# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 03:48:32 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 3-[(2-{[(benzyloxy)carbonyl]amino}ethyl)selanyl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[Se]CCNC(=O)OCc1ccccc1)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
 9U6  9U6  3-[(2-{[(benzyloxy)carbonyl]amino}ethyl)selanyl]-L-alanine  peptide  38  20  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_9U6
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
 9U6  C15  C   CR6   0   0.075   5.8355  -0.0041  -0.0780
 9U6  C17  C   CR16  0  -0.241   7.5099   1.1756  -1.3572
 9U6  C20  C   CR16  0  -0.282   6.0319   0.8888   0.9736
 9U6  C    C   C     0   0.555  -6.0903   1.6238  -0.0939
 9U6  CA   C   CH1   0  -0.229  -5.3345   0.3037  -0.0977
 9U6  CB   C   CH2   0  -0.588  -3.8505   0.6172   0.1713
 9U6  C8   C   CH2   0  -0.628  -1.0540  -0.1915   0.1955
 9U6  C9   C   CH2   0  -0.239   0.0379  -1.2477   0.2267
 9U6  C11  C   C     0   0.766   2.4713  -1.2956   0.1306
 9U6  C14  C   CH2   0  -0.237   4.8236  -1.1032   0.0447
 9U6  C16  C   CR16  0  -0.301   6.5793   0.1496  -1.2425
 9U6  C18  C   CR16  0  -0.262   7.6974   2.0619  -0.3065
 9U6  C19  C   CR16  0  -0.242   6.9558   1.9166   0.8607
 9U6  N    N   NH2   0  -0.775  -5.6222  -0.4009  -1.3226
 9U6  N10  N   NH1   0  -0.669   1.3252  -0.5983   0.0934
 9U6  O    O   O     0  -0.431  -6.5488   2.1510  -1.0736
 9U6  O12  O   O     0  -0.524   2.5439  -2.4994   0.2798
 9U6  O13  O   O2    0  -0.482   3.5309  -0.4923  -0.0204
 9U6  SE7  SE  SE    0   0.053  -2.8123  -1.0350   0.3767
 9U6  H17  H   HCR6  0   0.258   8.0852   1.2814  -2.2679
 9U6  H20  H   HCR6  0   0.255   5.4622   0.7776   1.8889
 9U6  HA   H   HCH1  0   0.287  -5.7247  -0.2896   0.7356
 9U6  HB2  H   HCH2  0   0.275  -3.4325   1.1779  -0.6693
 9U6  HB3  H   HCH2  0   0.282  -3.7313   1.2170   1.0741
 9U6  H6   H   HCH2  0   0.280  -0.9180   0.5223   1.0105
 9U6  H7   H   HCH2  0   0.279  -1.0309   0.3555  -0.7500
 9U6  H8   H   HCH2  0   0.246  -0.0029  -1.8058   1.1658
 9U6  H9   H   HCH2  0   0.246  -0.1082  -1.9651  -0.5851
 9U6  H14  H   HCH2  0   0.248   4.9432  -1.8291  -0.7621
 9U6  H15  H   HCH2  0   0.247   4.9386  -1.6316   0.9938
 9U6  H16  H   HCR6  0   0.256   6.4337  -0.5380  -2.0670
 9U6  H18  H   HCR6  0   0.259   8.4208   2.8622  -0.3932
 9U6  H19  H   HCR6  0   0.258   7.1023   2.6029   1.6847
 9U6  H    H   HNH2  0   0.349  -5.1640   0.0461  -2.1071
 9U6  H2   H   HNH2  0   0.360  -5.2570  -1.3425  -1.2747
 9U6  H10  H   HNH1  0   0.405   1.3615   0.4017  -0.0241
 9U6  HXT  H   HOH1  0   0.484  -6.6155   2.9994   1.0981
 9U6  OXT  O   OH1   0  -0.591  -6.1628   2.1429   1.1249

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
 9U6  C17  C16  aromatic  1.390  0.020  1.390
 9U6  C17  C18  aromatic  1.387  0.020  1.387
