# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:37:19 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{S})-2-azanyl-6-(phenylmethoxycarbonylamino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1ccccc1)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
 9VC  9VC  '(2~{S})-2-azanyl-6-(phenylmethoxycarbonylamino)hexanoic acid'  peptide  39  20  .  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_9VC
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
 9VC  C15  C  CR6    0   0.068   -9.4923  16.3507  10.4797
 9VC  C17  C  CR16   0  -0.240   -9.6535  16.4848   8.0738
 9VC  C20  C  CR16   0  -0.283   -9.3350  17.7342  10.5295
 9VC  C    C  C      0   0.415  -16.9397  18.9971  17.0065
 9VC  CA   C  CH1    0  -0.194  -16.1076  17.7420  17.3808
 9VC  CB   C  CH2    0  -0.413  -16.3717  16.5178  16.5147
 9VC  CG   C  CH2    0  -0.436  -15.7897  16.5876  15.1046
 9VC  CD   C  CH2    0  -0.453  -14.2677  16.5008  15.0576
 9VC  CE   C  CH2    0  -0.243  -13.7514  16.5296  13.6274
 9VC  C11  C  C      0   0.747  -11.6250  15.8958  12.5813
 9VC  C14  C  CH2    0  -0.243   -9.4522  15.5302  11.7391
 9VC  C16  C  CR16   0  -0.296   -9.6550  15.7358   9.2437
 9VC  C18  C  CR16   0  -0.265   -9.5017  17.8631   8.1312
 9VC  C19  C  CR16   0  -0.240   -9.3448  18.4861   9.3635
 9VC  N    N  NH2    0  -0.813  -16.4200  17.4205  18.7770
 9VC  NZ   N  NH1    0  -0.663  -12.3060  16.4703  13.5857
 9VC  O12  O  O      0  -0.508  -12.1144  15.3008  11.6437
 9VC  O13  O  O2     0  -0.486  -10.3009  16.0466  12.7591
 9VC  H17  H  HCR6   0   0.254   -9.7808  15.9914   7.1187
 9VC  H20  H  HCR6   0   0.252   -9.2027  18.2325  11.4826
 9VC  HA   H  HCH1   0   0.184  -15.0479  18.0270  17.2687
 9VC  HB2  H  HCH2   0   0.210  -17.4499  16.3541  16.4546
 9VC  HB3  H  HCH2   0   0.198  -15.9550  15.6341  17.0133
 9VC  HG2  H  HCH2   0   0.217  -16.1232  17.5055  14.6148
 9VC  HG3  H  HCH2   0   0.214  -16.2009  15.7633  14.5131
 9VC  HD2  H  HCH2   0   0.221  -13.9337  15.5788  15.5430
 9VC  HD3  H  HCH2   0   0.224  -13.8237  17.3283  15.6195
 9VC  HE2  H  HCH2   0   0.225  -14.1145  17.4320  13.1230
 9VC  HE3  H  HCH2   0   0.237  -14.1491  15.6776  13.0765
 9VC  H12  H  HCH2   0   0.249   -9.6873  14.4855  11.5254
 9VC  H13  H  HCH2   0   0.261   -8.4543  15.5587  12.1781
 9VC  H16  H  HCR6   0   0.251   -9.7862  14.6613   9.1925
 9VC  H18  H  HCR6   0   0.254   -9.5059  18.4501   7.2218
 9VC  H19  H  HCR6   0   0.254   -9.2239  19.5606   9.4163
 9VC  H    H  HNH2   0   0.329  -15.7550  16.7360  19.1176
 9VC  H2   H  HNH2   0   0.329  -16.2693  18.2520  19.3343
 9VC  HZ   H  HNH1   0   0.396  -11.7933  17.0129  14.2636
 9VC  O    O  O      0  -0.593  -17.7921  18.9083  16.1028
 9VC  OXT  O  OC    -1  -0.619  -16.6787  20.0158  17.6824

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
 9VC  C17  C18  aromatic  1.388  0.020  1.388
 9VC  C17  C16  aromatic  1.389  0.020  1.389
