# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:50:51 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: N~6~-({[(1R,8S,9s)-bicyclo[6.1.0]non-4-yn-9-yl]methoxy}carbonyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCC1[C@H]2CCC#CCC[C@@H]12)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
 9U9  9U9  N~6~-({[(1R,8S,9s)-bicyclo[6.1.0]non-4-yn-9-yl]methoxy}carbonyl)-L-lysine  peptide  48  23  .  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_9U9
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
 9U9  C15   C  CH1    0  -0.299  265.2626  47.7843  139.4510
 9U9  C17   C  CH2    0  -0.486  264.1577  50.2050  139.7296
 9U9  C20   C  CSP    0   0.006  266.3922  51.4305  137.9223
 9U9  C21   C  CH2    0  -0.459  267.2532  49.4053  138.8317
 9U9  C22   C  CH1    0  -0.216  265.9826  48.6664  138.4676
 9U9  C     C  C      0   0.394  259.4093  50.0786  146.9053
 9U9  CA    C  CH1    0  -0.213  260.3141  48.8217  146.7663
 9U9  CB    C  CH2    0  -0.434  259.8094  47.8104  145.7308
 9U9  CG    C  CH2    0  -0.426  260.1390  48.1060  144.2697
 9U9  CD    C  CH2    0  -0.430  261.6209  47.9749  143.9381
 9U9  CE    C  CH2    0  -0.272  261.8715  48.1103  142.4416
 9U9  C11   C  C      0   0.693  263.7895  46.6929  141.9270
 9U9  C14   C  CH2    0  -0.217  265.7707  47.6449  140.8660
 9U9  C16   C  CH1    0  -0.202  264.5768  49.0102  138.9002
 9U9  C18   C  CH2    0  -0.556  263.9763  51.4851  138.8843
 9U9  C19   C  CSP    0   0.026  265.2606  51.7038  138.2324
 9U9  C23   C  CH2    0  -0.560  267.5655  50.5669  137.8632
 9U9  N     N  NH2    0  -0.794  260.5579  48.1236  148.0285
 9U9  NZ    N  NH1    0  -0.662  263.2528  47.9187  142.0466
 9U9  O12   O  O      0  -0.503  263.1843  45.6611  142.1349
 9U9  O13   O  O2     0  -0.477  265.0815  46.6090  141.5716
 9U9  H15   H  HCH1   0   0.265  264.9238  46.8334  139.0505
 9U9  H171  H  HCH2   0   0.249  263.2051  49.9812  140.2173
 9U9  H172  H  HCH2   0   0.235  264.8819  50.4191  140.5191
 9U9  H211  H  HCH2   0   0.245  268.0881  48.6984  138.8161
 9U9  H212  H  HCH2   0   0.234  267.2063  49.8092  139.8455
 9U9  H22   H  HCH1   0   0.249  266.0341  48.2527  137.4637
 9U9  HA    H  HCH1   0   0.212  261.2908  49.1981  146.4284
 9U9  HB2   H  HCH2   0   0.213  258.7264  47.6929  145.8397
 9U9  HB3   H  HCH2   0   0.206  260.2436  46.8360  145.9795
 9U9  HG2   H  HCH2   0   0.221  259.7760  49.1007  144.0081
 9U9  HG3   H  HCH2   0   0.208  259.5844  47.3996  143.6432
 9U9  HD2   H  HCH2   0   0.217  261.9824  46.9990  144.2743
 9U9  HD3   H  HCH2   0   0.219  262.2072  48.7278  144.4720
 9U9  HE2   H  HCH2   0   0.244  261.5790  49.1048  142.1006
 9U9  HE3   H  HCH2   0   0.236  261.2493  47.4001  141.8944
 9U9  H141  H  HCH2   0   0.265  266.8056  47.3014  140.8580
 9U9  H142  H  HCH2   0   0.232  265.7677  48.5856  141.4262
 9U9  H16   H  HCH1   0   0.248  263.8330  48.7762  138.1428
 9U9  H181  H  HCH2   0   0.265  263.6826  52.3197  139.5236
 9U9  H182  H  HCH2   0   0.256  263.1764  51.3493  138.1523
 9U9  H231  H  HCH2   0   0.263  268.4825  51.0764  138.1648
 9U9  H232  H  HCH2   0   0.255  267.7306  50.1911  136.8503
 9U9  H     H  HNH2   0   0.326  260.6711  48.8315  148.7449
 9U9  H2    H  HNH2   0   0.321  259.7032  47.6436  148.2933
 9U9  HZ    H  HNH1   0   0.411  263.8395  48.7352  142.0258
 9U9  OXT   O  OC    -1  -0.609  259.3242  50.5796  148.0458
