# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 10:58:33 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]methoxycarbonylamino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1ccc(cc1)C2(N=N2)C(F)(F)F)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
 9VR  9VR  '(2~{S})-2-azanyl-6-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]methoxycarbonylamino]hexanoic acid'  peptide  45  27  .  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_9VR
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
 9VR  C10  C  CR16   0  -0.260  229.3407  46.5919  204.8892
 9VR  CE   C  CH2    0  -0.280  225.4131  44.6256  206.0467
 9VR  CB   C  CH2    0  -0.421  224.5030  47.3835  208.6479
 9VR  CA   C  CH1    0  -0.199  224.8934  48.7274  208.0237
 9VR  C26  C  CR16   0  -0.266  228.2258  46.6481  202.7656
 9VR  N1   N  N      0  -0.060  229.4042  50.9606  202.9496
 9VR  N2   N  N      0  -0.060  229.9483  50.9312  204.0288
 9VR  C3   C  CT     0  -0.177  228.7013  50.1862  203.9608
 9VR  C4   C  CT     0   1.058  227.4965  50.8276  204.5903
 9VR  F5   F  F      0  -0.295  226.3794  50.4924  203.9420
 9VR  F6   F  F      0  -0.300  227.5901  52.1576  204.5825
 9VR  F7   F  F      0  -0.296  227.3562  50.4356  205.8602
 9VR  C8   C  CR6    0   0.054  228.7288  48.7040  203.9066
 9VR  C9   C  CR16   0  -0.250  229.3008  47.9757  204.9447
 9VR  C11  C  CR6    0   0.004  228.7983  45.9154  203.8001
 9VR  C12  C  CH2    0  -0.256  228.8545  44.4114  203.7035
 9VR  O13  O  O2     0  -0.467  228.7875  43.7619  204.9631
 9VR  C14  C  C      0   0.703  227.6842  43.8039  205.7354
 9VR  O15  O  O      0  -0.499  227.7579  43.3229  206.8461
 9VR  NZ   N  NH1    0  -0.661  226.5696  44.3467  205.2161
 9VR  CD   C  CH2    0  -0.430  225.5693  45.9019  206.8642
 9VR  CG   C  CH2    0  -0.429  224.3235  46.2175  207.6808
 9VR  N    N  NH2    0  -0.793  225.1021  49.6855  209.1087
 9VR  C    C  C      0   0.387  223.8249  49.1621  206.9941
 9VR  O    O  O      0  -0.610  224.0479  48.9087  205.7916
 9VR  OXT  O  OC    -1  -0.609  222.8044  49.7112  207.4615
 9VR  C27  C  CR16   0  -0.249  228.1925  48.0333  202.8140
 9VR  H1   H  HCR6   0   0.267  229.7970  46.0457  205.7047
 9VR  HE2  H  HCH2   0   0.245  224.5535  44.7112  205.3807
 9VR  HE3  H  HCH2   0   0.240  225.2238  43.7711  206.6970
 9VR  HB2  H  HCH2   0   0.209  223.5741  47.5219  209.2122
 9VR  HB3  H  HCH2   0   0.209  225.2694  47.1197  209.3840
 9VR  HA   H  HCH1   0   0.201  225.8522  48.6081  207.5109
 9VR  H7   H  HCR6   0   0.267  227.7947  46.1335  201.9150
 9VR  H10  H  HCR6   0   0.269  229.7269  48.4890  205.7976
 9VR  H11  H  HCH2   0   0.258  228.0850  44.0387  203.0194
 9VR  H12  H  HCH2   0   0.291  229.8147  44.1060  203.2852
 9VR  HZ   H  HNH1   0   0.416  226.5809  44.8022  204.3191
 9VR  HD2  H  HCH2   0   0.216  226.4329  45.8016  207.5284
 9VR  HD3  H  HCH2   0   0.222  225.7844  46.7297  206.1852
 9VR  HG2  H  HCH2   0   0.214  223.4865  46.4066  207.0027
 9VR  HG3  H  HCH2   0   0.215  224.0423  45.3333  208.2620
 9VR  H    H  HNH2   0   0.330  225.4763  50.5423  208.7167
 9VR  H2   H  HNH2   0   0.320  224.1857  49.9462  209.4582
 9VR  H22  H  HCR6   0   0.270  227.7461  48.5875  201.9980

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
 9VR  N2   N1   double    1.209  0.020  1.209
 9VR  N2   C3   single    1.454  0.020  1.454
 9VR  N1   C3   single    1.455  0.020  1.455
