# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:56:58 2021
#   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  34  16  .  2022-08-10  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.662  44.1320  20.1599  -10.1545
 FF9  C1   C  CH2   0  -0.524  43.4253  21.2712   -9.3755
 FF9  N    N  NH2   0  -0.780  38.5989  26.4195  -15.1506
 FF9  CA   C  CH1   0  -0.194  39.0447  25.1224  -14.6844
 FF9  C    C  C     0   0.520  37.9131  24.2720  -14.1257
 FF9  O    O  O     0  -0.446  37.0424  24.7013  -13.4083
 FF9  CB   C  CH2   0  -0.430  40.1145  25.3115  -13.6045
 FF9  CG   C  CH2   0  -0.441  40.7274  24.0271  -13.0593
 FF9  CD   C  CH2   0  -0.425  41.8761  24.3193  -12.1034
 FF9  CE   C  CH2   0  -0.318  42.5063  23.0525  -11.5444
 FF9  NZ   N  N     0  -0.325  43.6047  23.3893  -10.6716
 FF9  CX1  C  C     0   0.108  43.9738  22.6218   -9.7382
 FF9  CX2  C  C     0   0.518  45.1594  23.0803   -8.9247
 FF9  O1   O  OH1   0  -0.578  45.5857  24.2879   -9.2466
 FF9  O2   O  O     0  -0.429  45.6632  22.3979   -8.0665
 FF9  OXT  O  OH1   0  -0.589  37.9894  22.9994  -14.4951
 FF9  H1   H  HCH3  0   0.244  43.7403  19.1860   -9.8635
 FF9  H2   H  HCH3  0   0.232  43.9823  20.2710  -11.2287
 FF9  H3   H  HCH3  0   0.234  45.2048  20.1587   -9.9633
 FF9  H4   H  HCH2  0   0.262  42.3563  21.2343   -9.5875
 FF9  H5   H  HCH2  0   0.260  43.5379  21.0986   -8.3059
 FF9  H7   H  HNH2  0   0.345  38.1235  26.9121  -14.4037
 FF9  H9   H  HCH1  0   0.259  39.4930  24.5922  -15.5283
 FF9  H10  H  HCH2  0   0.242  40.9010  25.9296  -14.0450
 FF9  H11  H  HCH2  0   0.228  39.6863  25.8934  -12.7812
 FF9  H12  H  HCH2  0   0.225  39.9744  23.4287  -12.5374
 FF9  H13  H  HCH2  0   0.222  41.0893  23.4110  -13.8890
 FF9  H14  H  HCH2  0   0.225  42.6432  24.9065  -12.6157
 FF9  H15  H  HCH2  0   0.224  41.5149  24.9345  -11.2736
 FF9  H16  H  HCH2  0   0.228  41.7418  22.4361  -11.0574
 FF9  H17  H  HCH2  0   0.248  42.9045  22.4502  -12.3692
 FF9  H18  H  HOH1  0   0.484  46.3473  24.5182   -8.6937
 FF9  HXT  H  HOH1  0   0.478  37.2747  22.4896  -14.0836
 FF9  H6   H  HNH2  0   0.355  37.9253  26.3156  -15.8989

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    double  1.231  0.020  1.231
 FF9  CG   CD   single  1.523  0.020  1.523
 FF9  CD   CE   single  1.521  0.020  1.521
 FF9  CE   NZ   single  1.443  0.020  1.443
 FF9  NZ   CX1  double  1.264  0.020  1.264
 FF9  C2   C1   single  1.530  0.020  1.530
 FF9  CX1  C1   single  1.502  0.020  1.502
 FF9  CX1  CX2  single  1.509  0.020  1.509
 FF9  CX2  O2   double  1.207  0.020  1.207
 FF9  CX2  O1   single  1.320  0.020  1.320
 FF9  C    OXT  single  1.327  0.020  1.327
 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
 FF9  O1   H18  single  0.850  0.020  0.980
