# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 10:21:34 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-({1-[(2S)-2-amino-2-carboxyethyl]-2,4-dioxo-1,2-dihydrothieno[3,4-d]pyrimidin-3(4H)-yl}methyl)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CN1C(=O)N(Cc2ccsc2C(O)=O)C(=O)c3cscc13)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
 3HU  3HU  '3-({1-[(2S)-2-amino-2-carboxyethyl]-2,4-dioxo-1,2-dihydrothieno[3,4-d]pyrimidin-3(4H)-yl}methyl)thiophene-2-carboxylic acid'  ligand  37  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3HU
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
 3HU  C     C  C      0   0.418  -4.2487   2.9409  -0.1793
 3HU  N     N  NH2    0  -0.785  -4.0412   1.0354   1.3859
 3HU  OXT   O  OC     0  -0.657  -3.6761   3.8911  -0.7486
 3HU  CA    C  CH1    0  -0.213  -3.3145   1.8933   0.4741
 3HU  CB    C  CH2    0  -0.318  -2.5935   1.1670  -0.6735
 3HU  OAB   O  O      0  -0.332   4.1867   1.0445   2.2484
 3HU  OAF   O  OC    -1  -0.794   5.9857   1.2539   0.9323
 3HU  CAH   C  CR15   0  -0.465   3.4924  -0.3752  -2.2792
 3HU  CAI   C  CR15   0  -0.147   2.4372  -0.4858  -1.4235
 3HU  CAJ   C  CR15   0  -0.514  -1.7084  -3.4619   0.2072
 3HU  CAK   C  CR15   0  -0.538  -3.2964  -1.7244  -0.5519
 3HU  SAN   S  S2     0   0.285  -3.3048  -3.4284  -0.3545
 3HU  SAO   S  S2     0   0.223   4.8700   0.2649  -1.5003
 3HU  CAP   C  C      0   0.359   4.8016   0.9456   1.1673
 3HU  CAR   C  CR5    0   0.152   2.7432  -0.0433  -0.1044
 3HU  CAS   C  CR5    0  -0.429   4.0379   0.3939   0.0004
 3HU  CAT   C  CR6    0   0.597   0.1619  -1.8599   0.6854
 3HU  CAU   C  CR6    0   0.712  -0.4269   0.4897   0.1780
 3HU  CAV   C  CR56   0   0.051  -1.1800  -2.2023   0.2536
 3HU  CAW   C  CR56   0   0.365  -2.0881  -1.2020  -0.1844
 3HU  NAY   N  NR6    0  -0.492   0.4402  -0.5059   0.6385
 3HU  NAZ   N  NR6    0  -0.588  -1.6838   0.1191  -0.2128
 3HU  O     O  O     -1  -0.602  -5.4733   2.7303  -0.1201
 3HU  HN    H  HNH2   0   0.337  -4.8577   0.6584   0.9235
 3HU  HNA   H  HNH2   0   0.361  -3.4742   0.2547   1.6916
 3HU  HA    H  HCH1   0   0.228  -2.5538   2.4314   1.0485
 3HU  HB    H  HCH2   0   0.232  -3.3175   0.6969  -1.3402
 3HU  HBA   H  HCH2   0   0.242  -2.0295   1.8774  -1.2726
 3HU  HAH   H  HCR5   0   0.281   3.5146  -0.6383  -3.3258
 3HU  HAI   H  HCR5   0   0.212   1.4760  -0.8688  -1.7372
 3HU  HAJ   H  HCR5   0   0.312  -1.2284  -4.3888   0.4798
