# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:46:37 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (2~{R})-2-azanyl-3-(6-fluoranyl-1~{H}-indol-3-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1c[nH]c2cc(F)ccc12)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
 E03  E03  '(2~{R})-2-azanyl-3-(6-fluoranyl-1~{H}-indol-3-yl)propanoic acid'  D-peptide  26  16  .  2022-09-22  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_E03
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
 E03  F1   F  F      0  -0.326   4.6561  -1.1668   0.5880
 E03  N    N  NH2    0  -0.799  -2.4343   0.8126   1.4438
 E03  CA   C  CH1    0  -0.197  -2.3344  -0.1753   0.3873
 E03  CB   C  CH2    0  -0.544  -1.6688   0.3541  -0.9060
 E03  CG   C  CR5    0   0.021  -0.2980   0.8895  -0.6674
 E03  CD1  C  CR15   0  -0.098   0.0867   2.1986  -0.6191
 E03  NE1  N  NR15   0  -0.689   1.4208   2.2927  -0.3135
 E03  CE2  C  CR56   0   0.370   1.9305   1.0441  -0.1449
 E03  CD2  C  CR56   0   0.021   0.8780   0.1254  -0.3587
 E03  CE3  C  CR16   0  -0.354   1.1408  -1.2427  -0.2454
 E03  CZ3  C  CR16   0  -0.425   2.4171  -1.6664   0.0720
 E03  CH2  C  CR6    0   0.500   3.4235  -0.7190   0.2751
 E03  CZ2  C  CR16   0  -0.466   3.2261   0.6372   0.1766
 E03  C    C  C      0   0.400  -3.7220  -0.7386   0.0131
 E03  O    O  O      0  -0.605  -4.7154  -0.0268   0.2623
 E03  OXT  O  OC    -1  -0.619  -3.7267  -1.8489  -0.5550
 E03  H4   H  HCH1   0   0.207  -1.7213  -1.0088   0.7497
 E03  H5   H  HCH2   0   0.228  -1.6331  -0.4546  -1.6413
 E03  H6   H  HCH2   0   0.232  -2.2998   1.1412  -1.3309
 E03  H7   H  HCR5   0   0.280  -0.4983   3.0891  -0.7888
 E03  H8   H  HNR5   0   0.409   1.9301   3.1540  -0.2106
 E03  H9   H  HCR6   0   0.251   0.3563  -1.9728  -0.4010
 E03  H10  H  HCR6   0   0.268   2.6461  -2.7195   0.1679
 E03  H11  H  HCR6   0   0.279   4.0312   1.3413   0.3422
 E03  H    H  HNH2   0   0.332  -1.5865   1.3673   1.4755
 E03  H2   H  HNH2   0   0.325  -3.1908   1.4471   1.2188

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
 E03  NE1  CD1  aromatic  1.372  0.020  1.372
 E03  NE1  CE2  aromatic  1.359  0.020  1.359
 E03  CD1  CG   aromatic  1.365  0.020  1.365
 E03  CZ2  CE2  aromatic  1.395  0.020  1.395
 E03  CZ2  CH2  aromatic  1.374  0.020  1.374
 E03  CE2  CD2  aromatic  1.413  0.020  1.413
 E03  CG   CD2  aromatic  1.436  0.020  1.436
 E03  CG   CB   single    1.491  0.020  1.491
 E03  F1   CH2  single    1.348  0.020  1.348
 E03  CH2  CZ3  aromatic  1.397  0.020  1.397
 E03  CD2  CE3  aromatic  1.398  0.020  1.398
 E03  CB   CA   single    1.521  0.033  1.521
 E03  CZ3  CE3  aromatic  1.382  0.020  1.382
 E03  N    CA   single    1.458  0.019  1.458
 E03  CA   C    single    1.525  0.021  1.525
 E03  C    O    deloc     1.231  0.020  1.231
 E03  C    OXT  deloc     1.247  0.020  1.247
 E03  N    H    single    0.860  0.020  0.860
 E03  N    H2   single    0.890  0.020  1.040
 E03  CA   H4   single    0.970  0.020  1.090
 E03  CB   H5   single    0.970  0.020  1.090
 E03  CB   H6   single    0.970  0.020  1.090
 E03  CD1  H7   single    0.930  0.020  1.080
 E03  NE1  H8   single    0.860  0.020  1.020
 E03  CE3  H9   single    0.930  0.020  1.080
 E03  CZ3  H10  single    0.930  0.020  1.080
 E03  CZ2  H11  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
 E03  H2   N    H    106.79  3.000
 E03  H2   N    CA   108.45  3.000
 E03  H    N    CA   114.00  3.000
 E03  H4   CA   C    107.79  3.000
 E03  H4   CA   CB   107.20  3.000
