# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 11:21:41 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: N~6~-(2-phenylethyl)-N~6~-propan-2-yl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N(CCCC[C@H](N)C(O)=O)CCc1ccccc1
#
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
 Y57  Y57  "N~6~-(2-phenylethyl)-N~6~-propan-2-yl-L-lysine"  L-peptide  48  21  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_Y57
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
 Y57  C10  C  CH1    0  -0.104   4.7567  -0.5467  32.2202
 Y57  N    N  NH2    0  -0.794  -0.0167   1.3517  37.3739
 Y57  CA   C  CH1    0  -0.188  -0.3094   1.8004  36.0132
 Y57  C    C  C      0   0.384  -1.5436   1.1232  35.3721
 Y57  O    O  O      0  -0.611  -1.6621  -0.1048  35.5726
 Y57  CB   C  CH2    0  -0.422   0.9282   1.5540  35.1472
 Y57  CG   C  CH2    0  -0.427   0.8217   2.0764  33.7179
 Y57  CD   C  CH2    0  -0.439   2.1434   2.0540  32.9544
 Y57  CE   C  CH2    0  -0.266   2.7016   0.6488  32.7573
 Y57  C01  C  CR6    0   0.128   4.1339   2.6828  28.7838
 Y57  C02  C  CR16   0  -0.308   2.9794   3.3682  28.4085
 Y57  C03  C  CR16   0  -0.239   2.7183   3.6502  27.0743
 Y57  C04  C  CR16   0  -0.272   3.6112   3.2470  26.0893
 Y57  C05  C  CR16   0  -0.238   4.7633   2.5598  26.4494
 Y57  C06  C  CR16   0  -0.310   5.0188   2.2801  27.7855
 Y57  C07  C  CH2    0  -0.512   4.3816   2.3289  30.2216
 Y57  C08  C  CH2    0  -0.294   3.7362   0.9857  30.5826
 Y57  C11  C  CH3    0  -0.659   6.1708  -0.3437  31.6884
 Y57  C12  C  CH3    0  -0.666   4.1674  -1.8630  31.7057
 Y57  NZ   N  NT     0  -0.412   3.9259   0.6294  31.9790
 Y57  H1   H  HCH1   0   0.221   4.8374  -0.6298  33.3093
 Y57  H2   H  HNH2   0   0.331  -0.7902   1.6104  37.9760
 Y57  H    H  HNH2   0   0.320  -0.0306   0.3371  37.3648
 Y57  HA   H  HCH1   0   0.192  -0.4834   2.8811  36.0518
 Y57  HB2  H  HCH2   0   0.205   1.1365   0.4786  35.1405
 Y57  HB3  H  HCH2   0   0.207   1.7854   2.0275  35.6380
 Y57  HG2  H  HCH2   0   0.214   0.4496   3.1049  33.7421
 Y57  HG3  H  HCH2   0   0.212   0.0782   1.5012  33.1589
 Y57  HD2  H  HCH2   0   0.206   2.8878   2.6622  33.4785
 Y57  HD3  H  HCH2   0   0.225   1.9878   2.5292  31.9810
 Y57  HE2  H  HCH2   0   0.183   1.9110   0.0161  32.3179
 Y57  HE3  H  HCH2   0   0.223   2.9263   0.2157  33.7356
 Y57  H15  H  HCR6   0   0.245   2.2795   3.6869  29.1731
 Y57  H16  H  HCR6   0   0.249   1.8180   4.1873  26.8036
 Y57  H17  H  HCR6   0   0.250   3.4112   3.4681  25.0487
 Y57  H18  H  HCR6   0   0.249   5.4654   2.2427  25.6887
 Y57  H19  H  HCR6   0   0.243   5.9209   1.7445  28.0595
