# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:40:00 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[(2-bromophenyl)methoxycarbonylamino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1ccccc1Br)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
 9VL  9VL  '(2~{S})-2-azanyl-6-[(2-bromophenyl)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_9VL
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
 9VL  C15  C   CR6    0   0.140  197.4803  37.1647  74.9247
 9VL  C20  C   CR16   0  -0.233  199.0652  38.9907  75.1124
 9VL  C21  C   CR16   0  -0.303  198.6295  37.7248  75.4747
 9VL  C    C   C      0   0.385  192.9385  36.2225  82.6738
 9VL  CA   C   CH1    0  -0.191  191.8531  35.3391  82.0154
 9VL  CB   C   CH2    0  -0.411  191.5347  35.8612  80.6135
 9VL  CG   C   CH2    0  -0.418  192.7176  35.8879  79.6543
 9VL  CD   C   CH2    0  -0.472  192.3100  36.3493  78.2600
 9VL  CE   C   CH2    0  -0.263  193.4611  36.4299  77.2701
 9VL  C11  C   C      0   0.739  195.1410  34.8320  76.3479
 9VL  C14  C   CH2    0  -0.237  197.0485  35.7921  75.3435
 9VL  C16  C   CR6    0  -0.158  196.7719  37.9264  73.9950
 9VL  C18  C   CR16   0  -0.218  197.1886  39.1959  73.6245
 9VL  C19  C   CR16   0  -0.260  198.3404  39.7271  74.1889
 9VL  N    N   NH2    0  -0.794  190.6056  35.2668  82.7759
 9VL  NZ   N   NH1    0  -0.660  194.0058  35.1081  77.0120
 9VL  O12  O   O      0  -0.520  195.5048  33.7174  76.0282
 9VL  O13  O   O2     0  -0.470  195.8452  35.9415  76.0916
 9VL  BR   BR  BR     0  -0.043  195.2076  37.2345  73.1862
 9VL  H20  H   HCR6   0   0.266  199.9639  39.3995  75.5542
 9VL  H21  H   HCR6   0   0.267  199.1923  37.1508  76.2006
 9VL  HA   H   HCH1   0   0.192  192.2401  34.3191  81.9168
 9VL  HB2  H   HCH2   0   0.200  191.1142  36.8700  80.6993
 9VL  HB3  H   HCH2   0   0.209  190.7427  35.2358  80.1886
 9VL  HG2  H   HCH2   0   0.211  193.1660  34.8908  79.6057
 9VL  HG3  H   HCH2   0   0.217  193.4994  36.5546  80.0288
 9VL  HD2  H   HCH2   0   0.237  191.8627  37.3448  78.3238
 9VL  HD3  H   HCH2   0   0.225  191.5282  35.6939  77.8602
 9VL  HE2  H   HCH2   0   0.236  194.2416  37.0751  77.6769
 9VL  HE3  H   HCH2   0   0.237  193.1134  36.8919  76.3407
 9VL  H12  H   HCH2   0   0.251  196.8896  35.1479  74.4759
 9VL  H13  H   HCH2   0   0.261  197.8226  35.3307  75.9603
 9VL  H18  H   HCR6   0   0.281  196.6269  39.7730  72.9022
 9VL  H19  H   HCR6   0   0.270  198.6658  40.7175  73.8993
 9VL  H    H   HNH2   0   0.332  190.7897  34.8069  83.6604
 9VL  H2   H   HNH2   0   0.321  190.3545  36.2167  83.0299
 9VL  HZ   H   HNH1   0   0.398  193.3953  34.3187  77.1571
 9VL  O    O   O      0  -0.612  192.5493  37.3235  83.1208
 9VL  OXT  O   OC    -1  -0.612  194.1066  35.7840  82.6856

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
 9VL  C20  C21  aromatic  1.387  0.020  1.387
 9VL  C20  C19  aromatic  1.386  0.020  1.386
