# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:22:27 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: N-({4-[(1R)-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
 DXZ  DXZ  'N-({4-[(1R)-4-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-1-(methylsulfanyl)butyl]phenyl}carbonyl)-L-glutamic acid'  ligand  58  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_DXZ
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
 DXZ  OE1   O  O      0  -0.609  -8.1803   2.1527  -2.2208
 DXZ  CD    C  C      0   0.412  -7.7659   2.3896  -1.0690
 DXZ  OE2   O  OC    -1  -0.634  -7.9419   3.4455  -0.4238
 DXZ  CG    C  CH2    0  -0.578  -6.9556   1.2954  -0.3538
 DXZ  CB    C  CH2    0  -0.440  -6.7914  -0.0123  -1.1113
 DXZ  CA    C  CH1    0  -0.198  -6.0431  -1.0784  -0.3111
 DXZ  C     C  C      0   0.413  -6.0858  -2.4556  -1.0238
 DXZ  OXT   O  OC    -1  -0.618  -7.2204  -2.9674  -1.1083
 DXZ  O     O  O      0  -0.599  -5.0171  -2.9203  -1.4553
 DXZ  N     N  NH1    0  -0.636  -4.6929  -0.6350  -0.0463
 DXZ  CAY   C  C      0   0.546  -3.9571  -1.1329   0.9557
 DXZ  OAF   O  O      0  -0.503  -4.4132  -1.8939   1.8029
 DXZ  CBB   C  CR6    0  -0.058  -2.5274  -0.6915   1.0256
 DXZ  CAK   C  CR16   0  -0.256  -1.6616  -1.4062   1.8479
 DXZ  CAM   C  CR16   0  -0.303  -0.3294  -1.0408   1.9597
 DXZ  CAJ   C  CR16   0  -0.284  -2.0255   0.4119   0.3347
 DXZ  CAL   C  CR16   0  -0.269  -0.6943   0.7750   0.4486
 DXZ  CBC   C  CR6    0   0.177   0.1755   0.0497   1.2589
 DXZ  CBG   C  CH1    0  -0.465   1.6411   0.3826   1.3527
 DXZ  SAV   S  S2     0  -0.020   1.9373   2.1598   1.6331
 DXZ  CAA   C  CH3    0  -0.763   1.0593   2.3989   3.1925
 DXZ  CAQ   C  CH2    0  -0.409   2.3838  -0.0507   0.0854
 DXZ  CAN   C  CH2    0  -0.409   3.8994   0.0770   0.1714
 DXZ  CAP   C  CH2    0  -0.516   4.5974  -0.5030  -1.0613
 DXZ  CBD   C  CR6    0  -0.218   6.0917  -0.3961  -0.9984
 DXZ  CBE   C  CR6    0   0.509   6.7242   0.7469  -1.5458
 DXZ  OAG   O  O      0  -0.519   6.1804   1.6966  -2.1109
 DXZ  NAU   N  NR16   0  -0.712   8.1164   0.7637  -1.4135
 DXZ  CAZ   C  CR6    0   0.682   8.8153  -0.2137  -0.7978
 DXZ  NAB   N  NH2    0  -0.828  10.1449  -0.0621  -0.6965
 DXZ  NAS   N  N      0  -0.528   8.2396  -1.2633  -0.2772
 DXZ  CBA   C  CR6    0   0.456   6.8901  -1.3459  -0.3707
 DXZ  NAC   N  NH2    0  -0.833   6.3685  -2.4637   0.1791
 DXZ  H1G   H  HCH2   0   0.222  -5.9752   1.7127  -0.0993
 DXZ  H2G   H  HCH2   0   0.217  -7.4306   1.0933   0.6136
 DXZ  H1B   H  HCH2   0   0.226  -7.7706  -0.4170  -1.3678
 DXZ  H2B   H  HCH2   0   0.209  -6.2773   0.1624  -2.0628
 DXZ  HA    H  HCH1   0   0.230  -6.5483  -1.1917   0.6522
 DXZ  HN    H  HNH1   0   0.390  -4.2161  -0.1850  -0.8109
