# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:45:00 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: N-(sulfanylacetyl)-L-tyrosyl-L-prolyl-L-methioninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](NC(=O)[C@@H]1CCCN1C(=O)[C@H](Cc2ccc(O)cc2)NC(=O)CS)C(N)=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
 SD2  SD2  N-(sulfanylacetyl)-L-tyrosyl-L-prolyl-L-methioninamide  L-peptide  62  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SD2
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
 SD2  CBE   C  CH3   0  -0.764  -6.3149  -3.4264   1.4416
 SD2  SBD   S  S2    0  -0.039  -6.8491  -1.8266   0.7966
 SD2  CBC   C  CH2   0  -0.544  -5.2518  -1.1815   0.2274
 SD2  CBB   C  CH2   0  -0.459  -5.4520   0.1921  -0.3961
 SD2  CAY   C  CH1   0  -0.190  -4.1429   0.7658  -0.9423
 SD2  CAZ   C  C     0   0.517  -4.4201   2.0552  -1.7274
 SD2  OBA   O  O     0  -0.475  -4.2920   3.1555  -1.2193
 SD2  NBF   N  NH2   0  -0.800  -4.8431   1.8536  -2.9814
 SD2  NAX   N  NH1   0  -0.637  -3.2260   1.0242   0.1335
 SD2  CAS   C  C     0   0.577  -1.9567   1.3935  -0.1071
 SD2  OAT   O  O     0  -0.483  -1.4520   1.3516  -1.2158
 SD2  CAR   C  CH1   0  -0.185  -1.2149   1.9384   1.1012
 SD2  CAU   C  CH2   0  -0.478  -1.3439   3.4699   1.1710
 SD2  CAV   C  CH2   0  -0.462   0.0240   3.9212   1.6705
 SD2  CAW   C  CH2   0  -0.295   0.9701   2.9525   0.9783
 SD2  NAQ   N  NT    0  -0.477   0.2124   1.7078   0.9867
 SD2  CAG   C  C     0   0.581   0.6651   0.4422   0.9855
 SD2  OAH   O  O     0  -0.477  -0.0994  -0.5021   1.1064
 SD2  CAF   C  CH1   0  -0.201   2.1778   0.2404   0.8439
 SD2  NAA   N  NH1   0  -0.632   2.5503  -1.0914   1.2459
 SD2  CAB   C  C     0   0.588   2.2627  -2.2239   0.5834
 SD2  OAC   O  O     0  -0.480   1.7784  -2.2804  -0.5333
 SD2  CAD   C  CH2   0  -0.687   2.6157  -3.4826   1.3527
 SD2  SAE   S  S2    0  -0.226   2.5745  -4.8801   0.1976
 SD2  CAI   C  CH2   0  -0.555   2.6869   0.6317  -0.5582
 SD2  CAJ   C  CR6   0   0.133   4.1785   0.4883  -0.6663
 SD2  CAK   C  CR16  0  -0.298   4.7724  -0.6396  -1.2267
 SD2  CAM   C  CR16  0  -0.326   6.1504  -0.7769  -1.2920
 SD2  CAO   C  CR6   0   0.338   6.9751   0.2257  -0.7889
 SD2  OAP   O  OH1   0  -0.635   8.3105   0.0496  -0.8720
 SD2  CAN   C  CR16  0  -0.370   6.3994   1.3631  -0.2288
 SD2  CAL   C  CR16  0  -0.294   5.0188   1.4823  -0.1734
 SD2  HBE1  H  HCH3  0   0.262  -5.6097  -3.3042   2.2622
 SD2  HBE2  H  HCH3  0   0.275  -7.1969  -3.9448   1.8129
 SD2  HBE3  H  HCH3  0   0.262  -5.8588  -4.0314   0.6589
 SD2  HBC1  H  HCH2  0   0.267  -4.5643  -1.1381   1.0743
 SD2  HBC2  H  HCH2  0   0.266  -4.8286  -1.8675  -0.5105
 SD2  HBB1  H  HCH2  0   0.268  -6.1698   0.1161  -1.2154
 SD2  HBB2  H  HCH2  0   0.258  -5.8797   0.8854   0.3346
 SD2  HAY   H  HCH1  0   0.279  -3.6987   0.0297  -1.6194
