# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:41:40 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: S-[(3S,4R)-4-hydroxy-1-oxononan-3-yl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@@H](O)[C@H](CC=O)SC[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
 HNC  HNC  S-[(3S,4R)-4-hydroxy-1-oxononan-3-yl]-L-cysteine  L-peptide  40  18  .  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_HNC
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
 HNC  C     C  C      0   0.422   1.6780  -0.3866  -11.4994
 HNC  N     N  NH2    0  -0.811   0.6502  -1.4162  -13.5145
 HNC  O     O  O      0  -0.593   0.9394   0.5827  -11.7573
 HNC  CA    C  CH1    0  -0.226   1.4508  -1.6835  -12.3313
 HNC  CB    C  CH2    0  -0.515   2.7904  -2.2958  -12.7221
 HNC  SG    S  S2     0  -0.030   2.5369  -3.8941  -13.5526
 HNC  CAA   C  CH3    0  -0.665  10.0064  -2.5718  -16.9022
 HNC  OAC   O  O      0  -0.385   3.6193  -5.7439  -16.2343
 HNC  OAE   O  OH1    0  -0.678   4.7247  -3.2486  -15.5924
 HNC  CAH   C  CH2    0  -0.424  10.1639  -3.1453  -15.4995
 HNC  CAI   C  CH2    0  -0.417   9.0344  -4.0836  -15.0830
 HNC  CAK   C  CH2    0  -0.577   4.1595  -6.0404  -13.8972
 HNC  CAL   C  CH2    0  -0.440   6.5874  -4.3575  -14.4779
 HNC  CAP   C  CH1    0   0.068   5.2198  -3.6842  -14.3534
 HNC  CAQ   C  CH1    0  -0.420   4.2361  -4.5547  -13.5470
 HNC  OXT   O  OC    -1  -0.600   2.5586  -0.4464  -10.6214
 HNC  HN    H  HNH2   0   0.333   0.0812  -2.2188  -13.7489
 HNC  HNA   H  HNH2   0   0.337   0.0165  -0.6588  -13.2930
 HNC  HA    H  HCH1   0   0.208   0.9542  -2.3899  -11.6448
 HNC  HB    H  HCH2   0   0.246   3.3205  -1.6156  -13.3919
 HNC  HBA   H  HCH2   0   0.252   3.4013  -2.4650  -11.8364
 HNC  HAA   H  HCH3   0   0.225  10.8689  -1.9646  -17.1795
 HNC  HAAA  H  HCH3   0   0.214   9.9122  -3.3686  -17.6429
 HNC  HAAB  H  HCH3   0   0.220   9.1225  -1.9389  -16.9879
 HNC  HOAE  H  HOH1   0   0.438   4.3092  -4.0088  -16.0263
 HNC  HAF   H  H      0   0.225   3.5113  -7.5343  -15.3488
 HNC  HAH   H  HCH2   0   0.218  11.1118  -3.6869  -15.4406
 HNC  HAHA  H  HCH2   0   0.209  10.2384  -2.3276  -14.7757
 HNC  HAI   H  HCH2   0   0.206   8.9708  -4.9128  -15.7965
 HNC  HAIA  H  HCH2   0   0.214   9.2866  -4.5350  -14.1180
 HNC  HAJ   H  HCH2   0   0.207   7.7471  -2.5585  -14.2830
 HNC  HAJA  H  HCH2   0   0.219   7.3769  -2.9946  -15.9381
 HNC  HAK   H  HCH2   0   0.298   3.5009  -6.5513  -13.1871
 HNC  HAKA  H  HCH2   0   0.307   5.1339  -6.5208  -13.7390
 HNC  HAL   H  HCH2   0   0.217   6.5227  -5.2185  -15.1528
 HNC  HALA  H  HCH2   0   0.218   6.8765  -4.7579  -13.4995
 HNC  HAP   H  HCH1   0   0.226   5.3654  -2.7740  -13.7603
