# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:12:27 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-(1H-pyrrolo[2,3-b]pyridin-3-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]c2ncccc12)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
 TRN  TRN  3-(1H-pyrrolo[2,3-b]pyridin-3-yl)-L-alanine  L-peptide  25  15  .  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_TRN
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
 TRN  N    N  NH2    0  -0.807  52.9909  78.8548  14.9455
 TRN  CA   C  CH1    0  -0.154  51.9842  78.6859  13.9017
 TRN  CB   C  CH2    0  -0.530  52.6236  79.0695  12.5603
 TRN  CG   C  CR5    0  -0.032  51.6998  78.9539  11.3931
 TRN  CD1  C  CR15   0  -0.059  50.7825  79.8727  10.9677
 TRN  CD2  C  CR56   0  -0.018  51.5721  77.8422  10.5003
 TRN  NE1  N  NR15   0  -0.670  50.0979  79.4028   9.8756
 TRN  CE2  C  CR56   0   0.456  50.5637  78.1658   9.5614
 TRN  CE3  C  CR16   0  -0.236  52.1900  76.6030  10.3548
 TRN  NZ2  N  N      0  -0.427  50.1506  77.4084   8.5566
 TRN  CH2  C  CR16   0  -0.093  50.7650  76.2390   8.4462
 TRN  CZ3  C  CR16   0  -0.346  51.7761  75.7978   9.3073
 TRN  C    C  C      0   0.399  51.4731  77.2252  13.8542
 TRN  O    O  O      0  -0.609  50.2360  77.0689  13.8263
 TRN  OXT  O  OC    -1  -0.607  52.3412  76.3301  13.8311
 TRN  H    H  HNH2   0   0.335  52.5999  78.5932  15.8425
 TRN  H2   H  HNH2   0   0.332  53.2125  79.8404  15.0285
 TRN  HA   H  HCH1   0   0.172  51.1138  79.3418  14.0490
 TRN  HB2  H  HCH2   0   0.231  52.9944  80.0970  12.6341
 TRN  HB3  H  HCH2   0   0.225  53.5009  78.4366  12.4049
 TRN  HD1  H  HCR5   0   0.280  50.5607  80.8501  11.3678
 TRN  HE1  H  HNR5   0   0.404  49.3801  79.9013   9.3759
 TRN  HE3  H  HCR6   0   0.250  52.9593  76.2755  11.0420
 TRN  HH2  H  HCR6   0   0.248  50.4426  75.6028   7.6292
 TRN  HZ3  H  HCR6   0   0.255  52.2222  74.8259   9.1451

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
 TRN  N    CA   single    1.458  0.019  1.458
 TRN  N    H    single    0.860  0.020  0.860
 TRN  N    H2   single    0.890  0.020  1.040
 TRN  CA   CB   single    1.530  0.020  1.530
 TRN  CA   C    single    1.525  0.021  1.525
 TRN  CA   HA   single    0.970  0.020  0.970
 TRN  CB   CG   single    1.493  0.020  1.493
 TRN  CB   HB2  single    0.970  0.020  1.090
 TRN  CB   HB3  single    0.970  0.020  1.090
 TRN  CG   CD1  aromatic  1.366  0.020  1.366
 TRN  CG   CD2  aromatic  1.432  0.020  1.432
 TRN  CD1  NE1  aromatic  1.372  0.020  1.372
 TRN  CD1  HD1  single    0.930  0.020  1.080
 TRN  CD2  CE2  aromatic  1.415  0.020  1.415
 TRN  CD2  CE3  aromatic  1.392  0.020  1.392
 TRN  NE1  CE2  aromatic  1.359  0.020  1.359
 TRN  NE1  HE1  single    0.860  0.020  1.020
 TRN  CE2  NZ2  aromatic  1.324  0.020  1.324
 TRN  CE3  CZ3  aromatic  1.385  0.020  1.385
 TRN  CE3  HE3  single    0.930  0.020  1.080
 TRN  NZ2  CH2  aromatic  1.326  0.020  1.326
 TRN  CH2  CZ3  aromatic  1.399  0.020  1.399
 TRN  CH2  HH2  single    0.930  0.020  1.080
 TRN  CZ3  HZ3  single    0.930  0.020  1.080
 TRN  C    O    deloc     1.231  0.020  1.231
 TRN  C    OXT  deloc     1.247  0.020  1.247

