# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 03:25:29 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  37  20  .  2022-07-24  2023-02-02
;
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   0.077   5.4250  -0.0681  -0.1880
 9U6  C17  C   CR16   0  -0.242   7.0977   1.0205  -1.5467
 9U6  C20  C   CR16   0  -0.289   5.7990   0.7332   0.8877
 9U6  C    C   C      0   0.408  -5.3012   1.3358  -0.9226
 9U6  CA   C   CH1    0  -0.199  -4.6070   0.1180  -0.2582
 9U6  CB   C   CH2    0  -0.601  -3.6101   0.6886   0.7623
 9U6  C8   C   CH2    0  -0.601  -0.8445  -0.2552   1.3863
 9U6  C9   C   CH2    0  -0.279  -0.4708  -0.6199  -0.0453
 9U6  C11  C   C      0   0.758   1.9447  -0.9929  -0.0413
 9U6  C14  C   CH2    0  -0.240   4.3087  -1.0565  -0.0393
 9U6  C16  C   CR16   0  -0.291   6.0816   0.0846  -1.4052
 9U6  C18  C   CR16   0  -0.262   7.4645   1.8151  -0.4687
 9U6  C19  C   CR16   0  -0.242   6.8134   1.6698   0.7502
 9U6  N    N   NH2    0  -0.795  -4.0351  -0.7601  -1.2564
 9U6  N10  N   NH1    0  -0.655   0.8838  -0.2308  -0.3646
 9U6  O12  O   O      0  -0.521   1.8848  -2.1201   0.4077
 9U6  O13  O   O2     0  -0.481   3.0899  -0.3492  -0.2965
 9U6  SE7  SE  SE     0   0.027  -2.6988  -0.6948   1.8318
 9U6  H17  H   HCR6   0   0.258   7.6044   1.1269  -2.4971
 9U6  H20  H   HCR6   0   0.255   5.2979   0.6199   1.8420
 9U6  HA   H   HCH1   0   0.219  -5.3708  -0.4390   0.2946
 9U6  HB2  H   HCH2   0   0.261  -2.8363   1.2674   0.2488
 9U6  HB3  H   HCH2   0   0.266  -4.1218   1.3589   1.4540
 9U6  H6   H   HCH2   0   0.276  -0.2230  -0.8087   2.0935
 9U6  H7   H   HCH2   0   0.270  -0.6824   0.8091   1.5688
 9U6  H8   H   HCH2   0   0.253  -0.5876  -1.6908  -0.2083
 9U6  H9   H   HCH2   0   0.250  -1.1282  -0.1143  -0.7526
 9U6  H14  H   HCH2   0   0.247   4.4185  -1.8796  -0.7492
 9U6  H15  H   HCH2   0   0.248   4.2975  -1.4766   0.9680
 9U6  H16  H   HCR6   0   0.255   5.8016  -0.5368  -2.2478
 9U6  H18  H   HCR6   0   0.259   8.2587   2.5427  -0.5748
 9U6  H19  H   HCR6   0   0.258   7.0983   2.2845   1.5942
 9U6  H    H   HNH2   0   0.330  -3.4534  -0.2163  -1.8816
 9U6  H2   H   HNH2   0   0.337  -3.4388  -1.4500  -0.8138
 9U6  H10  H   HNH1   0   0.402   1.0454   0.7197  -0.6576
 9U6  OXT  O   OC    -1  -0.614  -6.1774   1.9028  -0.2418
 9U6  O    O   O      0  -0.602  -4.8964   1.6704  -2.0517

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  1.389  0.020  1.389
 9U6  C17  C18  aromatic  1.389  0.020  1.389
 9U6  C16  C15  aromatic  1.391  0.020  1.391
 9U6  C18  C19  aromatic  1.389  0.020  1.389
 9U6  C15  C14  single    1.498  0.020  1.498
 9U6  C15  C20  aromatic  1.392  0.020  1.392
 9U6  C19  C20  aromatic  1.388  0.020  1.388
 9U6  C14  O13  single    1.433  0.020  1.433
 9U6  O13  C11  single    1.338  0.020  1.338
 9U6  C8   C9   single    1.524  0.020  1.524
 9U6  C8   SE7  single    1.957  0.020  1.957
