# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:48:52 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: N~6~-({[(1S,2E)-cyclooct-2-en-1-yl]oxy}carbonyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)O[C@H]/1CCCCC\C=C/1)C(O)=O
#
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
 9U0  9U0  N~6~-({[(1S,2E)-cyclooct-2-en-1-yl]oxy}carbonyl)-L-lysine  peptide  46  21  .  2019-07-05  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_9U0
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
 9U0  C15   C  C1     0  -0.223  263.5701  34.5829  138.7481
 9U0  C17   C  CH2    0  -0.485  263.8862  34.8857  136.3287
 9U0  C20   C  CH2    0  -0.447  262.7455  37.3154  138.4754
 9U0  C21   C  CH2    0  -0.454  262.9494  36.6377  139.8408
 9U0  C     C  C      0   0.380  255.9108  32.8787  146.0675
 9U0  O     O  O      0  -0.602  256.0982  32.6712  147.2826
 9U0  CA    C  CH1    0  -0.212  256.2480  34.2916  145.5206
 9U0  N     N  NH2    0  -0.785  256.5332  35.3018  146.5306
 9U0  CB    C  CH2    0  -0.424  257.4137  34.2001  144.5325
 9U0  CG    C  CH2    0  -0.414  257.7200  35.5168  143.8279
 9U0  CD    C  CH2    0  -0.481  258.7356  35.4001  142.6966
 9U0  CE    C  CH2    0  -0.226  260.1174  34.9762  143.1704
 9U0  NZ    N  NH1    0  -0.686  261.0489  34.9969  142.0585
 9U0  C11   C  C      0   0.696  262.2843  34.4756  142.1595
 9U0  O12   O  O      0  -0.510  262.7035  33.9324  143.1619
 9U0  C14   C  CH1    0  -0.039  262.7160  35.1132  139.8368
 9U0  C16   C  C1     0  -0.207  263.0754  34.5132  137.5158
 9U0  C18   C  CH2    0  -0.431  263.6768  36.4094  136.1649
 9U0  C19   C  CH2    0  -0.442  263.9017  37.2415  137.4402
 9U0  HC15  H  H      0   0.242  264.6460  34.6341  138.8993
 9U0  H3    H  HCH2   0   0.232  264.9460  34.6826  136.5016
 9U0  H4    H  HCH2   0   0.235  263.5881  34.3712  135.4131
 9U0  H5    H  HCH2   0   0.239  262.5613  38.3708  138.6879
 9U0  H6    H  HCH2   0   0.227  261.8149  36.9553  138.0256
 9U0  H7    H  HCH2   0   0.238  262.2801  37.1079  140.5678
 9U0  H8    H  HCH2   0   0.237  263.9670  36.8261  140.1963
 9U0  HA    H  HCH1   0   0.203  255.3730  34.6375  144.9555
 9U0  H     H  HNH2   0   0.330  255.7197  35.4017  147.1259
 9U0  H2    H  HNH2   0   0.320  257.2470  34.9297  147.1474
 9U0  HB2   H  HCH2   0   0.214  257.1798  33.4389  143.7842
 9U0  HB3   H  HCH2   0   0.208  258.3015  33.8409  145.0670
 9U0  HG2   H  HCH2   0   0.215  258.0646  36.2562  144.5542
 9U0  HG3   H  HCH2   0   0.216  256.7899  35.9148  143.4104
 9U0  HD2   H  HCH2   0   0.232  258.8140  36.3700  142.1948
 9U0  HD3   H  HCH2   0   0.226  258.3767  34.6883  141.9464
 9U0  HE2   H  HCH2   0   0.238  260.0827  33.9699  143.5898
 9U0  HE3   H  HCH2   0   0.226  260.4546  35.6448  143.9697
 9U0  HZ    H  HNH1   0   0.415  260.7700  35.5310  141.2525
 9U0  H23   H  HCH1   0   0.245  261.6666  34.8944  139.6074
 9U0  H24   H  H      0   0.238  261.9954  34.5143  137.3823
 9U0  H26   H  HCH2   0   0.232  264.3535  36.7674  135.3842
 9U0  H27   H  HCH2   0   0.222  262.6641  36.5922  135.7928
