# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:37:52 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[(2-chlorophenyl)methoxycarbonylamino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1ccccc1Cl)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
 9V6  9V6  '(2~{S})-2-azanyl-6-[(2-chlorophenyl)methoxycarbonylamino]hexanoic acid'  peptide  39  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_9V6
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
 9V6  C15  C   CR6    0   0.147  327.0075  30.7769  200.8842
 9V6  C20  C   CR16   0  -0.232  327.3535  29.1502  199.1208
 9V6  C21  C   CR16   0  -0.297  327.2780  29.4774  200.4660
 9V6  C    C   C      0   0.382  319.5478  33.2804  208.2553
 9V6  CA   C   CH1    0  -0.213  320.6825  32.4083  207.6495
 9V6  CB   C   CH2    0  -0.418  320.3980  32.1236  206.1741
 9V6  CG   C   CH2    0  -0.398  321.5328  31.4272  205.4351
 9V6  CD   C   CH2    0  -0.470  321.2063  31.2082  203.9628
 9V6  CE   C   CH2    0  -0.263  322.2743  30.4462  203.1958
 9V6  C11  C   C      0   0.755  324.6846  30.6299  202.8307
 9V6  C14  C   CH2    0  -0.260  326.9466  31.1057  202.3492
 9V6  C16  C   CR6    0  -0.092  326.8113  31.7428  199.8999
 9V6  C18  C   CR16   0  -0.200  326.8744  31.4345  198.5497
 9V6  C19  C   CR16   0  -0.271  327.1454  30.1308  198.1618
 9V6  N    N   NH2    0  -0.785  320.9593  31.1625  208.3520
 9V6  NZ   N   NH1    0  -0.657  323.5083  31.2014  203.1290
 9V6  O12  O   O      0  -0.509  324.8660  29.4406  202.6692
 9V6  O13  O   O2     0  -0.481  325.6580  31.5533  202.7547
 9V6  CL   CL  CL     0  -0.124  326.4929  33.3883  200.3500
 9V6  H20  H   HCR6   0   0.262  327.5661  28.1321  198.8232
 9V6  H21  H   HCR6   0   0.262  327.4324  28.7112  201.2151
 9V6  HA   H   HCH1   0   0.202  321.5984  33.0137  207.6911
 9V6  HB2  H   HCH2   0   0.215  320.1715  33.0683  205.6765
 9V6  HB3  H   HCH2   0   0.200  319.4888  31.5129  206.0977
 9V6  HG2  H   HCH2   0   0.211  321.7483  30.4634  205.9026
 9V6  HG3  H   HCH2   0   0.207  322.4447  32.0254  205.5320
 9V6  HD2  H   HCH2   0   0.223  321.0159  32.1695  203.4726
 9V6  HD3  H   HCH2   0   0.234  320.2758  30.6403  203.8775
 9V6  HE2  H   HCH2   0   0.236  321.9107  30.2152  202.1892
 9V6  HE3  H   HCH2   0   0.235  322.4693  29.4935  203.6909
 9V6  H12  H   HCH2   0   0.261  327.2651  30.2435  202.9371
 9V6  H13  H   HCH2   0   0.265  327.6157  31.9329  202.5860
 9V6  H18  H   HCR6   0   0.278  326.7166  32.2060  197.8082
 9V6  H19  H   HCR6   0   0.267  327.1958  29.8881  197.1086
 9V6  H    H   HNH2   0   0.330  321.0878  31.3699  209.3352
 9V6  H2   H   HNH2   0   0.319  320.1198  30.5935  208.3272
 9V6  HZ   H   HNH1   0   0.397  323.4498  32.2080  203.1374
 9V6  O    O   O      0  -0.617  319.3544  34.3822  207.6988
 9V6  OXT  O   OC    -1  -0.602  318.9299  32.8242  209.2372

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
