# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:42:51 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: N-({4-[(1S)-4-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-1-(methylsulfanyl)butyl]phenyl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@@H](CCCC1=C(N)N=C(N)NC1=O)c2ccc(cc2)C(=O)N[C@@H](CCC(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
 DXY  DXY  'N-({4-[(1S)-4-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-1-(methylsulfanyl)butyl]phenyl}carbonyl)-L-glutamic acid'  ligand  60  33  .  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_DXY
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
 DXY  OE1   O  OH1   0  -0.595    7.6117  -3.1137  -2.0016
 DXY  CD    C  C     0   0.555    7.6638  -1.7878  -2.0665
 DXY  OE2   O  O     0  -0.442    8.2514  -1.1915  -2.9340
 DXY  CG    C  CH2   0  -0.577    6.9053  -1.1486  -0.9369
 DXY  CB    C  CH2   0  -0.463    6.9442   0.3708  -0.9797
 DXY  CA    C  CH1   0  -0.198    6.1766   0.9743   0.2014
 DXY  C     C  C     0   0.551    6.3272   2.4897   0.2226
 DXY  OXT   O  OH1   0  -0.590    7.5554   2.8452   0.5688
 DXY  O     O  O     0  -0.428    5.4523   3.2650  -0.0587
 DXY  N     N  NH1   0  -0.656    4.7911   0.6020   0.1374
 DXY  CAY   C  C     0   0.555    3.9883   0.6761   1.2198
 DXY  OAF   O  O     0  -0.479    4.4022   1.0417   2.3099
 DXY  CBB   C  CR6   0  -0.057    2.5710   0.2574   1.0218
 DXY  CAK   C  CR16  0  -0.271    2.1696  -0.5796  -0.0145
 DXY  CAM   C  CR16  0  -0.304    0.8423  -0.9674  -0.1301
 DXY  CAJ   C  CR16  0  -0.254    1.6175   0.6846   1.9467
 DXY  CAL   C  CR16  0  -0.273    0.2961   0.2982   1.8255
 DXY  CBC   C  CR6   0   0.189   -0.1122  -0.5312   0.7810
 DXY  CBG   C  CH1   0  -0.469   -1.5480  -0.9534   0.6319
 DXY  SAV   S  S2    0  -0.018   -2.1244  -1.8523   2.1153
 DXY  CAA   C  CH3   0  -0.765   -0.9350  -3.2088   2.1572
 DXY  CAQ   C  CH2   0  -0.410   -2.4743   0.2398   0.3838
 DXY  CAN   C  CH2   0  -0.406   -3.9063  -0.1446   0.0360
 DXY  CAP   C  CH2   0  -0.516   -4.7715   1.0796  -0.2753
 DXY  CBD   C  CR6   0  -0.217   -6.1927   0.7262  -0.5960
 DXY  CBE   C  CR6   0   0.509   -6.5724   0.5530  -1.9505
 DXY  OAG   O  O     0  -0.519   -5.8615   0.7015  -2.9454
 DXY  NAU   N  NR16  0  -0.712   -7.9057   0.1764  -2.1409
 DXY  CAZ   C  CR6   0   0.682   -8.7707  -0.0306  -1.1250
 DXY  NAB   N  NH2   0  -0.827  -10.0137  -0.4323  -1.4316
 DXY  NAS   N  N     0  -0.528   -8.4263   0.1143   0.1263
 DXY  CBA   C  CR6   0   0.455   -7.1468   0.4782   0.3847
 DXY  NAC   N  NH2   0  -0.829   -6.8527   0.5534   1.7014
 DXY  H1G   H  HCH2  0   0.285    5.8773  -1.5204  -0.9663
 DXY  H2G   H  HCH2  0   0.289    7.3216  -1.5132   0.0072
 DXY  H1B   H  HCH2  0   0.274    7.9778   0.7139  -0.9409
 DXY  H2B   H  HCH2  0   0.259    6.5227   0.7402  -1.9183
