# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:48:23 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{S})-2-azanyl-6-(trimethylsilylmethoxycarbonylamino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Si](C)(C)COC(=O)NCCCC[C@H](N)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
 9VF  9VF  '(2~{S})-2-azanyl-6-(trimethylsilylmethoxycarbonylamino)hexanoic acid'  peptide  41  18  .  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_9VF
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
 9VF  CE   C   CH2    0  -0.271  125.3279  32.5888  14.4614
 9VF  CB   C   CH2    0  -0.432  123.1450  33.5000  17.5602
 9VF  C1   C   CH3    0  -0.971  130.6486  34.0752  11.2889
 9VF  C3   C   CH3    0  -0.973  129.7195  31.1354  10.9246
 9VF  C4   C   CH3    0  -0.982  127.6474  33.4092  11.1340
 9VF  C5   C   CH2    0  -0.507  129.4459  32.5740  13.6110
 9VF  C7   C   C      0   0.695  127.4554  31.3832  14.3756
 9VF  CG   C   CH2    0  -0.428  125.0166  32.9706  15.9025
 9VF  CD   C   CH2    0  -0.430  123.5142  33.0678  16.1429
 9VF  CA   C   CH1    0  -0.213  123.4197  34.9712  17.8970
 9VF  C    C   C      0   0.394  122.2907  35.9329  17.4300
 9VF  NZ   N   NH1    0  -0.667  126.7444  32.5068  14.1722
 9VF  N    N   NH2    0  -0.796  123.7561  35.0889  19.3161
 9VF  O6   O   O2     0  -0.467  128.7674  31.4167  14.1217
 9VF  O8   O   O      0  -0.513  126.9770  30.3367  14.7686
 9VF  OXT  O   OC    -1  -0.609  122.0896  36.9435  18.1354
 9VF  O    O   O      0  -0.600  121.6988  35.6487  16.3684
 9VF  SI   SI  SI     0   1.011  129.3318  32.7986  11.7124
 9VF  HE2  H   HCH2   0   0.241  124.9033  33.3317  13.7839
 9VF  HE3  H   HCH2   0   0.238  124.8594  31.6360  14.2128
 9VF  HB2  H   HCH2   0   0.214  122.0902  33.2755  17.7437
 9VF  HB3  H   HCH2   0   0.206  123.7114  32.8796  18.2631
 9VF  H11  H   HCH3   0   0.246  130.4519  35.0302  11.7796
 9VF  H12  H   HCH3   0   0.245  131.6418  33.7427  11.5953
 9VF  H13  H   HCH3   0   0.246  130.6789  34.2596  10.2135
 9VF  H31  H   HCH3   0   0.247  128.9769  30.3815  11.1914
 9VF  H32  H   HCH3   0   0.244  129.7264  31.2156   9.8360
 9VF  H33  H   HCH3   0   0.244  130.6972  30.7618  11.2336
 9VF  H41  H   HCH3   0   0.249  126.8640  32.6658  11.2842
 9VF  H42  H   HCH3   0   0.245  127.3456  34.3232  11.6491
 9VF  H43  H   HCH3   0   0.247  127.6866  33.6356  10.0663
 9VF  H51  H   HCH2   0   0.266  130.4989  32.3929  13.8405
 9VF  H52  H   HCH2   0   0.246  129.1858  33.4762  14.1768
 9VF  HG2  H   HCH2   0   0.216  125.4517  32.2273  16.5772
 9VF  HG3  H   HCH2   0   0.218  125.5039  33.9232  16.1299
 9VF  HD2  H   HCH2   0   0.219  123.0669  33.7607  15.4283
 9VF  HD3  H   HCH2   0   0.211  123.0692  32.0880  15.9417