 FF9  OXT  HXT  single  0.850  0.020  0.980

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   107.94  3.000
 FF9  H3   C2   H1   107.82  3.000
 FF9  H2   C2   H1   107.76  3.000
 FF9  H3   C2   C1   111.48  3.000
 FF9  H2   C2   C1   111.36  3.000
 FF9  H1   C2   C1   110.32  3.000
 FF9  H5   C1   H4   106.68  3.000
 FF9  H5   C1   CX1  109.99  3.000
 FF9  H4   C1   CX1  109.96  3.000
 FF9  H5   C1   C2   109.70  3.000
 FF9  H4   C1   C2   109.22  3.000
 FF9  CX1  C1   C2   111.19  3.000
 FF9  H7   N    H6   106.42  3.000
 FF9  H7   N    CA   110.03  3.000
 FF9  H6   N    CA   110.54  3.000
 FF9  H9   CA   CB   108.53  3.000
 FF9  H9   CA   C    108.51  3.000
 FF9  CB   CA   C    110.10  1.900
 FF9  H9   CA   N    108.19  3.000
 FF9  C    CA   N    111.00  2.800
 FF9  CB   CA   N    110.50  1.700
 FF9  OXT  C    O    123.22  3.000
 FF9  OXT  C    CA   113.00  3.000
 FF9  O    C    CA   120.80  1.700
 FF9  H11  CB   H10  106.49  3.000
 FF9  H11  CB   CG   109.63  3.000
 FF9  H10  CB   CG   109.35  3.000
 FF9  H11  CB   CA   108.81  3.000
 FF9  H10  CB   CA   106.76  3.000
 FF9  CG   CB   CA   115.41  3.000
 FF9  H13  CG   H12  106.33  3.000
 FF9  H13  CG   CD   109.53  3.000
 FF9  H12  CG   CD   108.95  3.000
 FF9  H13  CG   CB   109.63  3.000
 FF9  H12  CG   CB   110.78  3.000
 FF9  CD   CG   CB   111.48  3.000
 FF9  H15  CD   H14  106.55  3.000
 FF9  H15  CD   CE   109.04  3.000
 FF9  H14  CD   CE   109.19  3.000
 FF9  H15  CD   CG   109.57  3.000
 FF9  H14  CD   CG   109.77  3.000
 FF9  CE   CD   CG   112.54  3.000
 FF9  H17  CE   H16  106.18  3.000
 FF9  H17  CE   NZ   107.87  3.000
 FF9  H16  CE   NZ   113.17  3.000
 FF9  H17  CE   CD   109.36  3.000
 FF9  H16  CE   CD   110.04  3.000
 FF9  NZ   CE   CD   110.08  3.000
 FF9  CX1  NZ   CE   121.83  3.000
 FF9  CX2  CX1  NZ   116.30  3.000
 FF9  CX2  CX1  C1   115.46  3.000
 FF9  NZ   CX1  C1   128.16  3.000
 FF9  O2   CX2  O1   123.76  3.000
 FF9  O1   CX2  CX1  113.59  3.000
 FF9  O2   CX2  CX1  122.65  3.000
 FF9  H18  O1   CX2  109.40  3.000
 FF9  HXT  OXT  C    110.09  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  CONST_01  HXT  OXT  C    CA    180.00   0.0  0
 FF9  CONST_02  H18  O1   CX2  CX1   180.00   0.0  0
 FF9  Var_01    CX2  CX1  NZ   CE    178.43   0.0  2
 FF9  Var_02    NZ   CX1  C1   C2     88.17  30.0  2
 FF9  Var_03    O2   CX2  CX1  C1      2.12  30.0  2
 FF9  Var_04    CD   CG   CB   CA    174.04  30.0  3
 FF9  Var_05    CE   CD   CG   CB   -179.99  30.0  3
 FF9  Var_06    NZ   CE   CD   CG    178.71  30.0  3
 FF9  Var_07    H1   C2   C1   CX1   178.65  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-1  HXT  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-2  H18  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