 9VL  C21  C15  aromatic  1.392  0.020  1.392
 9VL  C19  C18  aromatic  1.388  0.020  1.388
 9VL  C15  C14  single    1.499  0.020  1.499
 9VL  C15  C16  aromatic  1.395  0.020  1.395
 9VL  C18  C16  aromatic  1.387  0.020  1.387
 9VL  C14  O13  single    1.425  0.020  1.425
 9VL  C16  BR   single    1.892  0.020  1.892
 9VL  O13  C11  single    1.339  0.020  1.339
 9VL  O12  C11  double    1.215  0.020  1.215
 9VL  C11  NZ   single    1.344  0.020  1.344
 9VL  CE   NZ   single    1.453  0.020  1.453
 9VL  CE   CD   single    1.520  0.020  1.520
 9VL  CD   CG   single    1.524  0.020  1.524
 9VL  CG   CB   single    1.523  0.020  1.523
 9VL  CB   CA   single    1.521  0.033  1.521
 9VL  O    C    deloc     1.231  0.020  1.231
 9VL  CA   C    single    1.525  0.021  1.525
 9VL  CA   N    single    1.458  0.019  1.458
 9VL  C    OXT  deloc     1.248  0.020  1.248
 9VL  C20  H20  single    0.930  0.020  1.080
 9VL  C21  H21  single    0.930  0.020  1.080
 9VL  CA   HA   single    0.970  0.020  0.970
 9VL  CB   HB2  single    0.970  0.020  1.090
 9VL  CB   HB3  single    0.970  0.020  1.090
 9VL  CG   HG2  single    0.970  0.020  1.090
 9VL  CG   HG3  single    0.970  0.020  1.090
 9VL  CD   HD2  single    0.970  0.020  1.090
 9VL  CD   HD3  single    0.970  0.020  1.090
 9VL  CE   HE2  single    0.970  0.020  1.090
 9VL  CE   HE3  single    0.970  0.020  1.090
 9VL  C14  H12  single    0.970  0.020  1.090
 9VL  C14  H13  single    0.970  0.020  1.090
 9VL  C18  H18  single    0.930  0.020  1.080
 9VL  C19  H19  single    0.930  0.020  1.080
 9VL  N    H    single    0.860  0.020  0.860
 9VL  N    H2   single    0.890  0.020  1.040
 9VL  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
 9VL  C16  C15  C14  122.68  3.000
 9VL  C16  C15  C21  117.58  3.000
 9VL  C14  C15  C21  119.74  3.000
 9VL  H20  C20  C19  120.39  3.000
 9VL  H20  C20  C21  119.95  3.000
 9VL  C19  C20  C21  119.65  3.000
 9VL  H21  C21  C20  119.70  3.000
 9VL  H21  C21  C15  118.73  3.000
 9VL  C20  C21  C15  121.57  3.000
 9VL  OXT  C    O    126.69  3.000
 9VL  OXT  C    CA   120.80  1.700
 9VL  O    C    CA   120.80  1.700
 9VL  HA   CA   N    110.00  3.000
 9VL  HA   CA   CB   109.00  3.000
 9VL  N    CA   CB   110.40  1.500
 9VL  HA   CA   C    110.00  3.000
 9VL  N    CA   C    111.00  2.800
 9VL  CB   CA   C    110.50  1.500
 9VL  HB3  CB   HB2  106.17  3.000
 9VL  HB3  CB   CG   109.11  3.000
 9VL  HB2  CB   CG   109.33  3.000
 9VL  HB3  CB   CA   108.14  3.000
 9VL  HB2  CB   CA   108.80  3.000
 9VL  CG   CB   CA   114.93  3.000
 9VL  HG3  CG   HG2  106.13  3.000
 9VL  HG3  CG   CD   108.66  3.000
 9VL  HG2  CG   CD   110.17  3.000
 9VL  HG3  CG   CB   110.50  3.000
 9VL  HG2  CG   CB   109.28  3.000
 9VL  CD   CG   CB   111.94  3.000
 9VL  HD3  CD   HD2  105.90  3.000
 9VL  HD3  CD   CE   109.53  3.000
 9VL  HD2  CD   CE   107.42  3.000