 E03  C    CA   CB   110.50  1.500
 E03  H4   CA   N    108.40  3.000
 E03  C    CA   N    111.00  2.800
 E03  CB   CA   N    110.40  1.500
 E03  H6   CB   H5   106.83  3.000
 E03  H6   CB   CG   109.51  3.000
 E03  H5   CB   CG   110.07  3.000
 E03  H6   CB   CA   108.81  3.000
 E03  H5   CB   CA   108.84  3.000
 E03  CG   CB   CA   112.61  3.000
 E03  CD2  CG   CD1  105.77  3.000
 E03  CD2  CG   CB   126.61  3.000
 E03  CD1  CG   CB   127.52  3.000
 E03  H7   CD1  NE1  120.38  3.000
 E03  H7   CD1  CG   129.27  3.000
 E03  NE1  CD1  CG   110.34  3.000
 E03  H8   NE1  CE2  125.74  3.000
 E03  H8   NE1  CD1  125.02  3.000
 E03  CE2  NE1  CD1  109.23  3.000
 E03  CZ2  CE2  CD2  122.46  3.000
 E03  CD2  CE2  NE1  107.40  3.000
 E03  CZ2  CE2  NE1  130.14  3.000
 E03  CE3  CD2  CE2  118.94  3.000
 E03  CE3  CD2  CG   133.81  3.000
 E03  CE2  CD2  CG   107.25  3.000
 E03  H9   CE3  CZ3  119.70  3.000
 E03  H9   CE3  CD2  120.80  3.000
 E03  CZ3  CE3  CD2  119.50  3.000
 E03  H10  CZ3  CH2  119.65  3.000
 E03  H10  CZ3  CE3  120.95  3.000
 E03  CH2  CZ3  CE3  119.40  3.000
 E03  CZ2  CH2  CZ3  123.74  3.000
 E03  CZ3  CH2  F1   117.85  3.000
 E03  CZ2  CH2  F1   118.41  3.000
 E03  H11  CZ2  CH2  121.62  3.000
 E03  H11  CZ2  CE2  122.43  3.000
 E03  CH2  CZ2  CE2  115.96  3.000
 E03  OXT  C    O    126.59  3.000
 E03  OXT  C    CA   120.80  1.700
 E03  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
 E03  CONST_01  CE2  NE1  CD1  CG      0.00   0.0  0
 E03  CONST_02  NE1  CE2  CD2  CG      0.00   0.0  0
 E03  CONST_03  CZ2  CE2  CD2  CG    180.00   0.0  0
 E03  CONST_04  CZ3  CE3  CD2  CG    180.00   0.0  0
 E03  CONST_05  CZ2  CE2  NE1  CD1   180.00   0.0  0
 E03  CONST_06  CD2  CE2  NE1  CD1     0.00   0.0  0
 E03  CONST_07  CE2  CD2  CG   CD1     0.00   0.0  0
 E03  CONST_08  CE3  CD2  CG   CD1   180.00   0.0  0
 E03  CONST_09  CD2  CG   CD1  NE1     0.00   0.0  0
 E03  CONST_10  CH2  CZ2  CE2  NE1   180.00   0.0  0
 E03  CONST_11  CE3  CD2  CE2  NE1   180.00   0.0  0
 E03  CONST_12  CZ3  CH2  CZ2  CE2     0.00   0.0  0
 E03  CONST_13  CZ3  CE3  CD2  CE2     0.00   0.0  0
 E03  CONST_14  CH2  CZ2  CE2  CD2     0.00   0.0  0
 E03  CONST_15  CH2  CZ3  CE3  CD2     0.00   0.0  0
 E03  CONST_16  CZ2  CE2  CD2  CE3     0.00   0.0  0
 E03  CONST_17  CZ2  CH2  CZ3  CE3     0.00   0.0  0
 E03  CONST_18  CE2  CZ2  CH2  F1    180.00   0.0  0
 E03  CONST_19  CE3  CZ3  CH2  F1    180.00   0.0  0
 E03  CONST_20  NE1  CD1  CG   CB    180.00   0.0  0
 E03  CONST_21  CE2  CD2  CG   CB    180.00   0.0  0
 E03  CONST_22  CE3  CD2  CG   CB      0.00   0.0  0
 E03  CONST_23  H8   NE1  CD1  CG    180.00   0.0  0
 E03  CONST_24  H9   CE3  CD2  CG      0.00   0.0  0
 E03  CONST_25  H11  CZ2  CE2  NE1     0.00   0.0  0
 E03  CONST_26  H7   CD1  NE1  CE2   180.00   0.0  0
 E03  CONST_27  H10  CZ3  CE3  CD2   180.00   0.0  0
 E03  Var_01    CD1  CG   CB   CA   -104.67  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
 E03  chir_01  CA  CB  N  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
 E03  plan-1  F1   0.020
 E03  plan-1  CB   0.020
 E03  plan-1  CG   0.020
 E03  plan-1  CD1  0.020
 E03  plan-1  NE1  0.020
 E03  plan-1  CE2  0.020
 E03  plan-1  CD2  0.020
 E03  plan-1  CE3  0.020
 E03  plan-1  CZ3  0.020
 E03  plan-1  CH2  0.020
 E03  plan-1  CZ2  0.020
 E03  plan-1  H7   0.020
 E03  plan-1  H8   0.020
 E03  plan-1  H9   0.020
 E03  plan-1  H10  0.020
 E03  plan-1  H11  0.020
 E03  plan-2  CA   0.020
 E03  plan-2  C    0.020
 E03  plan-2  O    0.020
 E03  plan-2  OXT  0.020

