# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 22:42:51 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: N~6~-{(1R)-2-{[(1S,2S)-1-carboxy-2-hydroxy-2-(methylsulfanyl)ethyl]oxy}-1-[(oxidosulfanyl)methyl]-2-oxoethyl}-6-oxo-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@H](O)[C@@H](OC(=O)[C@H](C[S@@H]=O)NC(=O)CCC[C@H](N)C(O)=O)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
 VAZ  VAZ  N~6~-{(1R)-2-{[(1S,2S)-1-carboxy-2-hydroxy-2-(methylsulfanyl)ethyl]oxy}-1-[(oxidosulfanyl)methyl]-2-oxoethyl}-6-oxo-L-lysine  ligand  46  26  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VAZ
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
 VAZ  SAQ   S  S2     0  -0.044   6.7566  -0.7386   0.3791
 VAZ  CAY   C  CH1    0  -0.113   5.1972   0.1671   0.0723
 VAZ  OAJ   O  OH1    0  -0.628   5.1956   1.4307   0.6567
 VAZ  CAZ   C  CH1    0  -0.097   4.0205  -0.6871   0.5438
 VAZ  CAU   C  C      0   0.399   4.0101  -2.0947  -0.1016
 VAZ  OAI   O  O      0  -0.585   3.3791  -2.2137  -1.1616
 VAZ  OAE   O  OC    -1  -0.588   4.6722  -2.9476   0.5120
 VAZ  OAP   O  O2     0  -0.451   2.8684   0.0730   0.1628
 VAZ  CAV   C  C      0   0.622   1.6933  -0.3533   0.5642
 VAZ  OAF   O  O      0  -0.435   1.5061  -1.2953   1.2895
 VAZ  CAX   C  CH1    0  -0.234   0.5825   0.5304   0.0120
 VAZ  CAN   C  CH2    0  -0.608   0.7846   1.9706   0.4895
 VAZ  SAR   S  S3     0   0.568  -0.4751   3.1279  -0.1510
 VAZ  OAG   O  O      0  -0.779  -0.0130   4.5003   0.2776
 VAZ  NAO   N  NH1    0  -0.639  -0.6890  -0.0113   0.4027
 VAZ  CAS   C  C      0   0.583  -1.7863   0.0970  -0.3722
 VAZ  OAC   O  O      0  -0.499  -1.7763   0.7456  -1.4094
 VAZ  CAL   C  CH2    0  -0.582  -2.9965  -0.6540   0.1281
 VAZ  CAK   C  CH2    0  -0.405  -4.3187  -0.1167  -0.3981
 VAZ  CB    C  CH2    0  -0.417  -5.4965  -0.9314   0.1190
 VAZ  CA    C  CH1    0  -0.215  -6.8555  -0.4404  -0.3859
 VAZ  C     C  C      0   0.385  -7.9503  -1.4596   0.0185
 VAZ  O     O  O     -1  -0.608  -8.7822  -1.1041   0.8770
 VAZ  OXT   O  OC     0  -0.624  -7.8944  -2.5743  -0.5427
 VAZ  N     N  NH2    0  -0.786  -7.0874   0.9281   0.0537
 VAZ  CAA   C  CH3    0  -0.765   7.9136   0.5194  -0.2133
 VAZ  HAA1  H  HCH3   0   0.271   8.8999   0.0593  -0.2280
 VAZ  HAA2  H  HCH3   0   0.259   7.6647   0.8332  -1.2266
 VAZ  HAA3  H  HCH3   0   0.261   7.9433   1.3890   0.4386
 VAZ  HAJ   H  HOH1   0   0.451   5.2817   1.3309   1.6127
