# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:19:34 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: N-methyl-L-tryptophan
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](Cc1c[nH]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
 E9M  E9M  'N-methyl-L-tryptophan    '  L-peptide  29  16  .  2019-03-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E9M
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
 E9M  N    N  NH1    0  -0.587  -4.2847  -3.1892  3.3325
 E9M  CA   C  CH1    0  -0.217  -3.3659  -2.0925  3.0551
 E9M  CG   C  CR5    0   0.014  -3.9552  -0.8051  5.1334
 E9M  CD1  C  CR15   0  -0.092  -4.5059  -1.3278  6.2695
 E9M  CD2  C  CR56   0   0.028  -4.7101   0.3810  4.8454
 E9M  CE2  C  CR56   0   0.352  -5.6906   0.5126  5.8549
 E9M  C    C  C      0   0.408  -2.2317  -2.5877  2.1126
 E9M  O    O  O      0  -0.596  -1.0606  -2.5211  2.5359
 E9M  CB   C  CH2    0  -0.540  -2.8460  -1.3735  4.3128
 E9M  CE3  C  CR16   0  -0.371  -4.6417   1.3495  3.8364
 E9M  NE1  N  NR15   0  -0.688  -5.5412  -0.5429  6.7041
 E9M  CZ3  C  CR16   0  -0.268  -5.5331   2.4044  3.8565
 E9M  CZ2  C  CR16   0  -0.306  -6.5931   1.5754  5.8789
 E9M  CH2  C  CR16   0  -0.283  -6.5002   2.5151  4.8699
 E9M  CN2  C  CH3    0  -0.529  -3.7045  -4.3175  4.0325
 E9M  OXT  O  OC    -1  -0.609  -2.5978  -3.0115  0.9995
 E9M  H    H  HNH1   0   0.337  -5.0588  -2.8321  3.8794
 E9M  HA   H  HCH1   0   0.216  -3.9480  -1.3572  2.4841
 E9M  HD1  H  HCR5   0   0.273  -4.2258  -2.2161  6.8150
 E9M  HB3  H  HCH2   0   0.226  -2.2457  -2.0539  4.9201
 E9M  HB2  H  HCH2   0   0.220  -2.1712  -0.5707  4.0048
 E9M  HE3  H  HCR6   0   0.237  -3.8996   1.2731  3.0505
 E9M  HE1  H  HNR5   0   0.403  -6.0921  -0.7154  7.5279
 E9M  HZ3  H  HCR6   0   0.240  -5.4893   3.1590  3.0815
 E9M  HZ2  H  HCR6   0   0.253  -7.3391   1.6649  6.6588
 E9M  HH2  H  HCR6   0   0.244  -7.1854   3.3531  4.8593
 E9M  HN3  H  HCH3   0   0.225  -4.4920  -5.0361  4.2622
 E9M  HN1  H  HCH3   0   0.219  -2.9815  -4.8308  3.3958
 E9M  HN2  H  HCH3   0   0.190  -3.1975  -4.0785  4.9769

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
 E9M  C    CA   single    1.525  0.021  1.525
 E9M  C    O    deloc     1.231  0.020  1.231
 E9M  CA   N    single    1.458  0.019  1.458
 E9M  CA   CB   single    1.530  0.020  1.530
 E9M  N    CN2  single    1.449  0.020  1.449
 E9M  CE3  CZ3  aromatic  1.381  0.020  1.381
 E9M  CE3  CD2  aromatic  1.400  0.020  1.400