 3HU  HAK   H  HCR5   0   0.326  -4.1774  -1.2263  -0.9203
 3HU  HAL   H  HCH2   0   0.288   2.1243  -0.7492   1.8191
 3HU  HALA  H  HCH2   0   0.302   1.6956   0.9068   1.5089
 3HU  OAE   O  O      0  -0.520  -0.0581   1.6454   0.1280
 3HU  CAL   C  CH2    0  -0.350   1.7731  -0.0709   1.0453
 3HU  OAD   O  O      0  -0.540   0.9857  -2.6742   1.0496

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
 3HU  CA   C     single    1.548  0.020  1.548
 3HU  C    O     deloc     1.244  0.020  1.244
 3HU  C    OXT   deloc     1.247  0.020  1.247
 3HU  N    CA    single    1.448  0.020  1.448
 3HU  N    HN    single    0.890  0.020  1.040
 3HU  N    HNA   single    0.890  0.020  1.040
 3HU  CB   CA    single    1.538  0.020  1.538
 3HU  CA   HA    single    0.970  0.020  1.090
 3HU  NAZ  CB    single    1.462  0.020  1.462
 3HU  CB   HB    single    0.970  0.020  1.090
 3HU  CB   HBA   single    0.970  0.020  1.090
 3HU  CAP  OAB   deloc     1.248  0.020  1.248
 3HU  OAD  CAT   double    1.214  0.020  1.214
 3HU  CAU  OAE   double    1.214  0.020  1.214
 3HU  CAP  OAF   deloc     1.246  0.020  1.246
 3HU  CAH  CAI   aromatic  1.363  0.020  1.363
 3HU  CAH  SAO   aromatic  1.707  0.020  1.707
 3HU  CAH  HAH   single    0.930  0.020  1.080
 3HU  CAI  CAR   aromatic  1.425  0.020  1.425
 3HU  CAI  HAI   single    0.930  0.020  1.080
 3HU  CAJ  SAN   aromatic  1.693  0.020  1.693
 3HU  CAJ  CAV   aromatic  1.367  0.020  1.367
 3HU  CAJ  HAJ   single    0.930  0.020  1.080
 3HU  SAN  CAK   aromatic  1.715  0.020  1.715
 3HU  CAK  CAW   aromatic  1.367  0.020  1.367
 3HU  CAK  HAK   single    0.930  0.020  1.080
 3HU  NAY  CAL   single    1.460  0.020  1.460
 3HU  CAR  CAL   single    1.505  0.020  1.505
 3HU  CAL  HAL   single    0.970  0.020  1.090
 3HU  CAL  HALA  single    0.970  0.020  1.090
 3HU  SAO  CAS   aromatic  1.721  0.020  1.721
 3HU  CAS  CAP   single    1.500  0.020  1.500
 3HU  CAR  CAS   aromatic  1.371  0.020  1.371
 3HU  CAV  CAT   single    1.451  0.020  1.451
 3HU  CAT  NAY   single    1.383  0.020  1.383
 3HU  NAY  CAU   single    1.398  0.020  1.398
 3HU  NAZ  CAU   single    1.367  0.020  1.367
 3HU  CAV  CAW   aromatic  1.420  0.020  1.420
 3HU  CAW  NAZ   single    1.382  0.020  1.382

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
 3HU  O     C    CA   117.34  3.000
 3HU  O     C    OXT  127.07  3.000
 3HU  CA    C    OXT  115.55  3.000
 3HU  HNA   N    HN   107.63  3.000
 3HU  HNA   N    CA   111.48  3.000