 9U9  O     O  O      0  -0.599  258.8695  50.5151  145.8676

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
 9U9  C23  C21   single  1.544  0.020  1.544
 9U9  C23  C20   single  1.458  0.020  1.458
 9U9  C21  C22   single  1.514  0.020  1.514
 9U9  C20  C19   triple  1.205  0.020  1.205
 9U9  C22  C15   single  1.505  0.020  1.505
 9U9  C22  C16   single  1.511  0.020  1.511
 9U9  C19  C18   single  1.457  0.020  1.457
 9U9  C15  C16   single  1.509  0.020  1.509
 9U9  C15  C14   single  1.510  0.020  1.510
 9U9  C16  C17   single  1.514  0.020  1.514
 9U9  C18  C17   single  1.545  0.020  1.545
 9U9  C14  O13   single  1.430  0.020  1.430
 9U9  O13  C11   single  1.343  0.020  1.343
 9U9  CE   NZ    single  1.449  0.020  1.449
 9U9  CE   CD    single  1.523  0.020  1.523
 9U9  C11  NZ    single  1.344  0.020  1.344
 9U9  C11  O12   double  1.214  0.020  1.214
 9U9  CD   CG    single  1.524  0.020  1.524
 9U9  CG   CB    single  1.527  0.020  1.527
 9U9  O    C     deloc   1.231  0.020  1.231
 9U9  CB   CA    single  1.521  0.033  1.521
 9U9  CA   C     single  1.525  0.021  1.525
 9U9  CA   N     single  1.458  0.019  1.458
 9U9  C    OXT   deloc   1.249  0.020  1.249
 9U9  C15  H15   single  0.970  0.020  1.090
 9U9  C17  H171  single  0.970  0.020  1.090
 9U9  C17  H172  single  0.970  0.020  1.090
 9U9  C21  H211  single  0.970  0.020  1.090
 9U9  C21  H212  single  0.970  0.020  1.090
 9U9  C22  H22   single  0.970  0.020  1.090
 9U9  CA   HA    single  0.970  0.020  0.970
 9U9  CB   HB2   single  0.970  0.020  1.090
 9U9  CB   HB3   single  0.970  0.020  1.090
 9U9  CG   HG2   single  0.970  0.020  1.090
 9U9  CG   HG3   single  0.970  0.020  1.090
 9U9  CD   HD2   single  0.970  0.020  1.090
 9U9  CD   HD3   single  0.970  0.020  1.090
 9U9  CE   HE2   single  0.970  0.020  1.090
 9U9  CE   HE3   single  0.970  0.020  1.090
 9U9  C14  H141  single  0.970  0.020  1.090
 9U9  C14  H142  single  0.970  0.020  1.090
 9U9  C16  H16   single  0.970  0.020  1.090
 9U9  C18  H181  single  0.970  0.020  1.090
 9U9  C18  H182  single  0.970  0.020  1.090
 9U9  C23  H231  single  0.970  0.020  1.090
 9U9  C23  H232  single  0.970  0.020  1.090
 9U9  N    H     single  0.860  0.020  0.860
 9U9  N    H2    single  0.890  0.020  1.040
 9U9  NZ   HZ    single  0.860  0.020  1.020

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
 9U9  H15   C15  C16   115.78  3.000
 9U9  H15   C15  C14   111.70  3.000
 9U9  C16   C15  C14   124.76  3.000
 9U9  H15   C15  C22   114.94  3.000
 9U9  C14   C15  C22   120.38  3.000
 9U9  C16   C15  C22    60.17  3.000
 9U9  H172  C17  H171  107.18  3.000
 9U9  H172  C17  C18   108.11  3.000
 9U9  H171  C17  C18   108.14  3.000
 9U9  H172  C17  C16   111.54  3.000
 9U9  H171  C17  C16   108.91  3.000
 9U9  C18   C17  C16   112.75  3.000
 9U9  C23   C20  C19   180.00  3.000
 9U9  H212  C21  H211  106.55  3.000
 9U9  H212  C21  C23   108.22  3.000
 9U9  H211  C21  C23   108.83  3.000
 9U9  H212  C21  C22   111.56  3.000
 9U9  H211  C21  C22   108.76  3.000
 9U9  C23   C21  C22   112.71  3.000
 9U9  H22   C22  C16   113.28  3.000
 9U9  H22   C22  C21   111.60  3.000
 9U9  C16   C22  C21   126.94  3.000
 9U9  H22   C22  C15   113.78  3.000
 9U9  C16   C22  C15    60.06  3.000
 9U9  C21   C22  C15   122.04  3.000
 9U9  O     C    OXT   126.12  3.000
 9U9  OXT   C    CA    120.80  1.700
 9U9  O     C    CA    120.80  1.700
