# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 22:35:41 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-formyl-L-tryptophan
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cn(C=O)c2ccccc12)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
 TRF  TRF  '1-formyl-L-tryptophan    '  L-peptide  28  17  .  2012-08-28  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_TRF
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
 TRF  N    N  NH2    0  -0.812  17.8372  -1.8404  -2.8340
 TRF  CA   C  CH1    0  -0.171  18.6207  -1.9931  -1.6089
 TRF  CB   C  CH2    0  -0.504  20.0263  -2.4317  -2.0017
 TRF  CG   C  CR5    0   0.008  20.9293  -2.7449  -0.8570
 TRF  CD1  C  CR15   0  -0.076  20.6589  -2.7282   0.4661
 TRF  NE1  N  NR5    0  -0.586  21.7903  -3.0998   1.1979
 TRF  CE2  C  CR56   0   0.368  22.8257  -3.3618   0.3059
 TRF  CZ2  C  CR16   0  -0.288  24.1405  -3.7568   0.5202
 TRF  CH2  C  CR16   0  -0.272  24.9396  -3.9320  -0.5997
 TRF  CZ3  C  CR16   0  -0.253  24.4470  -3.7218  -1.8910
 TRF  CE3  C  CR16   0  -0.365  23.1346  -3.3302  -2.0935
 TRF  CD2  C  CR56   0   0.034  22.3127  -3.1474  -0.9838
 TRF  C    C  C      0   0.397  18.6438  -0.6401  -0.8475
 TRF  C1   C  C1     0   0.259  21.8096  -3.1604   2.5641
 TRF  O1   O  O      0  -0.417  22.7713  -3.4658   3.2255
 TRF  O    O  O      0  -0.606  18.0949  -0.6200   0.2741
 TRF  OXT  O  OC    -1  -0.595  19.2002   0.3128  -1.4246
 TRF  H    H  HNH2   0   0.338  16.8970  -1.5441  -2.6000
 TRF  H2   H  HNH2   0   0.335  17.7274  -2.7493  -3.2689
 TRF  HA   H  HCH1   0   0.181  18.1937  -2.7565  -0.9416
 TRF  HB2  H  HCH2   0   0.235  19.9650  -3.3187  -2.6442
 TRF  HB3  H  HCH2   0   0.234  20.4775  -1.6491  -2.6180
 TRF  HD1  H  HCR5   0   0.297  19.7505  -2.4636   0.9848
 TRF  HZ2  H  HCR6   0   0.272  24.5375  -3.9236   1.5095
 TRF  HH2  H  HCR6   0   0.255  25.9693  -4.2373  -0.4671
 TRF  HZ3  H  HCR6   0   0.253  25.1020  -3.8661  -2.7402
 TRF  HE3  H  HCR6   0   0.250  22.7561  -3.1663  -3.0948
 TRF  HC1  H  H      0   0.228  20.8360  -2.8948   2.9990

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
 TRF  N    CA   single    1.458  0.019  1.458
 TRF  N    H    single    0.860  0.020  0.860
 TRF  N    H2   single    0.890  0.020  1.040
 TRF  CA   CB   single    1.530  0.020  1.530
 TRF  CA   C    single    1.525  0.021  1.525
 TRF  CA   HA   single    0.970  0.020  0.970
 TRF  CB   CG   single    1.491  0.020  1.491
 TRF  CB   HB2  single    0.970  0.020  1.090