 9U6  C9   N10  single    1.445  0.020  1.445
 9U6  N10  C11  single    1.346  0.020  1.346
 9U6  C11  O12  double    1.215  0.020  1.215
 9U6  SE7  CB   single    1.972  0.020  1.972
 9U6  CB   CA   single    1.521  0.033  1.521
 9U6  O    C    deloc     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  deloc     1.246  0.020  1.246
 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

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  120.20  3.000
 9U6  C16  C15  C20  119.07  3.000
 9U6  H17  C17  C18  120.12  3.000
 9U6  H17  C17  C16  119.89  3.000
 9U6  C18  C17  C16  119.99  3.000
 9U6  H20  C20  C19  119.72  3.000
 9U6  H20  C20  C15  119.73  3.000
 9U6  C19  C20  C15  120.54  3.000
 9U6  O    C    OXT  126.99  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  107.72  3.000
 9U6  HB3  CB   SE7  107.70  3.000
 9U6  HB2  CB   SE7  107.38  3.000
 9U6  HB3  CB   CA   110.19  3.000
 9U6  HB2  CB   CA   110.09  3.000
 9U6  SE7  CB   CA   113.55  3.000
 9U6  H7   C8   H6   107.53  3.000
 9U6  H7   C8   SE7  108.76  3.000
 9U6  H6   C8   SE7  106.14  3.000
 9U6  H7   C8   C9   110.72  3.000
 9U6  H6   C8   C9   110.34  3.000
 9U6  SE7  C8   C9   113.11  3.000
 9U6  H9   C9   H8   107.11  3.000
 9U6  H9   C9   N10  107.28  3.000
 9U6  H8   C9   N10  109.40  3.000
 9U6  H9   C9   C8   110.53  3.000
 9U6  H8   C9   C8   110.45  3.000
 9U6  N10  C9   C8   111.90  3.000
 9U6  O13  C11  O12  123.99  3.000
 9U6  O12  C11  N10  125.13  3.000
 9U6  O13  C11  N10  110.87  3.000
 9U6  H15  C14  H14  108.11  3.000
 9U6  H15  C14  O13  110.30  3.000
 9U6  H14  C14  O13  109.93  3.000
 9U6  H15  C14  C15  110.68  3.000
 9U6  H14  C14  C15  110.96  3.000
 9U6  O13  C14  C15  106.88  3.000
 9U6  H16  C16  C17  119.75  3.000
 9U6  H16  C16  C15  119.69  3.000
 9U6  C17  C16  C15  120.55  3.000
 9U6  H18  C18  C19  120.02  3.000
 9U6  H18  C18  C17  120.16  3.000
 9U6  C19  C18  C17  119.83  3.000
 9U6  H19  C19  C18  120.08  3.000
 9U6  H19  C19  C20  119.91  3.000
 9U6  C18  C19  C20  120.01  3.000
 9U6  H2   N    H    107.29  3.000
 9U6  H2   N    CA   110.14  3.000
 9U6  H    N    CA   114.00  3.000
 9U6  H10  N10  C11  118.54  3.000
 9U6  H10  N10  C9   117.94  3.000
 9U6  C11  N10  C9   122.24  3.000
 9U6  C14  O13  C11  117.15  3.000
 9U6  C8   SE7  CB    99.02  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  Var_01    O13  C14  C15  C20    85.64  30.0  2
 9U6  Var_02    C9   C8   SE7  CB    -71.39  30.0  1
 9U6  Var_03    C11  N10  C9   C8     82.99  30.0  3
 9U6  Var_04    O13  C11  N10  C9   -172.58  30.0  2
 9U6  Var_05    N10  C11  O13  C14  -178.13  30.0  3
 9U6  Var_06    SE7  C8   C9   N10   177.45  30.0  1
 9U6  Var_07    HB2  CB   SE7  C8      0.39  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  OXT  0.020
 9U6  plan-2  O    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

