# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:01:54 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-(cyclopentyldisulfanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSSC1CCCC1)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
 C5C  C5C  3-(cyclopentyldisulfanyl)-L-alanine  L-peptide  27  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_C5C
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
 C5C  N    N  NH2    0  -0.775  13.0117  20.5850  16.2790
 C5C  CA   C  CH1    0  -0.239  14.1939  21.3280  15.8723
 C5C  C    C  C      0   0.387  14.9215  22.1164  16.9966
 C5C  O    O  O      0  -0.593  14.2721  22.3394  18.0364
 C5C  CB   C  CH2    0  -0.525  13.8542  22.2829  14.7291
 C5C  SG   S  S2     0  -0.079  12.7569  23.6162  15.3391
 C5C  SD   S  S2     0  -0.059  12.2620  24.6187  13.6197
 C5C  C1   C  CH1    0  -0.373  10.6385  23.9793  13.0689
 C5C  C2   C  CH2    0  -0.428  10.6305  22.5382  12.5616
 C5C  C3   C  CH2    0  -0.464  10.2795  21.6756  13.7774
 C5C  C4   C  CH2    0  -0.439   9.4493  22.5789  14.7105
 C5C  C5   C  CH2    0  -0.434   9.5429  24.0071  14.1391
 C5C  OXT  O  OC    -1  -0.604  16.0817  22.4868  16.7339
 C5C  H    H  HNH2   0   0.341  13.3084  19.7807  16.8188
 C5C  H2   H  HNH2   0   0.330  12.4959  21.1562  16.9391
 C5C  HA   H  HCH1   0   0.240  14.9062  20.6138  15.4466
 C5C  HB2  H  HCH2   0   0.269  14.7600  22.7389  14.3320
 C5C  HB3  H  HCH2   0   0.269  13.3438  21.7468  13.9297
 C5C  H1   H  HCH1   0   0.287  10.4210  24.6852  12.2614
 C5C  H21  H  HCH2   0   0.238   9.8430  22.4536  11.8072
 C5C  H22  H  HCH2   0   0.241  11.5652  22.2514  12.0790
 C5C  H31  H  HCH2   0   0.232   9.7345  20.7780  13.4819
 C5C  H32  H  HCH2   0   0.236  11.1817  21.3395  14.2883
 C5C  H41  H  HCH2   0   0.229   8.4088  22.2555  14.7573
 C5C  H42  H  HCH2   0   0.227   9.8393  22.5377  15.7272
 C5C  H51  H  HCH2   0   0.244   9.7269  24.7615  14.9040
 C5C  H52  H  HCH2   0   0.243   8.6029  24.2775  13.6529

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
 C5C  N   CA   single  1.458  0.019  1.458
 C5C  N   H    single  0.860  0.020  0.860
 C5C  N   H2   single  0.890  0.020  1.040
 C5C  CA  C    single  1.525  0.021  1.525
 C5C  CA  CB   single  1.530  0.020  1.530
 C5C  CA  HA   single  0.970  0.020  0.970
 C5C  C   O    deloc   1.231  0.020  1.231
 C5C  C   OXT  deloc   1.246  0.020  1.246
 C5C  CB  SG   single  1.831  0.020  1.831
 C5C  CB  HB2  single  0.970  0.020  1.090
 C5C  CB  HB3  single  0.970  0.020  1.090
 C5C  SG  SD   single  2.051  0.020  2.051
 C5C  SD  C1   single  1.830  0.020  1.830
 C5C  C1  C2   single  1.528  0.020  1.528
 C5C  C1  C5   single  1.532  0.020  1.532
 C5C  C1  H1   single  0.970  0.020  1.090
 C5C  C2  C3   single  1.531  0.020  1.531
 C5C  C2  H21  single  0.970  0.020  1.090
 C5C  C2  H22  single  0.970  0.020  1.090
 C5C  C3  C4   single  1.541  0.020  1.541
 C5C  C3  H31  single  0.970  0.020  1.090
 C5C  C3  H32  single  0.970  0.020  1.090
 C5C  C4  C5   single  1.541  0.020  1.541
 C5C  C4  H41  single  0.970  0.020  1.090
 C5C  C4  H42  single  0.970  0.020  1.090
 C5C  C5  H51  single  0.970  0.020  1.090
 C5C  C5  H52  single  0.970  0.020  1.090

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
 C5C  H2   N   H    104.44  3.000
 C5C  H2   N   CA   107.93  3.000
 C5C  H    N   CA   114.00  3.000
 C5C  HA   CA  CB   109.00  3.000
 C5C  HA   CA  C    109.00  3.000
 C5C  CB   CA  C    110.10  1.900
 C5C  HA   CA  N    110.00  3.000
 C5C  CB   CA  N    110.50  1.700
 C5C  C    CA  N    111.00  2.800
 C5C  OXT  C   O    127.45  3.000
 C5C  OXT  C   CA   115.74  3.000
 C5C  O    C   CA   120.80  1.700
 C5C  HB3  CB  HB2  109.16  3.000
 C5C  HB3  CB  SG   108.78  3.000
 C5C  HB2  CB  SG   108.36  3.000
 C5C  HB3  CB  CA   110.22  3.000
 C5C  HB2  CB  CA   110.47  3.000
 C5C  SG   CB  CA   109.82  3.000
 C5C  SD   SG  CB   102.78  3.000
 C5C  C1   SD  SG   107.20  3.000
 C5C  H1   C1  C5   111.21  3.000
 C5C  H1   C1  C2   111.25  3.000
 C5C  C5   C1  C2   104.20  3.000
 C5C  H1   C1  SD    99.96  3.000
 C5C  C5   C1  SD   114.70  3.000
 C5C  C2   C1  SD   115.73  3.000
 C5C  H22  C2  H21  106.95  3.000
 C5C  H22  C2  C3   113.56  3.000
 C5C  H21  C2  C3   109.82  3.000
 C5C  H22  C2  C1   112.99  3.000
 C5C  H21  C2  C1   107.80  3.000
 C5C  C3   C2  C1   105.60  3.000
 C5C  H32  C3  H31  106.66  3.000
 C5C  H32  C3  C4   110.04  3.000
 C5C  H31  C3  C4   112.16  3.000
 C5C  H32  C3  C2   110.86  3.000
 C5C  H31  C3  C2   111.28  3.000
 C5C  C4   C3  C2   105.90  3.000
 C5C  H42  C4  H41  106.87  3.000
 C5C  H42  C4  C5   111.05  3.000
 C5C  H41  C4  C5   110.40  3.000
 C5C  H42  C4  C3   110.49  3.000
 C5C  H41  C4  C3   111.47  3.000
 C5C  C5   C4  C3   106.61  3.000
 C5C  H52  C5  H51  106.63  3.000
 C5C  H52  C5  C4   110.01  3.000
 C5C  H51  C5  C4   113.04  3.000
 C5C  H52  C5  C1   108.00  3.000
 C5C  H51  C5  C1   112.47  3.000
 C5C  C4   C5  C1   106.60  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
 C5C  Var_01  C4   C3  C2  C1   27.10  30.0  1
 C5C  Var_02  C3   C4  C5  C1  -11.31  30.0  1
 C5C  Var_03  C5   C4  C3  C2   -9.64  30.0  1
 C5C  Var_04  HB2  CB  SG  SD   65.80  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
 C5C  chir_01  CA  N   C   CB  positiv
 C5C  chir_02  C1  SD  C2  C5  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
 C5C  plan-1  CA   0.020
 C5C  plan-1  C    0.020
 C5C  plan-1  O    0.020
 C5C  plan-1  OXT  0.020