 TRF  CB   HB3  single    0.970  0.020  1.090
 TRF  CG   CD1  aromatic  1.351  0.020  1.351
 TRF  CG   CD2  aromatic  1.446  0.020  1.446
 TRF  CD1  NE1  aromatic  1.398  0.020  1.398
 TRF  CD1  HD1  single    0.930  0.020  1.080
 TRF  NE1  CE2  aromatic  1.392  0.020  1.392
 TRF  NE1  C1   single    1.368  0.020  1.368
 TRF  CE2  CZ2  aromatic  1.389  0.020  1.389
 TRF  CE2  CD2  aromatic  1.404  0.020  1.404
 TRF  CZ2  CH2  aromatic  1.387  0.020  1.387
 TRF  CZ2  HZ2  single    0.930  0.020  1.080
 TRF  CH2  CZ3  aromatic  1.398  0.020  1.398
 TRF  CH2  HH2  single    0.930  0.020  1.080
 TRF  CZ3  CE3  aromatic  1.385  0.020  1.385
 TRF  CZ3  HZ3  single    0.930  0.020  1.080
 TRF  CE3  CD2  aromatic  1.393  0.020  1.393
 TRF  CE3  HE3  single    0.930  0.020  1.080
 TRF  C    O    deloc     1.231  0.020  1.231
 TRF  C    OXT  deloc     1.245  0.020  1.245
 TRF  C1   O1   double    1.206  0.020  1.206
 TRF  C1   HC1  single    0.930  0.020  1.080

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
 TRF  H2   N    H    105.12  3.000
 TRF  H2   N    CA   108.90  3.000
 TRF  H    N    CA   114.00  3.000
 TRF  HA   CA   C    109.00  3.000
 TRF  HA   CA   CB   109.00  3.000
 TRF  C    CA   CB   110.10  1.900
 TRF  HA   CA   N    110.00  3.000
 TRF  C    CA   N    111.00  2.800
 TRF  CB   CA   N    110.50  1.700
 TRF  HB3  CB   HB2  105.76  3.000
 TRF  HB3  CB   CG   109.45  3.000
 TRF  HB2  CB   CG   108.28  3.000
 TRF  HB3  CB   CA   108.66  3.000
 TRF  HB2  CB   CA   109.40  3.000
 TRF  CG   CB   CA   114.91  3.000
 TRF  CD2  CG   CD1  106.31  3.000
 TRF  CD2  CG   CB   124.78  3.000
 TRF  CD1  CG   CB   128.91  3.000
 TRF  HD1  CD1  NE1  119.67  3.000
 TRF  HD1  CD1  CG   129.98  3.000
 TRF  NE1  CD1  CG   110.33  3.000
 TRF  C1   NE1  CE2  128.42  3.000
 TRF  C1   NE1  CD1  123.10  3.000
 TRF  CE2  NE1  CD1  108.47  3.000
 TRF  CD2  CE2  CZ2  122.05  3.000
 TRF  CD2  CE2  NE1  106.74  3.000
 TRF  CZ2  CE2  NE1  131.20  3.000
 TRF  HZ2  CZ2  CH2  120.59  3.000
 TRF  HZ2  CZ2  CE2  122.24  3.000
 TRF  CH2  CZ2  CE2  117.17  3.000
 TRF  HH2  CH2  CZ3  119.40  3.000
 TRF  HH2  CH2  CZ2  119.01  3.000
 TRF  CZ3  CH2  CZ2  121.59  3.000
 TRF  HZ3  CZ3  CE3  119.78  3.000
 TRF  HZ3  CZ3  CH2  119.44  3.000
 TRF  CE3  CZ3  CH2  120.77  3.000
 TRF  HE3  CE3  CD2  120.70  3.000
 TRF  HE3  CE3  CZ3  120.62  3.000
 TRF  CD2  CE3  CZ3  118.68  3.000
 TRF  CE3  CD2  CE2  119.74  3.000
 TRF  CE3  CD2  CG   132.12  3.000
 TRF  CE2  CD2  CG   108.14  3.000
 TRF  OXT  C    O    126.89  3.000