 9VL  HD3  CD   CG   110.10  3.000
 9VL  HD2  CD   CG   109.37  3.000
 9VL  CE   CD   CG   114.15  3.000
 9VL  HE3  CE   HE2  107.11  3.000
 9VL  HE3  CE   NZ   110.62  3.000
 9VL  HE2  CE   NZ   109.63  3.000
 9VL  HE3  CE   CD   109.55  3.000
 9VL  HE2  CE   CD   109.28  3.000
 9VL  NZ   CE   CD   110.57  3.000
 9VL  O13  C11  O12  123.52  3.000
 9VL  O12  C11  NZ   124.84  3.000
 9VL  O13  C11  NZ   111.63  3.000
 9VL  H13  C14  H12  107.61  3.000
 9VL  H13  C14  O13  110.27  3.000
 9VL  H12  C14  O13  110.86  3.000
 9VL  H13  C14  C15  109.91  3.000
 9VL  H12  C14  C15  111.11  3.000
 9VL  O13  C14  C15  107.10  3.000
 9VL  BR   C16  C18  117.97  3.000
 9VL  BR   C16  C15  120.33  3.000
 9VL  C18  C16  C15  121.69  3.000
 9VL  H18  C18  C19  119.87  3.000
 9VL  H18  C18  C16  120.72  3.000
 9VL  C19  C18  C16  119.41  3.000
 9VL  H19  C19  C18  119.41  3.000
 9VL  H19  C19  C20  120.50  3.000
 9VL  C18  C19  C20  120.10  3.000
 9VL  H2   N    H    104.54  3.000
 9VL  H2   N    CA   107.15  3.000
 9VL  H    N    CA   114.00  3.000
 9VL  HZ   NZ   C11  114.94  3.000
 9VL  HZ   NZ   CE   117.37  3.000
 9VL  C11  NZ   CE   126.26  3.000
 9VL  C14  O13  C11  117.25  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
 9VL  CONST_01  C19  C20  C21  C15     0.00   0.0  0
 9VL  CONST_02  C19  C18  C16  C15     0.00   0.0  0
 9VL  CONST_03  C16  C15  C21  C20     0.00   0.0  0
 9VL  CONST_04  C16  C18  C19  C20     0.00   0.0  0
 9VL  CONST_05  C18  C19  C20  C21     0.00   0.0  0
 9VL  CONST_06  C18  C16  C15  C21     0.00   0.0  0
 9VL  CONST_07  C14  C15  C21  C20   180.00   0.0  0
 9VL  CONST_08  BR   C16  C15  C21   180.00   0.0  0
 9VL  CONST_09  C18  C16  C15  C14   180.00   0.0  0
 9VL  CONST_10  BR   C16  C18  C19   180.00   0.0  0
 9VL  CONST_11  H20  C20  C21  C15   180.00   0.0  0
 9VL  CONST_12  H18  C18  C16  C15   180.00   0.0  0
 9VL  CONST_13  H19  C19  C20  C21   180.00   0.0  0
 9VL  CONST_14  H21  C21  C15  C16   180.00   0.0  0
 9VL  Var_01    O13  C14  C15  C21   111.33  30.0  2
 9VL  Var_02    CD   CG   CB   CA    177.01  30.0  1
 9VL  Var_03    CE   CD   CG   CB    178.46  30.0  1
 9VL  Var_04    NZ   CE   CD   CG     65.31  30.0  1
 9VL  Var_05    C11  NZ   CE   CD   -169.65  30.0  3
 9VL  Var_06    O13  C11  NZ   CE      8.75  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
 9VL  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
 9VL  plan-1  C15  0.020
 9VL  plan-1  C20  0.020
 9VL  plan-1  C21  0.020
 9VL  plan-1  C14  0.020
 9VL  plan-1  C16  0.020
 9VL  plan-1  C18  0.020
 9VL  plan-1  C19  0.020
 9VL  plan-1  BR   0.020
 9VL  plan-1  H20  0.020
 9VL  plan-1  H21  0.020
 9VL  plan-1  H18  0.020
 9VL  plan-1  H19  0.020
 9VL  plan-2  C    0.020
 9VL  plan-2  CA   0.020
 9VL  plan-2  O    0.020
 9VL  plan-2  OXT  0.020
 9VL  plan-3  C11  0.020
 9VL  plan-3  NZ   0.020
 9VL  plan-3  O12  0.020
 9VL  plan-3  O13  0.020

