# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 05:20:24 2021
#   Inital geometry file: a 157 line input string
#   Ligand name: ethyl N-[(2R)-2-[(4-tert-butylphenyl)(propanoyl)amino]-2-(pyridin-3-yl)acetyl]-beta-alaninate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CCNC(=O)[C@H](N(C(=O)CC)c1ccc(cc1)C(C)(C)C)c2cccnc2
#
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
 VEG  VEG  'ethyl N-[(2R)-2-[(4-tert-butylphenyl)(propanoyl)amino]-2-(pyridin-3-yl)acetyl]-beta-alaninate'  ligand  65  32  .  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_VEG
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
 VEG  N1   N  NT    0  -0.554   7.8150  -1.1740  21.3522
 VEG  C4   C  CH2   0  -0.283   8.3724   2.4122  24.0278
 VEG  C5   C  C     0   0.559   7.9048   1.2155  21.9400
 VEG  C6   C  CH1   0  -0.279   7.0703   0.0879  21.3086
 VEG  C7   C  C     0   0.535   7.1348  -2.2917  20.9550
 VEG  C8   C  CH2   0  -0.554   7.8811  -3.6067  20.9157
 VEG  C10  C  CR6   0   0.193   9.0533  -1.2550  22.0532
 VEG  C13  C  CR6   0   0.195  11.4795  -1.3502  23.4768
 VEG  C15  C  CR16  0  -0.222   9.0741  -1.6516  23.3856
 VEG  C17  C  CH3   0  -0.619  12.6607  -0.3078  25.4027
 VEG  C20  C  CR6   0   0.077   6.6975   0.4898  19.9072
 VEG  C21  C  CR16  0  -0.072   7.5954   0.3779  18.8519
 VEG  C22  C  CR16  0  -0.061   6.1456   1.3092  17.3717
 VEG  C24  C  CR16  0  -0.161   5.4587   1.0471  19.6351
 VEG  O3   O  O     0  -0.465   5.9661  -2.2209  20.6185
 VEG  C9   C  CH3   0  -0.639   7.3940  -4.5697  21.9946
 VEG  C14  C  CR16  0  -0.296  10.2700  -1.7029  24.0797
 VEG  C16  C  CT    0  -0.178  12.7672  -1.3613  24.2919
 VEG  C19  C  CH3   0  -0.609  12.9741  -2.7482  24.9139
 VEG  C18  C  CH3   0  -0.649  13.9926  -1.0280  23.4412
 VEG  C12  C  CR16  0  -0.287  11.4372  -0.9631  22.1411
 VEG  C11  C  CR16  0  -0.188  10.2445  -0.9134  21.4361
 VEG  N2   N  N     0  -0.376   7.3335   0.7700  17.6145
 VEG  C23  C  CR16  0  -0.302   5.1740   1.4684  18.3463
 VEG  O2   O  O     0  -0.413   8.7154   1.8488  21.2959
 VEG  N    N  NH1   0  -0.617   7.6485   1.4382  23.2366
 VEG  C3   C  CH2   0  -0.583   9.8780   2.1535  24.0942
 VEG  C2   C  C     0   0.606  10.6701   2.9398  23.0796
 VEG  O1   O  O     0  -0.418  10.4531   4.0875  22.7999
 VEG  O    O  O2    0  -0.449  11.6905   2.2327  22.5994
 VEG  C1   C  CH2   0  -0.185  12.5655   2.8685  21.6683
 VEG  C    C  CH3   0  -0.673  13.6370   3.6832  22.3627
 VEG  H1   H  HCH2  0   0.269   8.1815   3.4195  23.6539
 VEG  H2   H  HCH2  0   0.249   7.9487   2.3593  25.0278
 VEG  H3   H  HCH1  0   0.259   6.1442  -0.0297  21.8833
 VEG  H4   H  HCH2  0   0.259   8.9593  -3.4756  20.9894
 VEG  H5   H  HCH2  0   0.263   7.6801  -4.0372  19.9326
 VEG  H6   H  HCR6  0   0.238   8.1500  -1.9139  23.8865
 VEG  H7   H  HCH3  0   0.220  11.8137  -0.4862  26.0662
 VEG  H8   H  HCH3  0   0.219  13.5636  -0.3129  26.0164
 VEG  H9   H  HCH3  0   0.235  12.5476   0.6911  24.9794