 VAZ  HAZ   H  HCH1   0   0.254   4.0554  -0.7764   1.6348
 VAZ  HAX   H  HCH1   0   0.308   0.6607   0.4993  -1.0797
 VAZ  HAN1  H  HCH2   0   0.306   0.6958   2.0346   1.5758
 VAZ  HAN2  H  HCH2   0   0.310   1.7532   2.3695   0.1890
 VAZ  HAO   H  HNH1   0   0.406  -0.7325  -0.5480   1.2555
 VAZ  HAL1  H  HCH2   0   0.273  -2.8731  -1.7016  -0.1692
 VAZ  HAL2  H  HCH2   0   0.255  -2.9964  -0.6571   1.2219
 VAZ  HAK1  H  HCH2   0   0.226  -4.4419   0.9287  -0.1097
 VAZ  HAK2  H  HCH2   0   0.216  -4.3183  -0.1396  -1.4910
 VAZ  HBC1  H  HCH2   0   0.218  -5.3715  -1.9765  -0.1747
 VAZ  HBC2  H  HCH2   0   0.205  -5.4967  -0.9205   1.2164
 VAZ  HA    H  HCH1   0   0.207  -6.8096  -0.4292  -1.4816
 VAZ  HN1   H  HNH2   0   0.333  -7.9178   1.2792  -0.4083
 VAZ  HN2   H  HNH2   0   0.321  -7.3448   0.8962   1.0342
 VAZ  HAY   H  HCH1   0   0.274   5.1166   0.3308  -1.0057
 VAZ  HAR   H  HSH1   0   0.194  -0.0992   2.9408  -1.4497

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
 VAZ  SAQ  CAY   single  1.829  0.020  1.829
 VAZ  SAQ  CAA   single  1.809  0.020  1.809
 VAZ  CAY  OAJ   single  1.392  0.020  1.392
 VAZ  CAY  CAZ   single  1.529  0.020  1.529
 VAZ  CAZ  CAU   single  1.549  0.020  1.549
 VAZ  CAZ  OAP   single  1.432  0.020  1.432
 VAZ  CAU  OAI   deloc   1.239  0.020  1.239
 VAZ  CAU  OAE   deloc   1.242  0.020  1.242
 VAZ  OAP  CAV   single  1.313  0.020  1.313
 VAZ  CAV  OAF   double  1.203  0.020  1.203
 VAZ  CAV  CAX   single  1.523  0.020  1.523
 VAZ  CAX  CAN   single  1.531  0.020  1.531
 VAZ  CAX  NAO   single  1.436  0.020  1.436
 VAZ  CAN  SAR   single  1.827  0.020  1.827
 VAZ  SAR  OAG   double  1.510  0.020  1.510
 VAZ  NAO  CAS   single  1.348  0.020  1.348
 VAZ  CAS  OAC   double  1.223  0.020  1.223
 VAZ  CAS  CAL   single  1.510  0.020  1.510
 VAZ  CAL  CAK   single  1.521  0.020  1.521
 VAZ  CAK  CB    single  1.523  0.020  1.523
 VAZ  CB   CA    single  1.531  0.020  1.531
 VAZ  CA   C     single  1.550  0.020  1.550
 VAZ  CA   N     single  1.456  0.020  1.456
 VAZ  C    O     deloc   1.247  0.020  1.247
 VAZ  C    OXT   deloc   1.249  0.020  1.249
 VAZ  CAA  HAA1  single  0.970  0.020  1.090
 VAZ  CAA  HAA2  single  0.970  0.020  1.090
 VAZ  CAA  HAA3  single  0.970  0.020  1.090
 VAZ  OAJ  HAJ   single  0.850  0.020  0.980
 VAZ  CAZ  HAZ   single  0.970  0.020  1.090
 VAZ  CAX  HAX   single  0.970  0.020  1.090
 VAZ  CAN  HAN1  single  0.970  0.020  1.090