 DXY  HA    H  HCH1  0   0.296    6.6045   0.5831   1.1285
 DXY  HN    H  HNH1  0   0.409    4.3750   0.5310  -0.7778
 DXY  HAK   H  HCR6  0   0.254    2.8837  -0.9699  -0.7289
 DXY  HAM   H  HCR6  0   0.261    0.5519  -1.6286  -0.9376
 DXY  HAJ   H  HCR6  0   0.259    1.9134   1.3227   2.7690
 DXY  HAL   H  HCR6  0   0.253   -0.4243   0.6302   2.5631
 DXY  HBG   H  HCH1  0   0.285   -1.6272  -1.6372  -0.2189
 DXY  H1AA  H  HCH3  0   0.277   -1.2112  -3.8561   2.9878
 DXY  H2AA  H  HCH3  0   0.262   -0.9696  -3.7913   1.2376
 DXY  H3AA  H  HCH3  0   0.262    0.0791  -2.8469   2.3199
 DXY  H1AQ  H  HCH2  0   0.234   -2.4646   0.9029   1.2548
 DXY  H2AQ  H  HCH2  0   0.248   -2.0455   0.8146  -0.4423
 DXY  H1AN  H  HCH2  0   0.226   -3.9073  -0.8112  -0.8318
 DXY  H2AN  H  HCH2  0   0.223   -4.3565  -0.7088   0.8570
 DXY  H1AP  H  HCH2  0   0.223   -4.7214   1.7785   0.5672
 DXY  H2AP  H  HCH2  0   0.244   -4.3365   1.6193  -1.1191
 DXY  HNAU  H  HNR6  0   0.414   -8.2077   0.0422  -3.0964
 DXY  H1AB  H  HNH2  0   0.411  -10.3680  -0.3515  -2.3692
 DXY  H2AB  H  HNH2  0   0.408  -10.6948  -0.4420  -0.6920
 DXY  H1AC  H  HNH2  0   0.397   -6.0140   1.0137   2.0070
 DXY  H2AC  H  HNH2  0   0.390   -7.6194   0.5614   2.3520
 DXY  HOE1  H  HOH1  0   0.480    8.1002  -3.5023  -2.7426
 DXY  HOXT  H  HOH1  0   0.486    7.6500   3.8094   0.5368

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
 DXY  OE2  CD    double    1.206  0.020  1.206
 DXY  CD   OE1   single    1.328  0.020  1.328
 DXY  CD   CG    single    1.503  0.020  1.503
 DXY  CG   CB    single    1.521  0.020  1.521
 DXY  CB   CA    single    1.532  0.020  1.532
 DXY  CAA  SAV   single    1.805  0.020  1.805
 DXY  CA   N     single    1.436  0.020  1.436
 DXY  CA   C     single    1.523  0.020  1.523
 DXY  SAV  CBG   single    1.828  0.020  1.828
 DXY  OAF  CAY   double    1.222  0.020  1.222
 DXY  N    CAY   single    1.350  0.020  1.350
 DXY  CAY  CBB   single    1.491  0.020  1.491
 DXY  CBB  CAJ   aromatic  1.395  0.020  1.395
 DXY  CBB  CAK   aromatic  1.391  0.020  1.391
 DXY  CAJ  CAL   aromatic  1.382  0.020  1.382
 DXY  CAK  CAM   aromatic  1.388  0.020  1.388
 DXY  CAL  CBC   aromatic  1.395  0.020  1.395
 DXY  CAM  CBC   aromatic  1.390  0.020  1.390
 DXY  O    C     double    1.202  0.020  1.202
 DXY  C    OXT   single    1.325  0.020  1.325
 DXY  CBC  CBG   single    1.504  0.020  1.504
 DXY  CBG  CAQ   single    1.531  0.020  1.531
 DXY  CAQ  CAN   single    1.523  0.020  1.523
 DXY  CAN  CAP   single    1.531  0.020  1.531
 DXY  CAP  CBD   single    1.499  0.020  1.499
 DXY  NAC  CBA   single    1.351  0.020  1.351
 DXY  CBD  CBA   double    1.391  0.020  1.391
 DXY  CBD  CBE   single    1.417  0.020  1.417
 DXY  CBA  NAS   single    1.355  0.020  1.355
 DXY  CBE  OAG   double    1.232  0.020  1.232
 DXY  CBE  NAU   single    1.399  0.020  1.399
