# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:14:14 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (2~{S})-2-azanyl-3-(1-methylindol-3-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(C[C@H](N)C(O)=O)c2ccccc12
#
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
 EXL  EXL  '(2~{S})-2-azanyl-3-(1-methylindol-3-yl)propanoic acid'  L-peptide  29  16  .  2022-08-10  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_EXL
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
 EXL  C01  C  CH3    0  -0.527   -9.0740  134.3619   8.5490
 EXL  C03  C  CR15   0  -0.078   -9.6899  136.4030   9.8669
 EXL  C04  C  CR5    0  -0.013   -9.0683  137.4671  10.4593
 EXL  C05  C  CH2    0  -0.502   -9.7184  138.5768  11.2231
 EXL  C06  C  CH1    0  -0.222   -9.9280  138.2636  12.7116
 EXL  C08  C  C      0   0.390  -10.9269  137.0872  12.8799
 EXL  C11  C  CR56   0   0.018   -7.6684  137.2786  10.2191
 EXL  C12  C  CR16   0  -0.369   -6.5200  138.0075  10.5495
 EXL  C13  C  CR16   0  -0.269   -5.2870  137.5425  10.1344
 EXL  C14  C  CR16   0  -0.283   -5.1718  136.3533   9.3954
 EXL  C15  C  CR16   0  -0.315   -6.2864  135.6090   9.0566
 EXL  C16  C  CR56   0   0.367   -7.5291  136.0845   9.4748
 EXL  N02  N  NR5    0  -0.520   -8.7762  135.5683   9.2777
 EXL  N07  N  NH2    0  -0.785   -8.6399  138.1060  13.3696
 EXL  O09  O  O      0  -0.618  -12.0382  137.2410  12.3284
 EXL  O10  O  OC    -1  -0.601  -10.5562  136.1036  13.5486
 EXL  H1   H  HCH3   0   0.262  -10.1469  134.1899   8.5672
 EXL  H2   H  HCH3   0   0.247   -8.7554  134.4405   7.5090
 EXL  H3   H  HCH3   0   0.248   -8.5806  133.5000   8.9989
 EXL  H4   H  HCR5   0   0.272  -10.7432  136.1702   9.8218
 EXL  H5   H  HCH2   0   0.222   -9.1093  139.4808  11.1387
 EXL  H6   H  HCH2   0   0.230  -10.6863  138.8116  10.7805
 EXL  H7   H  HCH1   0   0.213  -10.4074  139.1492  13.1489
 EXL  H8   H  HCR6   0   0.235   -6.5959  138.9229  11.1241
 EXL  H9   H  HCR6   0   0.239   -4.3921  138.0990  10.3821
 EXL  H10  H  HCR6   0   0.243   -4.1919  136.0129   9.0858
 EXL  H11  H  HCR6   0   0.258   -6.1917  134.6936   8.4856
 EXL  H12  H  HNH2   0   0.330   -8.8043  137.8932  14.3462
 EXL  H13  H  HNH2   0   0.329   -8.1968  137.2687  13.0074

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
 EXL  C01  N02  single    1.441  0.020  1.441
 EXL  C15  C14  aromatic  1.382  0.020  1.382
 EXL  C15  C16  aromatic  1.395  0.020  1.395
 EXL  C14  C13  aromatic  1.405  0.020  1.405
 EXL  N02  C16  aromatic  1.364  0.020  1.364
 EXL  N02  C03  aromatic  1.371  0.020  1.371
 EXL  C16  C11  aromatic  1.414  0.020  1.414
 EXL  C03  C04  aromatic  1.367  0.020  1.367
 EXL  C13  C12  aromatic  1.382  0.020  1.382
 EXL  C11  C12  aromatic  1.400  0.020  1.400
 EXL  C11  C04  aromatic  1.433  0.020  1.433
 EXL  C04  C05  single    1.496  0.020  1.496
 EXL  C05  C06  single    1.535  0.020  1.535
 EXL  O09  C08  deloc     1.250  0.020  1.250
 EXL  C08  C06  single    1.552  0.020  1.552
 EXL  C08  O10  deloc     1.246  0.020  1.246
 EXL  C06  N07  single    1.455  0.020  1.455
 EXL  C01  H1   single    0.970  0.020  1.090
 EXL  C01  H2   single    0.970  0.020  1.090
 EXL  C01  H3   single    0.970  0.020  1.090
 EXL  C03  H4   single    0.930  0.020  1.080
 EXL  C05  H5   single    0.970  0.020  1.090
 EXL  C05  H6   single    0.970  0.020  1.090
 EXL  C06  H7   single    0.970  0.020  1.090
 EXL  C12  H8   single    0.930  0.020  1.080
 EXL  C13  H9   single    0.930  0.020  1.080
 EXL  C14  H10  single    0.930  0.020  1.080
 EXL  C15  H11  single    0.930  0.020  1.080
 EXL  N07  H12  single    0.890  0.020  1.040
 EXL  N07  H13  single    0.890  0.020  1.040

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
 EXL  H3   C01  H2   108.56  3.000
 EXL  H3   C01  H1   108.35  3.000
 EXL  H2   C01  H1   108.41  3.000
 EXL  H3   C01  N02  111.08  3.000