 9U9  HA    CA   N     110.00  3.000
 9U9  HA    CA   CB    109.00  3.000
 9U9  N     CA   CB    110.40  1.500
 9U9  HA    CA   C     110.00  3.000
 9U9  N     CA   C     111.00  2.800
 9U9  CB    CA   C     110.50  1.500
 9U9  HB3   CB   HB2   105.91  3.000
 9U9  HB3   CB   CG    107.69  3.000
 9U9  HB2   CB   CG    109.24  3.000
 9U9  HB3   CB   CA    107.64  3.000
 9U9  HB2   CB   CA    109.23  3.000
 9U9  CG    CB   CA    116.59  3.000
 9U9  HG3   CG   HG2   106.41  3.000
 9U9  HG3   CG   CD    108.20  3.000
 9U9  HG2   CG   CD    110.48  3.000
 9U9  HG3   CG   CB    108.26  3.000
 9U9  HG2   CG   CB    109.53  3.000
 9U9  CD    CG   CB    113.67  3.000
 9U9  HD3   CD   HD2   106.68  3.000
 9U9  HD3   CD   CE    109.28  3.000
 9U9  HD2   CD   CE    109.08  3.000
 9U9  HD3   CD   CG    110.85  3.000
 9U9  HD2   CD   CG    109.35  3.000
 9U9  CE    CD   CG    111.47  3.000
 9U9  HE3   CE   HE2   106.47  3.000
 9U9  HE3   CE   NZ    108.71  3.000
 9U9  HE2   CE   NZ    106.90  3.000
 9U9  HE3   CE   CD    109.93  3.000
 9U9  HE2   CE   CD    110.11  3.000
 9U9  NZ    CE   CD    114.38  3.000
 9U9  O13   C11  O12   118.16  3.000
 9U9  O12   C11  NZ    124.12  3.000
 9U9  O13   C11  NZ    117.71  3.000
 9U9  H142  C14  H141  106.08  3.000
 9U9  H142  C14  O13   111.63  3.000
 9U9  H141  C14  O13   103.46  3.000
 9U9  H142  C14  C15   113.53  3.000
 9U9  H141  C14  C15   109.97  3.000
 9U9  O13   C14  C15   111.54  3.000
 9U9  H16   C16  C22   112.84  3.000
 9U9  H16   C16  C17   111.24  3.000
 9U9  C22   C16  C17   126.46  3.000
 9U9  H16   C16  C15   112.99  3.000
 9U9  C17   C16  C15   124.55  3.000
 9U9  C22   C16  C15    59.77  3.000
 9U9  H182  C18  H181  106.88  3.000
 9U9  H182  C18  C19   111.36  3.000
 9U9  H181  C18  C19   112.62  3.000
 9U9  H182  C18  C17   110.46  3.000
 9U9  H181  C18  C17   110.16  3.000
 9U9  C19   C18  C17   105.41  3.000
 9U9  C18   C19  C20   180.00  3.000
 9U9  H232  C23  H231  106.84  3.000
 9U9  H232  C23  C21   110.68  3.000
 9U9  H231  C23  C21   110.35  3.000
 9U9  H232  C23  C20   111.27  3.000
 9U9  H231  C23  C20   112.85  3.000
 9U9  C21   C23  C20   104.91  3.000
 9U9  H2    N    H     103.88  3.000
 9U9  H2    N    CA    108.08  3.000
 9U9  H     N    CA    114.00  3.000
 9U9  HZ    NZ   C11   120.39  3.000
 9U9  HZ    NZ   CE    117.02  3.000
 9U9  C11   NZ   CE    121.71  3.000
 9U9  C14   O13  C11   123.30  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
 9U9  Var_01  H16  C16  C15  C22   103.94  30.0  1
 9U9  Var_02  H22  C22  C15  C16  -104.16  30.0  1
 9U9  Var_03  O13  C14  C15  C22  -170.73  30.0  3
 9U9  Var_04  CD   CG   CB   CA     68.81  30.0  1
 9U9  Var_05  CE   CD   CG   CB    172.98  30.0  1
 9U9  Var_06  NZ   CE   CD   CG   -176.62  30.0  2
 9U9  Var_07  C11  NZ   CE   CD     79.22  30.0  3
 9U9  Var_08  O13  C11  NZ   CE   -179.21  30.0  2
 9U9  Var_09  NZ   C11  O13  C14   -23.29  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
 9U9  chir_03  CA   CB   C    N    negativ
 9U9  chir_04  C15  C22  C16  C14  both
 9U9  chir_05  C22  C21  C15  C16  both
 9U9  chir_06  C16  C17  C15  C22  both

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
 9U9  plan-1  C    0.020
 9U9  plan-1  CA   0.020
 9U9  plan-1  OXT  0.020
 9U9  plan-1  O    0.020
 9U9  plan-2  C11  0.020
 9U9  plan-2  NZ   0.020
 9U9  plan-2  O12  0.020
 9U9  plan-2  O13  0.020

