# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:16:46 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: S-(2-iodobenzyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCc1ccccc1I)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
 ICY  ICY  S-(2-iodobenzyl)-L-cysteine  L-peptide  26  15  .  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_ICY
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
 ICY  C    C  C      0   0.427  17.2121  39.9228  -20.5295
 ICY  N    N  NH2    0  -0.810  16.0739  42.0211  -19.8580
 ICY  O    O  O      0  -0.594  17.4709  40.5308  -21.5854
 ICY  CA   C  CH1    0  -0.234  16.6483  40.7823  -19.3586
 ICY  CB   C  CH2    0  -0.515  15.6191  39.9933  -18.5596
 ICY  SG   S  S2     0  -0.032  15.0558  40.9693  -17.1314
 ICY  I    I  I      0   0.047  11.2314  41.3137  -17.4442
 ICY  C0   C  CH2    0  -0.626  13.9871  39.7392  -16.3178
 ICY  C1   C  CR6    0   0.168  13.1895  40.4220  -15.2501
 ICY  C2   C  CR6    0  -0.267  12.0240  41.1484  -15.4962
 ICY  C3   C  CR16   0  -0.213  11.3343  41.7881  -14.4747
 ICY  C4   C  CR16   0  -0.259  11.8126  41.7184  -13.1742
 ICY  C5   C  CR16   0  -0.236  12.9727  41.0090  -12.9024
 ICY  C6   C  CR16   0  -0.282  13.6471  40.3740  -13.9327
 ICY  OXT  O  OC    -1  -0.598  17.3919  38.7138  -20.2947
 ICY  HN   H  HNH2   0   0.333  16.1718  42.7611  -19.1755
 ICY  HNA  H  HNH2   0   0.337  16.6120  42.2971  -20.6695
 ICY  HA   H  HCH1   0   0.211  17.5083  40.9637  -18.6910
 ICY  HB   H  HCH2   0   0.247  14.7542  39.7534  -19.1834
 ICY  HBA  H  HCH2   0   0.254  16.0556  39.0648  -18.1957
 ICY  H0   H  HCH2   0   0.281  13.3473  39.2744  -17.0699
 ICY  H0A  H  HCH2   0   0.289  14.6052  38.9557  -15.8786
 ICY  H3   H  HCR6   0   0.277  10.4287  42.3419  -14.6823
 ICY  H4   H  HCR6   0   0.267  11.2736  42.2188  -12.3806
 ICY  H5   H  HCR6   0   0.264  13.3528  40.9492  -11.8912
 ICY  H6   H  HCR6   0   0.264  14.5535  39.8201  -13.7193

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
 ICY  C   CA   single    1.525  0.021  1.525
 ICY  C   OXT  deloc     1.245  0.020  1.245
 ICY  N   CA   single    1.458  0.019  1.458
 ICY  N   HN   single    0.890  0.020  1.040
 ICY  N   HNA  single    0.890  0.020  1.040
 ICY  O   C    deloc     1.231  0.020  1.231
 ICY  CA  CB   single    1.530  0.020  1.530
 ICY  CA  HA   single    0.970  0.020  0.970
 ICY  CB  SG   single    1.819  0.020  1.819
 ICY  CB  HB   single    0.970  0.020  1.090
 ICY  CB  HBA  single    0.970  0.020  1.090
 ICY  SG  C0   single    1.821  0.020  1.821
 ICY  I   C2   single    2.110  0.020  2.110
 ICY  C0  C1   single    1.497  0.020  1.497
 ICY  C0  H0   single    0.970  0.020  1.090
 ICY  C0  H0A  single    0.970  0.020  1.090
 ICY  C1  C6   aromatic  1.395  0.020  1.395
 ICY  C2  C1   aromatic  1.395  0.020  1.395
 ICY  C2  C3   aromatic  1.389  0.020  1.389
 ICY  C3  C4   aromatic  1.387  0.020  1.387
 ICY  C3  H3   single    0.930  0.020  1.080
 ICY  C4  C5   aromatic  1.387  0.020  1.387
 ICY  C4  H4   single    0.930  0.020  1.080
