# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 19:24:57 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[(~{E})-(1-oxidanyl-1-oxidanylidene-butan-2-ylidene)amino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=NCCCC[C@H](N)C(O)=O)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
 FF9  FF9  '(2~{S})-2-azanyl-6-[(~{E})-(1-oxidanyl-1-oxidanylidene-butan-2-ylidene)amino]hexanoic acid'  L-peptide  32  16  .  2022-08-10  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_FF9
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
 FF9  C2   C  CH3    0  -0.659  44.3681  20.3928  -10.7558
 FF9  C1   C  CH2    0  -0.515  43.6677  21.1495   -9.6254
 FF9  N    N  NH2    0  -0.794  39.0135  25.9892  -15.6490
 FF9  CA   C  CH1    0  -0.191  39.2173  24.8087  -14.8098
 FF9  C    C  C      0   0.384  37.9204  24.2480  -14.1791
 FF9  O    O  O      0  -0.612  37.1213  25.0940  -13.7222
 FF9  CB   C  CH2    0  -0.411  40.2298  25.1646  -13.7178
 FF9  CG   C  CH2    0  -0.425  40.6371  24.0091  -12.8111
 FF9  CD   C  CH2    0  -0.421  41.8326  24.3463  -11.9301
 FF9  CE   C  CH2    0  -0.313  42.2208  23.1947  -11.0143
 FF9  NZ   N  N      0  -0.356  43.4017  23.5228  -10.2398
 FF9  CX1  C  C      0   0.060  44.0349  22.6122   -9.6234
 FF9  CX2  C  C      0   0.373  45.3133  23.0116   -8.8529
 FF9  O1   O  OC    -1  -0.588  45.5271  24.2233   -8.6901
 FF9  O2   O  O      0  -0.586  46.0246  22.0601   -8.4726
 FF9  OXT  O  OC    -1  -0.614  37.7847  23.0071  -14.1564
 FF9  H1   H  HCH3   0   0.227  44.1061  19.3345  -10.7346
 FF9  H2   H  HCH3   0   0.221  44.0871  20.7823  -11.7352
 FF9  H3   H  HCH3   0   0.226  45.4498  20.4733  -10.6617
 FF9  H4   H  HCH2   0   0.236  42.5872  21.0280   -9.7252
 FF9  H5   H  HCH2   0   0.238  43.9495  20.7036   -8.6722
 FF9  H9   H  HCH1   0   0.192  39.6643  24.0306  -15.4380
 FF9  H10  H  HCH2   0   0.207  41.1224  25.5670  -14.2078
 FF9  H11  H  HCH2   0   0.200  39.8216  25.9797  -13.1092
 FF9  H12  H  HCH2   0   0.211  39.7954  23.7097  -12.1799
 FF9  H13  H  HCH2   0   0.203  40.8800  23.1339  -13.4240
 FF9  H14  H  HCH2   0   0.208  42.6892  24.6040  -12.5613
 FF9  H15  H  HCH2   0   0.209  41.6169  25.2337  -11.3261
 FF9  H16  H  HCH2   0   0.223  41.3841  22.9765  -10.3382
 FF9  H17  H  HCH2   0   0.213  42.3560  22.2918  -11.6224
 FF9  H6   H  HNH2   0   0.331  38.4306  25.7322  -16.4376
 FF9  H7   H  HNH2   0   0.321  38.4485  26.6428  -15.1170

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
 FF9  N    CA   single  1.458  0.019  1.458
 FF9  CA   CB   single  1.530  0.020  1.530
 FF9  CA   C    single  1.525  0.021  1.525
 FF9  CB   CG   single  1.524  0.020  1.524
 FF9  C    O    deloc   1.231  0.020  1.231
 FF9  CG   CD   single  1.523  0.020  1.523
 FF9  CD   CE   single  1.522  0.020  1.522
 FF9  CE   NZ   single  1.450  0.020  1.450
 FF9  NZ   CX1  double  1.269  0.020  1.269
 FF9  C2   C1   single  1.530  0.020  1.530
 FF9  CX1  C1   single  1.508  0.020  1.508
 FF9  CX1  CX2  single  1.545  0.020  1.545
 FF9  CX2  O2   deloc   1.247  0.020  1.247
 FF9  CX2  O1   deloc   1.241  0.020  1.241
 FF9  C    OXT  deloc   1.248  0.020  1.248
 FF9  C2   H1   single  0.970  0.020  1.090
 FF9  C2   H2   single  0.970  0.020  1.090
 FF9  C2   H3   single  0.970  0.020  1.090
 FF9  C1   H4   single  0.970  0.020  1.090