 DXZ  HAK   H  HCR6   0   0.255  -2.0310  -2.2563   2.4055
 DXZ  HAM   H  HCR6   0   0.255   0.3284  -1.6126   2.6038
 DXZ  HAJ   H  HCR6   0   0.250  -2.6687   1.0231  -0.2855
 DXZ  HAL   H  HCR6   0   0.252  -0.3344   1.6474  -0.0824
 DXZ  HBG   H  HCH1   0   0.281   2.0674  -0.1609   2.2019
 DXZ  H1AA  H  HCH3   0   0.275   1.1935   3.4397   3.4822
 DXZ  H2AA  H  HCH3   0   0.261  -0.0064   2.2015   3.0868
 DXZ  H3AA  H  HCH3   0   0.262   1.4698   1.7637   3.9762
 DXZ  H1AQ  H  HCH2   0   0.245   2.1237  -1.0981  -0.0976
 DXZ  H2AQ  H  HCH2   0   0.237   2.0047   0.5110  -0.7748
 DXZ  H1AN  H  HCH2   0   0.231   4.1913   1.1246   0.2771
 DXZ  H2AN  H  HCH2   0   0.218   4.2550  -0.4310   1.0745
 DXZ  H1AP  H  HCH2   0   0.224   4.2911  -1.5459  -1.1991
 DXZ  H2AP  H  HCH2   0   0.243   4.2367   0.0214  -1.9491
 DXZ  HNAU  H  HNR6   0   0.414   8.6001   1.5631  -1.7992
 DXZ  H1AB  H  HNH2   0   0.411  10.6296   0.6247  -1.2487
 DXZ  H2AB  H  HNH2   0   0.408  10.6833  -0.8536  -0.3882
 DXZ  H1AC  H  HNH2   0   0.402   5.3815  -2.5417   0.3448
 DXZ  H2AC  H  HNH2   0   0.391   6.9632  -3.0286   0.7604

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
 DXZ  OE1  CD    deloc     1.247  0.020  1.247
 DXZ  CD   OE2   deloc     1.250  0.020  1.250
 DXZ  CD   CG    single    1.538  0.020  1.538
 DXZ  CG   CB    single    1.520  0.020  1.520
 DXZ  CB   CA    single    1.529  0.020  1.529
 DXZ  CA   N     single    1.446  0.020  1.446
 DXZ  CA   C     single    1.551  0.020  1.551
 DXZ  SAV  CAA   single    1.805  0.020  1.805
 DXZ  SAV  CBG   single    1.823  0.020  1.823
 DXZ  OAF  CAY   double    1.227  0.020  1.227
 DXZ  N    CAY   single    1.339  0.020  1.339
 DXZ  CAY  CBB   single    1.498  0.020  1.498
 DXZ  CBB  CAK   aromatic  1.392  0.020  1.392
 DXZ  CBB  CAJ   aromatic  1.395  0.020  1.395
 DXZ  CAK  CAM   aromatic  1.386  0.020  1.386
 DXZ  CAJ  CAL   aromatic  1.385  0.020  1.385
 DXZ  CAM  CBC   aromatic  1.391  0.020  1.391
 DXZ  C    O     deloc     1.243  0.020  1.243
 DXZ  C    OXT   deloc     1.248  0.020  1.248
 DXZ  CAL  CBC   aromatic  1.393  0.020  1.393
 DXZ  CBC  CBG   single    1.506  0.020  1.506
 DXZ  CBG  CAQ   single    1.531  0.020  1.531
 DXZ  CAQ  CAN   single    1.523  0.020  1.523
 DXZ  CAN  CAP   single    1.531  0.020  1.531
 DXZ  CAP  CBD   single    1.499  0.020  1.499
 DXZ  NAC  CBA   single    1.350  0.020  1.350
 DXZ  CBD  CBA   double    1.391  0.020  1.391
 DXZ  CBD  CBE   single    1.416  0.020  1.416
 DXZ  CBA  NAS   single    1.355  0.020  1.355
 DXZ  NAS  CAZ   double    1.305  0.020  1.305
 DXZ  CBE  OAG   double    1.232  0.020  1.232
 DXZ  CBE  NAU   single    1.399  0.020  1.399
 DXZ  CAZ  NAU   single    1.350  0.020  1.350
 DXZ  CAZ  NAB   single    1.342  0.020  1.342