 SD2  HBF1  H  HNH2  0   0.409  -4.9092   0.9323  -3.3790
 SD2  HBF2  H  HNH2  0   0.405  -5.1043   2.6294  -3.5683
 SD2  HAX   H  HNH1  0   0.403  -3.6071   1.1804   1.0539
 SD2  HAR   H  HCH1  0   0.281  -1.5974   1.4793   2.0181
 SD2  HAU1  H  HCH2  0   0.254  -1.5389   3.8852   0.1802
 SD2  HAU2  H  HCH2  0   0.266  -2.1623   3.7726   1.8216
 SD2  HAV1  H  HCH2  0   0.259   0.2434   4.9589   1.4240
 SD2  HAV2  H  HCH2  0   0.247   0.0969   3.8058   2.7536
 SD2  HAW1  H  HCH2  0   0.249   1.1748   3.2825  -0.0445
 SD2  HAW2  H  HCH2  0   0.260   1.9220   2.8526   1.4991
 SD2  HAF   H  HCH1  0   0.290   2.6722   0.8978   1.5644
 SD2  HAA   H  HNH1  0   0.410   2.9293  -1.1819   2.1746
 SD2  HAD1  H  HCH2  0   0.298   3.5989  -3.3942   1.8156
 SD2  HAD2  H  HCH2  0   0.308   1.8859  -3.6255   2.1520
 SD2  HAE   H  HSH1  0   0.220   2.9768  -5.7985   1.0839
 SD2  HAI1  H  HCH2  0   0.276   2.1805   0.0390  -1.3170
 SD2  HAI2  H  HCH2  0   0.273   2.4117   1.6704  -0.7437
 SD2  HAK   H  HCR6  0   0.246   4.1524  -1.4316  -1.6280
 SD2  HAM   H  HCR6  0   0.260   6.5892  -1.6628  -1.7341
 SD2  HAP   H  HOH1  0   0.473   8.7718   0.8115  -0.5042
 SD2  HAN   H  HCR6  0   0.268   7.0241   2.1593   0.1608
 SD2  HAL   H  HCR6  0   0.248   4.5927   2.3793   0.2623

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
 SD2  CBE  SBD   single    1.806  0.020  1.806
 SD2  CBE  HBE1  single    0.970  0.020  1.090
 SD2  CBE  HBE2  single    0.970  0.020  1.090
 SD2  CBE  HBE3  single    0.970  0.020  1.090
 SD2  SBD  CBC   single    1.814  0.020  1.814
 SD2  CBC  CBB   single    1.522  0.020  1.522
 SD2  CBC  HBC1  single    0.970  0.020  1.090
 SD2  CBC  HBC2  single    0.970  0.020  1.090
 SD2  CBB  CAY   single    1.530  0.020  1.530
 SD2  CBB  HBB1  single    0.970  0.020  1.090
 SD2  CBB  HBB2  single    0.970  0.020  1.090
 SD2  CAY  CAZ   single    1.535  0.020  1.535
 SD2  CAY  NAX   single    1.437  0.020  1.437
 SD2  CAY  HAY   single    0.970  0.020  1.090
 SD2  CAZ  OBA   double    1.219  0.020  1.219
 SD2  CAZ  NBF   single    1.339  0.020  1.339
 SD2  NBF  HBF1  single    0.860  0.020  1.020
 SD2  NBF  HBF2  single    0.860  0.020  1.020
 SD2  NAX  CAS   single    1.344  0.020  1.344
 SD2  NAX  HAX   single    0.860  0.020  1.020
 SD2  CAS  OAT   double    1.219  0.020  1.219
 SD2  CAS  CAR   single    1.519  0.020  1.519
 SD2  CAR  CAU   single    1.539  0.020  1.539
 SD2  CAR  NAQ   single    1.450  0.020  1.450
 SD2  CAR  HAR   single    0.970  0.020  1.090
 SD2  CAU  CAV   single    1.525  0.020  1.525
 SD2  CAU  HAU1  single    0.970  0.020  1.090
 SD2  CAU  HAU2  single    0.970  0.020  1.090
 SD2  CAV  CAW   single    1.521  0.020  1.521
 SD2  CAV  HAV1  single    0.970  0.020  1.090
 SD2  CAV  HAV2  single    0.970  0.020  1.090
 SD2  CAW  NAQ   single    1.457  0.020  1.457
 SD2  CAW  HAW1  single    0.970  0.020  1.090