 E9M  CB   CG   single    1.492  0.020  1.492
 E9M  CZ3  CH2  aromatic  1.405  0.020  1.405
 E9M  CD2  CG   aromatic  1.435  0.020  1.435
 E9M  CD2  CE2  aromatic  1.413  0.020  1.413
 E9M  CG   CD1  aromatic  1.366  0.020  1.366
 E9M  CH2  CZ2  aromatic  1.382  0.020  1.382
 E9M  CE2  CZ2  aromatic  1.395  0.020  1.395
 E9M  CE2  NE1  aromatic  1.363  0.020  1.363
 E9M  CD1  NE1  aromatic  1.370  0.020  1.370
 E9M  C    OXT  deloc     1.246  0.020  1.246
 E9M  N    H    single    0.860  0.020  0.860
 E9M  CA   HA   single    0.970  0.020  0.970
 E9M  CD1  HD1  single    0.930  0.020  1.080
 E9M  CB   HB3  single    0.970  0.020  1.090
 E9M  CB   HB2  single    0.970  0.020  1.090
 E9M  CE3  HE3  single    0.930  0.020  1.080
 E9M  NE1  HE1  single    0.860  0.020  1.020
 E9M  CZ3  HZ3  single    0.930  0.020  1.080
 E9M  CZ2  HZ2  single    0.930  0.020  1.080
 E9M  CH2  HH2  single    0.930  0.020  1.080
 E9M  CN2  HN3  single    0.970  0.020  1.090
 E9M  CN2  HN1  single    0.970  0.020  1.090
 E9M  CN2  HN2  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
 E9M  H    N    CN2  108.64  3.000
 E9M  H    N    CA   114.00  3.000
 E9M  CN2  N    CA   115.18  3.000
 E9M  HA   CA   CB   109.00  3.000
 E9M  HA   CA   C    109.00  3.000
 E9M  CB   CA   C    110.10  1.900
 E9M  HA   CA   N    110.00  3.000
 E9M  CB   CA   N    110.50  1.700
 E9M  C    CA   N    111.00  2.800
 E9M  CB   CG   CD2  126.54  3.000
 E9M  CD2  CG   CD1  105.72  3.000
 E9M  CB   CG   CD1  127.67  3.000
 E9M  HD1  CD1  NE1  120.48  3.000
 E9M  HD1  CD1  CG   129.08  3.000
 E9M  NE1  CD1  CG   110.44  3.000
 E9M  CE3  CD2  CE2  118.96  3.000
 E9M  CE2  CD2  CG   107.37  3.000
 E9M  CE3  CD2  CG   133.67  3.000
 E9M  CZ2  CE2  NE1  130.58  3.000
 E9M  NE1  CE2  CD2  107.27  3.000
 E9M  CZ2  CE2  CD2  122.15  3.000
 E9M  OXT  C    O    126.68  3.000
 E9M  OXT  C    CA   115.80  3.000
 E9M  O    C    CA   120.80  1.700
 E9M  HB2  CB   HB3  105.96  3.000
 E9M  HB2  CB   CG   109.52  3.000
 E9M  HB3  CB   CG   109.89  3.000
 E9M  HB2  CB   CA   108.74  3.000
 E9M  HB3  CB   CA   110.43  3.000
 E9M  CG   CB   CA   112.10  3.000
 E9M  HE3  CE3  CZ3  120.43  3.000
 E9M  HE3  CE3  CD2  120.48  3.000
 E9M  CZ3  CE3  CD2  119.09  3.000
 E9M  HE1  NE1  CE2  125.66  3.000
 E9M  HE1  NE1  CD1  125.13  3.000
 E9M  CE2  NE1  CD1  109.20  3.000
 E9M  HZ3  CZ3  CH2  119.29  3.000
 E9M  HZ3  CZ3  CE3  119.72  3.000
 E9M  CH2  CZ3  CE3  120.98  3.000
 E9M  HZ2  CZ2  CH2  121.06  3.000
 E9M  HZ2  CZ2  CE2  121.41  3.000