 DXZ  CG   H1G   single    0.970  0.020  1.090
 DXZ  CG   H2G   single    0.970  0.020  1.090
 DXZ  CB   H1B   single    0.970  0.020  1.090
 DXZ  CB   H2B   single    0.970  0.020  1.090
 DXZ  CA   HA    single    0.970  0.020  1.090
 DXZ  N    HN    single    0.890  0.020  1.040
 DXZ  CAK  HAK   single    0.930  0.020  1.080
 DXZ  CAM  HAM   single    0.930  0.020  1.080
 DXZ  CAJ  HAJ   single    0.930  0.020  1.080
 DXZ  CAL  HAL   single    0.930  0.020  1.080
 DXZ  CBG  HBG   single    0.970  0.020  1.090
 DXZ  CAA  H1AA  single    0.970  0.020  1.090
 DXZ  CAA  H2AA  single    0.970  0.020  1.090
 DXZ  CAA  H3AA  single    0.970  0.020  1.090
 DXZ  CAQ  H1AQ  single    0.970  0.020  1.090
 DXZ  CAQ  H2AQ  single    0.970  0.020  1.090
 DXZ  CAN  H1AN  single    0.970  0.020  1.090
 DXZ  CAN  H2AN  single    0.970  0.020  1.090
 DXZ  CAP  H1AP  single    0.970  0.020  1.090
 DXZ  CAP  H2AP  single    0.970  0.020  1.090
 DXZ  NAU  HNAU  single    0.860  0.020  1.020
 DXZ  NAB  H1AB  single    0.890  0.020  1.040
 DXZ  NAB  H2AB  single    0.890  0.020  1.040
 DXZ  NAC  H1AC  single    0.890  0.020  1.040
 DXZ  NAC  H2AC  single    0.890  0.020  1.040

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
 DXZ  CG    CD   OE2   115.80  3.000
 DXZ  CG    CD   OE1   118.00  3.000
 DXZ  OE2   CD   OE1   126.20  3.000
 DXZ  H2G   CG   H1G   104.65  3.000
 DXZ  H2G   CG   CB    109.14  3.000
 DXZ  H1G   CG   CB    110.29  3.000
 DXZ  H2G   CG   CD    108.25  3.000
 DXZ  H1G   CG   CD    107.97  3.000
 DXZ  CB    CG   CD    115.93  3.000
 DXZ  H2B   CB   H1B   106.04  3.000
 DXZ  H2B   CB   CA    109.65  3.000
 DXZ  H1B   CB   CA    107.70  3.000
 DXZ  H2B   CB   CG    110.26  3.000
 DXZ  H1B   CB   CG    109.85  3.000
 DXZ  CA    CB   CG    113.08  3.000
 DXZ  HA    CA   N     107.57  3.000
 DXZ  HA    CA   C     107.46  3.000
 DXZ  N     CA   C     112.47  3.000
 DXZ  HA    CA   CB    107.89  3.000
 DXZ  C     CA   CB    111.41  3.000
 DXZ  N     CA   CB    109.83  3.000
 DXZ  O     C    OXT   127.24  3.000
 DXZ  OXT   C    CA    114.86  3.000
 DXZ  O     C    CA    117.89  3.000
 DXZ  HN    N    CAY   118.30  3.000
 DXZ  HN    N    CA    116.11  3.000
 DXZ  CAY   N    CA    122.42  3.000
 DXZ  CBB   CAY  OAF   120.36  3.000
 DXZ  CBB   CAY  N     116.73  3.000
 DXZ  OAF   CAY  N     122.90  3.000
 DXZ  CAJ   CBB  CAK   118.36  3.000
 DXZ  CAJ   CBB  CAY   123.59  3.000
 DXZ  CAK   CBB  CAY   118.04  3.000
 DXZ  HAK   CAK  CAM   119.59  3.000
 DXZ  HAK   CAK  CBB   119.72  3.000
 DXZ  CAM   CAK  CBB   120.69  3.000
 DXZ  HAM   CAM  CBC   119.52  3.000
 DXZ  HAM   CAM  CAK   119.49  3.000
 DXZ  CBC   CAM  CAK   120.99  3.000
 DXZ  HAJ   CAJ  CAL   118.06  3.000
 DXZ  HAJ   CAJ  CBB   121.10  3.000