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
 TRN  H2   N    H    105.25  3.000
 TRN  H2   N    CA   108.77  3.000
 TRN  H    N    CA   114.00  3.000
 TRN  HA   CA   C    109.00  3.000
 TRN  HA   CA   CB   109.00  3.000
 TRN  C    CA   CB   110.10  1.900
 TRN  HA   CA   N    110.00  3.000
 TRN  C    CA   N    111.00  2.800
 TRN  CB   CA   N    110.50  1.700
 TRN  HB3  CB   HB2  106.33  3.000
 TRN  HB3  CB   CG   109.92  3.000
 TRN  HB2  CB   CG   109.57  3.000
 TRN  HB3  CB   CA   108.29  3.000
 TRN  HB2  CB   CA   108.47  3.000
 TRN  CG   CB   CA   113.97  3.000
 TRN  CD2  CG   CD1  105.56  3.000
 TRN  CD2  CG   CB   127.08  3.000
 TRN  CD1  CG   CB   127.35  3.000
 TRN  HD1  CD1  NE1  120.19  3.000
 TRN  HD1  CD1  CG   129.17  3.000
 TRN  NE1  CD1  CG   110.64  3.000
 TRN  CE3  CD2  CE2  116.77  3.000
 TRN  CE3  CD2  CG   135.79  3.000
 TRN  CE2  CD2  CG   107.44  3.000
 TRN  HE1  NE1  CE2  125.49  3.000
 TRN  HE1  NE1  CD1  125.54  3.000
 TRN  CE2  NE1  CD1  108.96  3.000
 TRN  NZ2  CE2  NE1  126.10  3.000
 TRN  NZ2  CE2  CD2  126.50  3.000
 TRN  NE1  CE2  CD2  107.40  3.000
 TRN  HE3  CE3  CZ3  121.13  3.000
 TRN  HE3  CE3  CD2  121.23  3.000
 TRN  CZ3  CE3  CD2  117.65  3.000
 TRN  CH2  NZ2  CE2  115.03  3.000
 TRN  HH2  CH2  CZ3  119.56  3.000
 TRN  HH2  CH2  NZ2  116.26  3.000
 TRN  CZ3  CH2  NZ2  124.18  3.000
 TRN  HZ3  CZ3  CH2  119.28  3.000
 TRN  HZ3  CZ3  CE3  120.84  3.000
 TRN  CH2  CZ3  CE3  119.88  3.000
 TRN  OXT  C    O    126.87  3.000
 TRN  OXT  C    CA   116.61  3.000
 TRN  O    C    CA   120.80  1.700

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
 TRN  CONST_01  CE2  NE1  CD1  CG     0.00   0.0  0
 TRN  CONST_02  NE1  CE2  CD2  CG     0.00   0.0  0
 TRN  CONST_03  NZ2  CE2  CD2  CG   180.00   0.0  0
 TRN  CONST_04  CZ3  CE3  CD2  CG   180.00   0.0  0
 TRN  CONST_05  CE2  CD2  CG   CD1    0.00   0.0  0
 TRN  CONST_06  CE3  CD2  CG   CD1  180.00   0.0  0
 TRN  CONST_07  CD2  CE2  NE1  CD1    0.00   0.0  0
 TRN  CONST_08  NZ2  CE2  NE1  CD1  180.00   0.0  0
 TRN  CONST_09  NE1  CD1  CG   CD2    0.00   0.0  0
 TRN  CONST_10  CH2  NZ2  CE2  CD2    0.00   0.0  0
 TRN  CONST_11  CH2  CZ3  CE3  CD2    0.00   0.0  0
 TRN  CONST_12  CE3  CD2  CE2  NE1  180.00   0.0  0
 TRN  CONST_13  CH2  NZ2  CE2  NE1  180.00   0.0  0
 TRN  CONST_14  CZ3  CE3  CD2  CE2    0.00   0.0  0
 TRN  CONST_15  CZ3  CH2  NZ2  CE2    0.00   0.0  0
 TRN  CONST_16  NZ2  CE2  CD2  CE3    0.00   0.0  0
 TRN  CONST_17  NZ2  CH2  CZ3  CE3    0.00   0.0  0
 TRN  CONST_18  NE1  CD1  CG   CB   180.00   0.0  0
 TRN  CONST_19  CE2  CD2  CG   CB   180.00   0.0  0
 TRN  CONST_20  CE3  CD2  CG   CB     0.00   0.0  0
 TRN  CONST_21  HE1  NE1  CD1  CG   180.00   0.0  0
 TRN  CONST_22  HE3  CE3  CD2  CG     0.00   0.0  0
 TRN  CONST_23  HD1  CD1  CG   CD2  180.00   0.0  0
 TRN  CONST_24  HZ3  CZ3  CE3  CD2  180.00   0.0  0
 TRN  CONST_25  HH2  CH2  NZ2  CE2  180.00   0.0  0
 TRN  Var_01    CD1  CG   CB   CA    83.21  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
 TRN  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
 TRN  plan-1  CB   0.020
 TRN  plan-1  CG   0.020
 TRN  plan-1  CD1  0.020
 TRN  plan-1  CD2  0.020
 TRN  plan-1  NE1  0.020
 TRN  plan-1  CE2  0.020
 TRN  plan-1  CE3  0.020
 TRN  plan-1  NZ2  0.020
 TRN  plan-1  CH2  0.020
 TRN  plan-1  CZ3  0.020
 TRN  plan-1  HD1  0.020
 TRN  plan-1  HE1  0.020
 TRN  plan-1  HE3  0.020
 TRN  plan-1  HH2  0.020
 TRN  plan-1  HZ3  0.020
 TRN  plan-2  CA   0.020
 TRN  plan-2  C    0.020
 TRN  plan-2  O    0.020
 TRN  plan-2  OXT  0.020

