# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 02:06:11 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N~1~-[(1S)-1-benzyl-2-(dimethylamino)-2-oxoethyl]-2-oxo-N~4~-(2-pyridin-2-ylethyl)butanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)[C@H](Cc1ccccc1)NC(=O)C(=O)CC(=O)NCCc2ccccn2
#
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
 C48  C48  N~1~-[(1S)-1-benzyl-2-(dimethylamino)-2-oxoethyl]-2-oxo-N~4~-(2-pyridin-2-ylethyl)butanediamide  ligand  56  30  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C48
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
 C48  O1    O  O     0  -0.490   2.2570  -0.9311  -2.3445
 C48  O2    O  O     0  -0.347   0.1911  -0.7563   0.0507
 C48  O3    O  O     0  -0.448   2.0158   1.4666   1.9872
 C48  N5    N  NH1   0  -0.640   0.4507  -0.0371   2.6267
 C48  N8    N  N     0  -0.420   0.4086   0.4240  -7.2981
 C48  C9    C  C     0   0.543   1.6630   0.1079  -2.1000
 C48  C10   C  CH2   0  -0.700   1.8115   0.8030  -0.7627
 C48  C11   C  C     0   0.308   0.9903   0.1126   0.2864
 C48  C12   C  C     0   0.491   1.2088   0.5921   1.7287
 C48  C13   C  CH1   0  -0.181   0.4927   0.3058   4.0274
 C48  C14   C  CH2   0  -0.563  -0.5493  -0.4948   4.8210
 C48  C15   C  CR6   0   0.127  -1.9394  -0.2996   4.2809
 C48  C16   C  CR16  0  -0.326  -2.5738  -1.3159   3.5724
 C48  C17   C  CR16  0  -0.240  -3.8430  -1.1259   3.0382
 C48  C18   C  CR16  0  -0.266  -4.4938   0.0868   3.2098
 C48  C19   C  CR16  0  -0.239  -3.8704   1.1071   3.9197
 C48  C20   C  CR16  0  -0.296  -2.6034   0.9147   4.4492
 C48  C21   C  C     0   0.549   1.8825   0.1944   4.6697
 C48  C22   C  CH3   0  -0.526   2.3292  -2.0177   3.6039
 C48  C23   C  CH3   0  -0.528   4.0473  -0.8491   4.8708
 C48  C24   C  CH2   0  -0.236   0.5239   0.1404  -4.2620
 C48  C25   C  CH2   0  -0.543  -0.2742   1.1374  -5.0944
 C48  C26   C  CR6   0   0.254  -0.6029   0.5639  -6.4432
 C48  C27   C  CR16  0  -0.345  -1.8994   0.1737  -6.7640
 C48  C28   C  CR16  0  -0.149  -2.1485  -0.3758  -8.0122
 C48  C29   C  CR16  0  -0.329  -1.0940  -0.5216  -8.8998
 C48  C30   C  CR16  0  -0.081   0.1641  -0.1049  -8.4901
 C48  HN5   H  HNH1  0   0.411  -0.2168  -0.7181   2.2942
 C48  HN7   H  HNH1  0   0.409   0.3557   1.5435  -2.6826
 C48  H101  H  HCH2  0   0.318   1.5099   1.8546  -0.7919
 C48  H102  H  HCH2  0   0.320   2.8616   0.7998  -0.4629
 C48  H13   H  HCH1  0   0.300   0.2428   1.3655   4.1320
 C48  H141  H  HCH2  0   0.273  -0.3021  -1.5582   4.8237
 C48  H142  H  HCH2  0   0.290  -0.4922  -0.1617   5.8588
 C48  H16   H  HCR6  0   0.258  -2.0774  -2.2716   3.4437
 C48  H17   H  HCR6  0   0.259  -4.3204  -1.9274   2.4896
 C48  H18   H  HCR6  0   0.258  -5.4822   0.2387   2.7964
