    C6   C5   N1   C4    -77.68  30.0  3
 VEJ  Var_07    O2   C7   C6   C5    -62.94  30.0  3
 VEJ  Var_08    C    C1   C2   N     -79.73  30.0  3
 VEJ  Var_09    H8   C8   O2   C7    179.88  30.0  3
 VEJ  Var_10    H25  C    C1   C2   -175.84  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
 VEJ  chir_01  C3  C9  N  C4  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
 VEJ  plan-1  C15  0.020
 VEJ  plan-1  C17  0.020
 VEJ  plan-1  C20  0.020
 VEJ  plan-1  N    0.020
 VEJ  plan-1  C14  0.020
 VEJ  plan-1  C19  0.020
 VEJ  plan-1  C18  0.020
 VEJ  plan-1  C16  0.020
 VEJ  plan-1  H13  0.020
 VEJ  plan-1  H28  0.020
 VEJ  plan-1  H29  0.020
 VEJ  plan-1  H33  0.020
 VEJ  plan-2  C10  0.020
 VEJ  plan-2  C13  0.020
 VEJ  plan-2  C3   0.020
 VEJ  plan-2  C9   0.020
 VEJ  plan-2  C12  0.020
 VEJ  plan-2  C11  0.020
 VEJ  plan-2  N2   0.020
 VEJ  plan-2  H11  0.020
 VEJ  plan-2  H12  0.020
 VEJ  plan-2  H21  0.020
 VEJ  plan-2  H22  0.020
 VEJ  plan-3  N1   0.020
 VEJ  plan-3  C4   0.020
 VEJ  plan-3  C5   0.020
 VEJ  plan-3  O1   0.020
 VEJ  plan-3  C3   0.020
 VEJ  plan-3  H1   0.020
 VEJ  plan-4  C3   0.020
 VEJ  plan-4  N    0.020
 VEJ  plan-4  C2   0.020
 VEJ  plan-4  O    0.020
 VEJ  plan-4  C1   0.020
 VEJ  plan-4  C14  0.020