 E9M  CH2  CZ2  CE2  117.52  3.000
 E9M  HH2  CH2  CZ2  119.40  3.000
 E9M  HH2  CH2  CZ3  119.31  3.000
 E9M  CZ2  CH2  CZ3  121.29  3.000
 E9M  HN2  CN2  HN1  107.35  3.000
 E9M  HN2  CN2  HN3  107.19  3.000
 E9M  HN1  CN2  HN3  106.93  3.000
 E9M  HN2  CN2  N    115.52  3.000
 E9M  HN1  CN2  N    110.46  3.000
 E9M  HN3  CN2  N    109.01  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
 E9M  CONST_01  CZ3  CE3  CD2  CG   180.00   0.0  0
 E9M  CONST_02  CZ2  CE2  CD2  CG   180.00   0.0  0
 E9M  CONST_03  NE1  CE2  CD2  CG     0.00   0.0  0
 E9M  CONST_04  CE2  NE1  CD1  CG     0.00   0.0  0
 E9M  CONST_05  CE3  CD2  CG   CD1  180.00   0.0  0
 E9M  CONST_06  CE2  CD2  CG   CD1    0.00   0.0  0
 E9M  CONST_07  CD2  CE2  NE1  CD1    0.00   0.0  0
 E9M  CONST_08  CZ2  CE2  NE1  CD1  180.00   0.0  0
 E9M  CONST_09  CH2  CZ3  CE3  CD2    0.00   0.0  0
 E9M  CONST_10  NE1  CD1  CG   CD2    0.00   0.0  0
 E9M  CONST_11  CH2  CZ2  CE2  CD2    0.00   0.0  0
 E9M  CONST_12  CZ3  CE3  CD2  CE2    0.00   0.0  0
 E9M  CONST_13  CZ3  CH2  CZ2  CE2    0.00   0.0  0
 E9M  CONST_14  CZ2  CH2  CZ3  CE3    0.00   0.0  0
 E9M  CONST_15  CZ2  CE2  CD2  CE3    0.00   0.0  0
 E9M  CONST_16  NE1  CE2  CD2  CE3  180.00   0.0  0
 E9M  CONST_17  CH2  CZ2  CE2  NE1  180.00   0.0  0
 E9M  CONST_18  CB   CG   CD2  CE2  180.00   0.0  0
 E9M  CONST_19  CE3  CD2  CG   CB     0.00   0.0  0
 E9M  CONST_20  NE1  CD1  CG   CB   180.00   0.0  0
 E9M  CONST_21  HE3  CE3  CD2  CG     0.00   0.0  0
 E9M  CONST_22  HE1  NE1  CD1  CG   180.00   0.0  0
 E9M  CONST_23  HZ3  CZ3  CE3  CD2  180.00   0.0  0
 E9M  CONST_24  HD1  CD1  CG   CD2  180.00   0.0  0
 E9M  CONST_25  HZ2  CZ2  CE2  CD2  180.00   0.0  0
 E9M  CONST_26  HH2  CH2  CZ2  CE2  180.00   0.0  0
 E9M  Var_01    CD2  CG   CB   CA   -76.04  30.0  2
 E9M  Var_02    HN3  CN2  N    CA   175.21  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
 E9M  chir_01  CA  C  N  CB  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
 E9M  plan-1  CG   0.020
 E9M  plan-1  CD1  0.020
 E9M  plan-1  CD2  0.020
 E9M  plan-1  CE2  0.020
 E9M  plan-1  CB   0.020
 E9M  plan-1  CE3  0.020
 E9M  plan-1  NE1  0.020
 E9M  plan-1  CZ3  0.020
 E9M  plan-1  CZ2  0.020
 E9M  plan-1  CH2  0.020
 E9M  plan-1  HD1  0.020
 E9M  plan-1  HE3  0.020
 E9M  plan-1  HE1  0.020
 E9M  plan-1  HZ3  0.020
 E9M  plan-1  HZ2  0.020
 E9M  plan-1  HH2  0.020
 E9M  plan-2  CA   0.020
 E9M  plan-2  C    0.020
 E9M  plan-2  O    0.020
 E9M  plan-2  OXT  0.020