 C48  H19   H  HCR6  0   0.258  -4.3737   2.0549   4.0616
 C48  H20   H  HCR6  0   0.254  -2.1265   1.7161   5.0018
 C48  H221  H  HCH3  0   0.262   2.7883  -2.8844   4.0791
 C48  H222  H  HCH3  0   0.245   1.2607  -2.1972   3.5909
 C48  H223  H  HCH3  0   0.245   2.6890  -1.9692   2.5741
 C48  H231  H  HCH3  0   0.257   4.3691   0.1491   5.1486
 C48  H232  H  HCH3  0   0.242   4.1356  -1.5027   5.7414
 C48  H233  H  HCH3  0   0.246   4.7151  -1.2246   4.0955
 C48  H241  H  HCH2  0   0.246   1.4489  -0.1139  -4.7821
 C48  H242  H  HCH2  0   0.243  -0.0456  -0.7867  -4.1463
 C48  H251  H  HCH2  0   0.259  -1.1958   1.4034  -4.5720
 C48  H252  H  HCH2  0   0.263   0.3076   2.0541  -5.2180
 C48  H27   H  HCR6  0   0.266  -2.6988   0.2991  -6.0456
 C48  H28   H  HCR6  0   0.274  -3.1489  -0.6841  -8.2863
 C48  H29   H  HCR6  0   0.269  -1.2374  -0.9459  -9.8839
 C48  H30   H  HCR6  0   0.262   1.0134  -0.2020  -9.1575
 C48  N6    N  NT    0  -0.438   2.6898  -0.8344   4.3598
 C48  O4    O  O     0  -0.497   2.2005   1.0621   5.4729
 C48  N7    N  NH1   0  -0.632   0.8339   0.7028  -2.9647

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
 C48  O1   C9    double    1.222  0.020  1.222
 C48  O2   C11   double    1.204  0.020  1.204
 C48  O3   C12   double    1.218  0.020  1.218
 C48  O4   C21   double    1.224  0.020  1.224
 C48  N5   C12   single    1.333  0.020  1.333
 C48  N5   C13   single    1.443  0.020  1.443
 C48  N5   HN5   single    0.860  0.020  1.020
 C48  N6   C21   single    1.344  0.020  1.344
 C48  N6   C22   single    1.450  0.020  1.450
 C48  N6   C23   single    1.451  0.020  1.451
 C48  N7   C9    single    1.338  0.020  1.338
 C48  N7   C24   single    1.448  0.020  1.448
 C48  N7   HN7   single    0.860  0.020  1.020
 C48  N8   C26   aromatic  1.332  0.020  1.332
 C48  N8   C30   aromatic  1.327  0.020  1.327
 C48  C9   C10   single    1.514  0.020  1.514
 C48  C10  C11   single    1.501  0.020  1.501
 C48  C10  H101  single    0.970  0.020  1.090
 C48  C10  H102  single    0.970  0.020  1.090
 C48  C11  C12   single    1.535  0.020  1.535
 C48  C13  C14   single    1.535  0.020  1.535
 C48  C13  C21   single    1.535  0.020  1.535
 C48  C13  H13   single    0.970  0.020  1.090
 C48  C14  C15   single    1.504  0.020  1.504
 C48  C14  H141  single    0.970  0.020  1.090
 C48  C14  H142  single    0.970  0.020  1.090
 C48  C15  C16   aromatic  1.392  0.020  1.392
 C48  C15  C20   aromatic  1.394  0.020  1.394
 C48  C16  C17   aromatic  1.390  0.020  1.390
 C48  C16  H16   single    0.930  0.020  1.080
 C48  C17  C18   aromatic  1.387  0.020  1.387
 C48  C17  H17   single    0.930  0.020  1.080
 C48  C18  C19   aromatic  1.390  0.020  1.390
 C48  C18  H18   single    0.930  0.020  1.080
 C48  C19  C20   aromatic  1.387  0.020  1.387