 9VC  C18  C19  aromatic  1.390  0.020  1.390
 9VC  C16  C15  aromatic  1.390  0.020  1.390
 9VC  C19  C20  aromatic  1.387  0.020  1.387
 9VC  C15  C20  aromatic  1.393  0.020  1.393
 9VC  C15  C14  single    1.504  0.020  1.504
 9VC  C14  O13  single    1.424  0.020  1.424
 9VC  NZ   CE   single    1.447  0.020  1.447
 9VC  NZ   C11  single    1.343  0.020  1.343
 9VC  O13  C11  single    1.344  0.020  1.344
 9VC  CE   CD   single    1.521  0.020  1.521
 9VC  C11  O12  double    1.214  0.020  1.214
 9VC  CD   CG   single    1.525  0.020  1.525
 9VC  CG   CB   single    1.527  0.020  1.527
 9VC  O    C    deloc     1.231  0.020  1.231
 9VC  C    CA   single    1.525  0.021  1.525
 9VC  C    OXT  deloc     1.250  0.020  1.250
 9VC  CB   CA   single    1.521  0.033  1.521
 9VC  CA   N    single    1.458  0.019  1.458
 9VC  C17  H17  single    0.930  0.020  1.080
 9VC  C20  H20  single    0.930  0.020  1.080
 9VC  CA   HA   single    0.970  0.020  0.970
 9VC  CB   HB2  single    0.970  0.020  1.090
 9VC  CB   HB3  single    0.970  0.020  1.090
 9VC  CG   HG2  single    0.970  0.020  1.090
 9VC  CG   HG3  single    0.970  0.020  1.090
 9VC  CD   HD2  single    0.970  0.020  1.090
 9VC  CD   HD3  single    0.970  0.020  1.090
 9VC  CE   HE2  single    0.970  0.020  1.090
 9VC  CE   HE3  single    0.970  0.020  1.090
 9VC  C14  H12  single    0.970  0.020  1.090
 9VC  C14  H13  single    0.970  0.020  1.090
 9VC  C16  H16  single    0.930  0.020  1.080
 9VC  C18  H18  single    0.930  0.020  1.080
 9VC  C19  H19  single    0.930  0.020  1.080
 9VC  N    H    single    0.860  0.020  0.860
 9VC  N    H2   single    0.890  0.020  1.040
 9VC  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
 9VC  C16  C15  C14  120.43  3.000
 9VC  C14  C15  C20  120.59  3.000
 9VC  C16  C15  C20  118.96  3.000
 9VC  H17  C17  C18  120.13  3.000
 9VC  H17  C17  C16  119.82  3.000
 9VC  C18  C17  C16  120.05  3.000
 9VC  H20  C20  C19  119.40  3.000
 9VC  H20  C20  C15  120.12  3.000
 9VC  C19  C20  C15  120.48  3.000
 9VC  OXT  C    O    126.39  3.000
 9VC  OXT  C    CA   120.80  1.700
 9VC  O    C    CA   120.80  1.700
 9VC  HA   CA   N    110.00  3.000
 9VC  HA   CA   CB   109.00  3.000
 9VC  N    CA   CB   110.40  1.500
 9VC  HA   CA   C    110.00  3.000
 9VC  N    CA   C    111.00  2.800
 9VC  CB   CA   C    110.50  1.500
 9VC  HB3  CB   HB2  106.22  3.000
 9VC  HB3  CB   CG   108.17  3.000
 9VC  HB2  CB   CG   109.40  3.000
 9VC  HB3  CB   CA   108.87  3.000
 9VC  HB2  CB   CA   108.84  3.000
 9VC  CG   CB   CA   114.98  3.000
 9VC  HG3  CG   HG2  106.00  3.000
 9VC  HG3  CG   CD   108.38  3.000
 9VC  HG2  CG   CD   109.80  3.000
 9VC  HG3  CG   CB   108.74  3.000
 9VC  HG2  CG   CB   109.64  3.000
 9VC  CD   CG   CB   113.96  3.000
 9VC  HD3  CD   HD2  106.59  3.000
 9VC  HD3  CD   CE   109.32  3.000
 9VC  HD2  CD   CE   109.25  3.000
 9VC  HD3  CD   CG   110.24  3.000