 Y57  H20  H  HCH2   0   0.241   5.4543   2.2700  30.4192
 Y57  H21  H  HCH2   0   0.240   3.9797   3.1049  30.8768
 Y57  H22  H  HCH2   0   0.229   2.6679   1.0301  30.3396
 Y57  H23  H  HCH2   0   0.234   4.1464   0.2187  29.9179
 Y57  H24  H  HCH3   0   0.225   6.6065   0.5784  32.0748
 Y57  H25  H  HCH3   0   0.229   6.8090  -1.1735  31.9945
 Y57  H26  H  HCH3   0   0.217   6.2001  -0.3003  30.5976
 Y57  H27  H  HCH3   0   0.229   3.1684  -2.0424  32.1062
 Y57  H28  H  HCH3   0   0.215   4.0996  -1.8768  30.6158
 Y57  H29  H  HCH3   0   0.224   4.7957  -2.7045  32.0025
 Y57  OXT  O  OC    -1  -0.613  -2.2994   1.8430  34.6878

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
 Y57  C04  C05  aromatic  1.389  0.020  1.389
 Y57  C04  C03  aromatic  1.389  0.020  1.389
 Y57  C05  C06  aromatic  1.389  0.020  1.389
 Y57  C03  C02  aromatic  1.388  0.020  1.388
 Y57  C06  C01  aromatic  1.394  0.020  1.394
 Y57  C02  C01  aromatic  1.394  0.020  1.394
 Y57  C01  C07  single    1.501  0.020  1.501
 Y57  C07  C08  single    1.533  0.020  1.533
 Y57  C08  NZ   single    1.454  0.020  1.454
 Y57  C12  C10  single    1.531  0.020  1.531
 Y57  C11  C10  single    1.524  0.020  1.524
 Y57  NZ   C10  single    1.460  0.020  1.460
 Y57  NZ   CE   single    1.451  0.020  1.451
 Y57  CE   CD   single    1.525  0.020  1.525
 Y57  CD   CG   single    1.527  0.020  1.527
 Y57  CG   CB   single    1.526  0.020  1.526
 Y57  CB   CA   single    1.530  0.020  1.530
 Y57  C    O    deloc     1.231  0.020  1.231
 Y57  C    CA   single    1.525  0.021  1.525
 Y57  CA   N    single    1.458  0.019  1.458
 Y57  C10  H1   single    0.970  0.020  1.090
 Y57  N    H2   single    0.890  0.020  1.040
 Y57  N    H    single    0.860  0.020  0.860
 Y57  CA   HA   single    0.970  0.020  0.970
 Y57  CB   HB2  single    0.970  0.020  1.090
 Y57  CB   HB3  single    0.970  0.020  1.090
 Y57  CG   HG2  single    0.970  0.020  1.090
 Y57  CG   HG3  single    0.970  0.020  1.090
 Y57  CD   HD2  single    0.970  0.020  1.090
 Y57  CD   HD3  single    0.970  0.020  1.090
 Y57  CE   HE2  single    0.970  0.020  1.090
 Y57  CE   HE3  single    0.970  0.020  1.090
 Y57  C02  H15  single    0.930  0.020  1.080
 Y57  C03  H16  single    0.930  0.020  1.080
 Y57  C04  H17  single    0.930  0.020  1.080
 Y57  C05  H18  single    0.930  0.020  1.080
 Y57  C06  H19  single    0.930  0.020  1.080
 Y57  C07  H20  single    0.970  0.020  1.090
 Y57  C07  H21  single    0.970  0.020  1.090
 Y57  C08  H22  single    0.970  0.020  1.090
 Y57  C08  H23  single    0.970  0.020  1.090
 Y57  C11  H24  single    0.970  0.020  1.090