 9U0  H28   H  HCH2   0   0.223  264.8235  36.9130  137.9301
 9U0  H29   H  HCH2   0   0.235  264.1061  38.2623  137.1091
 9U0  O13   O  O2     0  -0.480  263.0929  34.5356  141.0922
 9U0  OXT   O  OC    -1  -0.618  255.4866  32.0578  145.2265

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
 9U0  C17  C16   single  1.485  0.020  1.485
 9U0  C17  C18   single  1.547  0.020  1.547
 9U0  C16  C15   double  1.330  0.020  1.330
 9U0  C18  C19   single  1.539  0.020  1.539
 9U0  C15  C14   single  1.482  0.020  1.482
 9U0  C19  C20   single  1.554  0.020  1.554
 9U0  C14  O13   single  1.432  0.020  1.432
 9U0  C14  C21   single  1.542  0.020  1.542
 9U0  C20  C21   single  1.538  0.020  1.538
 9U0  O13  C11   single  1.340  0.020  1.340
 9U0  C11  NZ    single  1.345  0.020  1.345
 9U0  C11  O12   double  1.215  0.020  1.215
 9U0  NZ   CE    single  1.451  0.020  1.451
 9U0  CE   CD    single  1.521  0.020  1.521
 9U0  CD   CG    single  1.525  0.020  1.525
 9U0  CG   CB    single  1.524  0.020  1.524
 9U0  N    CA    single  1.458  0.019  1.458
 9U0  CB   CA    single  1.530  0.020  1.530
 9U0  CA   C     single  1.525  0.021  1.525
 9U0  C    O     deloc   1.231  0.020  1.231
 9U0  C    OXT   deloc   1.249  0.020  1.249
 9U0  C15  HC15  single  0.930  0.020  1.086
 9U0  C17  H3    single  0.939  0.020  1.096
 9U0  C17  H4    single  0.939  0.020  1.096
 9U0  C20  H5    single  0.939  0.020  1.096
 9U0  C20  H6    single  0.939  0.020  1.096
 9U0  C21  H7    single  0.939  0.020  1.096
 9U0  C21  H8    single  0.939  0.020  1.096
 9U0  CA   HA    single  0.970  0.020  0.970
 9U0  N    H     single  0.860  0.020  0.860
 9U0  N    H2    single  0.868  0.020  1.013
 9U0  CB   HB2   single  0.939  0.020  1.096
 9U0  CB   HB3   single  0.939  0.020  1.096
 9U0  CG   HG2   single  0.939  0.020  1.096
 9U0  CG   HG3   single  0.939  0.020  1.096
 9U0  CD   HD2   single  0.939  0.020  1.096
 9U0  CD   HD3   single  0.939  0.020  1.096
 9U0  CE   HE2   single  0.939  0.020  1.096
 9U0  CE   HE3   single  0.939  0.020  1.096
 9U0  NZ   HZ    single  0.868  0.020  1.013
 9U0  C14  H23   single  0.939  0.020  1.096
 9U0  C16  H24   single  0.930  0.020  1.086
 9U0  C18  H26   single  0.939  0.020  1.096
 9U0  C18  H27   single  0.939  0.020  1.096
 9U0  C19  H28   single  0.939  0.020  1.096
 9U0  C19  H29   single  0.939  0.020  1.096

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
 9U0  HC15  C15  C16  119.95  3.000
 9U0  HC15  C15  C14  116.82  3.000
 9U0  C16   C15  C14  119.03  3.000
 9U0  H4    C17  H3   108.05  3.000
 9U0  H4    C17  C18  109.79  3.000
 9U0  H3    C17  C18  109.34  3.000
 9U0  H4    C17  C16  113.77  3.000
 9U0  H3    C17  C16  110.88  3.000
 9U0  C18   C17  C16  104.94  3.000
 9U0  H6    C20  H5   104.74  3.000
 9U0  H6    C20  C19  110.08  3.000
 9U0  H5    C20  C19  107.53  3.000
 9U0  H6    C20  C21  109.43  3.000
 9U0  H5    C20  C21  105.98  3.000
 9U0  C19   C20  C21  118.16  3.000
 9U0  H8    C21  H7   106.20  3.000
 9U0  H8    C21  C14  108.17  3.000
 9U0  H7    C21  C14  109.50  3.000
