# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:31:12 2021
#   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  30  16  .  2022-08-10  2023-02-16
;
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  -0.529   -9.1502  134.3953   8.4516
 EXL  C03  C  CR15  0  -0.075   -9.7701  136.4363   9.7711
 EXL  C04  C  CR5   0  -0.021   -9.1430  137.4726  10.4071
 EXL  C05  C  CH2   0  -0.526   -9.8046  138.5791  11.1633
 EXL  C06  C  CH1   0  -0.214   -9.9382  138.2968  12.6708
 EXL  C08  C  C     0   0.527  -10.8598  137.0941  12.8465
 EXL  C11  C  CR56  0   0.016   -7.7389  137.2529  10.2210
 EXL  C12  C  CR16  0  -0.368   -6.5842  137.9442  10.6079
 EXL  C13  C  CR16  0  -0.271   -5.3501  137.4470  10.2359
 EXL  C14  C  CR16  0  -0.282   -5.2398  136.2635   9.4871
 EXL  C15  C  CR16  0  -0.316   -6.3604  135.5581   9.0917
 EXL  C16  C  CR56  0   0.371   -7.6044  136.0664   9.4650
 EXL  N02  N  NR5   0  -0.520   -8.8561  135.5869   9.2092
 EXL  N07  N  NH2   0  -0.779   -8.6404  138.2279  13.2970
 EXL  O09  O  O     0  -0.456  -12.0107  137.0877  12.4786
 EXL  O10  O  OH1   0  -0.583  -10.2828  136.0573  13.4341
 EXL  H1   H  HCH3  0   0.264  -10.2243  134.2311   8.4483
 EXL  H2   H  HCH3  0   0.251   -8.8132  134.4921   7.4192
 EXL  H3   H  HCH3  0   0.252   -8.6700  133.5238   8.8958
 EXL  H4   H  HCR5  0   0.283  -10.8269  136.2372   9.6720
 EXL  H5   H  HCH2  0   0.254   -9.2386  139.5068  11.0560
 EXL  H6   H  HCH2  0   0.258  -10.7964  138.7703  10.7517
 EXL  H7   H  HCH1  0   0.280  -10.4779  139.1424  13.1098
 EXL  H8   H  HCR6  0   0.241   -6.6562  138.8503  11.1971
 EXL  H9   H  HCR6  0   0.245   -4.4499  137.9734  10.5261
 EXL  H10  H  HCR6  0   0.249   -4.2583  135.8962   9.2166
 EXL  H11  H  HCR6  0   0.262   -6.2690  134.6474   8.5128
 EXL  H12  H  HNH2  0   0.355   -8.7299  138.1050  14.2971
 EXL  H13  H  HNH2  0   0.354   -8.1133  137.4346  12.9548
 EXL  H15  H  HOH1  0   0.479  -10.9161  135.3274  13.5099

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    1.442  0.020  1.442
 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  1.365  0.020  1.365
 EXL  N02  C03  aromatic  1.368  0.020  1.368
 EXL  C16  C11  aromatic  1.413  0.020  1.413
 EXL  C03  C04  aromatic  1.368  0.020  1.368
 EXL  C13  C12  aromatic  1.381  0.020  1.381
 EXL  C11  C12  aromatic  1.400  0.020  1.400
 EXL  C11  C04  aromatic  1.433  0.020  1.433
 EXL  C04  C05  single    1.495  0.020  1.495
 EXL  C05  C06  single    1.540  0.020  1.540
 EXL  O09  C08  double    1.208  0.020  1.208
 EXL  C08  C06  single    1.525  0.020  1.525
 EXL  C08  O10  single    1.324  0.020  1.324
 EXL  C06  N07  single    1.443  0.020  1.443
 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
 EXL  O10  H15  single    0.850  0.020  0.980

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   108.71  3.000
 EXL  H3   C01  H1   108.42  3.000
 EXL  H2   C01  H1   108.43  3.000
 EXL  H3   C01  N02  110.90  3.000
 EXL  H2   C01  N02  111.16  3.000
 EXL  H1   C01  N02  109.15  3.000
 EXL  H4   C03  N02  120.09  3.000
 EXL  H4   C03  C04  129.11  3.000
 EXL  N02  C03  C04  110.79  3.000
 EXL  C11  C04  C05  127.79  3.000
 EXL  C05  C04  C03  126.38  3.000
 EXL  C11  C04  C03  105.82  3.000
 EXL  H6   C05  H5   106.58  3.000
 EXL  H6   C05  C06  108.83  3.000
 EXL  H5   C05  C06  107.27  3.000
 EXL  H6   C05  C04  109.96  3.000
 EXL  H5   C05  C04  110.48  3.000
 EXL  C06  C05  C04  113.46  3.000
 EXL  H7   C06  N07  107.84  3.000
 EXL  H7   C06  C08  105.36  3.000
 EXL  N07  C06  C08  117.12  3.000
 EXL  H7   C06  C05  107.08  3.000
 EXL  N07  C06  C05  110.84  3.000
 EXL  C08  C06  C05  108.04  3.000
 EXL  O10  C08  O09  123.09  3.000
 EXL  O10  C08  C06  113.90  3.000
 EXL  O09  C08  C06  123.00  3.000
 EXL  C16  C11  C12  118.93  3.000
 EXL  C12  C11  C04  134.13  3.000
 EXL  C16  C11  C04  106.94  3.000
 EXL  H8   C12  C13  120.46  3.000
 EXL  H8   C12  C11  120.56  3.000
 EXL  C13  C12  C11  118.98  3.000
 EXL  H9   C13  C14  119.16  3.000
 EXL  H9   C13  C12  119.72  3.000
 EXL  C14  C13  C12  121.12  3.000
 EXL  H10  C14  C15  119.38  3.000
 EXL  H10  C14  C13  119.36  3.000
 EXL  C15  C14  C13  121.25  3.000
 EXL  H11  C15  C16  121.65  3.000
 EXL  H11  C15  C14  120.92  3.000
 EXL  C16  C15  C14  117.43  3.000
 EXL  N02  C16  C15  129.79  3.000
 EXL  N02  C16  C11  107.94  3.000
 EXL  C15  C16  C11  122.28  3.000
 EXL  C16  N02  C03  108.51  3.000
 EXL  C03  N02  C01  126.32  3.000
 EXL  C16  N02  C01  125.15  3.000
 EXL  H13  N07  H12  106.57  3.000
 EXL  H13  N07  C06  111.06  3.000
 EXL  H12  N07  C06  110.81  3.000
 EXL  H15  O10  C08  109.85  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  CONST_29  H15  O10  C08  C06  180.00   0.0  0
 EXL  Var_01    C06  C05  C04  C03   93.14  30.0  2
 EXL  Var_02    H1   C01  N02  C03   -3.82  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
 EXL  plan-2  H15  0.020