 9V6  C19  C20  aromatic  1.387  0.020  1.387
 9V6  C19  C18  aromatic  1.387  0.020  1.387
 9V6  C20  C21  aromatic  1.386  0.020  1.386
 9V6  C18  C16  aromatic  1.386  0.020  1.386
 9V6  C21  C15  aromatic  1.392  0.020  1.392
 9V6  C16  C15  aromatic  1.393  0.020  1.393
 9V6  C16  CL   single    1.735  0.020  1.735
 9V6  C15  C14  single    1.503  0.020  1.503
 9V6  C14  O13  single    1.423  0.020  1.423
 9V6  O13  C11  single    1.344  0.020  1.344
 9V6  C11  O12  double    1.214  0.020  1.214
 9V6  C11  NZ   single    1.341  0.020  1.341
 9V6  NZ   CE   single    1.448  0.020  1.448
 9V6  CE   CD   single    1.520  0.020  1.520
 9V6  CD   CG   single    1.524  0.020  1.524
 9V6  O    C    deloc     1.231  0.020  1.231
 9V6  CG   CB   single    1.523  0.020  1.523
 9V6  CB   CA   single    1.521  0.033  1.521
 9V6  C    CA   single    1.525  0.021  1.525
 9V6  C    OXT  deloc     1.247  0.020  1.247
 9V6  CA   N    single    1.458  0.019  1.458
 9V6  C20  H20  single    0.930  0.020  1.080
 9V6  C21  H21  single    0.930  0.020  1.080
 9V6  CA   HA   single    0.970  0.020  0.970
 9V6  CB   HB2  single    0.970  0.020  1.090
 9V6  CB   HB3  single    0.970  0.020  1.090
 9V6  CG   HG2  single    0.970  0.020  1.090
 9V6  CG   HG3  single    0.970  0.020  1.090
 9V6  CD   HD2  single    0.970  0.020  1.090
 9V6  CD   HD3  single    0.970  0.020  1.090
 9V6  CE   HE2  single    0.970  0.020  1.090
 9V6  CE   HE3  single    0.970  0.020  1.090
 9V6  C14  H12  single    0.970  0.020  1.090
 9V6  C14  H13  single    0.970  0.020  1.090
 9V6  C18  H18  single    0.930  0.020  1.080
 9V6  C19  H19  single    0.930  0.020  1.080
 9V6  N    H    single    0.860  0.020  0.860
 9V6  N    H2   single    0.890  0.020  1.040
 9V6  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
 9V6  C16  C15  C14  122.11  3.000
 9V6  C14  C15  C21  120.34  3.000
 9V6  C16  C15  C21  117.55  3.000
 9V6  H20  C20  C19  120.30  3.000
 9V6  H20  C20  C21  119.98  3.000
 9V6  C19  C20  C21  119.72  3.000
 9V6  H21  C21  C20  119.78  3.000
 9V6  H21  C21  C15  118.72  3.000
 9V6  C20  C21  C15  121.50  3.000
 9V6  OXT  C    O    126.64  3.000
 9V6  OXT  C    CA   120.80  1.700
 9V6  O    C    CA   120.80  1.700
 9V6  HA   CA   N    110.00  3.000
 9V6  HA   CA   CB   109.00  3.000
 9V6  N    CA   CB   110.40  1.500
 9V6  HA   CA   C    110.00  3.000
 9V6  N    CA   C    111.00  2.800
 9V6  CB   CA   C    110.50  1.500
 9V6  HB3  CB   HB2  106.13  3.000
 9V6  HB3  CB   CG   109.21  3.000
 9V6  HB2  CB   CG   109.22  3.000
 9V6  HB3  CB   CA   108.95  3.000
 9V6  HB2  CB   CA   108.50  3.000
 9V6  CG   CB   CA   114.50  3.000
 9V6  HG3  CG   HG2  106.25  3.000
 9V6  HG3  CG   CD   110.02  3.000
 9V6  HG2  CG   CD   109.20  3.000
 9V6  HG3  CG   CB   109.14  3.000
 9V6  HG2  CG   CB   110.04  3.000
 9V6  CD   CG   CB   112.02  3.000
 9V6  HD3  CD   HD2  105.84  3.000
 9V6  HD3  CD   CE   107.35  3.000