 Y57  C11  H25  single    0.970  0.020  1.090
 Y57  C11  H26  single    0.970  0.020  1.090
 Y57  C12  H27  single    0.970  0.020  1.090
 Y57  C12  H28  single    0.970  0.020  1.090
 Y57  C12  H29  single    0.970  0.020  1.090
 Y57  C    OXT  deloc     1.248  0.020  1.248

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
 Y57  H1   C10  NZ   105.50  3.000
 Y57  H1   C10  C12  107.29  3.000
 Y57  NZ   C10  C12  114.71  3.000
 Y57  H1   C10  C11  106.78  3.000
 Y57  NZ   C10  C11  111.28  3.000
 Y57  C12  C10  C11  110.75  3.000
 Y57  H    N    H2   104.48  3.000
 Y57  H    N    CA   114.00  3.000
 Y57  H2   N    CA   108.76  3.000
 Y57  HA   CA   CB   109.00  3.000
 Y57  HA   CA   C    109.00  3.000
 Y57  CB   CA   C    110.10  1.900
 Y57  HA   CA   N    110.00  3.000
 Y57  C    CA   N    111.00  2.800
 Y57  CB   CA   N    110.50  1.700
 Y57  OXT  C    O    126.67  3.000
 Y57  OXT  C    CA   117.26  3.000
 Y57  O    C    CA   120.80  1.700
 Y57  HB3  CB   HB2  106.16  3.000
 Y57  HB3  CB   CG   109.05  3.000
 Y57  HB2  CB   CG   110.11  3.000
 Y57  HB3  CB   CA   108.04  3.000
 Y57  HB2  CB   CA   108.38  3.000
 Y57  CG   CB   CA   114.74  3.000
 Y57  HG3  CG   HG2  105.94  3.000
 Y57  HG3  CG   CD   108.98  3.000
 Y57  HG2  CG   CD   108.62  3.000
 Y57  HG3  CG   CB   110.25  3.000
 Y57  HG2  CG   CB   108.97  3.000
 Y57  CD   CG   CB   113.77  3.000
 Y57  HD3  CD   HD2  106.33  3.000
 Y57  HD3  CD   CE   109.71  3.000
 Y57  HD2  CD   CE   108.96  3.000
 Y57  HD3  CD   CG   108.38  3.000
 Y57  HD2  CD   CG   109.95  3.000
 Y57  CE   CD   CG   113.27  3.000
 Y57  HE3  CE   HE2  106.04  3.000
 Y57  HE3  CE   NZ   107.53  3.000
 Y57  HE2  CE   NZ   112.53  3.000
 Y57  HE3  CE   CD   108.94  3.000
 Y57  HE2  CE   CD   108.51  3.000
 Y57  NZ   CE   CD   112.99  3.000
 Y57  C07  C01  C06  120.88  3.000
 Y57  C07  C01  C02  120.68  3.000
 Y57  C06  C01  C02  118.37  3.000
 Y57  H15  C02  C03  119.77  3.000
 Y57  H15  C02  C01  119.28  3.000
 Y57  C03  C02  C01  120.95  3.000
 Y57  H16  C03  C04  120.08  3.000
 Y57  H16  C03  C02  119.82  3.000
 Y57  C04  C03  C02  120.10  3.000
 Y57  H17  C04  C05  120.23  3.000
 Y57  H17  C04  C03  120.23  3.000
 Y57  C05  C04  C03  119.53  3.000
 Y57  H18  C05  C06  119.84  3.000
 Y57  H18  C05  C04  120.05  3.000
 Y57  C06  C05  C04  120.11  3.000
 Y57  H19  C06  C05  119.72  3.000
 Y57  H19  C06  C01  119.34  3.000
 Y57  C05  C06  C01  120.94  3.000
 Y57  H21  C07  H20  106.92  3.000
 Y57  H21  C07  C08  109.04  3.000
 Y57  H20  C07  C08  108.88  3.000
 Y57  H21  C07  C01  110.27  3.000
 Y57  H20  C07  C01  110.36  3.000
