# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:09:41 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 3-(6H-selenopheno[2,3-b]pyrrol-4-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]c2[se]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
 23S  23S  3-(6H-selenopheno[2,3-b]pyrrol-4-yl)-L-alanine  L-peptide  23  14  .  2022-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_23S
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
 23S  CD2  C   CR5    0   0.033  -0.4715   0.0630   0.3749
 23S  CE2  C   CR5    0   0.043  -1.5731   0.8203   0.0099
 23S  NE1  N   NR15   0  -0.640  -1.1859   2.0983  -0.1874
 23S  CD1  C   CR15   0  -0.106   0.1653   2.1802   0.0497
 23S  CG   C   CR5    0  -0.009   0.6536   0.9457   0.4002
 23S  SEL  SE  SE     0   0.258  -3.1479  -0.1572  -0.0643
 23S  CZ2  C   C1     0  -0.518  -2.0884  -1.6296   0.4496
 23S  CZ3  C   C1     0  -0.254  -0.7834  -1.3142   0.6182
 23S  CB   C   CH2    0  -0.547   2.0734   0.6007   0.7102
 23S  CA   C   CH1    0  -0.195   2.8540   0.0076  -0.4878
 23S  N    N   NH2    0  -0.795   2.2374  -1.1493  -1.1074
 23S  C    C   C      0   0.398   4.2833  -0.3139  -0.0014
 23S  O    O   O      0  -0.606   4.5634  -1.5101   0.2083
 23S  OXT  O   OC    -1  -0.623   5.0286   0.6692   0.1889
 23S  HE1  H   HNR5   0   0.414  -1.7760   2.8708  -0.4465
 23S  HD1  H   HCR5   0   0.275   0.6784   3.1244  -0.0459
 23S  HZ2  H   H      0   0.286  -2.5416  -2.6026   0.5759
 23S  HZ3  H   H      0   0.257  -0.0480  -2.0544   0.9065
 23S  HB1  H   HCH2   0   0.233   2.6004   1.4918   1.0578
 23S  HB2  H   HCH2   0   0.222   2.0997  -0.1212   1.5348
 23S  HA   H   HCH1   0   0.207   2.9207   0.7958  -1.2460
 23S  H    H   HNH2   0   0.324   2.2404  -1.9207  -0.4514
 23S  HN2  H   HNH2   0   0.341   1.2687  -0.9497  -1.3252

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
 23S  CD2  CE2  aromatic  1.386  0.020  1.386
 23S  CD2  CG   aromatic  1.430  0.020  1.430
 23S  CD2  CZ3  aromatic  1.433  0.020  1.433
 23S  CE2  NE1  aromatic  1.350  0.020  1.350
 23S  CE2  SEL  aromatic  1.855  0.020  1.855
 23S  NE1  CD1  aromatic  1.374  0.020  1.374
 23S  NE1  HE1  single    0.860  0.020  1.020
 23S  CD1  CG   aromatic  1.373  0.020  1.373
 23S  CD1  HD1  single    0.930  0.020  1.080
 23S  CG   CB   single    1.494  0.020  1.494
 23S  SEL  CZ2  aromatic  1.885  0.020  1.885
 23S  CZ2  CZ3  aromatic  1.353  0.020  1.353
 23S  CZ2  HZ2  single    0.930  0.020  1.080
 23S  CZ3  HZ3  single    0.930  0.020  1.080
 23S  CB   CA   single    1.521  0.033  1.521
 23S  CB   HB1  single    0.970  0.020  1.090
 23S  CB   HB2  single    0.970  0.020  1.090
 23S  CA   N    single    1.458  0.019  1.458
 23S  CA   C    single    1.525  0.021  1.525
 23S  CA   HA   single    0.970  0.020  0.970
 23S  N    H    single    0.860  0.020  0.860
 23S  N    HN2  single    0.890  0.020  1.040
 23S  C    O    deloc     1.231  0.020  1.231
 23S  C    OXT  deloc     1.248  0.020  1.248

