# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 02:14:31 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[(3S,5S)-5-hydroxytetrahydrofuran-3-yl]-N~2~-(phenylcarbamothioyl)-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=S)Nc1ccccc1)C(=O)N[C@@H]2CO[C@H](O)C2
#
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
 D5G  D5G  N-[(3S,5S)-5-hydroxytetrahydrofuran-3-yl]-N~2~-(phenylcarbamothioyl)-L-leucinamide  ligand  49  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D5G
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
 D5G  CAK   C  CR16  0  -0.256   4.7992   1.3046  -1.0793
 D5G  CAI   C  CR16  0  -0.261   6.1280   1.4590  -1.4440
 D5G  CAH   C  CR16  0  -0.261   7.1486   1.1081  -0.5682
 D5G  CAJ   C  CR16  0  -0.254   6.8313   0.5990   0.6829
 D5G  CAL   C  CR16  0  -0.305   5.5035   0.4253   1.0487
 D5G  CAV   C  CR6   0   0.340   4.4840   0.7733   0.1684
 D5G  NAP   N  NH1   0  -0.730   3.1518   0.6440   0.6048
 D5G  CAU   C  C     0   0.402   2.1309   0.0368  -0.0425
 D5G  SAG   S  S1    0  -0.405   2.3047  -0.7354  -1.5245
 D5G  N     N  NH1   0  -0.622   0.9630   0.0948   0.6088
 D5G  CA    C  CH1   0  -0.192  -0.2570  -0.5488   0.1772
 D5G  CB    C  CH2   0  -0.396  -0.3384  -1.9844   0.7079
 D5G  CG    C  CH1   0  -0.259  -1.5805  -2.7776   0.3020
 D5G  CD2   C  CH3   0  -0.656  -1.6865  -2.9461  -1.2105
 D5G  CD1   C  CH3   0  -0.647  -1.5526  -4.1413   0.9869
 D5G  C     C  C     0   0.564  -1.4168   0.2866   0.7046
 D5G  O     O  O     0  -0.486  -1.4363   0.6800   1.8624
 D5G  NAQ   N  NH1   0  -0.654  -2.3994   0.5255  -0.1722
 D5G  CAZ   C  CR15  0  -0.085  -3.5962   1.2568   0.1678
 D5G  CAX   C  CH2   0  -0.170  -4.6161   0.4661   0.9858
 D5G  OAF   O  O     0  -0.504  -5.8192   1.1799   0.7930
 D5G  CAN   C  CH2   0  -0.575  -4.4265   1.6138  -1.0589
 D5G  CAM   C  CR15  0   0.295  -5.8554   1.7091  -0.5196
 D5G  OAE   O  OH1   0  -0.663  -6.7054   0.9895  -1.3520
 D5G  HAK   H  HCR6  0   0.264   4.0120   1.5994  -1.7581
 D5G  HAI   H  HCR6  0   0.259   6.3676   1.8717  -2.4154
 D5G  HAH   H  HCR6  0   0.258   8.1828   1.2371  -0.8586
 D5G  HAJ   H  HCR6  0   0.259   7.6162   0.3271   1.3766
 D5G  HAL   H  HCR6  0   0.269   5.2550   0.0150   2.0199
 D5G  HAP   H  HNH1  0   0.409   2.9844   0.9325   1.5588
 D5G  HN    H  HNH1  0   0.402   0.9358   0.5153   1.5285
 D5G  HA    H  HCH1  0   0.276  -0.2494  -0.5564  -0.9131
 D5G  HB1   H  HCH2  0   0.234  -0.2637  -1.9539   1.7991
 D5G  HB2   H  HCH2  0   0.237   0.5516  -2.5064   0.3429
 D5G  HG    H  HCH1  0   0.224  -2.4745  -2.2516   0.6574
 D5G  HD21  H  HCH3  0   0.217  -1.8315  -2.0009  -1.7354
 D5G  HD22  H  HCH3  0   0.222  -0.7814  -3.4071  -1.6123
 D5G  HD23  H  HCH3  0   0.234  -2.5300  -3.5864  -1.4724
 D5G  HD11  H  HCH3  0   0.216  -0.6898  -4.7256   0.6586
 D5G  HD12  H  HCH3  0   0.227  -1.4919  -4.0397   2.0717
