# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 00:39:04 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 3-(pentyldisulfanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCSSC[C@H](N)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
 PEC  PEC  3-(pentyldisulfanyl)-L-alanine  L-peptide  29  13  .  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_PEC
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
 PEC  N    N  NH2    0  -0.786  12.4294  20.2154  16.9921
 PEC  CA   C  CH1    0  -0.195  13.6678  20.3705  16.2568
 PEC  CB   C  CH2    0  -0.568  13.5087  20.8822  14.8238
 PEC  SG   S  S2     0  -0.067  12.8512  22.5808  14.7172
 PEC  SD   S  S2     0  -0.067  10.8116  22.3234  14.7590
 PEC  C1   C  CH2    0  -0.564  10.3288  22.2700  12.9967
 PEC  C2   C  CH2    0  -0.404   9.9184  23.6160  12.4222
 PEC  C3   C  CH2    0  -0.403  11.0284  24.6539  12.3512
 PEC  C4   C  CH2    0  -0.415  10.5593  25.9664  11.7347
 PEC  C5   C  CH3    0  -0.659  11.6631  27.0115  11.6601
 PEC  C    C  C      0   0.403  14.6818  21.2659  17.0180
 PEC  O    O  O      0  -0.591  14.2817  21.8425  18.0453
 PEC  OXT  O  OC    -1  -0.608  15.8180  21.3349  16.5082
 PEC  H    H  HNH2   0   0.328  12.1226  21.1215  17.3214
 PEC  H2   H  HNH2   0   0.330  11.7002  19.8612  16.3854
 PEC  HA   H  HCH1   0   0.223  14.1323  19.3801  16.1554
 PEC  HB2  H  HCH2   0   0.270  14.4790  20.9205  14.3264
 PEC  HB3  H  HCH2   0   0.273  12.8618  20.2357  14.2281
 PEC  H11  H  HCH2   0   0.273  11.1484  21.8179  12.4365
 PEC  H12  H  HCH2   0   0.280   9.4876  21.5744  12.9579
 PEC  H21  H  HCH2   0   0.229   9.5289  23.4352  11.4146
 PEC  H22  H  HCH2   0   0.224   9.0805  24.0111  13.0041
 PEC  H31  H  HCH2   0   0.210  11.4163  24.8494  13.3559
 PEC  H32  H  HCH2   0   0.208  11.8682  24.2571  11.7707
 PEC  H41  H  HCH2   0   0.211  10.1669  25.7768  10.7310
 PEC  H42  H  HCH2   0   0.211   9.7212  26.3582  12.3189
 PEC  H51  H  HCH3   0   0.225  11.3052  27.9415  11.2169
 PEC  H52  H  HCH3   0   0.216  12.0520  27.2470  12.6524
 PEC  H53  H  HCH3   0   0.215  12.5004  26.6591  11.0547

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
 PEC  N   CA   single  1.458  0.019  1.458
 PEC  N   H    single  0.860  0.020  0.860
 PEC  N   H2   single  0.890  0.020  1.040
 PEC  CA  CB   single  1.530  0.020  1.530
 PEC  CA  C    single  1.525  0.021  1.525
 PEC  CA  HA   single  0.970  0.020  0.970
 PEC  CB  SG   single  1.825  0.020  1.825
 PEC  CB  HB2  single  0.970  0.020  1.090
 PEC  CB  HB3  single  0.970  0.020  1.090
 PEC  SG  SD   single  2.056  0.020  2.056
 PEC  SD  C1   single  1.828  0.020  1.828
 PEC  C1  C2   single  1.520  0.020  1.520
 PEC  C1  H11  single  0.970  0.020  1.090
 PEC  C1  H12  single  0.970  0.020  1.090
 PEC  C2  C3   single  1.521  0.020  1.521