 HNC  HAQ   H  HCH1   0   0.287   4.5817  -4.5185  -12.5094
 HNC  CAF   C  C1     0   0.183   3.7259  -6.4561  -15.2627
 HNC  CAJ   C  CH2    0  -0.416   7.6726  -3.4083  -14.9711

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
 HNC  O    C     deloc   1.231  0.020  1.231
 HNC  CA   C     single  1.525  0.021  1.525
 HNC  C    OXT   deloc   1.245  0.020  1.245
 HNC  N    CA    single  1.458  0.019  1.458
 HNC  N    HN    single  0.890  0.020  1.040
 HNC  N    HNA   single  0.890  0.020  1.040
 HNC  CB   CA    single  1.530  0.020  1.530
 HNC  CA   HA    single  0.970  0.020  0.970
 HNC  SG   CB    single  1.819  0.020  1.819
 HNC  CB   HB    single  0.970  0.020  1.090
 HNC  CB   HBA   single  0.970  0.020  1.090
 HNC  CAQ  SG    single  1.823  0.020  1.823
 HNC  CAA  CAH   single  1.524  0.020  1.524
 HNC  CAA  HAA   single  0.970  0.020  1.090
 HNC  CAA  HAAA  single  0.970  0.020  1.090
 HNC  CAA  HAAB  single  0.970  0.020  1.090
 HNC  OAC  CAF   double  1.209  0.020  1.209
 HNC  OAE  CAP   single  1.404  0.020  1.404
 HNC  OAE  HOAE  single  0.850  0.020  0.980
 HNC  CAF  CAK   single  1.492  0.020  1.492
 HNC  CAF  HAF   single  0.930  0.020  1.080
 HNC  CAH  CAI   single  1.526  0.020  1.526
 HNC  CAH  HAH   single  0.970  0.020  1.090
 HNC  CAH  HAHA  single  0.970  0.020  1.090
 HNC  CAJ  CAI   single  1.524  0.020  1.524
 HNC  CAI  HAI   single  0.970  0.020  1.090
 HNC  CAI  HAIA  single  0.970  0.020  1.090
 HNC  CAJ  CAL   single  1.524  0.020  1.524
 HNC  CAJ  HAJ   single  0.970  0.020  1.090
 HNC  CAJ  HAJA  single  0.970  0.020  1.090
 HNC  CAK  CAQ   single  1.528  0.020  1.528
 HNC  CAK  HAK   single  0.970  0.020  1.090
 HNC  CAK  HAKA  single  0.970  0.020  1.090
 HNC  CAP  CAL   single  1.529  0.020  1.529
 HNC  CAL  HAL   single  0.970  0.020  1.090
 HNC  CAL  HALA  single  0.970  0.020  1.090
 HNC  CAP  CAQ   single  1.541  0.020  1.541
 HNC  CAP  HAP   single  0.970  0.020  1.090
 HNC  CAQ  HAQ   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
 HNC  OXT   C    CA    116.09  3.000
 HNC  OXT   C    O     127.07  3.000
 HNC  CA    C    O     120.80  1.700
 HNC  HNA   N    HN    107.00  3.000
 HNC  HNA   N    CA    107.72  3.000
 HNC  HN    N    CA    110.64  3.000
 HNC  HA    CA   CB    109.00  3.000
 HNC  HA    CA   N     110.00  3.000
 HNC  CB    CA   N     110.50  1.700
 HNC  HA    CA   C     109.00  3.000
 HNC  CB    CA   C     110.10  1.900
 HNC  N     CA   C     111.00  2.800
 HNC  HBA   CB   HB    108.86  3.000
 HNC  HBA   CB   SG    108.24  3.000
 HNC  HB    CB   SG    109.57  3.000
 HNC  HBA   CB   CA    110.30  3.000
 HNC  HB    CB   CA    109.50  3.000
 HNC  SG    CB   CA    110.35  3.000
 HNC  CAQ   SG   CB    100.78  3.000