 D5G  HD13  H  HCH3  0   0.229  -2.4499  -4.7169   0.7554
 D5G  HAQ   H  HNH1  0   0.409  -2.2912   0.2052  -1.1213
 D5G  HAZ   H  HCR5  0   0.273  -3.3176   2.1619   0.7136
 D5G  HAX1  H  HCH2  0   0.208  -4.6804  -0.5655   0.6129
 D5G  HAX2  H  HCH2  0   0.244  -4.3909   0.4353   2.0518
 D5G  HAN1  H  HCH2  0   0.279  -4.1040   2.5345  -1.5427
 D5G  HAN2  H  HCH2  0   0.256  -4.3736   0.8075  -1.7962
 D5G  HAM   H  HCR5  0   0.218  -6.1957   2.7456  -0.4247
 D5G  HAE   H  HOH1  0   0.459  -7.6172   1.2195  -1.1444

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
 D5G  CAK  CAI   aromatic  1.387  0.020  1.387
 D5G  CAK  CAV   aromatic  1.392  0.020  1.392
 D5G  CAK  HAK   single    0.930  0.020  1.080
 D5G  CAI  CAH   aromatic  1.390  0.020  1.390
 D5G  CAI  HAI   single    0.930  0.020  1.080
 D5G  CAH  CAJ   aromatic  1.388  0.020  1.388
 D5G  CAH  HAH   single    0.930  0.020  1.080
 D5G  CAJ  CAL   aromatic  1.388  0.020  1.388
 D5G  CAJ  HAJ   single    0.930  0.020  1.080
 D5G  CAL  CAV   aromatic  1.391  0.020  1.391
 D5G  CAL  HAL   single    0.930  0.020  1.080
 D5G  CAV  NAP   single    1.408  0.020  1.408
 D5G  NAP  CAU   single    1.353  0.020  1.353
 D5G  NAP  HAP   single    0.860  0.020  1.020
 D5G  CAU  SAG   double    1.680  0.020  1.680
 D5G  CAU  N     single    1.338  0.020  1.338
 D5G  N    CA    single    1.445  0.020  1.445
 D5G  N    HN    single    0.860  0.020  1.020
 D5G  CA   CB    single    1.533  0.020  1.533
 D5G  CA   C     single    1.524  0.020  1.524
 D5G  CA   HA    single    0.970  0.020  1.090
 D5G  CB   CG    single    1.529  0.020  1.529
 D5G  CB   HB1   single    0.970  0.020  1.090
 D5G  CB   HB2   single    0.970  0.020  1.090
 D5G  CG   CD2   single    1.526  0.020  1.526
 D5G  CG   CD1   single    1.526  0.020  1.526
 D5G  CG   HG    single    0.970  0.020  1.090
 D5G  CD2  HD21  single    0.970  0.020  1.090
 D5G  CD2  HD22  single    0.970  0.020  1.090
 D5G  CD2  HD23  single    0.970  0.020  1.090
 D5G  CD1  HD11  single    0.970  0.020  1.090
 D5G  CD1  HD12  single    0.970  0.020  1.090
 D5G  CD1  HD13  single    0.970  0.020  1.090
 D5G  C    O     double    1.223  0.020  1.223
 D5G  C    NAQ   single    1.338  0.020  1.338
 D5G  NAQ  CAZ   single    1.443  0.020  1.443
 D5G  NAQ  HAQ   single    0.860  0.020  1.020
 D5G  CAZ  CAX   single    1.528  0.020  1.528
 D5G  CAZ  CAN   single    1.524  0.020  1.524
 D5G  CAZ  HAZ   single    0.970  0.020  1.090
 D5G  CAX  OAF   single    1.412  0.020  1.412
 D5G  CAX  HAX1  single    0.970  0.020  1.090
 D5G  CAX  HAX2  single    0.970  0.020  1.090
 D5G  OAF  CAM   single    1.416  0.020  1.416
 D5G  CAN  CAM   single    1.530  0.020  1.530
 D5G  CAN  HAN1  single    0.970  0.020  1.090
 D5G  CAN  HAN2  single    0.970  0.020  1.090
 D5G  CAM  OAE   single    1.390  0.020  1.390