 PEC  C2  H21  single  0.970  0.020  1.090
 PEC  C2  H22  single  0.970  0.020  1.090
 PEC  C3  C4   single  1.524  0.020  1.524
 PEC  C3  H31  single  0.970  0.020  1.090
 PEC  C3  H32  single  0.970  0.020  1.090
 PEC  C4  C5   single  1.522  0.020  1.522
 PEC  C4  H41  single  0.970  0.020  1.090
 PEC  C4  H42  single  0.970  0.020  1.090
 PEC  C5  H51  single  0.970  0.020  1.090
 PEC  C5  H52  single  0.970  0.020  1.090
 PEC  C5  H53  single  0.970  0.020  1.090
 PEC  C   O    deloc   1.231  0.020  1.231
 PEC  C   OXT  deloc   1.247  0.020  1.247

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
 PEC  H2   N   H    106.85  3.000
 PEC  H2   N   CA   110.43  3.000
 PEC  H    N   CA   114.00  3.000
 PEC  HA   CA  C    109.00  3.000
 PEC  HA   CA  CB   109.00  3.000
 PEC  C    CA  CB   110.10  1.900
 PEC  HA   CA  N    110.00  3.000
 PEC  C    CA  N    111.00  2.800
 PEC  CB   CA  N    110.50  1.700
 PEC  HB3  CB  HB2  107.40  3.000
 PEC  HB3  CB  SG   107.81  3.000
 PEC  HB2  CB  SG   105.14  3.000
 PEC  HB3  CB  CA   112.01  3.000
 PEC  HB2  CB  CA   110.26  3.000
 PEC  SG   CB  CA   113.80  3.000
 PEC  SD   SG  CB   103.87  3.000
 PEC  C1   SD  SG   104.24  3.000
 PEC  H12  C1  H11  107.25  3.000
 PEC  H12  C1  C2   110.03  3.000
 PEC  H11  C1  C2   112.07  3.000
 PEC  H12  C1  SD   104.85  3.000
 PEC  H11  C1  SD   107.98  3.000
 PEC  C2   C1  SD   114.19  3.000
 PEC  H22  C2  H21  106.05  3.000
 PEC  H22  C2  C3   109.71  3.000
 PEC  H21  C2  C3   109.22  3.000
 PEC  H22  C2  C1   109.00  3.000
 PEC  H21  C2  C1   107.31  3.000
 PEC  C3   C2  C1   115.14  3.000
 PEC  H32  C3  H31  106.22  3.000
 PEC  H32  C3  C4   109.49  3.000
 PEC  H31  C3  C4   109.06  3.000
 PEC  H32  C3  C2   109.69  3.000
 PEC  H31  C3  C2   109.73  3.000
 PEC  C4   C3  C2   112.45  3.000
 PEC  H42  C4  H41  106.08  3.000
 PEC  H42  C4  C5   109.62  3.000
 PEC  H41  C4  C5   109.52  3.000
 PEC  H42  C4  C3   109.16  3.000
 PEC  H41  C4  C3   109.40  3.000
 PEC  C5   C4  C3   112.83  3.000
 PEC  H53  C5  H52  107.49  3.000
 PEC  H53  C5  H51  107.56  3.000
 PEC  H52  C5  H51  107.60  3.000
 PEC  H53  C5  C4   111.21  3.000
 PEC  H52  C5  C4   111.22  3.000
 PEC  H51  C5  C4   111.56  3.000
 PEC  OXT  C   O    127.22  3.000
 PEC  OXT  C   CA   115.25  3.000
 PEC  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
 PEC  Var_01  C2   C1  SD  SG   -93.14  30.0  3
 PEC  Var_02  C3   C2  C1  SD    65.55  30.0  3
 PEC  Var_03  C4   C3  C2  C1   178.57  30.0  3
 PEC  Var_04  C5   C4  C3  C2   179.97  30.0  3
 PEC  Var_05  HB2  CB  SG  SD   152.76  30.0  1
 PEC  Var_06  H51  C5  C4  C3  -179.95  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
 PEC  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
 PEC  plan-1  CA   0.020
 PEC  plan-1  C    0.020
 PEC  plan-1  O    0.020
 PEC  plan-1  OXT  0.020