 9U6  C16  C15  aromatic  1.390  0.020  1.390
 9U6  C18  C19  aromatic  1.390  0.020  1.390
 9U6  C15  C14  single    1.499  0.020  1.499
 9U6  C15  C20  aromatic  1.393  0.020  1.393
 9U6  C19  C20  aromatic  1.387  0.020  1.387
 9U6  C14  O13  single    1.431  0.020  1.431
 9U6  O13  C11  single    1.338  0.020  1.338
 9U6  C8   C9   single    1.520  0.020  1.520
 9U6  C8   SE7  single    1.959  0.020  1.959
 9U6  C9   N10  single    1.448  0.020  1.448
 9U6  N10  C11  single    1.342  0.020  1.342
 9U6  C11  O12  double    1.215  0.020  1.215
 9U6  SE7  CB   single    1.962  0.020  1.962
 9U6  CB   CA   single    1.521  0.033  1.521
 9U6  O    C    double    1.231  0.020  1.231
 9U6  CA   C    single    1.525  0.021  1.525
 9U6  CA   N    single    1.458  0.019  1.458
 9U6  C    OXT  single    1.327  0.020  1.327
 9U6  C17  H17  single    0.930  0.020  1.080
 9U6  C20  H20  single    0.930  0.020  1.080
 9U6  CA   HA   single    0.970  0.020  0.970
 9U6  CB   HB2  single    0.970  0.020  1.090
 9U6  CB   HB3  single    0.970  0.020  1.090
 9U6  C8   H6   single    0.970  0.020  1.090
 9U6  C8   H7   single    0.970  0.020  1.090
 9U6  C9   H8   single    0.970  0.020  1.090
 9U6  C9   H9   single    0.970  0.020  1.090
 9U6  C14  H14  single    0.970  0.020  1.090
 9U6  C14  H15  single    0.970  0.020  1.090
 9U6  C16  H16  single    0.930  0.020  1.080
 9U6  C18  H18  single    0.930  0.020  1.080
 9U6  C19  H19  single    0.930  0.020  1.080
 9U6  N    H    single    0.860  0.020  0.860
 9U6  N    H2   single    0.890  0.020  1.040
 9U6  N10  H10  single    0.860  0.020  1.020
 9U6  OXT  HXT  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
 9U6  C16  C15  C14  120.71  3.000
 9U6  C14  C15  C20  120.21  3.000
 9U6  C16  C15  C20  119.07  3.000
 9U6  H17  C17  C18  120.19  3.000
 9U6  H17  C17  C16  119.84  3.000
 9U6  C18  C17  C16  119.97  3.000
 9U6  H20  C20  C19  119.67  3.000
 9U6  H20  C20  C15  119.84  3.000
 9U6  C19  C20  C15  120.49  3.000
 9U6  O    C    OXT  123.76  3.000
 9U6  OXT  C    CA   120.80  1.700
 9U6  O    C    CA   120.80  1.700
 9U6  HA   CA   N    110.00  3.000
 9U6  HA   CA   CB   109.00  3.000
 9U6  N    CA   CB   110.40  1.500
 9U6  HA   CA   C    110.00  3.000
 9U6  N    CA   C    111.00  2.800
 9U6  CB   CA   C    110.50  1.500
 9U6  HB3  CB   HB2  108.22  3.000
 9U6  HB3  CB   SE7  108.58  3.000
 9U6  HB2  CB   SE7  108.06  3.000
 9U6  HB3  CB   CA   111.21  3.000
 9U6  HB2  CB   CA   109.78  3.000
 9U6  SE7  CB   CA   110.89  3.000
 9U6  H7   C8   H6   108.42  3.000
 9U6  H7   C8   SE7  108.34  3.000
 9U6  H6   C8   SE7  108.93  3.000
 9U6  H7   C8   C9   110.52  3.000
 9U6  H6   C8   C9   110.46  3.000
 9U6  SE7  C8   C9   110.11  3.000
 9U6  H9   C9   H8   107.34  3.000
 9U6  H9   C9   N10  110.16  3.000
 9U6  H8   C9   N10  109.95  3.000
 9U6  H9   C9   C8   110.17  3.000
