# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:43:40 2021
#   Inital geometry file: a 130 line input string
#   Ligand name: N-(4-tert-butylphenyl)-N-[(1R)-2-(methylamino)-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)NC)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
 VEV  VEV  N-(4-tert-butylphenyl)-N-[(1R)-2-(methylamino)-2-oxo-1-(pyridin-3-yl)ethyl]propanamide  ligand  53  26  .  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_VEV
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
 VEV  N1   N  NH1   0  -0.610   7.5300   1.4352  23.3076
 VEV  C4   C  C     0   0.541   7.8355   1.0637  22.0620
 VEV  C5   C  CH3   0  -0.517   8.3767   2.3178  24.0749
 VEV  C6   C  CR6   0   0.070   6.5718   0.3921  20.0408
 VEV  C7   C  CR16  0  -0.085   7.4600   0.1646  18.9958
 VEV  C8   C  CR16  0  -0.074   6.0915   1.1588  17.4720
 VEV  C10  C  CR16  0  -0.185   5.3847   1.0437  19.7422
 VEV  C13  C  CR16  0  -0.346  11.1689  -1.6814  22.1456
 VEV  C15  C  CR16  0  -0.314  10.0544  -1.6348  24.2512
 VEV  C17  C  CT    0  -0.174  12.5745  -1.8100  24.2864
 VEV  C20  C  CH3   0  -0.633  12.5509  -3.0257  25.2231
 VEV  O1   O  O     0  -0.463   8.7747   1.5185  21.4320
 VEV  C3   C  CH1   0  -0.286   6.8954   0.0083  21.4609
 VEV  C9   C  CR16  0  -0.321   5.1363   1.4372  18.4365
 VEV  N2   N  N     0  -0.405   7.2314   0.5320  17.7420
 VEV  N    N  NT    0  -0.557   7.5169  -1.3149  21.5670
 VEV  C2   C  C     0   0.560   6.7364  -2.3871  21.2380
 VEV  O    O  O     0  -0.471   5.5984  -2.2260  20.8350
 VEV  C1   C  CH2   0  -0.583   7.3656  -3.7563  21.3759
 VEV  C    C  CH3   0  -0.656   6.4193  -4.8840  21.0039
 VEV  C11  C  CR6   0   0.201   8.7732  -1.4726  22.2229
 VEV  C16  C  CR16  0  -0.219   8.8332  -1.5218  23.6109
 VEV  C14  C  CR6   0   0.207  11.2516  -1.7142  23.5353
 VEV  C19  C  CH3   0  -0.665  13.7699  -1.9553  23.3455
 VEV  C18  C  CH3   0  -0.629  12.7606  -0.5332  25.1182
 VEV  C12  C  CR16  0  -0.218   9.9478  -1.5538  21.4959
 VEV  H1   H  HNH1  0   0.410   6.7574   0.9927  23.7770
 VEV  H2   H  HCH3  0   0.255   7.8794   2.5437  25.0133
 VEV  H3   H  HCH3  0   0.239   9.3398   1.8538  24.2952
 VEV  H4   H  HCH3  0   0.246   8.5559   3.2517  23.5446
 VEV  H5   H  HCR6  0   0.260   8.3969  -0.3497  19.1768
 VEV  H6   H  HCR6  0   0.263   5.9295   1.4498  16.4401
 VEV  H7   H  HCR6  0   0.268   4.6568   1.2386  20.5208
 VEV  H8   H  HCR6  0   0.255  12.0613  -1.7448  21.5385
 VEV  H9   H  HCR6  0   0.253  10.0655  -1.6600  25.3337
 VEV  H10  H  HCH3  0   0.230  11.7468  -2.9612  25.9560
 VEV  H11  H  HCH3  0   0.229  12.4237  -3.9538  24.6631
 VEV  H12  H  HCH3  0   0.228  13.4922  -3.0928  25.7725
 VEV  H13  H  HCH1  0   0.286   5.9612   0.0003  22.0318
 VEV  H14  H  HCR6  0   0.271   4.2196   1.9441  18.1686
 VEV  H15  H  HCH2  0   0.270   7.7262  -3.8897  22.3990
 VEV  H16  H  HCH2  0   0.271   8.2610  -3.7877  20.7490
 VEV  H17  H  HCH3  0   0.234   6.9341  -5.8398  21.0964
 VEV  H18  H  HCH3  0   0.228   5.5488  -4.9123  21.6584
 VEV  H19  H  HCH3  0   0.228   6.0651  -4.7965  19.9777
 VEV  H20  H  HCR6  0   0.261   7.9232  -1.4735  24.1961