 ICY  C5  H5   single    0.930  0.020  1.080
 ICY  C6  C5   aromatic  1.386  0.020  1.386
 ICY  C6  H6   single    0.930  0.020  1.080

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
 ICY  OXT  C   CA  116.51  3.000
 ICY  OXT  C   O   127.16  3.000
 ICY  CA   C   O   120.80  1.700
 ICY  HNA  N   HN  106.86  3.000
 ICY  HNA  N   CA  107.33  3.000
 ICY  HN   N   CA  110.69  3.000
 ICY  HA   CA  CB  109.00  3.000
 ICY  HA   CA  N   110.00  3.000
 ICY  CB   CA  N   110.50  1.700
 ICY  HA   CA  C   109.00  3.000
 ICY  CB   CA  C   110.10  1.900
 ICY  N    CA  C   111.00  2.800
 ICY  HBA  CB  HB  108.72  3.000
 ICY  HBA  CB  SG  108.62  3.000
 ICY  HB   CB  SG  108.71  3.000
 ICY  HBA  CB  CA  110.26  3.000
 ICY  HB   CB  CA  110.42  3.000
 ICY  SG   CB  CA  110.07  3.000
 ICY  C0   SG  CB   99.79  3.000
 ICY  H0A  C0  H0  107.69  3.000
 ICY  H0A  C0  C1  110.02  3.000
 ICY  H0   C0  C1  111.92  3.000
 ICY  H0A  C0  SG  109.43  3.000
 ICY  H0   C0  SG  108.89  3.000
 ICY  C1   C0  SG  108.85  3.000
 ICY  C6   C1  C2  117.28  3.000
 ICY  C2   C1  C0  123.82  3.000
 ICY  C6   C1  C0  118.87  3.000
 ICY  C3   C2  C1  121.67  3.000
 ICY  C3   C2  I   117.17  3.000
 ICY  C1   C2  I   121.17  3.000
 ICY  H3   C3  C4  119.62  3.000
 ICY  H3   C3  C2  120.70  3.000
 ICY  C4   C3  C2  119.68  3.000
 ICY  H4   C4  C5  120.64  3.000
 ICY  H4   C4  C3  119.50  3.000
 ICY  C5   C4  C3  119.85  3.000
 ICY  H5   C5  C6  119.91  3.000
 ICY  C6   C5  C4  119.73  3.000
 ICY  H5   C5  C4  120.35  3.000
 ICY  H6   C6  C5  119.67  3.000
 ICY  H6   C6  C1  118.55  3.000
 ICY  C5   C6  C1  121.78  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
 ICY  CONST_01  C4  C5  C6  C1     0.00   0.0  0
 ICY  CONST_02  C4  C3  C2  C1     0.00   0.0  0
 ICY  CONST_03  C5  C6  C1  C2     0.00   0.0  0
 ICY  CONST_04  C5  C4  C3  C2     0.00   0.0  0
 ICY  CONST_05  C6  C1  C2  C3     0.00   0.0  0
 ICY  CONST_06  C6  C5  C4  C3     0.00   0.0  0
 ICY  CONST_07  C6  C1  C2  I    180.00   0.0  0
 ICY  CONST_08  C4  C3  C2  I    180.00   0.0  0
 ICY  CONST_09  C5  C6  C1  C0   180.00   0.0  0
 ICY  CONST_10  C3  C2  C1  C0   180.00   0.0  0
 ICY  CONST_11  H5  C5  C6  C1   180.00   0.0  0
 ICY  CONST_12  H3  C3  C2  C1   180.00   0.0  0
 ICY  CONST_13  H6  C6  C1  C2   180.00   0.0  0
 ICY  CONST_14  H4  C4  C3  C2   180.00   0.0  0
 ICY  Var_01    C6  C1  C0  SG   -96.70  30.0  2
 ICY  Var_02    C1  C0  SG  CB  -168.65  30.0  3
 ICY  Var_03    HB  CB  SG  C0    63.80  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
 ICY  chir_01  CA  C  N  CB  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
 ICY  plan-1  I    0.020
 ICY  plan-1  C0   0.020
 ICY  plan-1  C1   0.020
 ICY  plan-1  C2   0.020
 ICY  plan-1  C3   0.020
 ICY  plan-1  C4   0.020
 ICY  plan-1  C5   0.020
 ICY  plan-1  C6   0.020
 ICY  plan-1  H3   0.020
 ICY  plan-1  H4   0.020
 ICY  plan-1  H5   0.020
 ICY  plan-1  H6   0.020
 ICY  plan-2  C    0.020
 ICY  plan-2  O    0.020
 ICY  plan-2  CA   0.020
 ICY  plan-2  OXT  0.020