 C48  C19  H19   single    0.930  0.020  1.080
 C48  C20  H20   single    0.930  0.020  1.080
 C48  C22  H221  single    0.970  0.020  1.090
 C48  C22  H222  single    0.970  0.020  1.090
 C48  C22  H223  single    0.970  0.020  1.090
 C48  C23  H231  single    0.970  0.020  1.090
 C48  C23  H232  single    0.970  0.020  1.090
 C48  C23  H233  single    0.970  0.020  1.090
 C48  C24  C25   single    1.524  0.020  1.524
 C48  C24  H241  single    0.970  0.020  1.090
 C48  C24  H242  single    0.970  0.020  1.090
 C48  C25  C26   single    1.502  0.020  1.502
 C48  C25  H251  single    0.970  0.020  1.090
 C48  C25  H252  single    0.970  0.020  1.090
 C48  C26  C27   aromatic  1.391  0.020  1.391
 C48  C27  C28   aromatic  1.386  0.020  1.386
 C48  C27  H27   single    0.930  0.020  1.080
 C48  C28  C29   aromatic  1.386  0.020  1.386
 C48  C28  H28   single    0.930  0.020  1.080
 C48  C29  C30   aromatic  1.387  0.020  1.387
 C48  C29  H29   single    0.930  0.020  1.080
 C48  C30  H30   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
 C48  HN5   N5   C13   119.94  3.000
 C48  HN5   N5   C12   118.19  3.000
 C48  C13   N5   C12   121.69  3.000
 C48  C30   N8   C26   118.60  3.000
 C48  C10   C9   N7    115.31  3.000
 C48  C10   C9   O1    121.30  3.000
 C48  N7    C9   O1    123.39  3.000
 C48  H102  C10  H101  105.97  3.000
 C48  H102  C10  C11   109.45  3.000
 C48  H101  C10  C11   108.06  3.000
 C48  H102  C10  C9    109.60  3.000
 C48  H101  C10  C9    112.98  3.000
 C48  C11   C10  C9    110.64  3.000
 C48  C12   C11  C10   115.79  3.000
 C48  C12   C11  O2    120.25  3.000
 C48  C10   C11  O2    123.95  3.000
 C48  C11   C12  N5    113.85  3.000
 C48  C11   C12  O3    121.20  3.000
 C48  N5    C12  O3    124.95  3.000
 C48  H13   C13  C21   103.72  3.000
 C48  H13   C13  C14   107.51  3.000
 C48  C21   C13  C14   111.13  3.000
 C48  H13   C13  N5    108.45  3.000
 C48  C21   C13  N5    114.54  3.000
 C48  C14   C13  N5    110.99  3.000
 C48  H142  C14  H141  106.45  3.000
 C48  H142  C14  C15   110.50  3.000
 C48  H141  C14  C15   109.67  3.000
 C48  H142  C14  C13   107.27  3.000
 C48  H141  C14  C13   110.83  3.000
 C48  C15   C14  C13   111.96  3.000
 C48  C20   C15  C16   118.71  3.000
 C48  C20   C15  C14   120.66  3.000
 C48  C16   C15  C14   120.61  3.000
 C48  H16   C16  C17   119.52  3.000
 C48  H16   C16  C15   119.69  3.000
 C48  C17   C16  C15   120.79  3.000
 C48  H17   C17  C18   120.21  3.000
 C48  H17   C17  C16   119.76  3.000
 C48  C18   C17  C16   120.03  3.000
 C48  H18   C18  C19   120.10  3.000
 C48  H18   C18  C17   120.27  3.000
 C48  C19   C18  C17   119.63  3.000
 C48  H19   C19  C20   119.75  3.000
 C48  H19   C19  C18   120.06  3.000
 C48  C20   C19  C18   120.19  3.000