 VEV  H21  H  HCH3  0   0.238  14.6881  -2.0217  23.9312
 VEV  H22  H  HCH3  0   0.231  13.7045  -2.8589  22.7365
 VEV  H23  H  HCH3  0   0.230  13.8743  -1.1012  22.6743
 VEV  H24  H  HCH3  0   0.229  11.9648  -0.4084  25.8547
 VEV  H25  H  HCH3  0   0.227  13.7082  -0.5678  25.6603
 VEV  H26  H  HCH3  0   0.229  12.7708   0.3547  24.4834
 VEV  H27  H  HCR6  0   0.261   9.9175  -1.5231  20.4144

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
 VEV  C8   N2   aromatic  1.329  0.020  1.329
 VEV  C8   C9   aromatic  1.386  0.020  1.386
 VEV  N2   C7   aromatic  1.326  0.020  1.326
 VEV  C9   C10  aromatic  1.386  0.020  1.386
 VEV  C7   C6   aromatic  1.390  0.020  1.390
 VEV  C10  C6   aromatic  1.387  0.020  1.387
 VEV  C6   C3   single    1.506  0.020  1.506
 VEV  C    C1   single    1.518  0.020  1.518
 VEV  O1   C4   double    1.219  0.020  1.219
 VEV  O    C2   double    1.218  0.020  1.218
 VEV  C3   N    single    1.466  0.020  1.466
 VEV  C3   C4   single    1.536  0.020  1.536
 VEV  C2   C1   single    1.513  0.020  1.513
 VEV  C2   N    single    1.366  0.020  1.366
 VEV  C12  C13  aromatic  1.389  0.020  1.389
 VEV  C12  C11  aromatic  1.384  0.020  1.384
 VEV  N    C11  single    1.426  0.020  1.426
 VEV  C4   N1   single    1.335  0.020  1.335
 VEV  C13  C14  aromatic  1.393  0.020  1.393
 VEV  C11  C16  aromatic  1.390  0.020  1.390
 VEV  N1   C5   single    1.444  0.020  1.444
 VEV  C19  C17  single    1.528  0.020  1.528
 VEV  C14  C15  aromatic  1.397  0.020  1.397
 VEV  C14  C17  single    1.524  0.020  1.524
 VEV  C16  C15  aromatic  1.384  0.020  1.384
 VEV  C17  C18  single    1.535  0.020  1.535
 VEV  C17  C20  single    1.535  0.020  1.535
 VEV  N1   H1   single    0.860  0.020  1.020
 VEV  C5   H2   single    0.970  0.020  1.090
 VEV  C5   H3   single    0.970  0.020  1.090
 VEV  C5   H4   single    0.970  0.020  1.090
 VEV  C7   H5   single    0.930  0.020  1.080
 VEV  C8   H6   single    0.930  0.020  1.080
 VEV  C10  H7   single    0.930  0.020  1.080
 VEV  C13  H8   single    0.930  0.020  1.080
 VEV  C15  H9   single    0.930  0.020  1.080
 VEV  C20  H10  single    0.970  0.020  1.090
 VEV  C20  H11  single    0.970  0.020  1.090
 VEV  C20  H12  single    0.970  0.020  1.090
 VEV  C3   H13  single    0.970  0.020  1.090
 VEV  C9   H14  single    0.930  0.020  1.080
 VEV  C1   H15  single    0.970  0.020  1.090
 VEV  C1   H16  single    0.970  0.020  1.090
 VEV  C    H17  single    0.970  0.020  1.090
 VEV  C    H18  single    0.970  0.020  1.090
 VEV  C    H19  single    0.970  0.020  1.090
 VEV  C16  H20  single    0.930  0.020  1.080
 VEV  C19  H21  single    0.970  0.020  1.090
 VEV  C19  H22  single    0.970  0.020  1.090
 VEV  C19  H23  single    0.970  0.020  1.090
 VEV  C18  H24  single    0.970  0.020  1.090
 VEV  C18  H25  single    0.970  0.020  1.090
 VEV  C18  H26  single    0.970  0.020  1.090
 VEV  C12  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
 VEV  H1   N1   C5   118.11  3.000
 VEV  H1   N1   C4   119.23  3.000
 VEV  C5   N1   C4   122.12  3.000
 VEV  C3   C4   O1   121.72  3.000
 VEV  C3   C4   N1   114.59  3.000