 9V6  HD2  CD   CE   109.65  3.000
 9V6  HD3  CD   CG   109.41  3.000
 9V6  HD2  CD   CG   110.08  3.000
 9V6  CE   CD   CG   114.15  3.000
 9V6  HE3  CE   HE2  106.99  3.000
 9V6  HE3  CE   NZ   108.90  3.000
 9V6  HE2  CE   NZ   110.52  3.000
 9V6  HE3  CE   CD   109.54  3.000
 9V6  HE2  CE   CD   109.66  3.000
 9V6  NZ   CE   CD   111.14  3.000
 9V6  O13  C11  O12  123.88  3.000
 9V6  O12  C11  NZ   125.32  3.000
 9V6  O13  C11  NZ   110.79  3.000
 9V6  H13  C14  H12  107.66  3.000
 9V6  H13  C14  O13  104.79  3.000
 9V6  H12  C14  O13  111.06  3.000
 9V6  H13  C14  C15  110.67  3.000
 9V6  H12  C14  C15  109.91  3.000
 9V6  O13  C14  C15  112.54  3.000
 9V6  CL   C16  C18  118.15  3.000
 9V6  CL   C16  C15  120.00  3.000
 9V6  C18  C16  C15  121.84  3.000
 9V6  H18  C18  C19  120.48  3.000
 9V6  H18  C18  C16  120.16  3.000
 9V6  C19  C18  C16  119.36  3.000
 9V6  H19  C19  C18  119.49  3.000
 9V6  H19  C19  C20  120.49  3.000
 9V6  C18  C19  C20  120.03  3.000
 9V6  H2   N    H    104.10  3.000
 9V6  H2   N    CA   108.10  3.000
 9V6  H    N    CA   114.00  3.000
 9V6  HZ   NZ   C11  118.56  3.000
 9V6  HZ   NZ   CE   118.08  3.000
 9V6  C11  NZ   CE   122.36  3.000
 9V6  C14  O13  C11  117.12  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
 9V6  CONST_01  C19  C20  C21  C15     0.00   0.0  0
 9V6  CONST_02  C19  C18  C16  C15     0.00   0.0  0
 9V6  CONST_03  C16  C18  C19  C20     0.00   0.0  0
 9V6  CONST_04  C16  C15  C21  C20     0.00   0.0  0
 9V6  CONST_05  C18  C19  C20  C21     0.00   0.0  0
 9V6  CONST_06  C18  C16  C15  C21     0.00   0.0  0
 9V6  CONST_07  C14  C15  C21  C20   180.00   0.0  0
 9V6  CONST_08  CL   C16  C15  C21   180.00   0.0  0
 9V6  CONST_09  C18  C16  C15  C14   180.00   0.0  0
 9V6  CONST_10  CL   C16  C18  C19   180.00   0.0  0
 9V6  CONST_11  H20  C20  C21  C15   180.00   0.0  0
 9V6  CONST_12  H18  C18  C16  C15   180.00   0.0  0
 9V6  CONST_13  H19  C19  C20  C21   180.00   0.0  0
 9V6  CONST_14  H21  C21  C15  C16   180.00   0.0  0
 9V6  Var_01    O13  C14  C15  C21  -116.98  30.0  2
 9V6  Var_02    CD   CG   CB   CA   -178.32  30.0  2
 9V6  Var_03    CE   CD   CG   CB   -176.74  30.0  1
 9V6  Var_04    NZ   CE   CD   CG    -64.94  30.0  2
 9V6  Var_05    C11  NZ   CE   CD    161.96  30.0  2
 9V6  Var_06    O13  C11  NZ   CE    176.33  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
 9V6  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
 9V6  plan-1  C15  0.020
 9V6  plan-1  C20  0.020
 9V6  plan-1  C21  0.020
 9V6  plan-1  C14  0.020
 9V6  plan-1  C16  0.020
 9V6  plan-1  C18  0.020
 9V6  plan-1  C19  0.020
 9V6  plan-1  CL   0.020
 9V6  plan-1  H20  0.020
 9V6  plan-1  H21  0.020
 9V6  plan-1  H18  0.020
 9V6  plan-1  H19  0.020
 9V6  plan-2  C    0.020
 9V6  plan-2  CA   0.020
 9V6  plan-2  O    0.020
 9V6  plan-2  OXT  0.020
 9V6  plan-3  C11  0.020
 9V6  plan-3  NZ   0.020
 9V6  plan-3  O12  0.020
 9V6  plan-3  O13  0.020