 VEG  H10  H  HCR6  0   0.241   8.5716  -0.0652  19.0132
 VEG  H11  H  HCR6  0   0.243   5.9547   1.6263  16.3525
 VEG  H12  H  HCR6  0   0.235   4.7181   1.1513  20.4186
 VEG  H13  H  HCH3  0   0.235   7.8530  -5.5475  21.8569
 VEG  H14  H  HCH3  0   0.220   7.6560  -4.2211  22.9934
 VEG  H15  H  HCH3  0   0.229   6.3136  -4.7002  21.9521
 VEG  H16  H  HCR6  0   0.227  10.2454  -2.0111  25.1173
 VEG  H17  H  HCH3  0   0.218  12.1553  -3.0318  25.5755
 VEG  H18  H  HCH3  0   0.224  13.0622  -3.5177  24.1454
 VEG  H19  H  HCH3  0   0.219  13.8899  -2.7652  25.5081
 VEG  H20  H  HCH3  0   0.229  14.8906  -1.0544  24.0602
 VEG  H21  H  HCH3  0   0.224  14.1355  -1.7410  22.6277
 VEG  H22  H  HCH3  0   0.229  13.9316  -0.0265  23.0116
 VEG  H23  H  HCR6  0   0.231  12.3432  -0.6825  21.6235
 VEG  H24  H  HCR6  0   0.243  10.2485  -0.5999  20.4013
 VEG  H25  H  HCR6  0   0.241   4.2169   1.9056  18.0988
 VEG  H26  H  HNH1  0   0.374   6.9853   0.8534  23.7131
 VEG  H27  H  HCH2  0   0.288  10.0904   1.0868  24.0273
 VEG  H28  H  HCH2  0   0.262  10.2395   2.4792  25.0748
 VEG  H29  H  HCH2  0   0.240  11.9947   3.4822  20.9702
 VEG  H30  H  HCH2  0   0.215  13.0147   2.0499  21.1049
 VEG  H31  H  HCH3  0   0.220  14.3192   4.0998  21.6208
 VEG  H32  H  HCH3  0   0.245  13.2105   4.5133  22.9237
 VEG  H33  H  HCH3  0   0.220  14.2241   3.0668  23.0441

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
 VEG  C22  N2   aromatic  1.327  0.020  1.327
 VEG  C22  C23  aromatic  1.385  0.020  1.385
 VEG  N2   C21  aromatic  1.324  0.020  1.324
 VEG  C23  C24  aromatic  1.385  0.020  1.385
 VEG  C21  C20  aromatic  1.390  0.020  1.390
 VEG  C8   C9   single    1.526  0.020  1.526
 VEG  C8   C7   single    1.513  0.020  1.513
 VEG  C24  C20  aromatic  1.385  0.020  1.385
 VEG  C20  C6   single    1.505  0.020  1.505
 VEG  O2   C5   double    1.214  0.020  1.214
 VEG  C7   O3   double    1.218  0.020  1.218
 VEG  C7   N1   single    1.367  0.020  1.367
 VEG  C6   N1   single    1.466  0.020  1.466
 VEG  C6   C5   single    1.538  0.020  1.538
 VEG  C11  C12  aromatic  1.386  0.020  1.386
 VEG  C11  C10  aromatic  1.384  0.020  1.384
 VEG  N1   C10  single    1.425  0.020  1.425
 VEG  O1   C2   double    1.201  0.020  1.201
 VEG  C5   N    single    1.340  0.020  1.340
 VEG  C12  C13  aromatic  1.391  0.020  1.391
 VEG  C10  C15  aromatic  1.390  0.020  1.390
 VEG  C    C1   single    1.515  0.020  1.515
 VEG  C1   O    single    1.427  0.020  1.427
 VEG  C2   O    single    1.331  0.020  1.331
 VEG  C2   C3   single    1.508  0.020  1.508
 VEG  N    C4   single    1.449  0.020  1.449
 VEG  C4   C3   single    1.529  0.020  1.529
 VEG  C18  C16  single    1.529  0.020  1.529
 VEG  C13  C14  aromatic  1.397  0.020  1.397
 VEG  C13  C16  single    1.524  0.020  1.524
 VEG  C15  C14  aromatic  1.384  0.020  1.384
 VEG  C16  C17  single    1.535  0.020  1.535
 VEG  C16  C19  single    1.534  0.020  1.534
 VEG  C4   H1   single    0.970  0.020  1.090