 SD2  CAW  HAW2  single    0.970  0.020  1.090
 SD2  NAQ  CAG   single    1.344  0.020  1.344
 SD2  CAG  OAH   double    1.221  0.020  1.221
 SD2  CAG  CAF   single    1.533  0.020  1.533
 SD2  CAF  NAA   single    1.440  0.020  1.440
 SD2  CAF  CAI   single    1.542  0.020  1.542
 SD2  CAF  HAF   single    0.970  0.020  1.090
 SD2  NAA  CAB   single    1.343  0.020  1.343
 SD2  NAA  HAA   single    0.860  0.020  1.020
 SD2  CAB  OAC   double    1.218  0.020  1.218
 SD2  CAB  CAD   single    1.517  0.020  1.517
 SD2  CAD  SAE   single    1.814  0.020  1.814
 SD2  CAD  HAD1  single    0.970  0.020  1.090
 SD2  CAD  HAD2  single    0.970  0.020  1.090
 SD2  SAE  HAE   single    1.200  0.020  1.300
 SD2  CAI  CAJ   single    1.502  0.020  1.502
 SD2  CAI  HAI1  single    0.970  0.020  1.090
 SD2  CAI  HAI2  single    0.970  0.020  1.090
 SD2  CAJ  CAK   aromatic  1.392  0.020  1.392
 SD2  CAJ  CAL   aromatic  1.392  0.020  1.392
 SD2  CAK  CAM   aromatic  1.386  0.020  1.386
 SD2  CAK  HAK   single    0.930  0.020  1.080
 SD2  CAM  CAO   aromatic  1.392  0.020  1.392
 SD2  CAM  HAM   single    0.930  0.020  1.080
 SD2  CAO  OAP   single    1.350  0.020  1.350
 SD2  CAO  CAN   aromatic  1.392  0.020  1.392
 SD2  OAP  HAP   single    0.850  0.020  0.980
 SD2  CAN  CAL   aromatic  1.387  0.020  1.387
 SD2  CAN  HAN   single    0.930  0.020  1.080
 SD2  CAL  HAL   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
 SD2  HBE3  CBE  HBE2  108.65  3.000
 SD2  HBE3  CBE  HBE1  109.43  3.000
 SD2  HBE2  CBE  HBE1  108.74  3.000
 SD2  HBE3  CBE  SBD   111.05  3.000
 SD2  HBE2  CBE  SBD   107.70  3.000
 SD2  HBE1  CBE  SBD   111.18  3.000
 SD2  CBC   SBD  CBE    99.59  3.000
 SD2  HBC2  CBC  HBC1  107.76  3.000
 SD2  HBC2  CBC  CBB   109.93  3.000
 SD2  HBC1  CBC  CBB   111.39  3.000
 SD2  HBC2  CBC  SBD   109.25  3.000
 SD2  HBC1  CBC  SBD   108.98  3.000
 SD2  CBB   CBC  SBD   109.49  3.000
 SD2  HBB2  CBB  HBB1  106.75  3.000
 SD2  HBB2  CBB  CAY   109.59  3.000
 SD2  HBB1  CBB  CAY   108.70  3.000
 SD2  HBB2  CBB  CBC   110.47  3.000
 SD2  HBB1  CBB  CBC   109.33  3.000
 SD2  CAY   CBB  CBC   111.85  3.000
 SD2  HAY   CAY  NAX   108.97  3.000
 SD2  HAY   CAY  CAZ   108.78  3.000
 SD2  NAX   CAY  CAZ   110.31  3.000
 SD2  HAY   CAY  CBB   108.42  3.000
 SD2  NAX   CAY  CBB   110.25  3.000
 SD2  CAZ   CAY  CBB   110.06  3.000
 SD2  NBF   CAZ  OBA   124.04  3.000
 SD2  NBF   CAZ  CAY   114.19  3.000
 SD2  OBA   CAZ  CAY   121.75  3.000
 SD2  HBF2  NBF  HBF1  117.27  3.000
 SD2  HBF2  NBF  CAZ   120.78  3.000
 SD2  HBF1  NBF  CAZ   121.95  3.000
 SD2  HAX   NAX  CAS   118.55  3.000
 SD2  HAX   NAX  CAY   118.04  3.000
 SD2  CAS   NAX  CAY   121.21  3.000
 SD2  CAR   CAS  OAT   122.25  3.000
 SD2  CAR   CAS  NAX   114.68  3.000
 SD2  OAT   CAS  NAX   123.00  3.000
 SD2  HAR   CAR  NAQ   110.08  3.000
 SD2  HAR   CAR  CAU   110.50  3.000