 DXZ  CAL   CAJ  CBB   120.83  3.000
 DXZ  HAL   CAL  CBC   119.82  3.000
 DXZ  HAL   CAL  CAJ   119.37  3.000
 DXZ  CBC   CAL  CAJ   120.79  3.000
 DXZ  CBG   CBC  CAL   121.94  3.000
 DXZ  CBG   CBC  CAM   119.68  3.000
 DXZ  CAL   CBC  CAM   118.34  3.000
 DXZ  HBG   CBG  CAQ   108.22  3.000
 DXZ  HBG   CBG  SAV   107.54  3.000
 DXZ  CAQ   CBG  SAV   108.92  3.000
 DXZ  HBG   CBG  CBC   108.52  3.000
 DXZ  CAQ   CBG  CBC   110.97  3.000
 DXZ  SAV   CBG  CBC   112.53  3.000
 DXZ  CAA   SAV  CBG   100.54  3.000
 DXZ  H3AA  CAA  H2AA  109.45  3.000
 DXZ  H3AA  CAA  H1AA  108.64  3.000
 DXZ  H2AA  CAA  H1AA  108.65  3.000
 DXZ  H3AA  CAA  SAV   111.16  3.000
 DXZ  H2AA  CAA  SAV   111.59  3.000
 DXZ  H1AA  CAA  SAV   107.25  3.000
 DXZ  H2AQ  CAQ  H1AQ  106.09  3.000
 DXZ  H2AQ  CAQ  CAN   110.23  3.000
 DXZ  H1AQ  CAQ  CAN   109.03  3.000
 DXZ  H2AQ  CAQ  CBG   109.70  3.000
 DXZ  H1AQ  CAQ  CBG   107.09  3.000
 DXZ  CAN   CAQ  CBG   114.34  3.000
 DXZ  H2AN  CAN  H1AN  106.15  3.000
 DXZ  H2AN  CAN  CAP   109.88  3.000
 DXZ  H1AN  CAN  CAP   108.63  3.000
 DXZ  H2AN  CAN  CAQ   109.31  3.000
 DXZ  H1AN  CAN  CAQ   110.59  3.000
 DXZ  CAP   CAN  CAQ   112.12  3.000
 DXZ  H2AP  CAP  H1AP  105.22  3.000
 DXZ  H2AP  CAP  CBD   109.21  3.000
 DXZ  H1AP  CAP  CBD   110.60  3.000
 DXZ  H2AP  CAP  CAN   108.78  3.000
 DXZ  H1AP  CAP  CAN   109.54  3.000
 DXZ  CBD   CAP  CAN   113.18  3.000
 DXZ  CBA   CBD  CBE   117.99  3.000
 DXZ  CBE   CBD  CAP   119.10  3.000
 DXZ  CBA   CBD  CAP   122.85  3.000
 DXZ  NAU   CBE  OAG   118.27  3.000
 DXZ  NAU   CBE  CBD   114.69  3.000
 DXZ  OAG   CBE  CBD   127.04  3.000
 DXZ  HNAU  NAU  CAZ   119.92  3.000
 DXZ  HNAU  NAU  CBE   116.73  3.000
 DXZ  CAZ   NAU  CBE   123.35  3.000
 DXZ  NAS   CAZ  NAB   119.84  3.000
 DXZ  NAB   CAZ  NAU   117.75  3.000
 DXZ  NAS   CAZ  NAU   122.39  3.000
 DXZ  H2AB  NAB  H1AB  116.59  3.000
 DXZ  H2AB  NAB  CAZ   117.69  3.000
 DXZ  H1AB  NAB  CAZ   120.87  3.000
 DXZ  CBA   NAS  CAZ   117.43  3.000
 DXZ  NAC   CBA  NAS   114.01  3.000
 DXZ  NAS   CBA  CBD   124.14  3.000
 DXZ  NAC   CBA  CBD   121.83  3.000
 DXZ  H2AC  NAC  H1AC  116.26  3.000
 DXZ  H2AC  NAC  CBA   118.17  3.000
 DXZ  H1AC  NAC  CBA   120.75  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
 DXZ  CONST_01  CBC   CAM  CAK  CBB     0.00   0.0  0
 DXZ  CONST_02  CBC   CAL  CAJ  CBB     0.00   0.0  0
 DXZ  CONST_03  CAL   CAJ  CBB  CAK     0.00   0.0  0
 DXZ  CONST_04  CAL   CBC  CAM  CAK     0.00   0.0  0
 DXZ  CONST_05  CAJ   CBB  CAK  CAM     0.00   0.0  0
 DXZ  CONST_06  CAJ   CAL  CBC  CAM     0.00   0.0  0
 DXZ  CONST_07  CAZ   NAS  CBA  CBD     0.00   0.0  0
 DXZ  CONST_08  CAZ   NAU  CBE  CBD     0.00   0.0  0
 DXZ  CONST_09  NAS   CAZ  NAU  CBE     0.00   0.0  0