 9VF  HA   H   HCH1   0   0.212  124.3168  35.2812  17.3409
 9VF  HZ   H   HNH1   0   0.412  127.1988  33.3683  13.9223
 9VF  H    H   HNH2   0   0.326  123.7126  36.0733  19.5544
 9VF  H2   H   HNH2   0   0.322  123.0033  34.6726  19.8554

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
 9VF  C1  SI   single  1.882  0.020  1.882
 9VF  C3  SI   single  1.881  0.020  1.881
 9VF  C4  SI   single  1.883  0.020  1.883
 9VF  SI  C5   single  1.915  0.020  1.915
 9VF  C5  O6   single  1.436  0.020  1.436
 9VF  NZ  CE   single  1.448  0.020  1.448
 9VF  NZ  C7   single  1.345  0.020  1.345
 9VF  O8  C7   double  1.216  0.020  1.216
 9VF  CE  CG   single  1.523  0.020  1.523
 9VF  C7  O6   single  1.337  0.020  1.337
 9VF  CG  CD   single  1.525  0.020  1.525
 9VF  CD  CB   single  1.527  0.020  1.527
 9VF  O   C    deloc   1.231  0.020  1.231
 9VF  CB  CA   single  1.521  0.033  1.521
 9VF  C   CA   single  1.525  0.021  1.525
 9VF  C   OXT  deloc   1.249  0.020  1.249
 9VF  CA  N    single  1.458  0.019  1.458
 9VF  CE  HE2  single  0.970  0.020  1.090
 9VF  CE  HE3  single  0.970  0.020  1.090
 9VF  CB  HB2  single  0.970  0.020  1.090
 9VF  CB  HB3  single  0.970  0.020  1.090
 9VF  C1  H11  single  0.970  0.020  1.090
 9VF  C1  H12  single  0.970  0.020  1.090
 9VF  C1  H13  single  0.970  0.020  1.090
 9VF  C3  H31  single  0.970  0.020  1.090
 9VF  C3  H32  single  0.970  0.020  1.090
 9VF  C3  H33  single  0.970  0.020  1.090
 9VF  C4  H41  single  0.970  0.020  1.090
 9VF  C4  H42  single  0.970  0.020  1.090
 9VF  C4  H43  single  0.970  0.020  1.090
 9VF  C5  H51  single  0.970  0.020  1.090
 9VF  C5  H52  single  0.970  0.020  1.090
 9VF  CG  HG2  single  0.970  0.020  1.090
 9VF  CG  HG3  single  0.970  0.020  1.090
 9VF  CD  HD2  single  0.970  0.020  1.090
 9VF  CD  HD3  single  0.970  0.020  1.090
 9VF  CA  HA   single  0.970  0.020  0.970
 9VF  NZ  HZ   single  0.860  0.020  1.020
 9VF  N   H    single  0.860  0.020  0.860
 9VF  N   H2   single  0.890  0.020  1.040

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
 9VF  HE3  CE  HE2  106.62  3.000
 9VF  HE3  CE  NZ   108.98  3.000
 9VF  HE2  CE  NZ   107.16  3.000
 9VF  HE3  CE  CG   110.31  3.000
 9VF  HE2  CE  CG   109.71  3.000
 9VF  NZ   CE  CG   113.77  3.000
 9VF  HB3  CB  HB2  105.94  3.000
 9VF  HB3  CB  CA   108.04  3.000
 9VF  HB2  CB  CA   109.43  3.000
 9VF  HB3  CB  CD   108.08  3.000
 9VF  HB2  CB  CD   109.32  3.000
 9VF  CA   CB  CD   115.59  3.000
 9VF  H13  C1  H12  107.63  3.000
 9VF  H13  C1  H11  107.46  3.000
 9VF  H12  C1  H11  107.73  3.000
 9VF  H13  C1  SI   110.83  3.000
 9VF  H12  C1  SI   111.52  3.000
 9VF  H11  C1  SI   111.48  3.000
 9VF  H33  C3  H32  107.57  3.000