 DXY  NAS  CAZ   double    1.306  0.020  1.306
 DXY  NAU  CAZ   single    1.350  0.020  1.350
 DXY  CAZ  NAB   single    1.342  0.020  1.342
 DXY  CG   H1G   single    0.970  0.020  1.090
 DXY  CG   H2G   single    0.970  0.020  1.090
 DXY  CB   H1B   single    0.970  0.020  1.090
 DXY  CB   H2B   single    0.970  0.020  1.090
 DXY  CA   HA    single    0.970  0.020  1.090
 DXY  N    HN    single    0.860  0.020  1.020
 DXY  CAK  HAK   single    0.930  0.020  1.080
 DXY  CAM  HAM   single    0.930  0.020  1.080
 DXY  CAJ  HAJ   single    0.930  0.020  1.080
 DXY  CAL  HAL   single    0.930  0.020  1.080
 DXY  CBG  HBG   single    0.970  0.020  1.090
 DXY  CAA  H1AA  single    0.970  0.020  1.090
 DXY  CAA  H2AA  single    0.970  0.020  1.090
 DXY  CAA  H3AA  single    0.970  0.020  1.090
 DXY  CAQ  H1AQ  single    0.970  0.020  1.090
 DXY  CAQ  H2AQ  single    0.970  0.020  1.090
 DXY  CAN  H1AN  single    0.970  0.020  1.090
 DXY  CAN  H2AN  single    0.970  0.020  1.090
 DXY  CAP  H1AP  single    0.970  0.020  1.090
 DXY  CAP  H2AP  single    0.970  0.020  1.090
 DXY  NAU  HNAU  single    0.860  0.020  1.020
 DXY  NAB  H1AB  single    0.890  0.020  1.040
 DXY  NAB  H2AB  single    0.890  0.020  1.040
 DXY  NAC  H1AC  single    0.890  0.020  1.040
 DXY  NAC  H2AC  single    0.890  0.020  1.040
 DXY  OE1  HOE1  single    0.850  0.020  0.980
 DXY  OXT  HOXT  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
 DXY  HOE1  OE1  CD    110.07  3.000
 DXY  CG    CD   OE2   125.19  3.000
 DXY  CG    CD   OE1   111.58  3.000
 DXY  OE2   CD   OE1   123.23  3.000
 DXY  H2G   CG   H1G   105.52  3.000
 DXY  H2G   CG   CB    110.33  3.000
 DXY  H1G   CG   CB    111.28  3.000
 DXY  H2G   CG   CD    108.34  3.000
 DXY  H1G   CG   CD    108.04  3.000
 DXY  CB    CG   CD    113.01  3.000
 DXY  H2B   CB   H1B   106.85  3.000
 DXY  H2B   CB   CA    109.61  3.000
 DXY  H1B   CB   CA    108.88  3.000
 DXY  H2B   CB   CG    110.61  3.000
 DXY  H1B   CB   CG    109.74  3.000
 DXY  CA    CB   CG    111.04  3.000
 DXY  HA    CA   N     108.81  3.000
 DXY  HA    CA   C     107.79  3.000
 DXY  N     CA   C     110.73  3.000
 DXY  HA    CA   CB    108.46  3.000
 DXY  C     CA   CB    110.68  3.000
 DXY  N     CA   CB    110.29  3.000
 DXY  O     C    OXT   124.25  3.000
 DXY  OXT   C    CA    111.24  3.000
 DXY  O     C    CA    124.50  3.000
 DXY  HOXT  OXT  C     110.41  3.000
 DXY  HN    N    CAY   119.12  3.000
 DXY  HN    N    CA    117.19  3.000
 DXY  CAY   N    CA    121.59  3.000
 DXY  CBB   CAY  OAF   121.63  3.000
 DXY  CBB   CAY  N     116.32  3.000
 DXY  OAF   CAY  N     122.03  3.000
 DXY  CAJ   CBB  CAK   118.74  3.000
 DXY  CAK   CBB  CAY   122.82  3.000
 DXY  CAJ   CBB  CAY   118.40  3.000
 DXY  HAK   CAK  CAM   118.37  3.000
 DXY  HAK   CAK  CBB   121.20  3.000
 DXY  CAM   CAK  CBB   120.40  3.000