 9VR  C27  C26  aromatic  1.386  0.020  1.386
 9VR  C27  C8   aromatic  1.390  0.020  1.390
 9VR  C3   C8   single    1.483  0.020  1.483
 9VR  C3   C4   single    1.503  0.020  1.503
 9VR  C26  C11  aromatic  1.391  0.020  1.391
 9VR  C8   C9   aromatic  1.391  0.020  1.391
 9VR  F6   C4   single    1.333  0.020  1.333
 9VR  C4   F7   single    1.336  0.020  1.336
 9VR  C4   F5   single    1.334  0.020  1.334
 9VR  C11  C12  single    1.508  0.020  1.508
 9VR  C11  C10  aromatic  1.392  0.020  1.392
 9VR  C9   C10  aromatic  1.386  0.020  1.386
 9VR  C12  O13  single    1.419  0.020  1.419
 9VR  NZ   CE   single    1.451  0.020  1.451
 9VR  NZ   C14  single    1.344  0.020  1.344
 9VR  O13  C14  single    1.347  0.020  1.347
 9VR  CE   CD   single    1.524  0.020  1.524
 9VR  C14  O15  double    1.213  0.020  1.213
 9VR  CD   CG   single    1.523  0.020  1.523
 9VR  CG   CB   single    1.525  0.020  1.525
 9VR  O    C    deloc     1.231  0.020  1.231
 9VR  CB   CA   single    1.521  0.033  1.521
 9VR  C    CA   single    1.525  0.021  1.525
 9VR  C    OXT  deloc     1.250  0.020  1.250
 9VR  CA   N    single    1.458  0.019  1.458
 9VR  C10  H1   single    0.930  0.020  1.080
 9VR  CE   HE2  single    0.970  0.020  1.090
 9VR  CE   HE3  single    0.970  0.020  1.090
 9VR  CB   HB2  single    0.970  0.020  1.090
 9VR  CB   HB3  single    0.970  0.020  1.090
 9VR  CA   HA   single    0.970  0.020  0.970
 9VR  C26  H7   single    0.930  0.020  1.080
 9VR  C9   H10  single    0.930  0.020  1.080
 9VR  C12  H11  single    0.970  0.020  1.090
 9VR  C12  H12  single    0.970  0.020  1.090
 9VR  NZ   HZ   single    0.860  0.020  1.020
 9VR  CD   HD2  single    0.970  0.020  1.090
 9VR  CD   HD3  single    0.970  0.020  1.090
 9VR  CG   HG2  single    0.970  0.020  1.090
 9VR  CG   HG3  single    0.970  0.020  1.090
 9VR  N    H    single    0.860  0.020  0.860
 9VR  N    H2   single    0.890  0.020  1.040
 9VR  C27  H22  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
 9VR  H1   C10  C11  120.57  3.000
 9VR  H1   C10  C9   119.08  3.000
 9VR  C11  C10  C9   120.36  3.000
 9VR  HE3  CE   HE2  106.79  3.000
 9VR  HE3  CE   CD   110.75  3.000
 9VR  HE2  CE   CD   110.04  3.000
 9VR  HE3  CE   NZ   109.21  3.000
 9VR  HE2  CE   NZ   107.08  3.000
 9VR  CD   CE   NZ   112.73  3.000
 9VR  HB3  CB   HB2  106.12  3.000
 9VR  HB3  CB   CG   108.93  3.000
 9VR  HB2  CB   CG   108.86  3.000
 9VR  HB3  CB   CA   107.87  3.000
 9VR  HB2  CB   CA   108.37  3.000
 9VR  CG   CB   CA   116.24  3.000
 9VR  HA   CA   C    110.00  3.000
 9VR  HA   CA   N    110.00  3.000
 9VR  C    CA   N    111.00  2.800
 9VR  HA   CA   CB   109.00  3.000
 9VR  N    CA   CB   110.40  1.500
 9VR  C    CA   CB   110.50  1.500
 9VR  H7   C26  C27  119.49  3.000
 9VR  H7   C26  C11  119.83  3.000
 9VR  C27  C26  C11  120.67  3.000
 9VR  C3   N1   N2    65.42  3.000
 9VR  C3   N2   N1    65.46  3.000
 9VR  C8   C3   C4   117.16  3.000
 9VR  C4   C3   N2   116.69  3.000
 9VR  C8   C3   N2   119.85  3.000
 9VR  C4   C3   N1   116.82  3.000
 9VR  C8   C3   N1   119.84  3.000
 9VR  N2   C3   N1    49.12  3.000
 9VR  F7   C4   F6   107.79  3.000
 9VR  F7   C4   F5   107.46  3.000
 9VR  F6   C4   F5   107.85  3.000
 9VR  F5   C4   C3   111.12  3.000
 9VR  F7   C4   C3   110.91  3.000
 9VR  F6   C4   C3   111.53  3.000
 9VR  C27  C8   C9   119.52  3.000
 9VR  C9   C8   C3   120.23  3.000