 HNC  HAAB  CAA  HAAA  107.48  3.000
 HNC  HAAB  CAA  HAA   107.33  3.000
 HNC  HAAA  CAA  HAA   107.58  3.000
 HNC  HAAB  CAA  CAH   112.00  3.000
 HNC  HAAA  CAA  CAH   111.03  3.000
 HNC  HAA   CAA  CAH   111.22  3.000
 HNC  HOAE  OAE  CAP   107.65  3.000
 HNC  HAHA  CAH  HAH   105.99  3.000
 HNC  HAHA  CAH  CAI   109.22  3.000
 HNC  HAH   CAH  CAI   108.80  3.000
 HNC  HAHA  CAH  CAA   109.55  3.000
 HNC  HAH   CAH  CAA   109.01  3.000
 HNC  CAI   CAH  CAA   113.96  3.000
 HNC  HAIA  CAI  HAI   105.98  3.000
 HNC  HAIA  CAI  CAJ   108.89  3.000
 HNC  HAI   CAI  CAJ   109.34  3.000
 HNC  HAIA  CAI  CAH   108.88  3.000
 HNC  HAI   CAI  CAH   109.29  3.000
 HNC  CAJ   CAI  CAH   114.13  3.000
 HNC  HAKA  CAK  HAK   103.67  3.000
 HNC  HAKA  CAK  CAQ   110.36  3.000
 HNC  HAK   CAK  CAQ   109.58  3.000
 HNC  HAKA  CAK  CAF   105.54  3.000
 HNC  HAK   CAK  CAF   106.78  3.000
 HNC  CAQ   CAK  CAF   119.68  3.000
 HNC  HALA  CAL  HAL   106.16  3.000
 HNC  HALA  CAL  CAP   108.91  3.000
 HNC  HAL   CAL  CAP   110.07  3.000
 HNC  HALA  CAL  CAJ   109.19  3.000
 HNC  HAL   CAL  CAJ   109.40  3.000
 HNC  CAP   CAL  CAJ   112.89  3.000
 HNC  HAP   CAP  CAQ   105.70  3.000
 HNC  HAP   CAP  CAL   106.91  3.000
 HNC  CAQ   CAP  CAL   111.39  3.000
 HNC  HAP   CAP  OAE   105.47  3.000
 HNC  CAQ   CAP  OAE   114.33  3.000
 HNC  CAL   CAP  OAE   112.35  3.000
 HNC  HAQ   CAQ  CAP   106.01  3.000
 HNC  HAQ   CAQ  CAK   105.38  3.000
 HNC  CAP   CAQ  CAK   117.46  3.000
 HNC  HAQ   CAQ  SG    106.58  3.000
 HNC  CAP   CAQ  SG    112.87  3.000
 HNC  CAK   CAQ  SG    107.75  3.000
 HNC  HAF   CAF  CAK   113.61  3.000
 HNC  HAF   CAF  OAC   119.73  3.000
 HNC  CAK   CAF  OAC   126.65  3.000
 HNC  HAJA  CAJ  HAJ   106.29  3.000
 HNC  HAJA  CAJ  CAL   109.24  3.000
 HNC  HAJ   CAJ  CAL   109.16  3.000
 HNC  HAJA  CAJ  CAI   110.16  3.000
 HNC  HAJ   CAJ  CAI   109.21  3.000
 HNC  CAL   CAJ  CAI   112.58  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
 HNC  Var_01  CAJ  CAI  CAH  CAA   -64.61  30.0  3
 HNC  Var_02  CAQ  CAK  CAF  OAC    12.87  30.0  3
 HNC  Var_03  CAL  CAJ  CAI  CAH  -176.76  30.0  1
 HNC  Var_04  CAP  CAL  CAJ  CAI   179.59  30.0  3
 HNC  Var_05  HAA  CAA  CAH  CAI  -176.07  30.0  3
 HNC  Var_06  HB   CB   SG   CAQ    71.90  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
 HNC  chir_01  CA   C    N    CB   negativ
 HNC  chir_02  CAP  OAE  CAL  CAQ  positiv
 HNC  chir_03  CAQ  SG   CAK  CAP  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
 HNC  plan-1  C    0.020
 HNC  plan-1  O    0.020
 HNC  plan-1  CA   0.020
 HNC  plan-1  OXT  0.020
 HNC  plan-2  OAC  0.020
 HNC  plan-2  CAK  0.020
 HNC  plan-2  HAF  0.020
 HNC  plan-2  CAF  0.020