 FF9  C1   H5   single  0.970  0.020  1.090
 FF9  N    H6   single  0.890  0.020  1.040
 FF9  N    H7   single  0.890  0.020  1.040
 FF9  CA   H9   single  0.970  0.020  1.090
 FF9  CB   H10  single  0.970  0.020  1.090
 FF9  CB   H11  single  0.970  0.020  1.090
 FF9  CG   H12  single  0.970  0.020  1.090
 FF9  CG   H13  single  0.970  0.020  1.090
 FF9  CD   H14  single  0.970  0.020  1.090
 FF9  CD   H15  single  0.970  0.020  1.090
 FF9  CE   H16  single  0.970  0.020  1.090
 FF9  CE   H17  single  0.970  0.020  1.090

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
 FF9  H3   C2   H2   107.89  3.000
 FF9  H3   C2   H1   107.98  3.000
 FF9  H2   C2   H1   107.58  3.000
 FF9  H3   C2   C1   110.76  3.000
 FF9  H2   C2   C1   111.65  3.000
 FF9  H1   C2   C1   110.83  3.000
 FF9  H5   C1   H4   106.88  3.000
 FF9  H5   C1   CX1  109.44  3.000
 FF9  H4   C1   CX1  110.42  3.000
 FF9  H5   C1   C2   109.00  3.000
 FF9  H4   C1   C2   109.30  3.000
 FF9  CX1  C1   C2   111.67  3.000
 FF9  H7   N    H6   104.53  3.000
 FF9  H7   N    CA   107.26  3.000
 FF9  H6   N    CA   108.77  3.000
 FF9  H9   CA   CB   107.72  3.000
 FF9  H9   CA   C    108.56  3.000
 FF9  CB   CA   C    110.10  1.900
 FF9  H9   CA   N    107.53  3.000
 FF9  C    CA   N    111.00  2.800
 FF9  CB   CA   N    110.50  1.700
 FF9  OXT  C    O    126.62  3.000
 FF9  OXT  C    CA   117.30  3.000
 FF9  O    C    CA   120.80  1.700
 FF9  H11  CB   H10  106.19  3.000
 FF9  H11  CB   CG   109.45  3.000
 FF9  H10  CB   CG   109.08  3.000
 FF9  H11  CB   CA   108.82  3.000
 FF9  H10  CB   CA   107.78  3.000
 FF9  CG   CB   CA   115.14  3.000
 FF9  H13  CG   H12  105.95  3.000
 FF9  H13  CG   CD   109.06  3.000
 FF9  H12  CG   CD   109.32  3.000
 FF9  H13  CG   CB   109.39  3.000
 FF9  H12  CG   CB   110.19  3.000
 FF9  CD   CG   CB   112.71  3.000
 FF9  H15  CD   H14  106.35  3.000
 FF9  H15  CD   CE   109.36  3.000
 FF9  H14  CD   CE   108.99  3.000
 FF9  H15  CD   CG   110.12  3.000
 FF9  H14  CD   CG   109.44  3.000
 FF9  CE   CD   CG   112.39  3.000
 FF9  H17  CE   H16  105.77  3.000
 FF9  H17  CE   NZ   112.46  3.000
 FF9  H16  CE   NZ   109.68  3.000
 FF9  H17  CE   CD   108.71  3.000
 FF9  H16  CE   CD   109.07  3.000
 FF9  NZ   CE   CD   110.98  3.000
 FF9  CX1  NZ   CE   120.23  3.000
 FF9  CX2  CX1  NZ   118.01  3.000
 FF9  CX2  CX1  C1   116.92  3.000
 FF9  NZ   CX1  C1   125.02  3.000
 FF9  O2   CX2  O1   127.34  3.000
 FF9  O1   CX2  CX1  117.41  3.000
 FF9  O2   CX2  CX1  115.26  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
 FF9  Var_01  CX2  CX1  NZ   CE   177.97   0.0  2
 FF9  Var_02  NZ   CX1  C1   C2    90.94  30.0  2
 FF9  Var_03  O2   CX2  CX1  C1    10.13  30.0  2
 FF9  Var_04  CD   CG   CB   CA   168.81  30.0  3
 FF9  Var_05  CE   CD   CG   CB   179.20  30.0  3
 FF9  Var_06  NZ   CE   CD   CG   177.07  30.0  3
 FF9  Var_07  H1   C2   C1   CX1  179.07  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
 FF9  chir_01  CA  N  CB  C  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
 FF9  plan-1  CA   0.020
 FF9  plan-1  C    0.020
 FF9  plan-1  O    0.020
 FF9  plan-1  OXT  0.020
 FF9  plan-2  CX1  0.020
 FF9  plan-2  CX2  0.020
 FF9  plan-2  O1   0.020
 FF9  plan-2  O2   0.020
 FF9  plan-3  C1   0.020
 FF9  plan-3  CE   0.020
 FF9  plan-3  NZ   0.020
 FF9  plan-3  CX1  0.020
 FF9  plan-3  CX2  0.020