 C48  H20   C20  C19   119.61  3.000
 C48  H20   C20  C15   119.73  3.000
 C48  C19   C20  C15   120.66  3.000
 C48  C13   C21  N6    120.19  3.000
 C48  C13   C21  O4    117.27  3.000
 C48  N6    C21  O4    122.53  3.000
 C48  H223  C22  H222  108.73  3.000
 C48  H223  C22  H221  107.92  3.000
 C48  H222  C22  H221  106.79  3.000
 C48  H223  C22  N6    111.94  3.000
 C48  H222  C22  N6    112.76  3.000
 C48  H221  C22  N6    108.48  3.000
 C48  H233  C23  H232  108.13  3.000
 C48  H233  C23  H231  108.51  3.000
 C48  H232  C23  H231  108.81  3.000
 C48  H233  C23  N6    109.05  3.000
 C48  H232  C23  N6    111.25  3.000
 C48  H231  C23  N6    111.01  3.000
 C48  H242  C24  H241  107.11  3.000
 C48  H242  C24  C25   109.84  3.000
 C48  H241  C24  C25   109.63  3.000
 C48  H242  C24  N7    110.24  3.000
 C48  H241  C24  N7    109.64  3.000
 C48  C25   C24  N7    110.33  3.000
 C48  H252  C25  H251  107.40  3.000
 C48  H252  C25  C26   109.58  3.000
 C48  H251  C25  C26   109.74  3.000
 C48  H252  C25  C24   109.37  3.000
 C48  H251  C25  C24   109.87  3.000
 C48  C26   C25  C24   110.81  3.000
 C48  C27   C26  C25   121.20  3.000
 C48  C27   C26  N8    122.02  3.000
 C48  C25   C26  N8    116.76  3.000
 C48  H27   C27  C28   120.73  3.000
 C48  H27   C27  C26   120.18  3.000
 C48  C28   C27  C26   119.09  3.000
 C48  H28   C28  C29   120.75  3.000
 C48  H28   C28  C27   120.46  3.000
 C48  C29   C28  C27   118.79  3.000
 C48  H29   C29  C30   120.46  3.000
 C48  H29   C29  C28   121.55  3.000
 C48  C30   C29  C28   117.99  3.000
 C48  H30   C30  C29   120.11  3.000
 C48  H30   C30  N8    116.37  3.000
 C48  C29   C30  N8    123.52  3.000
 C48  C23   N6   C22   114.10  3.000
 C48  C23   N6   C21   119.26  3.000
 C48  C22   N6   C21   126.55  3.000
 C48  HN7   N7   C24   118.26  3.000
 C48  HN7   N7   C9    118.97  3.000
 C48  C24   N7   C9    122.64  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
 C48  CONST_01  C28   C27  C26  N8      0.00   0.0  0
 C48  CONST_02  C28   C29  C30  N8      0.00   0.0  0
 C48  CONST_03  C18   C17  C16  C15     0.00   0.0  0
 C48  CONST_04  C18   C19  C20  C15     0.00   0.0  0
 C48  CONST_05  C19   C20  C15  C16     0.00   0.0  0
 C48  CONST_06  C19   C18  C17  C16     0.00   0.0  0
 C48  CONST_07  C20   C15  C16  C17     0.00   0.0  0
 C48  CONST_08  C20   C19  C18  C17     0.00   0.0  0
 C48  CONST_09  C29   C30  N8   C26     0.00   0.0  0
 C48  CONST_10  C29   C28  C27  C26     0.00   0.0  0
 C48  CONST_11  C30   N8   C26  C27     0.00   0.0  0
 C48  CONST_12  C30   C29  C28  C27     0.00   0.0  0
 C48  CONST_13  C17   C16  C15  C14   180.00   0.0  0
 C48  CONST_14  C19   C20  C15  C14   180.00   0.0  0
 C48  CONST_15  C30   N8   C26  C25   180.00   0.0  0