 VEG  C4   H2   single    0.970  0.020  1.090
 VEG  C6   H3   single    0.970  0.020  1.090
 VEG  C8   H4   single    0.970  0.020  1.090
 VEG  C8   H5   single    0.970  0.020  1.090
 VEG  C15  H6   single    0.930  0.020  1.080
 VEG  C17  H7   single    0.970  0.020  1.090
 VEG  C17  H8   single    0.970  0.020  1.090
 VEG  C17  H9   single    0.970  0.020  1.090
 VEG  C21  H10  single    0.930  0.020  1.080
 VEG  C22  H11  single    0.930  0.020  1.080
 VEG  C24  H12  single    0.930  0.020  1.080
 VEG  C9   H13  single    0.970  0.020  1.090
 VEG  C9   H14  single    0.970  0.020  1.090
 VEG  C9   H15  single    0.970  0.020  1.090
 VEG  C14  H16  single    0.930  0.020  1.080
 VEG  C19  H17  single    0.970  0.020  1.090
 VEG  C19  H18  single    0.970  0.020  1.090
 VEG  C19  H19  single    0.970  0.020  1.090
 VEG  C18  H20  single    0.970  0.020  1.090
 VEG  C18  H21  single    0.970  0.020  1.090
 VEG  C18  H22  single    0.970  0.020  1.090
 VEG  C12  H23  single    0.930  0.020  1.080
 VEG  C11  H24  single    0.930  0.020  1.080
 VEG  C23  H25  single    0.930  0.020  1.080
 VEG  N    H26  single    0.860  0.020  1.020
 VEG  C3   H27  single    0.970  0.020  1.090
 VEG  C3   H28  single    0.970  0.020  1.090
 VEG  C1   H29  single    0.970  0.020  1.090
 VEG  C1   H30  single    0.970  0.020  1.090
 VEG  C    H31  single    0.970  0.020  1.090
 VEG  C    H32  single    0.970  0.020  1.090
 VEG  C    H33  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
 VEG  C10  N1   C7   121.91  3.000
 VEG  C10  N1   C6   120.32  3.000
 VEG  C7   N1   C6   116.26  3.000
 VEG  H2   C4   H1   106.96  3.000
 VEG  H2   C4   C3   109.60  3.000
 VEG  H1   C4   C3   110.08  3.000
 VEG  H2   C4   N    105.95  3.000
 VEG  H1   C4   N    110.25  3.000
 VEG  C3   C4   N    113.70  3.000
 VEG  N    C5   O2   123.67  3.000
 VEG  N    C5   C6   114.52  3.000
 VEG  O2   C5   C6   121.80  3.000
 VEG  H3   C6   C20  107.91  3.000
 VEG  H3   C6   C5   108.77  3.000
 VEG  C20  C6   C5   108.71  3.000
 VEG  H3   C6   N1   108.74  3.000
 VEG  C5   C6   N1   110.08  3.000
 VEG  C20  C6   N1   112.54  3.000
 VEG  O3   C7   C8   121.11  3.000
 VEG  O3   C7   N1   120.66  3.000
 VEG  C8   C7   N1   118.22  3.000
 VEG  H5   C8   H4   106.90  3.000
 VEG  H5   C8   C9   109.20  3.000
 VEG  H4   C8   C9   110.14  3.000
 VEG  H5   C8   C7   105.99  3.000
 VEG  H4   C8   C7   112.47  3.000
 VEG  C9   C8   C7   111.89  3.000
 VEG  C11  C10  C15  119.00  3.000
 VEG  C15  C10  N1   120.04  3.000
 VEG  C11  C10  N1   120.95  3.000
 VEG  C12  C13  C16  122.76  3.000
 VEG  C16  C13  C14  119.93  3.000
 VEG  C12  C13  C14  117.28  3.000
 VEG  H6   C15  C14  119.76  3.000
 VEG  H6   C15  C10  119.96  3.000
 VEG  C14  C15  C10  120.28  3.000
 VEG  H9   C17  H8   107.95  3.000
 VEG  H9   C17  H7   107.78  3.000
 VEG  H8   C17  H7   107.43  3.000
 VEG  H9   C17  C16  110.79  3.000
 VEG  H8   C17  C16  110.26  3.000
 VEG  H7   C17  C16  112.45  3.000
 VEG  C24  C20  C21  117.44  3.000