 TRF  OXT  C    CA   116.50  3.000
 TRF  O    C    CA   120.80  1.700
 TRF  HC1  C1   O1   123.39  3.000
 TRF  HC1  C1   NE1  111.85  3.000
 TRF  O1   C1   NE1  124.76  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
 TRF  CONST_01  CE2  NE1  CD1  CG     0.00   0.0  0
 TRF  CONST_02  NE1  CE2  CD2  CG     0.00   0.0  0
 TRF  CONST_03  CZ2  CE2  CD2  CG   180.00   0.0  0
 TRF  CONST_04  CZ3  CE3  CD2  CG   180.00   0.0  0
 TRF  CONST_05  CE2  CD2  CG   CD1    0.00   0.0  0
 TRF  CONST_06  CE3  CD2  CG   CD1  180.00   0.0  0
 TRF  CONST_07  CZ2  CE2  NE1  CD1  180.00   0.0  0
 TRF  CONST_08  CD2  CE2  NE1  CD1    0.00   0.0  0
 TRF  CONST_09  CD2  CG   CD1  NE1    0.00   0.0  0
 TRF  CONST_10  CH2  CZ2  CE2  NE1  180.00   0.0  0
 TRF  CONST_11  CE3  CD2  CE2  NE1  180.00   0.0  0
 TRF  CONST_12  CZ3  CH2  CZ2  CE2    0.00   0.0  0
 TRF  CONST_13  CZ3  CE3  CD2  CE2    0.00   0.0  0
 TRF  CONST_14  CE3  CD2  CE2  CZ2    0.00   0.0  0
 TRF  CONST_15  CE3  CZ3  CH2  CZ2    0.00   0.0  0
 TRF  CONST_16  CD2  CE2  CZ2  CH2    0.00   0.0  0
 TRF  CONST_17  CD2  CE3  CZ3  CH2    0.00   0.0  0
 TRF  CONST_18  NE1  CD1  CG   CB   180.00   0.0  0
 TRF  CONST_19  CE2  CD2  CG   CB   180.00   0.0  0
 TRF  CONST_20  CE3  CD2  CG   CB     0.00   0.0  0
 TRF  CONST_21  C1   NE1  CD1  CG   180.00   0.0  0
 TRF  CONST_22  C1   NE1  CE2  CZ2    0.00   0.0  0
 TRF  CONST_23  C1   NE1  CE2  CD2  180.00   0.0  0
 TRF  CONST_24  HE3  CE3  CD2  CG     0.00   0.0  0
 TRF  CONST_25  HZ2  CZ2  CE2  NE1    0.00   0.0  0
 TRF  CONST_26  HD1  CD1  NE1  CE2  180.00   0.0  0
 TRF  CONST_27  HH2  CH2  CZ2  CE2  180.00   0.0  0
 TRF  CONST_28  HZ3  CZ3  CH2  CZ2  180.00   0.0  0
 TRF  CONST_29  O1   C1   NE1  CD1  180.00   0.0  0
 TRF  CONST_30  O1   C1   NE1  CE2    0.00   0.0  0
 TRF  Var_01    CD1  CG   CB   CA     2.06  30.0  2

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
 TRF  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
 TRF  plan-1  CB   0.020
 TRF  plan-1  CG   0.020
 TRF  plan-1  CD1  0.020
 TRF  plan-1  NE1  0.020
 TRF  plan-1  CE2  0.020
 TRF  plan-1  CZ2  0.020
 TRF  plan-1  CH2  0.020
 TRF  plan-1  CZ3  0.020
 TRF  plan-1  CE3  0.020
 TRF  plan-1  CD2  0.020
 TRF  plan-1  C1   0.020
 TRF  plan-1  O1   0.020
 TRF  plan-1  HD1  0.020
 TRF  plan-1  HZ2  0.020
 TRF  plan-1  HH2  0.020
 TRF  plan-1  HZ3  0.020
 TRF  plan-1  HE3  0.020
 TRF  plan-1  HC1  0.020
 TRF  plan-2  CA   0.020
 TRF  plan-2  C    0.020
 TRF  plan-2  O    0.020
 TRF  plan-2  OXT  0.020