 D5G  CAM  HAM   single    0.970  0.020  1.090
 D5G  OAE  HAE   single    0.850  0.020  0.980

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
 D5G  HAK   CAK  CAV   120.14  3.000
 D5G  HAK   CAK  CAI   120.17  3.000
 D5G  CAV   CAK  CAI   119.68  3.000
 D5G  HAI   CAI  CAH   119.95  3.000
 D5G  HAI   CAI  CAK   119.39  3.000
 D5G  CAH   CAI  CAK   120.65  3.000
 D5G  HAH   CAH  CAJ   120.28  3.000
 D5G  HAH   CAH  CAI   120.18  3.000
 D5G  CAJ   CAH  CAI   119.53  3.000
 D5G  HAJ   CAJ  CAL   119.56  3.000
 D5G  HAJ   CAJ  CAH   120.29  3.000
 D5G  CAL   CAJ  CAH   120.15  3.000
 D5G  HAL   CAL  CAV   119.61  3.000
 D5G  HAL   CAL  CAJ   120.20  3.000
 D5G  CAV   CAL  CAJ   120.19  3.000
 D5G  NAP   CAV  CAL   118.31  3.000
 D5G  NAP   CAV  CAK   121.81  3.000
 D5G  CAL   CAV  CAK   119.78  3.000
 D5G  HAP   NAP  CAU   117.05  3.000
 D5G  HAP   NAP  CAV   115.03  3.000
 D5G  CAU   NAP  CAV   127.38  3.000
 D5G  N     CAU  SAG   122.64  3.000
 D5G  N     CAU  NAP   113.97  3.000
 D5G  SAG   CAU  NAP   123.39  3.000
 D5G  HN    N    CA    115.71  3.000
 D5G  HN    N    CAU   118.94  3.000
 D5G  CA    N    CAU   124.88  3.000
 D5G  HA    CA   C     110.81  3.000
 D5G  HA    CA   CB    109.88  3.000
 D5G  C     CA   CB    110.69  3.000
 D5G  HA    CA   N     107.20  3.000
 D5G  C     CA   N     107.16  3.000
 D5G  CB    CA   N     111.01  3.000
 D5G  HB2   CB   HB1   106.88  3.000
 D5G  HB2   CB   CG    108.95  3.000
 D5G  HB1   CB   CG    109.56  3.000
 D5G  HB2   CB   CA    106.74  3.000
 D5G  HB1   CB   CA    108.40  3.000
 D5G  CG    CB   CA    115.93  3.000
 D5G  HG    CG   CD1   107.34  3.000
 D5G  HG    CG   CD2   108.52  3.000
 D5G  CD1   CG   CD2   110.34  3.000
 D5G  HG    CG   CB    109.12  3.000
 D5G  CD1   CG   CB    109.25  3.000
 D5G  CD2   CG   CB    112.15  3.000
 D5G  HD23  CD2  HD22  107.74  3.000
 D5G  HD23  CD2  HD21  106.88  3.000
 D5G  HD22  CD2  HD21  107.39  3.000
 D5G  HD23  CD2  CG    110.89  3.000
 D5G  HD22  CD2  CG    110.71  3.000
 D5G  HD21  CD2  CG    112.99  3.000
 D5G  HD13  CD1  HD12  107.81  3.000
 D5G  HD13  CD1  HD11  107.68  3.000
 D5G  HD12  CD1  HD11  107.73  3.000
 D5G  HD13  CD1  CG    111.18  3.000
 D5G  HD12  CD1  CG    111.34  3.000
 D5G  HD11  CD1  CG    110.94  3.000
 D5G  NAQ   C    O     123.44  3.000
 D5G  NAQ   C    CA    115.46  3.000
 D5G  O     C    CA    121.08  3.000
 D5G  HAQ   NAQ  CAZ   118.18  3.000
 D5G  HAQ   NAQ  C     118.79  3.000
 D5G  CAZ   NAQ  C     123.01  3.000
 D5G  HAZ   CAZ  CAN   110.30  3.000
 D5G  HAZ   CAZ  CAX   109.35  3.000
 D5G  CAN   CAZ  CAX   100.86  3.000
 D5G  HAZ   CAZ  NAQ   109.02  3.000
 D5G  CAN   CAZ  NAQ   112.39  3.000
 D5G  CAX   CAZ  NAQ   114.67  3.000
 D5G  HAX2  CAX  HAX1  108.51  3.000
 D5G  HAX2  CAX  OAF   108.90  3.000
 D5G  HAX1  CAX  OAF   112.23  3.000
 D5G  HAX2  CAX  CAZ   113.59  3.000