 9U0  H8    C21  C20  109.62  3.000
 9U0  H7    C21  C20  108.62  3.000
 9U0  C14   C21  C20  114.40  3.000
 9U0  CA    C    O    120.80  1.700
 9U0  O     C    OXT  126.71  3.000
 9U0  CA    C    OXT  115.76  3.000
 9U0  HA    CA   CB   109.00  3.000
 9U0  HA    CA   N    110.00  3.000
 9U0  CB    CA   N    110.50  1.700
 9U0  HA    CA   C    109.00  3.000
 9U0  CB    CA   C    110.10  1.900
 9U0  N     CA   C    111.00  2.800
 9U0  H2    N    H    104.12  3.000
 9U0  H2    N    CA   107.76  3.000
 9U0  H     N    CA   114.00  3.000
 9U0  HB3   CB   HB2  106.19  3.000
 9U0  HB3   CB   CG   110.21  3.000
 9U0  HB2   CB   CG   109.16  3.000
 9U0  HB3   CB   CA   108.74  3.000
 9U0  HB2   CB   CA   108.70  3.000
 9U0  CG    CB   CA   113.56  3.000
 9U0  HG3   CG   HG2  106.00  3.000
 9U0  HG3   CG   CD   108.11  3.000
 9U0  HG2   CG   CD   109.57  3.000
 9U0  HG3   CG   CB   108.65  3.000
 9U0  HG2   CG   CB   109.93  3.000
 9U0  CD    CG   CB   114.25  3.000
 9U0  HD3   CD   HD2  106.58  3.000
 9U0  HD3   CD   CE   109.28  3.000
 9U0  HD2   CD   CE   108.94  3.000
 9U0  HD3   CD   CG   109.86  3.000
 9U0  HD2   CD   CG   108.66  3.000
 9U0  CE    CD   CG   113.29  3.000
 9U0  HE3   CE   HE2  107.00  3.000
 9U0  HE3   CE   NZ   110.66  3.000
 9U0  HE2   CE   NZ   109.17  3.000
 9U0  HE3   CE   CD   109.69  3.000
 9U0  HE2   CE   CD   110.36  3.000
 9U0  NZ    CE   CD   109.92  3.000
 9U0  HZ    NZ   C11  121.37  3.000
 9U0  HZ    NZ   CE   116.33  3.000
 9U0  C11   NZ   CE   121.79  3.000
 9U0  O13   C11  O12  117.96  3.000
 9U0  O12   C11  NZ   123.53  3.000
 9U0  O13   C11  NZ   118.49  3.000
 9U0  H23   C14  O13  110.78  3.000
 9U0  H23   C14  C21  110.04  3.000
 9U0  O13   C14  C21  110.89  3.000
 9U0  H23   C14  C15  109.06  3.000
 9U0  C21   C14  C15  105.57  3.000
 9U0  O13   C14  C15  110.36  3.000
 9U0  H24   C16  C17  116.33  3.000
 9U0  H24   C16  C15  118.87  3.000
 9U0  C17   C16  C15  121.64  3.000
 9U0  H27   C18  H26  105.97  3.000
 9U0  H27   C18  C19  109.07  3.000
 9U0  H26   C18  C19  108.91  3.000
 9U0  H27   C18  C17  109.02  3.000
 9U0  H26   C18  C17  108.32  3.000
 9U0  C19   C18  C17  115.15  3.000
 9U0  H29   C19  H28  104.99  3.000
 9U0  H29   C19  C18  106.34  3.000
 9U0  H28   C19  C18  109.37  3.000
 9U0  H29   C19  C20  107.26  3.000
 9U0  H28   C19  C20  110.05  3.000
 9U0  C18   C19  C20  117.97  3.000
 9U0  C14   O13  C11  123.86  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
 9U0  Var_01  CD   CG   CB  CA  -171.46  30.0  1
 9U0  Var_02  CE   CD   CG  CB   -64.20  30.0  1
 9U0  Var_03  NZ   CE   CD  CG  -175.24  30.0  1
 9U0  Var_04  C11  NZ   CE  CD  -169.85  30.0  1
 9U0  Var_05  O13  C11  NZ  CE  -179.72  30.0  1

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
 9U0  chir_01  CA   N    CB   C    negativ
 9U0  chir_02  C14  C15  O13  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
 9U0  plan-1  C    0.020
 9U0  plan-1  O    0.020
 9U0  plan-1  CA   0.020
 9U0  plan-1  OXT  0.020
 9U0  plan-2  NZ   0.020
 9U0  plan-2  C11  0.020
 9U0  plan-2  O12  0.020
 9U0  plan-2  O13  0.020