 VEV  O1   C4   N1   123.68  3.000
 VEV  H4   C5   H3   108.52  3.000
 VEV  H4   C5   H2   108.53  3.000
 VEV  H3   C5   H2   108.55  3.000
 VEV  H4   C5   N1   111.23  3.000
 VEV  H3   C5   N1   111.40  3.000
 VEV  H2   C5   N1   108.53  3.000
 VEV  C3   C6   C10  120.44  3.000
 VEV  C3   C6   C7   121.99  3.000
 VEV  C10  C6   C7   117.51  3.000
 VEV  H5   C7   N2   115.99  3.000
 VEV  H5   C7   C6   120.29  3.000
 VEV  N2   C7   C6   123.72  3.000
 VEV  H6   C8   N2   116.63  3.000
 VEV  H6   C8   C9   120.37  3.000
 VEV  N2   C8   C9   123.00  3.000
 VEV  H7   C10  C9   120.36  3.000
 VEV  H7   C10  C6   120.32  3.000
 VEV  C9   C10  C6   119.32  3.000
 VEV  H8   C13  C12  117.93  3.000
 VEV  H8   C13  C14  120.66  3.000
 VEV  C12  C13  C14  121.41  3.000
 VEV  H9   C15  C14  120.14  3.000
 VEV  H9   C15  C16  118.27  3.000
 VEV  C14  C15  C16  121.59  3.000
 VEV  C18  C17  C19  108.53  3.000
 VEV  C18  C17  C14  108.66  3.000
 VEV  C19  C17  C14  112.42  3.000
 VEV  C18  C17  C20  109.27  3.000
 VEV  C14  C17  C20  109.70  3.000
 VEV  C19  C17  C20  108.21  3.000
 VEV  H12  C20  H11  107.84  3.000
 VEV  H12  C20  H10  107.53  3.000
 VEV  H11  C20  H10  108.02  3.000
 VEV  H12  C20  C17  110.03  3.000
 VEV  H11  C20  C17  111.23  3.000
 VEV  H10  C20  C17  112.01  3.000
 VEV  H13  C3   N    108.51  3.000
 VEV  H13  C3   C6   108.07  3.000
 VEV  N    C3   C6   112.92  3.000
 VEV  H13  C3   C4   108.86  3.000
 VEV  N    C3   C4   109.42  3.000
 VEV  C6   C3   C4   108.98  3.000
 VEV  H14  C9   C10  121.23  3.000
 VEV  H14  C9   C8   120.40  3.000
 VEV  C10  C9   C8   118.37  3.000
 VEV  C8   N2   C7   118.08  3.000
 VEV  C11  N    C2   121.82  3.000
 VEV  C11  N    C3   120.44  3.000
 VEV  C2   N    C3   116.66  3.000
 VEV  C1   C2   O    122.57  3.000
 VEV  C1   C2   N    116.78  3.000
 VEV  O    C2   N    120.64  3.000
 VEV  H16  C1   H15  105.25  3.000
 VEV  H16  C1   C    110.40  3.000
 VEV  H15  C1   C    110.14  3.000
 VEV  H16  C1   C2   108.31  3.000
 VEV  H15  C1   C2   109.44  3.000
 VEV  C    C1   C2   112.99  3.000
 VEV  H19  C    H18  107.95  3.000
 VEV  H19  C    H17  107.71  3.000
 VEV  H18  C    H17  107.68  3.000
 VEV  H19  C    C1   111.95  3.000
 VEV  H18  C    C1   111.72  3.000
 VEV  H17  C    C1   109.65  3.000
 VEV  C12  C11  C16  119.07  3.000
 VEV  C16  C11  N    120.08  3.000
 VEV  C12  C11  N    120.84  3.000
 VEV  H20  C16  C11  120.11  3.000
 VEV  H20  C16  C15  119.69  3.000
 VEV  C11  C16  C15  120.20  3.000
 VEV  C17  C14  C15  119.65  3.000
 VEV  C17  C14  C13  123.01  3.000
 VEV  C15  C14  C13  117.33  3.000
 VEV  H23  C19  H22  108.09  3.000
 VEV  H23  C19  H21  107.29  3.000
 VEV  H22  C19  H21  107.42  3.000
 VEV  H23  C19  C17  112.28  3.000
 VEV  H22  C19  C17  112.04  3.000
 VEV  H21  C19  C17  109.49  3.000
 VEV  H26  C18  H25  107.83  3.000
 VEV  H26  C18  H24  107.83  3.000
 VEV  H25  C18  H24  107.53  3.000
 VEV  H26  C18  C17  111.26  3.000
 VEV  H25  C18  C17  110.35  3.000
 VEV  H24  C18  C17  111.86  3.000
 VEV  H27  C12  C11  119.97  3.000
 VEV  H27  C12  C13  119.64  3.000
 VEV  C11  C12  C13  120.39  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