 D5G  HAX1  CAX  CAZ   110.07  3.000
 D5G  OAF   CAX  CAZ   103.53  3.000
 D5G  CAM   OAF  CAX   109.72  3.000
 D5G  HAN2  CAN  HAN1  108.03  3.000
 D5G  HAN2  CAN  CAM   109.19  3.000
 D5G  HAN1  CAN  CAM   112.36  3.000
 D5G  HAN2  CAN  CAZ   110.09  3.000
 D5G  HAN1  CAN  CAZ   113.23  3.000
 D5G  CAM   CAN  CAZ   103.87  3.000
 D5G  HAM   CAM  OAE   110.60  3.000
 D5G  HAM   CAM  CAN   112.31  3.000
 D5G  OAE   CAM  CAN   109.12  3.000
 D5G  HAM   CAM  OAF   106.34  3.000
 D5G  OAE   CAM  OAF   112.16  3.000
 D5G  CAN   CAM  OAF   106.23  3.000
 D5G  HAE   OAE  CAM   109.04  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
 D5G  CONST_01  CAJ   CAH  CAI  CAK    0.00   0.0  0
 D5G  CONST_02  CAJ   CAL  CAV  CAK    0.00   0.0  0
 D5G  CONST_03  CAL   CAV  CAK  CAI    0.00   0.0  0
 D5G  CONST_04  CAL   CAJ  CAH  CAI    0.00   0.0  0
 D5G  CONST_05  CAV   CAK  CAI  CAH    0.00   0.0  0
 D5G  CONST_06  CAV   CAL  CAJ  CAH    0.00   0.0  0
 D5G  CONST_07  NAP   CAV  CAK  CAI  180.00   0.0  0
 D5G  CONST_08  NAP   CAV  CAL  CAJ  180.00   0.0  0
 D5G  CONST_09  HAH   CAH  CAI  CAK  180.00   0.0  0
 D5G  CONST_10  HAL   CAL  CAV  CAK  180.00   0.0  0
 D5G  CONST_11  HAJ   CAJ  CAH  CAI  180.00   0.0  0
 D5G  CONST_12  HAK   CAK  CAI  CAH  180.00   0.0  0
 D5G  CONST_13  HAI   CAI  CAH  CAJ  180.00   0.0  0
 D5G  CONST_17  CAZ   NAQ  C    CA   180.00   0.0  0
 D5G  CONST_18  CAZ   NAQ  C    O      0.00   0.0  0
 D5G  CONST_19  SAG   CAU  NAP  CAV    0.00   0.0  0
 D5G  CONST_20  N     CAU  NAP  CAV  180.00   0.0  0
 D5G  CONST_21  CA    N    CAU  NAP  180.00   0.0  0
 D5G  CONST_22  CA    N    CAU  SAG    0.00   0.0  0
 D5G  CONST_23  HAQ   NAQ  C    CA     0.00   0.0  0
 D5G  CONST_24  HN    N    CAU  NAP    0.00   0.0  0
 D5G  Var_01    HAX1  CAX  OAF  CAM  -83.88  30.0  1
 D5G  Var_02    CD2   CG   CB   CA    61.22  30.0  3
 D5G  Var_03    HD21  CD2  CG   CB   -64.94  30.0  3
 D5G  Var_04    HD11  CD1  CG   CB   -62.86  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
 D5G  chir_01  CA   N    CB   C    negativ
 D5G  chir_02  CAZ  NAQ  CAX  CAN  positiv
 D5G  chir_03  CAM  OAE  OAF  CAN  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
 D5G  plan-1  CAK  0.020
 D5G  plan-1  CAI  0.020
 D5G  plan-1  CAH  0.020
 D5G  plan-1  CAJ  0.020
 D5G  plan-1  CAL  0.020
 D5G  plan-1  CAV  0.020
 D5G  plan-1  NAP  0.020
 D5G  plan-1  HAK  0.020
 D5G  plan-1  HAI  0.020
 D5G  plan-1  HAH  0.020
 D5G  plan-1  HAJ  0.020
 D5G  plan-1  HAL  0.020
 D5G  plan-2  CAV  0.020
 D5G  plan-2  NAP  0.020
 D5G  plan-2  CAU  0.020
 D5G  plan-2  SAG  0.020
 D5G  plan-2  N    0.020
 D5G  plan-2  CA   0.020
 D5G  plan-2  HAP  0.020
 D5G  plan-2  HN   0.020
 D5G  plan-3  CA   0.020
 D5G  plan-3  C    0.020
 D5G  plan-3  O    0.020
 D5G  plan-3  NAQ  0.020
 D5G  plan-3  CAZ  0.020
 D5G  plan-3  HAQ  0.020