 9VR  C27  C8   C3   120.25  3.000
 9VR  H10  C9   C8   120.10  3.000
 9VR  H10  C9   C10  119.58  3.000
 9VR  C8   C9   C10  120.32  3.000
 9VR  C12  C11  C26  119.54  3.000
 9VR  C12  C11  C10  121.34  3.000
 9VR  C26  C11  C10  119.10  3.000
 9VR  H12  C12  H11  106.48  3.000
 9VR  H12  C12  O13  104.71  3.000
 9VR  H11  C12  O13  111.44  3.000
 9VR  H12  C12  C11  109.67  3.000
 9VR  H11  C12  C11  110.68  3.000
 9VR  O13  C12  C11  113.45  3.000
 9VR  C14  O13  C12  122.23  3.000
 9VR  NZ   C14  O15  124.36  3.000
 9VR  O15  C14  O13  117.58  3.000
 9VR  NZ   C14  O13  118.05  3.000
 9VR  HZ   NZ   C14  121.19  3.000
 9VR  HZ   NZ   CE   115.62  3.000
 9VR  C14  NZ   CE   121.16  3.000
 9VR  HD3  CD   HD2  106.95  3.000
 9VR  HD3  CD   CG   109.72  3.000
 9VR  HD2  CD   CG   109.83  3.000
 9VR  HD3  CD   CE   108.76  3.000
 9VR  HD2  CD   CE   109.26  3.000
 9VR  CG   CD   CE   112.17  3.000
 9VR  HG3  CG   HG2  105.80  3.000
 9VR  HG3  CG   CD   109.11  3.000
 9VR  HG2  CG   CD   109.24  3.000
 9VR  HG3  CG   CB   108.11  3.000
 9VR  HG2  CG   CB   110.55  3.000
 9VR  CD   CG   CB   113.71  3.000
 9VR  H2   N    H    104.44  3.000
 9VR  H2   N    CA   107.16  3.000
 9VR  H    N    CA   114.00  3.000
 9VR  OXT  C    O    126.52  3.000
 9VR  OXT  C    CA   120.80  1.700
 9VR  O    C    CA   120.80  1.700
 9VR  H22  C27  C8   120.30  3.000
 9VR  H22  C27  C26  119.67  3.000
 9VR  C8   C27  C26  120.03  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
 9VR  CONST_01  C27  C26  C11  C10     0.00   0.0  0
 9VR  CONST_02  C27  C8   C9   C10     0.00   0.0  0
 9VR  CONST_03  C9   C8   C27  C26     0.00   0.0  0
 9VR  CONST_04  C9   C10  C11  C26     0.00   0.0  0
 9VR  CONST_05  C11  C26  C27  C8      0.00   0.0  0
 9VR  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 9VR  CONST_07  C3   C8   C9   C10   180.00   0.0  0
 9VR  CONST_08  C3   C8   C27  C26   180.00   0.0  0
 9VR  CONST_09  C12  C11  C10  C9    180.00   0.0  0
 9VR  CONST_10  C27  C26  C11  C12   180.00   0.0  0
 9VR  CONST_11  H7   C26  C11  C10   180.00   0.0  0
 9VR  CONST_12  H1   C10  C11  C26   180.00   0.0  0
 9VR  CONST_13  H22  C27  C8   C3      0.00   0.0  0
 9VR  CONST_14  H10  C9   C8   C3      0.00   0.0  0
 9VR  Var_01    C8   C3   N2   N1    105.19  30.0  1
 9VR  Var_02    C27  C8   C3   N1    -61.82  30.0  2
 9VR  Var_03    O13  C12  C11  C10    32.52  30.0  2
 9VR  Var_04    F6   C4   C3   N1    -27.76  30.0  3
 9VR  Var_05    O13  C14  NZ   CE   -169.89  30.0  2
 9VR  Var_06    CB   CG   CD   CE    172.53  30.0  3
 9VR  Var_07    CD   CG   CB   CA     59.00  30.0  1
 9VR  Var_08    NZ   C14  O13  C12     7.95  30.0  3
 9VR  Var_09    CD   CE   NZ   C14    78.75  30.0  3
 9VR  Var_10    CG   CD   CE   NZ    177.31  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
 9VR  chir_01  CA  CB  C   N   negativ
 9VR  chir_02  C3  N1  C8  C4  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
 9VR  plan-1  C10  0.020
 9VR  plan-1  C26  0.020
 9VR  plan-1  C3   0.020
 9VR  plan-1  C8   0.020
 9VR  plan-1  C9   0.020
 9VR  plan-1  C11  0.020
 9VR  plan-1  C12  0.020
 9VR  plan-1  C27  0.020
 9VR  plan-1  H1   0.020
 9VR  plan-1  H7   0.020
 9VR  plan-1  H10  0.020
 9VR  plan-1  H22  0.020
 9VR  plan-2  O13  0.020
 9VR  plan-2  C14  0.020
 9VR  plan-2  O15  0.020
 9VR  plan-2  NZ   0.020
 9VR  plan-3  CA   0.020
 9VR  plan-3  C    0.020
 9VR  plan-3  O    0.020
 9VR  plan-3  OXT  0.020