 9VC  HD2  CD   CG   109.81  3.000
 9VC  CE   CD   CG   111.51  3.000
 9VC  HE3  CE   HE2  106.87  3.000
 9VC  HE3  CE   NZ   108.53  3.000
 9VC  HE2  CE   NZ   110.58  3.000
 9VC  HE3  CE   CD   109.67  3.000
 9VC  HE2  CE   CD   109.64  3.000
 9VC  NZ   CE   CD   111.43  3.000
 9VC  O13  C11  O12  123.66  3.000
 9VC  O12  C11  NZ   125.68  3.000
 9VC  O13  C11  NZ   110.65  3.000
 9VC  H13  C14  H12  107.51  3.000
 9VC  H13  C14  O13  104.33  3.000
 9VC  H12  C14  O13  111.03  3.000
 9VC  H13  C14  C15  110.32  3.000
 9VC  H12  C14  C15  110.64  3.000
 9VC  O13  C14  C15  112.72  3.000
 9VC  H16  C16  C17  119.66  3.000
 9VC  H16  C16  C15  119.66  3.000
 9VC  C17  C16  C15  120.68  3.000
 9VC  H18  C18  C19  120.16  3.000
 9VC  H18  C18  C17  120.22  3.000
 9VC  C19  C18  C17  119.62  3.000
 9VC  H19  C19  C18  120.06  3.000
 9VC  H19  C19  C20  119.74  3.000
 9VC  C18  C19  C20  120.20  3.000
 9VC  H2   N    H    105.79  3.000
 9VC  H2   N    CA   108.20  3.000
 9VC  H    N    CA   114.00  3.000
 9VC  HZ   NZ   C11  118.38  3.000
 9VC  HZ   NZ   CE   117.79  3.000
 9VC  C11  NZ   CE   123.07  3.000
 9VC  C14  O13  C11  116.85  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
 9VC  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 9VC  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 9VC  CONST_03  C20  C19  C18  C17     0.00   0.0  0
 9VC  CONST_04  C20  C15  C16  C17     0.00   0.0  0
 9VC  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 9VC  CONST_06  C19  C20  C15  C16     0.00   0.0  0
 9VC  CONST_07  C14  C15  C16  C17   180.00   0.0  0
 9VC  CONST_08  C19  C20  C15  C14   180.00   0.0  0
 9VC  CONST_09  H17  C17  C16  C15   180.00   0.0  0
 9VC  CONST_10  H19  C19  C20  C15   180.00   0.0  0
 9VC  CONST_11  H18  C18  C19  C20   180.00   0.0  0
 9VC  CONST_12  H16  C16  C15  C20   180.00   0.0  0
 9VC  CONST_13  H20  C20  C15  C16   180.00   0.0  0
 9VC  Var_01    O13  C14  C15  C20    49.56  30.0  2
 9VC  Var_02    CD   CG   CB   CA     70.15  30.0  2
 9VC  Var_03    CE   CD   CG   CB    178.13  30.0  1
 9VC  Var_04    NZ   CE   CD   CG    179.01  30.0  1
 9VC  Var_05    C11  NZ   CE   CD    148.94  30.0  1
 9VC  Var_06    O13  C11  NZ   CE    176.60  30.0  2
 9VC  Var_07    NZ   C11  O13  C14  -177.61  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
 9VC  chir_01  CA  C  CB  N  positiv

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
 9VC  plan-1  C15  0.020
 9VC  plan-1  C17  0.020
 9VC  plan-1  C20  0.020
 9VC  plan-1  C14  0.020
 9VC  plan-1  C16  0.020
 9VC  plan-1  C18  0.020
 9VC  plan-1  C19  0.020
 9VC  plan-1  H17  0.020
 9VC  plan-1  H20  0.020
 9VC  plan-1  H16  0.020
 9VC  plan-1  H18  0.020
 9VC  plan-1  H19  0.020
 9VC  plan-2  C    0.020
 9VC  plan-2  CA   0.020
 9VC  plan-2  O    0.020
 9VC  plan-2  OXT  0.020
 9VC  plan-3  C11  0.020
 9VC  plan-3  NZ   0.020
 9VC  plan-3  O12  0.020
 9VC  plan-3  O13  0.020