 Y57  C08  C07  C01  111.26  3.000
 Y57  H23  C08  H22  105.00  3.000
 Y57  H23  C08  NZ   111.26  3.000
 Y57  H22  C08  NZ   110.49  3.000
 Y57  H23  C08  C07  108.25  3.000
 Y57  H22  C08  C07  108.81  3.000
 Y57  NZ   C08  C07  112.71  3.000
 Y57  H26  C11  H25  107.15  3.000
 Y57  H26  C11  H24  108.03  3.000
 Y57  H25  C11  H24  108.06  3.000
 Y57  H26  C11  C10  112.25  3.000
 Y57  H25  C11  C10  110.10  3.000
 Y57  H24  C11  C10  111.07  3.000
 Y57  H29  C12  H28  107.31  3.000
 Y57  H29  C12  H27  107.50  3.000
 Y57  H28  C12  H27  107.90  3.000
 Y57  H29  C12  C10  110.48  3.000
 Y57  H28  C12  C10  111.72  3.000
 Y57  H27  C12  C10  111.73  3.000
 Y57  C08  NZ   CE   113.70  3.000
 Y57  CE   NZ   C10  113.73  3.000
 Y57  C08  NZ   C10  115.49  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
 Y57  CONST_01  C04  C05  C06  C01     0.00   0.0  0
 Y57  CONST_02  C04  C03  C02  C01     0.00   0.0  0
 Y57  CONST_03  C05  C04  C03  C02     0.00   0.0  0
 Y57  CONST_04  C05  C06  C01  C02     0.00   0.0  0
 Y57  CONST_05  C06  C05  C04  C03     0.00   0.0  0
 Y57  CONST_06  C06  C01  C02  C03     0.00   0.0  0
 Y57  CONST_07  C07  C01  C02  C03   180.00   0.0  0
 Y57  CONST_08  C07  C01  C06  C05   180.00   0.0  0
 Y57  CONST_09  H18  C05  C06  C01   180.00   0.0  0
 Y57  CONST_10  H16  C03  C02  C01   180.00   0.0  0
 Y57  CONST_11  H17  C04  C03  C02   180.00   0.0  0
 Y57  CONST_12  H19  C06  C01  C02   180.00   0.0  0
 Y57  CONST_13  H18  C05  C04  C03   180.00   0.0  0
 Y57  CONST_14  H19  C06  C05  C04   180.00   0.0  0
 Y57  CONST_15  H15  C02  C03  C04   180.00   0.0  0
 Y57  CONST_16  H16  C03  C04  C05   180.00   0.0  0
 Y57  CONST_17  H17  C04  C05  C06   180.00   0.0  0
 Y57  CONST_18  H15  C02  C01  C06   180.00   0.0  0
 Y57  Var_01    C08  C07  C01  C02    87.17  30.0  2
 Y57  Var_02    C08  C07  C01  C06   -89.77  30.0  2
 Y57  Var_03    H20  C07  C01  C02  -151.85  30.0  2
 Y57  Var_04    H21  C07  C01  C02   -33.95  30.0  2
 Y57  Var_05    H20  C07  C01  C06    31.21  30.0  2
 Y57  Var_06    H21  C07  C01  C06   149.11  30.0  2
 Y57  Var_07    NZ   C08  C07  C01  -178.43  30.0  3
 Y57  Var_08    H22  C08  C07  C01   -55.52  30.0  3
 Y57  Var_09    H23  C08  C07  C01    58.07  30.0  3
 Y57  Var_10    C07  C08  NZ   C10  -114.01  30.0  2
 Y57  Var_11    CD   CE   NZ   C10   156.38  30.0  3
 Y57  Var_12    CD   CG   CB   CA    169.34  30.0  1
 Y57  Var_13    CE   CD   CG   CB     63.18  30.0  1
 Y57  Var_14    NZ   CE   CD   CG    177.38  30.0  3
 Y57  Var_15    C08  NZ   CE   CD    -68.68  30.0  1
 Y57  Var_16    C07  C08  NZ   CE    111.87  30.0  2