 9VF  H33  C3  H31  107.69  3.000
 9VF  H32  C3  H31  107.40  3.000
 9VF  H33  C3  SI   111.64  3.000
 9VF  H32  C3  SI   110.73  3.000
 9VF  H31  C3  SI   111.61  3.000
 9VF  H43  C4  H42  107.32  3.000
 9VF  H43  C4  H41  107.56  3.000
 9VF  H42  C4  H41  107.90  3.000
 9VF  H43  C4  SI   109.60  3.000
 9VF  H42  C4  SI   111.95  3.000
 9VF  H41  C4  SI   112.30  3.000
 9VF  H52  C5  H51  104.87  3.000
 9VF  H52  C5  SI   113.64  3.000
 9VF  H51  C5  SI   106.56  3.000
 9VF  H52  C5  O6   111.58  3.000
 9VF  H51  C5  O6   104.31  3.000
 9VF  SI   C5  O6   114.77  3.000
 9VF  O8   C7  O6   117.98  3.000
 9VF  O6   C7  NZ   117.98  3.000
 9VF  O8   C7  NZ   124.04  3.000
 9VF  HG3  CG  HG2  106.64  3.000
 9VF  HG3  CG  CD   110.53  3.000
 9VF  HG2  CG  CD   109.75  3.000
 9VF  HG3  CG  CE   108.90  3.000
 9VF  HG2  CG  CE   109.38  3.000
 9VF  CD   CG  CE   111.51  3.000
 9VF  HD3  CD  HD2  106.34  3.000
 9VF  HD3  CD  CG   108.33  3.000
 9VF  HD2  CD  CG   109.95  3.000
 9VF  HD3  CD  CB   109.00  3.000
 9VF  HD2  CD  CB   109.20  3.000
 9VF  CG   CD  CB   113.74  3.000
 9VF  HA   CA  N    110.00  3.000
 9VF  HA   CA  C    110.00  3.000
 9VF  N    CA  C    111.00  2.800
 9VF  HA   CA  CB   109.00  3.000
 9VF  N    CA  CB   110.40  1.500
 9VF  C    CA  CB   110.50  1.500
 9VF  O    C   OXT  126.03  3.000
 9VF  OXT  C   CA   120.80  1.700
 9VF  O    C   CA   120.80  1.700
 9VF  HZ   NZ  C7   120.95  3.000
 9VF  HZ   NZ  CE   116.31  3.000
 9VF  C7   NZ  CE   122.29  3.000
 9VF  H2   N   H    103.97  3.000
 9VF  H2   N   CA   108.17  3.000
 9VF  H    N   CA   114.00  3.000
 9VF  C7   O6  C5   123.48  3.000
 9VF  C5   SI  C4   113.32  3.000
 9VF  C5   SI  C3   107.41  3.000
 9VF  C4   SI  C3   110.03  3.000
 9VF  C5   SI  C1   105.12  3.000
 9VF  C4   SI  C1   109.68  3.000
 9VF  C3   SI  C1   111.18  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
 9VF  Var_01  O8   C7  NZ  CE     2.67  30.0  2
 9VF  Var_02  CB   CD  CG  CE  -177.81  30.0  3
 9VF  Var_03  O6   C5  SI  C1  -165.39  30.0  3
 9VF  Var_04  NZ   C7  O6  C5    -1.76  30.0  1
 9VF  Var_05  CG   CE  NZ  C7    86.97  30.0  3
 9VF  Var_06  SI   C5  O6  C7   -82.53  30.0  1
 9VF  Var_07  CA   CB  CD  CG    72.03  30.0  3
 9VF  Var_08  NZ   CE  CG  CD   178.92  30.0  1
 9VF  Var_09  H31  C3  SI  C1   178.21  30.0  3
 9VF  Var_10  H41  C4  SI  C1   175.28  30.0  3
 9VF  Var_11  H11  C1  SI  C3  -177.49  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
 9VF  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
 9VF  plan-1  CA   0.020
 9VF  plan-1  C    0.020
 9VF  plan-1  OXT  0.020
 9VF  plan-1  O    0.020
 9VF  plan-2  C7   0.020
 9VF  plan-2  NZ   0.020
 9VF  plan-2  O6   0.020
 9VF  plan-2  O8   0.020

