# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:58:59 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: 3-[(2-fluoroethyl)disulfanyl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSSCCF)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
 EFC  EFC  3-[(2-fluoroethyl)disulfanyl]-L-alanine  L-peptide  20  11  .  2012-08-28  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_EFC
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
 EFC  N    N  NH2    0  -0.793  13.1344  20.4859  16.1444
 EFC  CA   C  CH1    0  -0.210  14.1765  21.3629  15.6492
 EFC  CB   C  CH2    0  -0.554  13.7113  22.3605  14.5801
 EFC  SG   S  S2     0  -0.063  12.5087  23.5374  15.2973
 EFC  SD   S  S2     0  -0.057  11.7685  24.4519  13.6133
 EFC  C1   C  CH2    0  -0.615  10.3817  23.3877  13.1088
 EFC  C2   C  CH2    0   0.009   9.0971  23.6797  13.8382
 EFC  F2   F  F      0  -0.372   9.2440  23.4594  15.2007
 EFC  C    C  C      0   0.403  14.8546  22.1506  16.7990
 EFC  O    O  O      0  -0.591  14.1595  22.3653  17.8117
 EFC  OXT  O  OC    -1  -0.599  16.0144  22.5443  16.5806
 EFC  H    H  HNH2   0   0.333  12.5966  20.9811  16.8443
 EFC  H2   H  HNH2   0   0.333  12.4943  20.2367  15.4002
 EFC  HA   H  HCH1   0   0.230  14.9452  20.7562  15.1573
 EFC  HB2  H  HCH2   0   0.265  14.5571  22.9161  14.1754
 EFC  HB3  H  HCH2   0   0.271  13.2195  21.8313  13.7614
 EFC  H11  H  HCH2   0   0.289  10.2271  23.5896  12.0461
 EFC  H12  H  HCH2   0   0.289  10.6795  22.3427  13.2013
 EFC  H21  H  HCH2   0   0.214   8.7944  24.7176  13.6914
 EFC  H22  H  HCH2   0   0.220   8.3031  23.0267  13.4688

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
 EFC  N   CA   single  1.458  0.019  1.458
 EFC  N   H    single  0.860  0.020  0.860
 EFC  N   H2   single  0.890  0.020  1.040
 EFC  CA  CB   single  1.530  0.020  1.530
 EFC  CA  C    single  1.525  0.021  1.525
 EFC  CA  HA   single  0.970  0.020  0.970
 EFC  CB  SG   single  1.829  0.020  1.829
 EFC  CB  HB2  single  0.970  0.020  1.090
 EFC  CB  HB3  single  0.970  0.020  1.090
 EFC  SG  SD   single  2.054  0.020  2.054
 EFC  SD  C1   single  1.819  0.020  1.819
 EFC  C1  C2   single  1.506  0.020  1.506
 EFC  C1  H11  single  0.970  0.020  1.090
 EFC  C1  H12  single  0.970  0.020  1.090
 EFC  C2  F2   single  1.388  0.020  1.388
 EFC  C2  H21  single  0.970  0.020  1.090
 EFC  C2  H22  single  0.970  0.020  1.090
 EFC  C   O    deloc   1.231  0.020  1.231
 EFC  C   OXT  deloc   1.244  0.020  1.244

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
 EFC  H2   N   H    107.02  3.000
 EFC  H2   N   CA   110.62  3.000
 EFC  H    N   CA   114.00  3.000
 EFC  HA   CA  C    109.00  3.000
 EFC  HA   CA  CB   109.00  3.000
 EFC  C    CA  CB   110.10  1.900
 EFC  HA   CA  N    110.00  3.000
 EFC  C    CA  N    111.00  2.800
 EFC  CB   CA  N    110.50  1.700
 EFC  HB3  CB  HB2  108.56  3.000
 EFC  HB3  CB  SG   108.04  3.000
 EFC  HB2  CB  SG   109.14  3.000
 EFC  HB3  CB  CA   110.11  3.000
 EFC  HB2  CB  CA   110.78  3.000
 EFC  SG   CB  CA   110.15  3.000
 EFC  SD   SG  CB   101.65  3.000
 EFC  C1   SD  SG   103.98  3.000
 EFC  H12  C1  H11  107.35  3.000
 EFC  H12  C1  C2   112.19  3.000
 EFC  H11  C1  C2   108.34  3.000
 EFC  H12  C1  SD   109.20  3.000
 EFC  H11  C1  SD   105.63  3.000
 EFC  C2   C1  SD   113.73  3.000
 EFC  H22  C2  H21  108.75  3.000
 EFC  H22  C2  F2   108.30  3.000
 EFC  H21  C2  F2   108.21  3.000
 EFC  H22  C2  C1   109.90  3.000
 EFC  H21  C2  C1   110.85  3.000
 EFC  F2   C2  C1   110.76  3.000
 EFC  OXT  C   O    127.43  3.000
 EFC  OXT  C   CA   116.00  3.000
 EFC  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
 EFC  Var_01  C2   C1  SD  SG   83.50  30.0  3
 EFC  Var_02  F2   C2  C1  SD  -61.94  30.0  3
 EFC  Var_03  HB2  CB  SG  SD   69.91  30.0  1

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
 EFC  chir_01  CA  N  CB  C  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
 EFC  plan-1  CA   0.020
 EFC  plan-1  C    0.020
 EFC  plan-1  O    0.020
 EFC  plan-1  OXT  0.020

