# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:46:58 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: N~2~-[(2Z,4E)-7-methylocta-2,4-dienoyl]-L-asparagine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C\C=C\C=C/C(=O)N[C@@H](CC(N)=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
 AFA  AFA  N~2~-[(2Z,4E)-7-methylocta-2,4-dienoyl]-L-asparagine  L-peptide  38  19  .  2012-08-28  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AFA
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
 AFA  N     N  NH1    0  -0.639  14.6436  22.9851  27.1637
 AFA  CA    C  CH1    0  -0.192  15.0330  22.3143  25.9472
 AFA  CB    C  CH2    0  -0.598  15.0746  20.8100  26.1921
 AFA  CG    C  C      0   0.526  16.0907  20.4224  27.2482
 AFA  OD1   O  O      0  -0.489  17.2252  20.8782  27.2516
 AFA  ND2   N  NH2    0  -0.803  15.6625  19.5323  28.1572
 AFA  C     C  C      0   0.413  14.1124  22.6384  24.7324
 AFA  O     O  O      0  -0.585  13.0953  23.3165  24.9458
 AFA  OXT   O  OC    -1  -0.606  14.5038  22.1623  23.6490
 AFA  C1    C  C      0   0.547  14.9231  24.2819  27.4032
 AFA  O1    O  O      0  -0.505  15.6733  24.9375  26.6853
 AFA  C2    C  C1     0  -0.409  14.2688  24.8154  28.6184
 AFA  C3    C  C1     0  -0.197  14.3622  26.0662  29.0997
 AFA  C4    C  C1     0  -0.270  15.1046  27.2008  28.5885
 AFA  C5    C  C1     0  -0.184  15.0492  28.3963  29.1912
 AFA  C6    C  CH2    0  -0.474  15.7793  29.6095  28.7249
 AFA  C7    C  CH1    0  -0.230  16.8385  30.1276  29.7121
 AFA  C8    C  CH3    0  -0.650  17.5970  31.2936  29.0862
 AFA  C9    C  CH3    0  -0.657  16.2276  30.5429  31.0462
 AFA  H     H  HNH1   0   0.389  13.9105  22.5574  27.7082
 AFA  HA    H  HCH1   0   0.243  16.0414  22.6441  25.6916
 AFA  HB2   H  HCH2   0   0.281  15.3594  20.3161  25.2611
 AFA  HB3   H  HCH2   0   0.252  14.0776  20.4386  26.4471
 AFA  HD21  H  HNH2   0   0.404  14.7288  19.1606  28.1424
 AFA  HD22  H  HNH2   0   0.395  16.2874  19.1877  28.8682
 AFA  H2    H  H      0   0.254  13.6426  24.1229  29.1704
 AFA  H3    H  H      0   0.253  13.7961  26.2681  30.0052
 AFA  H4    H  H      0   0.256  15.7088  27.0759  27.7003
 AFA  H5    H  H      0   0.251  14.4298  28.5022  30.0790
 AFA  H61   H  HCH2   0   0.239  16.2565  29.3989  27.7640
 AFA  H62   H  HCH2   0   0.231  15.0564  30.4161  28.5497
 AFA  H7    H  HCH1   0   0.221  17.5501  29.3146  29.8940
 AFA  H81   H  HCH3   0   0.214  16.9248  32.1314  28.8855
 AFA  H82   H  HCH3   0   0.225  18.0632  31.0084  28.1416
 AFA  H83   H  HCH3   0   0.226  18.3843  31.6546  29.7499
 AFA  H91   H  HCH3   0   0.228  16.9930  30.9357  31.7171
 AFA  H92   H  HCH3   0   0.215  15.4803  31.3267  30.9005
 AFA  H93   H  HCH3   0   0.228  15.7424  29.7114  31.5584

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