 9U6  H8   C9   C8   110.22  3.000
 9U6  N10  C9   C8   108.98  3.000
 9U6  O13  C11  O12  124.14  3.000
 9U6  O12  C11  N10  124.69  3.000
 9U6  O13  C11  N10  111.17  3.000
 9U6  H15  C14  H14  107.99  3.000
 9U6  H15  C14  O13  109.94  3.000
 9U6  H14  C14  O13  110.43  3.000
 9U6  H15  C14  C15  110.78  3.000
 9U6  H14  C14  C15  110.68  3.000
 9U6  O13  C14  C15  107.04  3.000
 9U6  H16  C16  C17  119.71  3.000
 9U6  H16  C16  C15  119.69  3.000
 9U6  C17  C16  C15  120.59  3.000
 9U6  H18  C18  C19  120.07  3.000
 9U6  H18  C18  C17  120.14  3.000
 9U6  C19  C18  C17  119.79  3.000
 9U6  H19  C19  C18  120.04  3.000
 9U6  H19  C19  C20  119.88  3.000
 9U6  C18  C19  C20  120.08  3.000
 9U6  H2   N    H    106.52  3.000
 9U6  H2   N    CA   110.04  3.000
 9U6  H    N    CA   114.00  3.000
 9U6  H10  N10  C11  119.22  3.000
 9U6  H10  N10  C9   119.20  3.000
 9U6  C11  N10  C9   121.58  3.000
 9U6  C14  O13  C11  116.98  3.000
 9U6  C8   SE7  CB    95.89  3.000
 9U6  HXT  OXT  C    110.24  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
 9U6  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 9U6  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 9U6  CONST_03  C20  C15  C16  C17     0.00   0.0  0
 9U6  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 9U6  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 9U6  CONST_06  C19  C20  C15  C16     0.00   0.0  0
 9U6  CONST_07  C14  C15  C16  C17   180.00   0.0  0
 9U6  CONST_08  C19  C20  C15  C14   180.00   0.0  0
 9U6  CONST_09  H17  C17  C16  C15   180.00   0.0  0
 9U6  CONST_10  H19  C19  C20  C15   180.00   0.0  0
 9U6  CONST_11  H16  C16  C15  C20   180.00   0.0  0
 9U6  CONST_12  H18  C18  C19  C20   180.00   0.0  0
 9U6  CONST_13  H20  C20  C15  C16   180.00   0.0  0
 9U6  CONST_14  HXT  OXT  C    CA    180.00   0.0  0
 9U6  Var_01    O13  C14  C15  C20    71.71  30.0  2
 9U6  Var_02    C9   C8   SE7  CB   -176.59  30.0  1
 9U6  Var_03    C11  N10  C9   C8    177.93  30.0  3
 9U6  Var_04    O13  C11  N10  C9    179.62  30.0  2
 9U6  Var_05    N10  C11  O13  C14   177.97  30.0  3
 9U6  Var_06    SE7  C8   C9   N10  -179.91  30.0  1
 9U6  Var_07    HB2  CB   SE7  C8     45.15  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
 9U6  chir_01  CA  CB  C  N  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
 9U6  plan-1  C15  0.020
 9U6  plan-1  C17  0.020
 9U6  plan-1  C20  0.020
 9U6  plan-1  C14  0.020
 9U6  plan-1  C16  0.020
 9U6  plan-1  C18  0.020
 9U6  plan-1  C19  0.020
 9U6  plan-1  H17  0.020
 9U6  plan-1  H20  0.020
 9U6  plan-1  H16  0.020
 9U6  plan-1  H18  0.020
 9U6  plan-1  H19  0.020
 9U6  plan-2  C    0.020
 9U6  plan-2  CA   0.020
 9U6  plan-2  O    0.020
 9U6  plan-2  HXT  0.020
 9U6  plan-2  OXT  0.020
 9U6  plan-3  C11  0.020
 9U6  plan-3  N10  0.020
 9U6  plan-3  O12  0.020
 9U6  plan-3  O13  0.020