 3HU  HN    N    CA   109.77  3.000
 3HU  HA    CA   CB   107.34  3.000
 3HU  HA    CA   N    108.04  3.000
 3HU  CB    CA   N    115.19  3.000
 3HU  HA    CA   C    107.95  3.000
 3HU  CB    CA   C    106.71  3.000
 3HU  N     CA   C    111.34  3.000
 3HU  HBA   CB   HB   106.81  3.000
 3HU  HBA   CB   NAZ  108.61  3.000
 3HU  HB    CB   NAZ  107.25  3.000
 3HU  HBA   CB   CA   110.24  3.000
 3HU  HB    CB   CA   110.40  3.000
 3HU  NAZ   CB   CA   113.27  3.000
 3HU  HAH   CAH  SAO  121.15  3.000
 3HU  HAH   CAH  CAI  127.22  3.000
 3HU  SAO   CAH  CAI  111.63  3.000
 3HU  HAI   CAI  CAR  124.73  3.000
 3HU  HAI   CAI  CAH  122.33  3.000
 3HU  CAR   CAI  CAH  112.94  3.000
 3HU  HAJ   CAJ  CAV  127.67  3.000
 3HU  HAJ   CAJ  SAN  121.37  3.000
 3HU  CAV   CAJ  SAN  110.96  3.000
 3HU  HAK   CAK  CAW  129.67  3.000
 3HU  HAK   CAK  SAN  119.66  3.000
 3HU  CAW   CAK  SAN  110.67  3.000
 3HU  CAK   SAN  CAJ   93.05  3.000
 3HU  CAS   SAO  CAH   92.05  3.000
 3HU  CAS   CAP  OAF  115.36  3.000
 3HU  CAS   CAP  OAB  116.90  3.000
 3HU  OAF   CAP  OAB  127.74  3.000
 3HU  CAS   CAR  CAL  123.81  3.000
 3HU  CAS   CAR  CAI  111.89  3.000
 3HU  CAL   CAR  CAI  124.29  3.000
 3HU  CAR   CAS  CAP  131.14  3.000
 3HU  CAR   CAS  SAO  111.48  3.000
 3HU  CAP   CAS  SAO  117.38  3.000
 3HU  NAY   CAT  CAV  114.02  3.000
 3HU  NAY   CAT  OAD  122.02  3.000
 3HU  CAV   CAT  OAD  123.95  3.000
 3HU  NAZ   CAU  NAY  118.11  3.000
 3HU  NAZ   CAU  OAE  121.69  3.000
 3HU  NAY   CAU  OAE  120.20  3.000
 3HU  CAW   CAV  CAT  121.13  3.000
 3HU  CAW   CAV  CAJ  113.04  3.000
 3HU  CAT   CAV  CAJ  125.82  3.000
 3HU  NAZ   CAW  CAV  119.51  3.000
 3HU  NAZ   CAW  CAK  128.21  3.000
 3HU  CAV   CAW  CAK  112.27  3.000
 3HU  CAU   NAY  CAT  125.69  3.000
 3HU  CAU   NAY  CAL  116.48  3.000
 3HU  CAT   NAY  CAL  117.77  3.000
 3HU  CAW   NAZ  CAU  121.47  3.000
 3HU  CAW   NAZ  CB   120.64  3.000
 3HU  CAU   NAZ  CB   117.88  3.000
 3HU  HALA  CAL  HAL  106.33  3.000
 3HU  HALA  CAL  NAY  108.81  3.000
 3HU  HAL   CAL  NAY  107.90  3.000
 3HU  HALA  CAL  CAR  110.86  3.000
 3HU  HAL   CAL  CAR  110.30  3.000
 3HU  NAY   CAL  CAR  112.41  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
 3HU  CONST_01  CAS  CAR  CAI  CAH    0.00   0.0  0
 3HU  CONST_02  CAR  CAS  SAO  CAH    0.00   0.0  0
 3HU  CONST_03  CAS  SAO  CAH  CAI    0.00   0.0  0
 3HU  CONST_04  SAO  CAS  CAR  CAI    0.00   0.0  0
 3HU  CONST_05  CAW  CAK  SAN  CAJ    0.00   0.0  0