 AFA  N    CA    single  1.458  0.019  1.458
 AFA  N    C1    single  1.348  0.020  1.348
 AFA  N    H     single  0.860  0.020  0.860
 AFA  CA   CB    single  1.530  0.020  1.530
 AFA  CA   C     single  1.525  0.021  1.525
 AFA  CA   HA    single  0.970  0.020  0.970
 AFA  CB   CG    single  1.516  0.020  1.516
 AFA  CB   HB2   single  0.970  0.020  1.090
 AFA  CB   HB3   single  0.970  0.020  1.090
 AFA  CG   OD1   double  1.223  0.020  1.223
 AFA  CG   ND2   single  1.342  0.020  1.342
 AFA  ND2  HD21  single  0.860  0.020  1.020
 AFA  ND2  HD22  single  0.860  0.020  1.020
 AFA  C    O     deloc   1.231  0.020  1.231
 AFA  C    OXT   deloc   1.246  0.020  1.246
 AFA  C1   O1    double  1.228  0.020  1.228
 AFA  C1   C2    single  1.480  0.020  1.480
 AFA  C2   C3    double  1.343  0.020  1.343
 AFA  C2   H2    single  0.930  0.020  1.080
 AFA  C3   C4    single  1.449  0.020  1.449
 AFA  C3   H3    single  0.930  0.020  1.080
 AFA  C4   C5    double  1.340  0.020  1.340
 AFA  C4   H4    single  0.930  0.020  1.080
 AFA  C5   C6    single  1.491  0.020  1.491
 AFA  C5   H5    single  0.930  0.020  1.080
 AFA  C6   C7    single  1.538  0.020  1.538
 AFA  C6   H61   single  0.970  0.020  1.090
 AFA  C6   H62   single  0.970  0.020  1.090
 AFA  C7   C8    single  1.525  0.020  1.525
 AFA  C7   C9    single  1.525  0.020  1.525
 AFA  C7   H7    single  0.970  0.020  1.090
 AFA  C8   H81   single  0.970  0.020  1.090
 AFA  C8   H82   single  0.970  0.020  1.090
 AFA  C8   H83   single  0.970  0.020  1.090
 AFA  C9   H91   single  0.970  0.020  1.090
 AFA  C9   H92   single  0.970  0.020  1.090
 AFA  C9   H93   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
 AFA  H     N    C1    117.56  3.000
 AFA  H     N    CA    114.00  3.000
 AFA  C1    N    CA    122.76  3.000
 AFA  HA    CA   C     109.00  3.000
 AFA  HA    CA   CB    109.00  3.000
 AFA  C     CA   CB    110.10  1.900
 AFA  HA    CA   N     110.00  3.000
 AFA  C     CA   N     111.00  2.800
 AFA  CB    CA   N     110.50  1.700
 AFA  HB3   CB   HB2   106.44  3.000
 AFA  HB3   CB   CG    111.20  3.000
 AFA  HB2   CB   CG    107.67  3.000
 AFA  HB3   CB   CA    110.33  3.000
 AFA  HB2   CB   CA    108.45  3.000
 AFA  CG    CB   CA    112.48  3.000
 AFA  ND2   CG   OD1   122.77  3.000
 AFA  ND2   CG   CB    115.31  3.000
 AFA  OD1   CG   CB    121.91  3.000
 AFA  HD22  ND2  HD21  117.40  3.000
 AFA  HD22  ND2  CG    120.46  3.000
 AFA  HD21  ND2  CG    122.11  3.000
 AFA  OXT   C    O     128.00  3.000
 AFA  OXT   C    CA    114.37  3.000
 AFA  O     C    CA    120.80  1.700
 AFA  C2    C1   O1    123.90  3.000
 AFA  C2    C1   N     113.65  3.000
 AFA  O1    C1   N     122.44  3.000
 AFA  H2    C2   C3    116.89  3.000
 AFA  H2    C2   C1    116.30  3.000
 AFA  C3    C2   C1    126.81  3.000