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
 23S  CZ3  CD2  CG   139.59  3.000
 23S  CZ3  CD2  CE2  113.39  3.000
 23S  CG   CD2  CE2  107.02  3.000
 23S  SEL  CE2  NE1  137.44  3.000
 23S  SEL  CE2  CD2  113.42  3.000
 23S  NE1  CE2  CD2  109.14  3.000
 23S  HE1  NE1  CD1  125.12  3.000
 23S  HE1  NE1  CE2  126.61  3.000
 23S  CD1  NE1  CE2  108.26  3.000
 23S  HD1  CD1  CG   129.82  3.000
 23S  HD1  CD1  NE1  120.30  3.000
 23S  CG   CD1  NE1  109.88  3.000
 23S  CB   CG   CD1  126.77  3.000
 23S  CB   CG   CD2  127.51  3.000
 23S  CD1  CG   CD2  105.70  3.000
 23S  CZ2  SEL  CE2   85.61  3.000
 23S  HZ2  CZ2  CZ3  126.85  3.000
 23S  HZ2  CZ2  SEL  119.95  3.000
 23S  CZ3  CZ2  SEL  113.20  3.000
 23S  HZ3  CZ3  CZ2  121.94  3.000
 23S  HZ3  CZ3  CD2  123.68  3.000
 23S  CZ2  CZ3  CD2  114.38  3.000
 23S  HB2  CB   HB1  106.64  3.000
 23S  HB2  CB   CA   108.53  3.000
 23S  HB1  CB   CA   108.40  3.000
 23S  HB2  CB   CG   109.33  3.000
 23S  HB1  CB   CG   109.65  3.000
 23S  CA   CB   CG   114.03  3.000
 23S  HA   CA   C    110.00  3.000
 23S  HA   CA   N    110.00  3.000
 23S  C    CA   N    111.00  2.800
 23S  HA   CA   CB   109.00  3.000
 23S  C    CA   CB   110.50  1.500
 23S  N    CA   CB   110.40  1.500
 23S  HN2  N    H    106.99  3.000
 23S  HN2  N    CA   109.97  3.000
 23S  H    N    CA   114.00  3.000
 23S  OXT  C    O    126.58  3.000
 23S  OXT  C    CA   120.80  1.700
 23S  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
 23S  CONST_01  CD1  NE1  CE2  CD2    0.00   0.0  0
 23S  CONST_02  CZ2  SEL  CE2  CD2    0.00   0.0  0
 23S  CONST_03  NE1  CD1  CG   CD2    0.00   0.0  0
 23S  CONST_04  SEL  CZ2  CZ3  CD2    0.00   0.0  0
 23S  CONST_05  CD1  CG   CD2  CE2    0.00   0.0  0
 23S  CONST_06  CZ2  CZ3  CD2  CE2    0.00   0.0  0
 23S  CONST_07  CG   CD1  NE1  CE2    0.00   0.0  0
 23S  CONST_08  CZ3  CZ2  SEL  CE2    0.00   0.0  0
 23S  CONST_09  CG   CD2  CE2  NE1    0.00   0.0  0
 23S  CONST_10  CZ3  CD2  CE2  NE1  180.00   0.0  0
 23S  CONST_11  CZ2  SEL  CE2  NE1  180.00   0.0  0
 23S  CONST_12  SEL  CE2  NE1  CD1  180.00   0.0  0
 23S  CONST_13  CZ3  CD2  CG   CD1  180.00   0.0  0
 23S  CONST_14  SEL  CE2  CD2  CG   180.00   0.0  0
 23S  CONST_15  CZ2  CZ3  CD2  CG   180.00   0.0  0
 23S  CONST_16  CZ3  CD2  CE2  SEL    0.00   0.0  0
 23S  CONST_17  CB   CG   CD2  CE2  180.00   0.0  0
 23S  CONST_18  CB   CG   CD1  NE1  180.00   0.0  0
 23S  CONST_19  CB   CG   CD2  CZ3    0.00   0.0  0
 23S  CONST_20  HE1  NE1  CE2  CD2  180.00   0.0  0
 23S  CONST_21  HD1  CD1  CG   CD2  180.00   0.0  0
 23S  CONST_22  HZ2  CZ2  CZ3  CD2  180.00   0.0  0
 23S  CONST_23  HZ3  CZ3  CD2  CE2  180.00   0.0  0
 23S  Var_01    CA   CB   CG   CD2   81.95  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
 23S  chir_01  CA  CB  N  C  positiv

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
 23S  plan-1  CD2  0.020
 23S  plan-1  CE2  0.020
 23S  plan-1  NE1  0.020
 23S  plan-1  CD1  0.020
 23S  plan-1  CG   0.020
 23S  plan-1  SEL  0.020
 23S  plan-1  CZ2  0.020
 23S  plan-1  CZ3  0.020
 23S  plan-1  CB   0.020
 23S  plan-1  HE1  0.020
 23S  plan-1  HD1  0.020
 23S  plan-1  HZ2  0.020
 23S  plan-1  HZ3  0.020
 23S  plan-2  CA   0.020
 23S  plan-2  C    0.020
 23S  plan-2  O    0.020
 23S  plan-2  OXT  0.020