 SD2  NAQ   CAR  CAU   104.15  3.000
 SD2  HAR   CAR  CAS   110.20  3.000
 SD2  NAQ   CAR  CAS   111.15  3.000
 SD2  CAU   CAR  CAS   110.62  3.000
 SD2  HAU2  CAU  HAU1  107.60  3.000
 SD2  HAU2  CAU  CAV   113.36  3.000
 SD2  HAU1  CAU  CAV   110.18  3.000
 SD2  HAU2  CAU  CAR   111.53  3.000
 SD2  HAU1  CAU  CAR   110.64  3.000
 SD2  CAV   CAU  CAR   103.55  3.000
 SD2  HAV2  CAV  HAV1  108.17  3.000
 SD2  HAV2  CAV  CAW   110.04  3.000
 SD2  HAV1  CAV  CAW   112.25  3.000
 SD2  HAV2  CAV  CAU   110.72  3.000
 SD2  HAV1  CAV  CAU   112.87  3.000
 SD2  CAW   CAV  CAU   102.74  3.000
 SD2  HAW2  CAW  HAW1  108.12  3.000
 SD2  HAW2  CAW  NAQ   111.91  3.000
 SD2  HAW1  CAW  NAQ   111.12  3.000
 SD2  HAW2  CAW  CAV   112.60  3.000
 SD2  HAW1  CAW  CAV   110.47  3.000
 SD2  NAQ   CAW  CAV   102.59  3.000
 SD2  CAG   NAQ  CAW   128.99  3.000
 SD2  CAG   NAQ  CAR   118.76  3.000
 SD2  CAW   NAQ  CAR   112.11  3.000
 SD2  CAF   CAG  OAH   121.69  3.000
 SD2  CAF   CAG  NAQ   117.16  3.000
 SD2  OAH   CAG  NAQ   121.15  3.000
 SD2  HAF   CAF  CAI   107.29  3.000
 SD2  HAF   CAF  NAA   104.78  3.000
 SD2  CAI   CAF  NAA   113.77  3.000
 SD2  HAF   CAF  CAG   107.83  3.000
 SD2  CAI   CAF  CAG   112.11  3.000
 SD2  NAA   CAF  CAG   110.57  3.000
 SD2  HAA   NAA  CAB   117.37  3.000
 SD2  HAA   NAA  CAF   115.96  3.000
 SD2  CAB   NAA  CAF   125.92  3.000
 SD2  CAD   CAB  OAC   121.25  3.000
 SD2  CAD   CAB  NAA   113.56  3.000
 SD2  OAC   CAB  NAA   125.18  3.000
 SD2  HAD2  CAD  HAD1  107.61  3.000
 SD2  HAD2  CAD  SAE   110.50  3.000
 SD2  HAD1  CAD  SAE   110.69  3.000
 SD2  HAD2  CAD  CAB   108.93  3.000
 SD2  HAD1  CAD  CAB   110.98  3.000
 SD2  SAE   CAD  CAB   108.13  3.000
 SD2  HAE   SAE  CAD    95.75  3.000
 SD2  HAI2  CAI  HAI1  106.43  3.000
 SD2  HAI2  CAI  CAJ   109.22  3.000
 SD2  HAI1  CAI  CAJ   111.10  3.000
 SD2  HAI2  CAI  CAF   108.24  3.000
 SD2  HAI1  CAI  CAF   110.02  3.000
 SD2  CAJ   CAI  CAF   111.65  3.000
 SD2  CAL   CAJ  CAK   117.62  3.000
 SD2  CAL   CAJ  CAI   120.38  3.000
 SD2  CAK   CAJ  CAI   121.98  3.000
 SD2  HAK   CAK  CAM   118.63  3.000
 SD2  HAK   CAK  CAJ   119.83  3.000
 SD2  CAM   CAK  CAJ   121.54  3.000
 SD2  HAM   CAM  CAO   119.77  3.000
 SD2  HAM   CAM  CAK   120.20  3.000
 SD2  CAO   CAM  CAK   120.03  3.000
 SD2  CAN   CAO  OAP   122.72  3.000
 SD2  CAN   CAO  CAM   119.25  3.000
 SD2  OAP   CAO  CAM   118.03  3.000
 SD2  HAP   OAP  CAO   110.30  3.000
 SD2  HAN   CAN  CAL   119.74  3.000
 SD2  HAN   CAN  CAO   120.40  3.000
 SD2  CAL   CAN  CAO   119.86  3.000
 SD2  HAL   CAL  CAN   118.57  3.000
 SD2  HAL   CAL  CAJ   119.73  3.000
 SD2  CAN   CAL  CAJ   121.70  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
 SD2  CONST_01  CAO   CAM  CAK  CAJ     0.00   0.0  0
 SD2  CONST_02  CAO   CAN  CAL  CAJ     0.00   0.0  0
 SD2  CONST_03  CAN   CAL  CAJ  CAK     0.00   0.0  0