 DXY  HAM   CAM  CBC   119.74  3.000
 DXY  HAM   CAM  CAK   119.28  3.000
 DXY  CBC   CAM  CAK   120.98  3.000
 DXY  HAJ   CAJ  CAL   119.53  3.000
 DXY  HAJ   CAJ  CBB   119.83  3.000
 DXY  CAL   CAJ  CBB   120.64  3.000
 DXY  HAL   CAL  CBC   119.84  3.000
 DXY  HAL   CAL  CAJ   119.37  3.000
 DXY  CBC   CAL  CAJ   120.78  3.000
 DXY  CBG   CBC  CAL   121.37  3.000
 DXY  CBG   CBC  CAM   120.17  3.000
 DXY  CAL   CBC  CAM   118.46  3.000
 DXY  HBG   CBG  CAQ   108.49  3.000
 DXY  HBG   CBG  SAV   107.51  3.000
 DXY  CAQ   CBG  SAV   108.91  3.000
 DXY  HBG   CBG  CBC   108.76  3.000
 DXY  CAQ   CBG  CBC   112.03  3.000
 DXY  SAV   CBG  CBC   111.02  3.000
 DXY  CAA   SAV  CBG   100.41  3.000
 DXY  H3AA  CAA  H2AA  109.48  3.000
 DXY  H3AA  CAA  H1AA  108.66  3.000
 DXY  H2AA  CAA  H1AA  108.55  3.000
 DXY  H3AA  CAA  SAV   111.56  3.000
 DXY  H2AA  CAA  SAV   111.19  3.000
 DXY  H1AA  CAA  SAV   107.30  3.000
 DXY  H2AQ  CAQ  H1AQ  106.21  3.000
 DXY  H2AQ  CAQ  CAN   109.19  3.000
 DXY  H1AQ  CAQ  CAN   110.06  3.000
 DXY  H2AQ  CAQ  CBG   107.14  3.000
 DXY  H1AQ  CAQ  CBG   109.74  3.000
 DXY  CAN   CAQ  CBG   114.16  3.000
 DXY  H2AN  CAN  H1AN  106.31  3.000
 DXY  H2AN  CAN  CAP   109.43  3.000
 DXY  H1AN  CAN  CAP   108.99  3.000
 DXY  H2AN  CAN  CAQ   110.24  3.000
 DXY  H1AN  CAN  CAQ   109.61  3.000
 DXY  CAP   CAN  CAQ   112.08  3.000
 DXY  H2AP  CAP  H1AP  105.11  3.000
 DXY  H2AP  CAP  CBD   109.20  3.000
 DXY  H1AP  CAP  CBD   110.98  3.000
 DXY  H2AP  CAP  CAN   109.10  3.000
 DXY  H1AP  CAP  CAN   109.14  3.000
 DXY  CBD   CAP  CAN   113.00  3.000
 DXY  CBA   CBD  CBE   117.93  3.000
 DXY  CBE   CBD  CAP   119.15  3.000
 DXY  CBA   CBD  CAP   122.79  3.000
 DXY  NAU   CBE  OAG   118.21  3.000
 DXY  NAU   CBE  CBD   114.73  3.000
 DXY  OAG   CBE  CBD   127.06  3.000
 DXY  HNAU  NAU  CAZ   119.96  3.000
 DXY  HNAU  NAU  CBE   116.70  3.000
 DXY  CAZ   NAU  CBE   123.34  3.000
 DXY  NAS   CAZ  NAB   119.77  3.000
 DXY  NAB   CAZ  NAU   117.87  3.000
 DXY  NAS   CAZ  NAU   122.34  3.000
 DXY  H2AB  NAB  H1AB  116.61  3.000
 DXY  H2AB  NAB  CAZ   117.54  3.000
 DXY  H1AB  NAB  CAZ   121.02  3.000
 DXY  CBA   NAS  CAZ   117.48  3.000
 DXY  NAC   CBA  NAS   113.97  3.000
 DXY  NAS   CBA  CBD   124.14  3.000
 DXY  NAC   CBA  CBD   121.87  3.000
 DXY  H2AC  NAC  H1AC  115.86  3.000
 DXY  H2AC  NAC  CBA   117.71  3.000
 DXY  H1AC  NAC  CBA   120.25  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
 DXY  CONST_01  CBC   CAL  CAJ  CBB     0.00   0.0  0
 DXY  CONST_02  CBC   CAM  CAK  CBB     0.00   0.0  0
 DXY  CONST_03  CAL   CAJ  CBB  CAK     0.00   0.0  0
 DXY  CONST_04  CAL   CBC  CAM  CAK     0.00   0.0  0
 DXY  CONST_05  CAJ   CBB  CAK  CAM     0.00   0.0  0
 DXY  CONST_06  CAJ   CAL  CBC  CAM     0.00   0.0  0
 DXY  CONST_07  CAZ   NAS  CBA  CBD     0.00   0.0  0