 3HU  CONST_06  CAK  CAW  CAV  CAJ    0.00   0.0  0
 3HU  CONST_07  CAV  CAJ  SAN  CAK    0.00   0.0  0
 3HU  CONST_08  CAW  CAV  CAJ  SAN    0.00   0.0  0
 3HU  CONST_09  CAV  CAW  CAK  SAN    0.00   0.0  0
 3HU  CONST_10  CAR  CAI  CAH  SAO    0.00   0.0  0
 3HU  CONST_11  NAZ  CAU  NAY  CAT    0.00   0.0  0
 3HU  CONST_12  CAV  CAT  NAY  CAU    0.00   0.0  0
 3HU  CONST_13  NAY  CAU  NAZ  CAW    0.00   0.0  0
 3HU  CONST_14  CAL  CAR  CAI  CAH  180.00   0.0  0
 3HU  CONST_15  CAP  CAS  SAO  CAH  180.00   0.0  0
 3HU  CONST_16  CAP  CAS  CAR  CAI  180.00   0.0  0
 3HU  CONST_17  SAO  CAS  CAR  CAL  180.00   0.0  0
 3HU  CONST_18  NAY  CAU  NAZ  CB   180.00   0.0  0
 3HU  CONST_19  CAU  NAY  CAT  OAD  180.00   0.0  0
 3HU  CONST_20  CAT  NAY  CAU  OAE  180.00   0.0  0
 3HU  CONST_21  CAW  NAZ  CAU  OAE  180.00   0.0  0
 3HU  CONST_22  CAV  CAT  NAY  CAL  180.00   0.0  0
 3HU  CONST_23  NAZ  CAU  NAY  CAL  180.00   0.0  0
 3HU  CONST_24  HAK  CAK  SAN  CAJ  180.00   0.0  0
 3HU  CONST_25  HAJ  CAJ  SAN  CAK  180.00   0.0  0
 3HU  CONST_26  HAI  CAI  CAH  SAO  180.00   0.0  0
 3HU  CONST_27  HAH  CAH  CAI  CAR  180.00   0.0  0
 3HU  CONST_28  OAE  CAU  NAZ  CB     0.00   0.0  0
 3HU  CONST_29  CAL  NAY  CAT  OAD    0.00   0.0  0
 3HU  CONST_30  CAL  NAY  CAU  OAE    0.00   0.0  0
 3HU  Var_01    NAY  CAL  CAR  CAI   -4.51  30.0  2
 3HU  Var_02    CAT  NAY  CAL  CAR   89.72  30.0  1
 3HU  Var_03    CAU  NAZ  CB   CA   -83.27  30.0  2
 3HU  Var_04    SAO  CAS  CAP  OAB  179.48  30.0  2

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
 3HU  chir_01  CA  C  N  CB  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
 3HU  plan-1  CAH  0.020
 3HU  plan-1  CAI  0.020
 3HU  plan-1  SAO  0.020
 3HU  plan-1  CAP  0.020
 3HU  plan-1  CAR  0.020
 3HU  plan-1  CAS  0.020
 3HU  plan-1  HAH  0.020
 3HU  plan-1  HAI  0.020
 3HU  plan-1  CAL  0.020
 3HU  plan-2  CB   0.020
 3HU  plan-2  CAJ  0.020
 3HU  plan-2  CAK  0.020
 3HU  plan-2  SAN  0.020
 3HU  plan-2  CAT  0.020
 3HU  plan-2  CAU  0.020
 3HU  plan-2  CAV  0.020
 3HU  plan-2  CAW  0.020
 3HU  plan-2  NAY  0.020
 3HU  plan-2  NAZ  0.020
 3HU  plan-2  HAJ  0.020
 3HU  plan-2  HAK  0.020
 3HU  plan-2  OAE  0.020
 3HU  plan-2  CAL  0.020
 3HU  plan-2  OAD  0.020
 3HU  plan-3  C    0.020
 3HU  plan-3  OXT  0.020
 3HU  plan-3  CA   0.020
 3HU  plan-3  O    0.020
 3HU  plan-4  OAB  0.020
 3HU  plan-4  OAF  0.020
 3HU  plan-4  CAP  0.020
 3HU  plan-4  CAS  0.020