 VAZ  CAN  HAN2  single  0.970  0.020  1.090
 VAZ  NAO  HAO   single  0.860  0.020  1.020
 VAZ  CAL  HAL1  single  0.970  0.020  1.090
 VAZ  CAL  HAL2  single  0.970  0.020  1.090
 VAZ  CAK  HAK1  single  0.970  0.020  1.090
 VAZ  CAK  HAK2  single  0.970  0.020  1.090
 VAZ  CB   HBC1  single  0.970  0.020  1.090
 VAZ  CB   HBC2  single  0.970  0.020  1.090
 VAZ  CA   HA    single  0.970  0.020  1.090
 VAZ  N    HN1   single  0.890  0.020  1.040
 VAZ  N    HN2   single  0.890  0.020  1.040
 VAZ  CAY  HAY   single  0.970  0.020  1.090
 VAZ  SAR  HAR   single  1.200  0.020  1.300

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
 VAZ  CAA   SAQ  CAY    98.40  3.000
 VAZ  HAY   CAY  CAZ   109.34  3.000
 VAZ  HAY   CAY  OAJ   106.14  3.000
 VAZ  CAZ   CAY  OAJ   112.14  3.000
 VAZ  HAY   CAY  SAQ   107.60  3.000
 VAZ  CAZ   CAY  SAQ   109.14  3.000
 VAZ  OAJ   CAY  SAQ   112.33  3.000
 VAZ  HAJ   OAJ  CAY   108.78  3.000
 VAZ  HAZ   CAZ  OAP   109.51  3.000
 VAZ  HAZ   CAZ  CAU   109.96  3.000
 VAZ  OAP   CAZ  CAU   111.48  3.000
 VAZ  HAZ   CAZ  CAY   109.17  3.000
 VAZ  OAP   CAZ  CAY   103.93  3.000
 VAZ  CAU   CAZ  CAY   112.62  3.000
 VAZ  OAE   CAU  OAI   128.91  3.000
 VAZ  OAE   CAU  CAZ   114.50  3.000
 VAZ  OAI   CAU  CAZ   116.56  3.000
 VAZ  CAV   OAP  CAZ   117.81  3.000
 VAZ  CAX   CAV  OAF   124.00  3.000
 VAZ  CAX   CAV  OAP   110.70  3.000
 VAZ  OAF   CAV  OAP   125.28  3.000
 VAZ  HAX   CAX  NAO   108.89  3.000
 VAZ  HAX   CAX  CAN   109.17  3.000
 VAZ  NAO   CAX  CAN   112.76  3.000
 VAZ  HAX   CAX  CAV   107.03  3.000
 VAZ  NAO   CAX  CAV   109.16  3.000
 VAZ  CAN   CAX  CAV   109.67  3.000
 VAZ  HAN2  CAN  HAN1  108.98  3.000
 VAZ  HAN2  CAN  SAR   106.52  3.000
 VAZ  HAN1  CAN  SAR   104.81  3.000
 VAZ  HAN2  CAN  CAX   112.07  3.000
 VAZ  HAN1  CAN  CAX   110.78  3.000
 VAZ  SAR   CAN  CAX   113.31  3.000
 VAZ  HAR   SAR  OAG   108.08  3.000
 VAZ  HAR   SAR  CAN    93.26  3.000
 VAZ  OAG   SAR  CAN   105.38  3.000
 VAZ  HAO   NAO  CAS   119.60  3.000
 VAZ  HAO   NAO  CAX   117.96  3.000
 VAZ  CAS   NAO  CAX   122.28  3.000
 VAZ  CAL   CAS  OAC   123.45  3.000
 VAZ  CAL   CAS  NAO   114.97  3.000
 VAZ  OAC   CAS  NAO   121.57  3.000
 VAZ  HAL2  CAL  HAL1  105.58  3.000
 VAZ  HAL2  CAL  CAK   110.31  3.000
 VAZ  HAL1  CAL  CAK   109.98  3.000
 VAZ  HAL2  CAL  CAS   109.44  3.000
 VAZ  HAL1  CAL  CAS   107.18  3.000
 VAZ  CAK   CAL  CAS   113.98  3.000
 VAZ  HAK2  CAK  HAK1  106.52  3.000