 DXY  CONST_08  CAZ   NAU  CBE  CBD     0.00   0.0  0
 DXY  CONST_09  NAS   CAZ  NAU  CBE     0.00   0.0  0
 DXY  CONST_10  CBA   NAS  CAZ  NAU     0.00   0.0  0
 DXY  CONST_11  CAL   CAJ  CBB  CAY   180.00   0.0  0
 DXY  CONST_12  CAM   CAK  CBB  CAY   180.00   0.0  0
 DXY  CONST_13  CBG   CBC  CAM  CAK   180.00   0.0  0
 DXY  CONST_14  CBG   CBC  CAL  CAJ   180.00   0.0  0
 DXY  CONST_15  NAB   CAZ  NAU  CBE   180.00   0.0  0
 DXY  CONST_16  CAZ   NAU  CBE  OAG   180.00   0.0  0
 DXY  CONST_17  NAC   CBA  NAS  CAZ   180.00   0.0  0
 DXY  CONST_18  CBA   NAS  CAZ  NAB   180.00   0.0  0
 DXY  CONST_19  HAL   CAL  CAJ  CBB   180.00   0.0  0
 DXY  CONST_20  HAM   CAM  CAK  CBB   180.00   0.0  0
 DXY  CONST_21  HAJ   CAJ  CBB  CAK   180.00   0.0  0
 DXY  CONST_22  HAK   CAK  CBB  CAJ   180.00   0.0  0
 DXY  CONST_23  HNAU  NAU  CBE  CBD   180.00   0.0  0
 DXY  CONST_25  H2AC  NAC  CBA  CBD   180.00   0.0  0
 DXY  CONST_27  H2AB  NAB  CAZ  NAU   180.00   0.0  0
 DXY  CONST_28  CBB   CAY  N    CA    180.00   0.0  0
 DXY  CONST_30  OAF   CAY  N    CA      0.00   0.0  0
 DXY  CONST_31  HOE1  OE1  CD   OE2     0.00   0.0  0
 DXY  CONST_32  HOXT  OXT  C    CA    180.00   0.0  0
 DXY  Var_01    CAJ   CBB  CAY  N    -160.66  30.0  2
 DXY  Var_02    CBA   CBD  CAP  CAN    81.83  30.0  3
 DXY  Var_03    CBD   CAP  CAN  CAQ  -178.94  30.0  3
 DXY  Var_04    CB    CG   CD   OE1   179.98  30.0  3
 DXY  Var_05    CA    CB   CG   CD   -179.14  30.0  3
 DXY  Var_06    CAP   CAN  CAQ  CBG  -176.95  30.0  3
 DXY  Var_07    H1AA  CAA  SAV  CBG  -177.18  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
 DXY  chir_01  CA   CB   N    C    positiv
 DXY  chir_02  CBG  SAV  CBC  CAQ  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
 DXY  plan-1  CAY   0.020
 DXY  plan-1  CBB   0.020
 DXY  plan-1  CAK   0.020
 DXY  plan-1  CAM   0.020
 DXY  plan-1  CAJ   0.020
 DXY  plan-1  CAL   0.020
 DXY  plan-1  CBC   0.020
 DXY  plan-1  CBG   0.020
 DXY  plan-1  HAK   0.020
 DXY  plan-1  HAM   0.020
 DXY  plan-1  HAJ   0.020
 DXY  plan-1  HAL   0.020
 DXY  plan-2  CAP   0.020
 DXY  plan-2  CBD   0.020
 DXY  plan-2  CBE   0.020
 DXY  plan-2  OAG   0.020
 DXY  plan-2  NAU   0.020
 DXY  plan-2  CAZ   0.020
 DXY  plan-2  NAB   0.020
 DXY  plan-2  NAS   0.020
 DXY  plan-2  CBA   0.020
 DXY  plan-2  NAC   0.020
 DXY  plan-2  HNAU  0.020
 DXY  plan-2  H1AB  0.020
 DXY  plan-2  H2AB  0.020
 DXY  plan-2  H1AC  0.020
 DXY  plan-2  H2AC  0.020
 DXY  plan-3  CA    0.020
 DXY  plan-3  N     0.020
 DXY  plan-3  CAY   0.020
 DXY  plan-3  OAF   0.020
 DXY  plan-3  CBB   0.020
 DXY  plan-3  HN    0.020
 DXY  plan-4  OE1   0.020
 DXY  plan-4  CD    0.020
 DXY  plan-4  OE2   0.020
 DXY  plan-4  CG    0.020
 DXY  plan-4  HOE1  0.020
 DXY  plan-5  CA    0.020
 DXY  plan-5  C     0.020
 DXY  plan-5  OXT   0.020
 DXY  plan-5  O     0.020
 DXY  plan-5  HOXT  0.020