 VEV  CONST_01  C8   N2   C7   C6      0.00   0.0  0
 VEV  CONST_02  C8   C9   C10  C6      0.00   0.0  0
 VEV  CONST_03  C9   C8   N2   C7      0.00   0.0  0
 VEV  CONST_04  C9   C10  C6   C7      0.00   0.0  0
 VEV  CONST_05  N2   C8   C9   C10     0.00   0.0  0
 VEV  CONST_06  N2   C7   C6   C10     0.00   0.0  0
 VEV  CONST_07  C16  C11  C12  C13     0.00   0.0  0
 VEV  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 VEV  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 VEV  CONST_10  C12  C11  C16  C15     0.00   0.0  0
 VEV  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 VEV  CONST_12  C14  C15  C16  C11     0.00   0.0  0
 VEV  CONST_13  N    C11  C12  C13   180.00   0.0  0
 VEV  CONST_14  N    C11  C16  C15   180.00   0.0  0
 VEV  CONST_15  C12  C13  C14  C17   180.00   0.0  0
 VEV  CONST_16  C16  C15  C14  C17   180.00   0.0  0
 VEV  CONST_17  N2   C7   C6   C3    180.00   0.0  0
 VEV  CONST_18  C9   C10  C6   C3    180.00   0.0  0
 VEV  CONST_19  H14  C9   C10  C6    180.00   0.0  0
 VEV  CONST_20  H6   C8   N2   C7    180.00   0.0  0
 VEV  CONST_21  H7   C10  C6   C7    180.00   0.0  0
 VEV  CONST_22  H5   C7   N2   C8    180.00   0.0  0
 VEV  CONST_23  H9   C15  C14  C13   180.00   0.0  0
 VEV  CONST_24  H8   C13  C14  C15   180.00   0.0  0
 VEV  CONST_25  H27  C12  C11  C16   180.00   0.0  0
 VEV  CONST_26  H20  C16  C15  C14   180.00   0.0  0
 VEV  CONST_31  C11  N    C2   O     180.00   0.0  0
 VEV  CONST_32  C11  N    C2   C1      0.00   0.0  0
 VEV  CONST_33  O1   C4   N1   C5      0.00   0.0  0
 VEV  CONST_34  C3   C4   N1   C5    180.00   0.0  0
 VEV  CONST_35  O    C2   N    C3      0.00   0.0  0
 VEV  CONST_36  C1   C2   N    C3    180.00   0.0  0
 VEV  CONST_37  H1   N1   C4   O1    180.00   0.0  0
 VEV  Var_01    C19  C17  C14  C13    -3.69  30.0  2
 VEV  Var_02    H21  C19  C17  C14  -179.87  30.0  3
 VEV  Var_03    H24  C18  C17  C14    60.98  30.0  3
 VEV  Var_04    H10  C20  C17  C14   -59.80  30.0  3
 VEV  Var_05    C    C1   C2   N     179.34  30.0  3
 VEV  Var_06    H2   C5   N1   C4    174.95  30.0  3
 VEV  Var_07    H17  C    C1   C2    178.47  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
 VEV  chir_01  C3  C6  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
 VEV  plan-1  C6   0.020
 VEV  plan-1  C7   0.020
 VEV  plan-1  C8   0.020
 VEV  plan-1  C10  0.020
 VEV  plan-1  C3   0.020
 VEV  plan-1  C9   0.020
 VEV  plan-1  N2   0.020
 VEV  plan-1  H5   0.020
 VEV  plan-1  H6   0.020
 VEV  plan-1  H7   0.020
 VEV  plan-1  H14  0.020
 VEV  plan-2  C13  0.020
 VEV  plan-2  C15  0.020
 VEV  plan-2  C17  0.020
 VEV  plan-2  N    0.020
 VEV  plan-2  C11  0.020
 VEV  plan-2  C16  0.020
 VEV  plan-2  C14  0.020
 VEV  plan-2  C12  0.020
 VEV  plan-2  H8   0.020
 VEV  plan-2  H9   0.020
 VEV  plan-2  H20  0.020
 VEV  plan-2  H27  0.020
 VEV  plan-3  N1   0.020
 VEV  plan-3  C4   0.020
 VEV  plan-3  C5   0.020
 VEV  plan-3  O1   0.020
 VEV  plan-3  C3   0.020
 VEV  plan-3  H1   0.020
 VEV  plan-4  C3   0.020
 VEV  plan-4  N    0.020
 VEV  plan-4  C2   0.020
 VEV  plan-4  O    0.020
 VEV  plan-4  C1   0.020
 VEV  plan-4  C11  0.020