 VAZ  HAK2  CAK  CB    109.19  3.000
 VAZ  HAK1  CAK  CB    109.60  3.000
 VAZ  HAK2  CAK  CAL   109.76  3.000
 VAZ  HAK1  CAK  CAL   110.18  3.000
 VAZ  CB    CAK  CAL   111.46  3.000
 VAZ  HBC2  CB   HBC1  106.16  3.000
 VAZ  HBC2  CB   CA    109.06  3.000
 VAZ  HBC1  CB   CA    108.64  3.000
 VAZ  HBC2  CB   CAK   109.54  3.000
 VAZ  HBC1  CB   CAK   109.39  3.000
 VAZ  CA    CB   CAK   113.77  3.000
 VAZ  HA    CA   N     107.38  3.000
 VAZ  HA    CA   C     107.28  3.000
 VAZ  N     CA   C     115.27  3.000
 VAZ  HA    CA   CB    107.20  3.000
 VAZ  N     CA   CB    110.08  3.000
 VAZ  C     CA   CB    109.28  3.000
 VAZ  OXT   C    O     126.40  3.000
 VAZ  OXT   C    CA    115.98  3.000
 VAZ  O     C    CA    117.61  3.000
 VAZ  HN2   N    HN1   104.11  3.000
 VAZ  HN2   N    CA    107.63  3.000
 VAZ  HN1   N    CA    108.58  3.000
 VAZ  HAA3  CAA  HAA2  109.48  3.000
 VAZ  HAA3  CAA  HAA1  108.75  3.000
 VAZ  HAA2  CAA  HAA1  108.43  3.000
 VAZ  HAA3  CAA  SAQ   112.17  3.000
 VAZ  HAA2  CAA  SAQ   111.02  3.000
 VAZ  HAA1  CAA  SAQ   106.86  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
 VAZ  CONST_01  OAC   CAS  NAO  CAX     0.00   0.0  0
 VAZ  CONST_02  CAL   CAS  NAO  CAX   180.00   0.0  0
 VAZ  CONST_03  HAO   NAO  CAS  OAC   180.00   0.0  0
 VAZ  Var_01    OAF   CAV  OAP  CAZ     4.21  30.0  3
 VAZ  Var_02    OAG   SAR  CAN  CAX  -173.06  30.0  3
 VAZ  Var_03    CAK   CAL  CAS  NAO   157.18  30.0  3
 VAZ  Var_04    CB    CAK  CAL  CAS   178.86  30.0  3
 VAZ  Var_05    CA    CB   CAK  CAL  -179.65  30.0  3
 VAZ  Var_06    HAA1  CAA  SAQ  CAY  -171.84  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
 VAZ  chir_01  CAY  SAQ  OAJ  CAZ  positiv
 VAZ  chir_02  CAZ  OAP  CAY  CAU  positiv
 VAZ  chir_03  CAX  NAO  CAN  CAV  negativ
 VAZ  chir_05  CA   CB   C    N    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
 VAZ  plan-1  CAX  0.020
 VAZ  plan-1  NAO  0.020
 VAZ  plan-1  CAS  0.020
 VAZ  plan-1  OAC  0.020
 VAZ  plan-1  CAL  0.020
 VAZ  plan-1  HAO  0.020
 VAZ  plan-2  CAZ  0.020
 VAZ  plan-2  CAU  0.020
 VAZ  plan-2  OAI  0.020
 VAZ  plan-2  OAE  0.020
 VAZ  plan-3  CA   0.020
 VAZ  plan-3  C    0.020
 VAZ  plan-3  O    0.020
 VAZ  plan-3  OXT  0.020
 VAZ  plan-4  OAP  0.020
 VAZ  plan-4  CAV  0.020
 VAZ  plan-4  OAF  0.020
 VAZ  plan-4  CAX  0.020
 VAZ  plan-5  CAN  0.020
 VAZ  plan-5  SAR  0.020
 VAZ  plan-5  OAG  0.020
 VAZ  plan-5  HAR  0.020