 SD2  CONST_04  CAN   CAO  CAM  CAK     0.00   0.0  0
 SD2  CONST_05  CAL   CAJ  CAK  CAM     0.00   0.0  0
 SD2  CONST_06  CAL   CAN  CAO  CAM     0.00   0.0  0
 SD2  CONST_07  CAM   CAK  CAJ  CAI   180.00   0.0  0
 SD2  CONST_08  CAN   CAL  CAJ  CAI   180.00   0.0  0
 SD2  CONST_09  OAP   CAO  CAM  CAK   180.00   0.0  0
 SD2  CONST_10  CAL   CAN  CAO  OAP   180.00   0.0  0
 SD2  CONST_11  HAM   CAM  CAK  CAJ   180.00   0.0  0
 SD2  CONST_12  HAN   CAN  CAL  CAJ   180.00   0.0  0
 SD2  CONST_13  HAL   CAL  CAJ  CAK   180.00   0.0  0
 SD2  CONST_14  HAK   CAK  CAM  CAO   180.00   0.0  0
 SD2  CONST_15  OAH   CAG  NAQ  CAR     0.00   0.0  0
 SD2  CONST_16  CAF   CAG  NAQ  CAR   180.00   0.0  0
 SD2  CONST_17  OAH   CAG  NAQ  CAW   180.00   0.0  0
 SD2  CONST_18  CAF   CAG  NAQ  CAW     0.00   0.0  0
 SD2  CONST_19  CAR   CAS  NAX  CAY   180.00   0.0  0
 SD2  CONST_20  HAX   NAX  CAS  CAR     0.00   0.0  0
 SD2  CONST_21  OAT   CAS  NAX  CAY     0.00   0.0  0
 SD2  CONST_22  OAC   CAB  NAA  CAF     0.00   0.0  0
 SD2  CONST_23  CAD   CAB  NAA  CAF   180.00   0.0  0
 SD2  CONST_24  HBF1  NBF  CAZ  CAY     0.00   0.0  0
 SD2  CONST_25  HBF2  NBF  CAZ  CAY   180.00   0.0  0
 SD2  CONST_26  HAA   NAA  CAB  OAC   180.00   0.0  0
 SD2  Var_01    CAW   CAV  CAU  CAR    36.87  30.0  1
 SD2  Var_02    CAV   CAW  NAQ  CAR    23.13  30.0  1
 SD2  Var_03    NAQ   CAW  CAV  CAU   -36.47  30.0  1
 SD2  Var_04    CAK   CAJ  CAI  CAF    97.71  30.0  2
 SD2  Var_05    CBB   CBC  SBD  CBE   179.08  30.0  3
 SD2  Var_06    CAY   CBB  CBC  SBD  -177.90  30.0  3
 SD2  Var_07    SAE   CAD  CAB  NAA  -165.76  30.0  3
 SD2  Var_08    HBE1  CBE  SBD  CBC    61.84  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
 SD2  chir_01  CAY  CBB  CAZ  NAX  negativ
 SD2  chir_02  CAR  NAQ  CAS  CAU  positiv
 SD2  chir_03  CAF  NAA  CAG  CAI  positiv

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
 SD2  plan-1  CAI   0.020
 SD2  plan-1  CAJ   0.020
 SD2  plan-1  CAK   0.020
 SD2  plan-1  CAM   0.020
 SD2  plan-1  CAO   0.020
 SD2  plan-1  OAP   0.020
 SD2  plan-1  CAN   0.020
 SD2  plan-1  CAL   0.020
 SD2  plan-1  HAK   0.020
 SD2  plan-1  HAM   0.020
 SD2  plan-1  HAN   0.020
 SD2  plan-1  HAL   0.020
 SD2  plan-2  CAY   0.020
 SD2  plan-2  NAX   0.020
 SD2  plan-2  CAS   0.020
 SD2  plan-2  OAT   0.020
 SD2  plan-2  CAR   0.020
 SD2  plan-2  HAX   0.020
 SD2  plan-3  CAR   0.020
 SD2  plan-3  CAW   0.020
 SD2  plan-3  NAQ   0.020
 SD2  plan-3  CAG   0.020
 SD2  plan-3  OAH   0.020
 SD2  plan-3  CAF   0.020
 SD2  plan-4  CAF   0.020
 SD2  plan-4  NAA   0.020
 SD2  plan-4  CAB   0.020
 SD2  plan-4  OAC   0.020
 SD2  plan-4  CAD   0.020
 SD2  plan-4  HAA   0.020
 SD2  plan-5  CAY   0.020
 SD2  plan-5  CAZ   0.020
 SD2  plan-5  OBA   0.020
 SD2  plan-5  NBF   0.020
 SD2  plan-5  HBF1  0.020
 SD2  plan-5  HBF2  0.020