 AFA  H3    C3   C4    114.54  3.000
 AFA  H3    C3   C2    115.80  3.000
 AFA  C4    C3   C2    129.66  3.000
 AFA  H4    C4   C5    119.71  3.000
 AFA  H4    C4   C3    119.04  3.000
 AFA  C5    C4   C3    121.25  3.000
 AFA  H5    C5   C6    117.06  3.000
 AFA  H5    C5   C4    118.52  3.000
 AFA  C6    C5   C4    124.41  3.000
 AFA  H62   C6   H61   106.79  3.000
 AFA  H62   C6   C7    107.98  3.000
 AFA  H61   C6   C7    109.18  3.000
 AFA  H62   C6   C5    109.00  3.000
 AFA  H61   C6   C5    109.38  3.000
 AFA  C7    C6   C5    114.25  3.000
 AFA  H7    C7   C9    108.48  3.000
 AFA  H7    C7   C8    108.20  3.000
 AFA  C9    C7   C8    110.49  3.000
 AFA  H7    C7   C6    107.70  3.000
 AFA  C9    C7   C6    112.18  3.000
 AFA  C8    C7   C6    109.67  3.000
 AFA  H83   C8   H82   107.74  3.000
 AFA  H83   C8   H81   107.57  3.000
 AFA  H82   C8   H81   107.71  3.000
 AFA  H83   C8   C7    111.23  3.000
 AFA  H82   C8   C7    111.58  3.000
 AFA  H81   C8   C7    110.83  3.000
 AFA  H93   C9   H92   107.77  3.000
 AFA  H93   C9   H91   107.33  3.000
 AFA  H92   C9   H91   107.67  3.000
 AFA  H93   C9   C7    112.43  3.000
 AFA  H92   C9   C7    110.65  3.000
 AFA  H91   C9   C7    110.79  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
 AFA  CONST_01  O1    C1   N   CA     0.00   0.0  0
 AFA  CONST_02  C2    C1   N   CA   180.00   0.0  0
 AFA  CONST_03  HD21  ND2  CG  CB     0.00   0.0  0
 AFA  CONST_04  HD22  ND2  CG  CB   180.00   0.0  0
 AFA  CONST_05  H     N    C1  O1   180.00   0.0  0
 AFA  Var_01    C4    C3   C2  C1    -0.25   0.0  2
 AFA  Var_02    C6    C5   C4  C3  -179.83   0.0  2
 AFA  Var_03    C3    C2   C1  N   -179.84  30.0  2
 AFA  Var_04    OD1   CG   CB  CA   -46.07  30.0  3
 AFA  Var_05    C5    C4   C3  C2   178.19  30.0  2
 AFA  Var_06    C7    C6   C5  C4  -115.91  30.0  3
 AFA  Var_07    C8    C7   C6  C5   175.36  30.0  3
 AFA  Var_08    H81   C8   C7  C6    62.74  30.0  3
 AFA  Var_09    H91   C9   C7  C6  -178.20  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
 AFA  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
 AFA  plan-1  CB    0.020
 AFA  plan-1  CG    0.020
 AFA  plan-1  OD1   0.020
 AFA  plan-1  ND2   0.020
 AFA  plan-1  HD21  0.020
 AFA  plan-1  HD22  0.020
 AFA  plan-2  C3    0.020
 AFA  plan-2  C4    0.020
 AFA  plan-2  C5    0.020
 AFA  plan-2  C6    0.020
 AFA  plan-2  H4    0.020
 AFA  plan-2  H5    0.020
 AFA  plan-3  N     0.020
 AFA  plan-3  CA    0.020
 AFA  plan-3  C1    0.020
 AFA  plan-3  O1    0.020
 AFA  plan-3  C2    0.020
 AFA  plan-3  H     0.020
 AFA  plan-4  CA    0.020
 AFA  plan-4  C     0.020
 AFA  plan-4  O     0.020
 AFA  plan-4  OXT   0.020
 AFA  plan-5  C1    0.020
 AFA  plan-5  C2    0.020
 AFA  plan-5  C3    0.020
 AFA  plan-5  C4    0.020
 AFA  plan-5  H2    0.020
 AFA  plan-5  H3    0.020