 EXL  H2   C01  N02  111.20  3.000
 EXL  H1   C01  N02  109.16  3.000
 EXL  H4   C03  N02  120.07  3.000
 EXL  H4   C03  C04  129.01  3.000
 EXL  N02  C03  C04  110.92  3.000
 EXL  C11  C04  C05  127.44  3.000
 EXL  C05  C04  C03  126.94  3.000
 EXL  C11  C04  C03  105.61  3.000
 EXL  H6   C05  H5   106.57  3.000
 EXL  H6   C05  C06  108.45  3.000
 EXL  H5   C05  C06  108.64  3.000
 EXL  H6   C05  C04  109.78  3.000
 EXL  H5   C05  C04  109.38  3.000
 EXL  C06  C05  C04  113.77  3.000
 EXL  H7   C06  N07  107.08  3.000
 EXL  H7   C06  C08  106.68  3.000
 EXL  N07  C06  C08  116.01  3.000
 EXL  H7   C06  C05  106.33  3.000
 EXL  N07  C06  C05  109.86  3.000
 EXL  C08  C06  C05  110.33  3.000
 EXL  O10  C08  O09  126.76  3.000
 EXL  O10  C08  C06  117.71  3.000
 EXL  O09  C08  C06  115.53  3.000
 EXL  C16  C11  C12  118.89  3.000
 EXL  C12  C11  C04  133.91  3.000
 EXL  C16  C11  C04  107.19  3.000
 EXL  H8   C12  C13  120.41  3.000
 EXL  H8   C12  C11  120.51  3.000
 EXL  C13  C12  C11  119.08  3.000
 EXL  H9   C13  C14  119.19  3.000
 EXL  H9   C13  C12  119.73  3.000
 EXL  C14  C13  C12  121.08  3.000
 EXL  H10  C14  C15  119.37  3.000
 EXL  H10  C14  C13  119.40  3.000
 EXL  C15  C14  C13  121.23  3.000
 EXL  H11  C15  C16  121.62  3.000
 EXL  H11  C15  C14  120.91  3.000
 EXL  C16  C15  C14  117.47  3.000
 EXL  N02  C16  C15  129.96  3.000
 EXL  N02  C16  C11  107.79  3.000
 EXL  C15  C16  C11  122.25  3.000
 EXL  C16  N02  C03  108.48  3.000
 EXL  C03  N02  C01  126.13  3.000
 EXL  C16  N02  C01  125.38  3.000
 EXL  H13  N07  H12  103.99  3.000
 EXL  H13  N07  C06  108.33  3.000
 EXL  H12  N07  C06  108.37  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
 EXL  CONST_01  C15  C16  N02  C03  180.00   0.0  0
 EXL  CONST_02  C11  C16  N02  C03    0.00   0.0  0
 EXL  CONST_03  C16  C11  C04  C03    0.00   0.0  0
 EXL  CONST_04  C12  C11  C04  C03  180.00   0.0  0
 EXL  CONST_05  C16  N02  C03  C04    0.00   0.0  0
 EXL  CONST_06  C15  C16  C11  C04  180.00   0.0  0
 EXL  CONST_07  N02  C16  C11  C04    0.00   0.0  0
 EXL  CONST_08  C13  C12  C11  C04  180.00   0.0  0
 EXL  CONST_09  C14  C15  C16  C11    0.00   0.0  0
 EXL  CONST_10  C14  C13  C12  C11    0.00   0.0  0
 EXL  CONST_11  N02  C03  C04  C11    0.00   0.0  0
 EXL  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 EXL  CONST_13  C15  C16  C11  C12    0.00   0.0  0
 EXL  CONST_14  N02  C16  C11  C12  180.00   0.0  0
 EXL  CONST_15  C16  C15  C14  C13    0.00   0.0  0
 EXL  CONST_16  C16  C11  C12  C13    0.00   0.0  0
 EXL  CONST_17  N02  C16  C15  C14  180.00   0.0  0
 EXL  CONST_18  C15  C16  N02  C01    0.00   0.0  0
 EXL  CONST_19  C11  C16  N02  C01  180.00   0.0  0
 EXL  CONST_20  C04  C03  N02  C01  180.00   0.0  0
 EXL  CONST_21  N02  C03  C04  C05  180.00   0.0  0
 EXL  CONST_22  C16  C11  C04  C05  180.00   0.0  0
 EXL  CONST_23  C12  C11  C04  C05    0.00   0.0  0
 EXL  CONST_24  H8   C12  C11  C04    0.00   0.0  0
 EXL  CONST_25  H11  C15  C16  C11  180.00   0.0  0
 EXL  CONST_26  H9   C13  C12  C11  180.00   0.0  0
 EXL  CONST_27  H4   C03  C04  C11  180.00   0.0  0
 EXL  CONST_28  H10  C14  C13  C12  180.00   0.0  0
 EXL  Var_01    C06  C05  C04  C03   86.63  30.0  2
 EXL  Var_02    H1   C01  N02  C03   -2.07  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
 EXL  chir_01  C06  C05  C08  N07  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
 EXL  plan-1  C01  0.020
 EXL  plan-1  C03  0.020
 EXL  plan-1  C04  0.020
 EXL  plan-1  C05  0.020
 EXL  plan-1  C11  0.020
 EXL  plan-1  C12  0.020
 EXL  plan-1  C13  0.020
 EXL  plan-1  C14  0.020
 EXL  plan-1  C15  0.020
 EXL  plan-1  C16  0.020
 EXL  plan-1  N02  0.020
 EXL  plan-1  H4   0.020
 EXL  plan-1  H8   0.020
 EXL  plan-1  H9   0.020
 EXL  plan-1  H10  0.020
 EXL  plan-1  H11  0.020
 EXL  plan-2  C06  0.020
 EXL  plan-2  C08  0.020
 EXL  plan-2  O09  0.020
 EXL  plan-2  O10  0.020