 DXZ  CONST_10  CBA   NAS  CAZ  NAU     0.00   0.0  0
 DXZ  CONST_11  CAM   CAK  CBB  CAY   180.00   0.0  0
 DXZ  CONST_12  CAL   CAJ  CBB  CAY   180.00   0.0  0
 DXZ  CONST_13  CBG   CBC  CAM  CAK   180.00   0.0  0
 DXZ  CONST_14  CBG   CBC  CAL  CAJ   180.00   0.0  0
 DXZ  CONST_15  NAB   CAZ  NAU  CBE   180.00   0.0  0
 DXZ  CONST_16  CAZ   NAU  CBE  OAG   180.00   0.0  0
 DXZ  CONST_17  NAC   CBA  NAS  CAZ   180.00   0.0  0
 DXZ  CONST_18  CBA   NAS  CAZ  NAB   180.00   0.0  0
 DXZ  CONST_19  HAM   CAM  CAK  CBB   180.00   0.0  0
 DXZ  CONST_20  HAL   CAL  CAJ  CBB   180.00   0.0  0
 DXZ  CONST_21  HAJ   CAJ  CBB  CAK   180.00   0.0  0
 DXZ  CONST_22  HAK   CAK  CBB  CAJ   180.00   0.0  0
 DXZ  CONST_23  HNAU  NAU  CBE  CBD   180.00   0.0  0
 DXZ  CONST_24  H1AC  NAC  CBA  CBD     0.00   0.0  0
 DXZ  CONST_25  H2AC  NAC  CBA  CBD   180.00   0.0  0
 DXZ  CONST_26  H1AB  NAB  CAZ  NAU     0.00   0.0  0
 DXZ  CONST_27  H2AB  NAB  CAZ  NAU   180.00   0.0  0
 DXZ  CONST_28  CBB   CAY  N    CA    180.00   0.0  0
 DXZ  CONST_29  HN    N    CAY  CBB     0.00   0.0  0
 DXZ  CONST_30  OAF   CAY  N    CA      0.00   0.0  0
 DXZ  Var_01    CAK   CBB  CAY  N    -165.59  30.0  2
 DXZ  Var_02    CBA   CBD  CAP  CAN    85.82  30.0  3
 DXZ  Var_03    CBD   CAP  CAN  CAQ  -179.70  30.0  3
 DXZ  Var_04    CB    CG   CD   OE1    -2.70  30.0  3
 DXZ  Var_05    CA    CB   CG   CD   -176.83  30.0  3
 DXZ  Var_06    CAP   CAN  CAQ  CBG   174.06  30.0  3
 DXZ  Var_07    H1AA  CAA  SAV  CBG   178.32  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
 DXZ  chir_01  CA   CB   N    C    positiv
 DXZ  chir_02  CBG  SAV  CBC  CAQ  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
 DXZ  plan-1  CAY   0.020
 DXZ  plan-1  CBB   0.020
 DXZ  plan-1  CAK   0.020
 DXZ  plan-1  CAM   0.020
 DXZ  plan-1  CAJ   0.020
 DXZ  plan-1  CAL   0.020
 DXZ  plan-1  CBC   0.020
 DXZ  plan-1  CBG   0.020
 DXZ  plan-1  HAK   0.020
 DXZ  plan-1  HAM   0.020
 DXZ  plan-1  HAJ   0.020
 DXZ  plan-1  HAL   0.020
 DXZ  plan-2  CAP   0.020
 DXZ  plan-2  CBD   0.020
 DXZ  plan-2  CBE   0.020
 DXZ  plan-2  OAG   0.020
 DXZ  plan-2  NAU   0.020
 DXZ  plan-2  CAZ   0.020
 DXZ  plan-2  NAB   0.020
 DXZ  plan-2  NAS   0.020
 DXZ  plan-2  CBA   0.020
 DXZ  plan-2  NAC   0.020
 DXZ  plan-2  HNAU  0.020
 DXZ  plan-2  H1AB  0.020
 DXZ  plan-2  H2AB  0.020
 DXZ  plan-2  H1AC  0.020
 DXZ  plan-2  H2AC  0.020
 DXZ  plan-3  CA    0.020
 DXZ  plan-3  N     0.020
 DXZ  plan-3  CAY   0.020
 DXZ  plan-3  OAF   0.020
 DXZ  plan-3  CBB   0.020
 DXZ  plan-3  HN    0.020
 DXZ  plan-4  OE1   0.020
 DXZ  plan-4  CD    0.020
 DXZ  plan-4  OE2   0.020
 DXZ  plan-4  CG    0.020
 DXZ  plan-5  CA    0.020
 DXZ  plan-5  C     0.020
 DXZ  plan-5  OXT   0.020
 DXZ  plan-5  O     0.020