 Y57  Var_17    C12  C10  NZ   CE     68.77  30.0  3
 Y57  Var_18    C11  C10  NZ   CE   -164.53  30.0  3
 Y57  Var_19    C12  C10  NZ   C08   -65.34  30.0  3
 Y57  Var_20    C11  C10  NZ   C08    61.37  30.0  3
 Y57  Var_21    H22  C08  NZ   C10   124.01  30.0  2
 Y57  Var_22    H23  C08  NZ   C10     7.79  30.0  2
 Y57  Var_23    HE2  CE   NZ   C10   -80.29  30.0  3
 Y57  Var_24    HE3  CE   NZ   C10    36.12  30.0  3
 Y57  Var_25    HG2  CG   CB   CA     47.98  30.0  1
 Y57  Var_26    HG3  CG   CB   CA    -67.89  30.0  1
 Y57  Var_27    HD2  CD   CG   CB    -58.99  30.0  1
 Y57  Var_28    HD3  CD   CG   CB   -174.83  30.0  1
 Y57  Var_29    HE2  CE   CD   CG     51.85  30.0  3
 Y57  Var_30    HE3  CE   CD   CG    -63.18  30.0  3
 Y57  Var_31    HB2  CB   CG   CD    -68.09  30.0  3
 Y57  Var_32    HB3  CB   CG   CD     48.01  30.0  3
 Y57  Var_33    H22  C08  NZ   CE    -10.10  30.0  2
 Y57  Var_34    H23  C08  NZ   CE   -126.33  30.0  2
 Y57  Var_35    H1   C10  NZ   CE    -49.09  30.0  3
 Y57  Var_36    HG2  CG   CD   CE   -175.27  30.0  3
 Y57  Var_37    HG3  CG   CD   CE    -60.29  30.0  3
 Y57  Var_38    H1   C10  NZ   C08   176.81  30.0  3
 Y57  Var_39    HE2  CE   NZ   C08    54.65  30.0  3
 Y57  Var_40    HE3  CE   NZ   C08   171.06  30.0  3
 Y57  Var_41    H27  C12  C10  C11   177.91  30.0  3
 Y57  Var_42    H28  C12  C10  C11   -61.09  30.0  3
 Y57  Var_43    H29  C12  C10  C11    58.29  30.0  3
 Y57  Var_44    H24  C11  C10  C12  -178.36  30.0  3
 Y57  Var_45    H25  C11  C10  C12   -58.70  30.0  3
 Y57  Var_46    H26  C11  C10  C12    60.57  30.0  3
 Y57  Var_47    H20  C07  C08  NZ     59.73  30.0  1
 Y57  Var_48    H21  C07  C08  NZ    -56.60  30.0  1
 Y57  Var_49    H27  C12  C10  NZ    -55.10  30.0  3
 Y57  Var_50    H28  C12  C10  NZ     65.89  30.0  3
 Y57  Var_51    H29  C12  C10  NZ   -174.73  30.0  3
 Y57  Var_52    H24  C11  C10  NZ     52.79  30.0  3
 Y57  Var_53    H25  C11  C10  NZ    172.45  30.0  3
 Y57  Var_54    H26  C11  C10  NZ    -68.28  30.0  3
 Y57  Var_55    HD2  CD   CE   NZ    -59.91  30.0  3
 Y57  Var_56    HD3  CD   CE   NZ     56.13  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
 Y57  chir_01  CA  CB  C  N  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
 Y57  plan-1  C01  0.020
 Y57  plan-1  C02  0.020
 Y57  plan-1  C03  0.020
 Y57  plan-1  C04  0.020
 Y57  plan-1  C05  0.020
 Y57  plan-1  C06  0.020
 Y57  plan-1  C07  0.020
 Y57  plan-1  H15  0.020
 Y57  plan-1  H16  0.020
 Y57  plan-1  H17  0.020
 Y57  plan-1  H18  0.020
 Y57  plan-1  H19  0.020
 Y57  plan-2  CA   0.020
 Y57  plan-2  C    0.020
 Y57  plan-2  O    0.020
 Y57  plan-2  OXT  0.020