 C48  CONST_16  C28   C27  C26  C25   180.00   0.0  0
 C48  CONST_17  H27   C27  C26  N8    180.00   0.0  0
 C48  CONST_18  H29   C29  C30  N8    180.00   0.0  0
 C48  CONST_19  H17   C17  C16  C15   180.00   0.0  0
 C48  CONST_20  H19   C19  C20  C15   180.00   0.0  0
 C48  CONST_21  H20   C20  C15  C16   180.00   0.0  0
 C48  CONST_22  H18   C18  C17  C16   180.00   0.0  0
 C48  CONST_23  H16   C16  C17  C18   180.00   0.0  0
 C48  CONST_24  H30   C30  N8   C26   180.00   0.0  0
 C48  CONST_25  H28   C28  C27  C26   180.00   0.0  0
 C48  CONST_26  C24   N7   C9   O1      0.00   0.0  0
 C48  CONST_27  C13   N5   C12  O3      0.00   0.0  0
 C48  CONST_28  C22   N6   C21  O4    180.00   0.0  0
 C48  CONST_29  C23   N6   C21  O4      0.00   0.0  0
 C48  CONST_30  C10   C11  C12  N5    180.00   0.0  0
 C48  CONST_31  C24   N7   C9   C10   180.00   0.0  0
 C48  CONST_32  C13   N5   C12  C11   180.00   0.0  0
 C48  CONST_33  C22   N6   C21  C13     0.00   0.0  0
 C48  CONST_34  C23   N6   C21  C13   180.00   0.0  0
 C48  CONST_35  HN7   N7   C9   O1    180.00   0.0  0
 C48  CONST_36  HN5   N5   C12  O3    180.00   0.0  0
 C48  Var_01    C24   C25  C26  N8    -70.71  30.0  2
 C48  Var_02    C16   C15  C14  C13   107.24  30.0  2
 C48  Var_03    C26   C25  C24  N7   -179.95  30.0  3
 C48  Var_04    C11   C10  C9   O1    -77.84  30.0  3
 C48  Var_05    C9    C10  C11  O2     -9.26  30.0  1
 C48  Var_06    C25   C24  N7   C9   -171.55  30.0  3
 C48  Var_07    H221  C22  N6   C21  -138.72  30.0  3
 C48  Var_08    H231  C23  N6   C21   -21.00  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
 C48  chir_01  C13  N5  C14  C21  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
 C48  plan-1  N8   0.020
 C48  plan-1  C25  0.020
 C48  plan-1  C26  0.020
 C48  plan-1  C27  0.020
 C48  plan-1  C28  0.020
 C48  plan-1  C29  0.020
 C48  plan-1  C30  0.020
 C48  plan-1  H27  0.020
 C48  plan-1  H28  0.020
 C48  plan-1  H29  0.020
 C48  plan-1  H30  0.020
 C48  plan-2  C14  0.020
 C48  plan-2  C15  0.020
 C48  plan-2  C16  0.020
 C48  plan-2  C17  0.020
 C48  plan-2  C18  0.020
 C48  plan-2  C19  0.020
 C48  plan-2  C20  0.020
 C48  plan-2  H16  0.020
 C48  plan-2  H17  0.020
 C48  plan-2  H18  0.020
 C48  plan-2  H19  0.020
 C48  plan-2  H20  0.020
 C48  plan-3  O1   0.020
 C48  plan-3  C9   0.020
 C48  plan-3  C10  0.020
 C48  plan-3  C24  0.020
 C48  plan-3  HN7  0.020
 C48  plan-3  N7   0.020
 C48  plan-4  O2   0.020
 C48  plan-4  O3   0.020
 C48  plan-4  N5   0.020
 C48  plan-4  C10  0.020
 C48  plan-4  C11  0.020
 C48  plan-4  C12  0.020
 C48  plan-4  C13  0.020
 C48  plan-4  HN5  0.020
 C48  plan-5  C13  0.020
 C48  plan-5  C21  0.020
 C48  plan-5  C22  0.020
 C48  plan-5  C23  0.020
 C48  plan-5  N6   0.020
 C48  plan-5  O4   0.020