 VEG  C24  C20  C6   120.79  3.000
 VEG  C21  C20  C6   121.70  3.000
 VEG  H10  C21  N2   115.99  3.000
 VEG  H10  C21  C20  120.10  3.000
 VEG  N2   C21  C20  123.90  3.000
 VEG  H11  C22  C23  120.28  3.000
 VEG  H11  C22  N2   116.64  3.000
 VEG  C23  C22  N2   123.08  3.000
 VEG  H12  C24  C23  120.20  3.000
 VEG  H12  C24  C20  120.53  3.000
 VEG  C23  C24  C20  119.26  3.000
 VEG  H15  C9   H14  108.22  3.000
 VEG  H15  C9   H13  107.79  3.000
 VEG  H14  C9   H13  107.56  3.000
 VEG  H15  C9   C8   111.39  3.000
 VEG  H14  C9   C8   111.67  3.000
 VEG  H13  C9   C8   110.04  3.000
 VEG  H16  C14  C15  118.14  3.000
 VEG  H16  C14  C13  120.35  3.000
 VEG  C15  C14  C13  121.51  3.000
 VEG  C18  C16  C19  108.34  3.000
 VEG  C19  C16  C17  109.67  3.000
 VEG  C18  C16  C17  107.98  3.000
 VEG  C19  C16  C13  109.72  3.000
 VEG  C17  C16  C13  108.88  3.000
 VEG  C18  C16  C13  112.22  3.000
 VEG  H19  C19  H18  107.74  3.000
 VEG  H19  C19  H17  107.20  3.000
 VEG  H18  C19  H17  107.74  3.000
 VEG  H19  C19  C16  110.35  3.000
 VEG  H18  C19  C16  111.28  3.000
 VEG  H17  C19  C16  112.33  3.000
 VEG  H22  C18  H21  108.27  3.000
 VEG  H22  C18  H20  106.95  3.000
 VEG  H21  C18  H20  107.42  3.000
 VEG  H22  C18  C16  111.99  3.000
 VEG  H21  C18  C16  112.18  3.000
 VEG  H20  C18  C16  109.81  3.000
 VEG  H23  C12  C11  117.94  3.000
 VEG  H23  C12  C13  120.44  3.000
 VEG  C11  C12  C13  121.62  3.000
 VEG  H24  C11  C12  119.59  3.000
 VEG  H24  C11  C10  120.10  3.000
 VEG  C12  C11  C10  120.31  3.000
 VEG  C22  N2   C21  117.93  3.000
 VEG  H25  C23  C24  121.20  3.000
 VEG  H25  C23  C22  120.42  3.000
 VEG  C24  C23  C22  118.38  3.000
 VEG  H26  N    C5   119.24  3.000
 VEG  H26  N    C4   117.54  3.000
 VEG  C5   N    C4   122.99  3.000
 VEG  H28  C3   H27  106.38  3.000
 VEG  H28  C3   C2   105.90  3.000
 VEG  H27  C3   C2   111.51  3.000
 VEG  H28  C3   C4   108.28  3.000
 VEG  H27  C3   C4   110.78  3.000
 VEG  C2   C3   C4   113.55  3.000
 VEG  O    C2   O1   124.20  3.000
 VEG  O    C2   C3   111.61  3.000
 VEG  O1   C2   C3   124.05  3.000
 VEG  C1   O    C2   117.95  3.000
 VEG  H30  C1   H29  107.89  3.000
 VEG  H30  C1   C    110.44  3.000
 VEG  H29  C1   C    111.16  3.000
 VEG  H30  C1   O    104.79  3.000
 VEG  H29  C1   O    110.32  3.000
 VEG  C    C1   O    111.98  3.000
 VEG  H33  C    H32  108.65  3.000
 VEG  H33  C    H31  107.71  3.000
 VEG  H32  C    H31  107.71  3.000
 VEG  H33  C    C1   111.31  3.000
 VEG  H32  C    C1   111.67  3.000
 VEG  H31  C    C1   109.64  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
 VEG  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 VEG  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 VEG  CONST_03  C12  C11  C10  C15     0.00   0.0  0
 VEG  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 VEG  CONST_05  C22  N2   C21  C20     0.00   0.0  0
 VEG  CONST_06  C22  C23  C24  C20     0.00   0.0  0
 VEG  CONST_07  C23  C22  N2   C21     0.00   0.0  0
 VEG  CONST_08  C23  C24  C20  C21     0.00   0.0  0
 VEG  CONST_09  N2   C22  C23  C24     0.00   0.0  0
 VEG  CONST_10  N2   C21  C20  C24     0.00   0.0  0
 VEG  CONST_11  C11  C12  C13  C14     0.00   0.0  0
 VEG  CONST_12  C11  C10  C15  C14     0.00   0.0  0
 VEG  CONST_13  C12  C11  C10  N1    180.00   0.0  0
 VEG  CONST_14  C14  C15  C10  N1    180.00   0.0  0
 VEG  CONST_15  N2   C21  C20  C6    180.00   0.0  0
 VEG  CONST_16  C23  C24  C20  C6    180.00   0.0  0
 VEG  CONST_17  C16  C13  C14  C15   180.00   0.0  0
 VEG  CONST_18  C11  C12  C13  C16   180.00   0.0  0
 VEG  CONST_19  H23  C12  C11  C10   180.00   0.0  0
 VEG  CONST_20  H16  C14  C15  C10   180.00   0.0  0
 VEG  CONST_21  H24  C11  C12  C13   180.00   0.0  0
 VEG  CONST_22  H6   C15  C14  C13   180.00   0.0  0
 VEG  CONST_23  H25  C23  C24  C20   180.00   0.0  0
 VEG  CONST_24  H11  C22  N2   C21   180.00   0.0  0
 VEG  CONST_25  H12  C24  C20  C21   180.00   0.0  0
 VEG  CONST_26  H10  C21  N2   C22   180.00   0.0  0
 VEG  CONST_33  O2   C5   N    C4      0.00   0.0  0
 VEG  CONST_34  C6   C5   N    C4    180.00   0.0  0
 VEG  CONST_35  C8   C7   N1   C6    180.00   0.0  0
 VEG  CONST_36  O3   C7   N1   C6      0.00   0.0  0
 VEG  CONST_37  H26  N    C5   C6      0.00   0.0  0
 VEG  Var_01    C12  C13  C16  C17   114.24  30.0  2
 VEG  Var_02    H20  C18  C16  C13  -179.57  30.0  3
 VEG  Var_03    H7   C17  C16  C13    58.79  30.0  3
 VEG  Var_04    H17  C19  C16  C13   -59.93  30.0  3
 VEG  Var_05    C9   C8   C7   N1    111.00  30.0  2
 VEG  Var_06    O1   C2   C3   C4     40.97  30.0  2
 VEG  Var_07    C3   C4   N    C5    -59.21  30.0  3
 VEG  Var_08    C2   C3   C4   N      95.80  30.0  3
 VEG  Var_09    C    C1   O    C2     84.09  30.0  1
 VEG  Var_10    H13  C9   C8   C7    172.47  30.0  3
 VEG  Var_11    H31  C    C1   O     176.48  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
 VEG  chir_01  C6  C20  N1  C5  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
 VEG  plan-1  C6   0.020
 VEG  plan-1  C20  0.020
 VEG  plan-1  C21  0.020
 VEG  plan-1  C22  0.020
 VEG  plan-1  C24  0.020
 VEG  plan-1  N2   0.020
 VEG  plan-1  C23  0.020
 VEG  plan-1  H10  0.020
 VEG  plan-1  H11  0.020
 VEG  plan-1  H12  0.020
 VEG  plan-1  H25  0.020
 VEG  plan-2  C3   0.020
 VEG  plan-2  C2   0.020
 VEG  plan-2  O1   0.020
 VEG  plan-2  O    0.020
 VEG  plan-3  N1   0.020
 VEG  plan-3  C10  0.020
 VEG  plan-3  C13  0.020
 VEG  plan-3  C15  0.020
 VEG  plan-3  C14  0.020
 VEG  plan-3  C16  0.020
 VEG  plan-3  C12  0.020
 VEG  plan-3  C11  0.020
 VEG  plan-3  H6   0.020
 VEG  plan-3  H16  0.020
 VEG  plan-3  H23  0.020
 VEG  plan-3  H24  0.020
 VEG  plan-4  C4   0.020
 VEG  plan-4  C5   0.020
 VEG  plan-4  C6   0.020
 VEG  plan-4  O2   0.020
 VEG  plan-4  N    0.020
 VEG  plan-4  H26  0.020
 VEG  plan-5  N1   0.020
 VEG  plan-5  C6   0.020
 VEG  plan-5  C7   0.020
 VEG  plan-5  C8   0.020
 VEG  plan-5  C10  0.020
 VEG  plan-5  O3   0.020

