# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 00:59:21 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(1~{S})-1-(dioxidanyl)-1-oxidanyl-ethyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[n]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@](C)(O)OO)c(N)n1
#
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
 AUJ  AUJ  '2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(1~{S})-1-(dioxidanyl)-1-oxidanyl-ethyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate'  ligand  54  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AUJ
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
 AUJ  CAB   C  CH3   0  -0.744   1.1097  478.2561  50.8368
 AUJ  OAH   O  OH1   0  -0.657   0.5246  475.2827  46.1990
 AUJ  OAG   O  O     0  -0.679   2.1418  484.3935  48.5494
 AUJ  CAC   C  CH3   0  -0.747  -1.0937  476.7876  45.2535
 AUJ  OAI   O  OH1   0  -0.731  -2.4672  484.1425  47.9494
 AUJ  OAK   O  OH1   0  -0.721  -0.0939  485.3609  49.5316
 AUJ  CAO   C  CH2   0  -0.542  -0.4631  480.6494  49.5005
 AUJ  CAP   C  CH2   0  -0.428   1.6245  476.1183  48.9210
 AUJ  CAX   C  CR5   0   0.495   0.5582  478.2901  49.4526
 AUJ  CAZ   C  CR5   0  -0.338  -0.1429  479.3142  48.9202
 AUJ  OAF   O  O     0  -0.675  -1.7485  484.6346  45.4662
 AUJ  OAJ   O  OH1   0  -0.725  -1.5949  482.3120  46.6784
 AUJ  OAS   O  O2    0  -0.588   0.1392  482.9725  49.4674
 AUJ  OAT   O  O2    0  -0.699  -0.0032  484.2181  47.2436
 AUJ  SAU   S  S2    0   0.150  -0.6085  478.9675  47.2720
 AUJ  CBA   C  CR5   0  -0.129   0.2063  477.4151  47.3060
 AUJ  CBC   C  CT    0   0.488  -0.4127  476.2781  46.5211
 AUJ  NBB   N  NR5   0  -0.464   0.7350  477.2273  48.5935
 AUJ  PBD   P  P     0   1.474  -1.5047  483.8973  46.7142
 AUJ  PBE   P  P     0   1.485   0.6870  484.2526  48.7125
 AUJ  N1    N  N     0  -0.446   5.0943  476.3844  50.3301
 AUJ  C2    C  CR6   0   0.354   5.7136  476.9544  49.3027
 AUJ  N3    N  N     0  -0.470   5.1412  477.3212  48.1671
 AUJ  C4    C  CR6   0   0.462   3.8310  477.1026  48.0090
 AUJ  C5    C  CR6   0  -0.055   3.0774  476.4876  49.0352
 AUJ  C6    C  CR16  0  -0.082   3.7906  476.1673  50.1673
 AUJ  OBC1  O  O2    0  -0.307  -1.3173  475.6895  47.4310
 AUJ  OC11  O  OH1   0  -0.452  -2.0154  474.6194  46.8250
 AUJ  H1    H  HCH3  0   0.269   0.6518  479.0328  51.4447
 AUJ  H2    H  HCH3  0   0.262   0.9128  477.3017  51.3253
 AUJ  H3    H  HCH3  0   0.269   2.1874  478.4202  50.8528
 AUJ  H4    H  HOH1  0   0.456   1.0904  475.6057  45.4893
 AUJ  H5    H  HCH3  0   0.250  -1.9521  477.4223  45.4729
 AUJ  H6    H  HCH3  0   0.253  -0.3903  477.3669  44.6541
 AUJ  H7    H  HCH3  0   0.269  -1.4378  475.9524  44.6453
 AUJ  H8    H  HOH1  0   0.510  -2.7695  485.0554  48.0513
 AUJ  H9    H  HOH1  0   0.510   0.2610  486.2550  49.4288
 AUJ  H10   H  HCH3  0   0.245   7.6225  477.5406  48.5154
 AUJ  H11   H  HCH3  0   0.255   7.3479  477.9981  50.1992
 AUJ  H12   H  HCH3  0   0.251   7.6972  476.3252  49.8035
 AUJ  H13   H  HCH2  0   0.239   0.7686  481.6029  48.0134
 AUJ  H14   H  HCH2  0   0.261   1.5416  481.4517  49.5927
 AUJ  H15   H  HCH2  0   0.274  -0.5221  480.5900  50.5886
 AUJ  H16   H  HCH2  0   0.270  -1.4425  480.9837  49.1527
 AUJ  H17   H  HCH2  0   0.283   1.3000  475.6705  49.8624
 AUJ  H18   H  HCH2  0   0.311   1.4952  475.3537  48.1602
 AUJ  H19   H  HNH2  0   0.394   3.8769  477.9926  46.1970
 AUJ  H20   H  HNH2  0   0.430   2.2972  477.5471  46.7054
 AUJ  H21   H  HOH1  0   0.508  -1.1983  481.9051  45.8957
 AUJ  H23   H  HCR6  0   0.263   3.2719  475.7002  51.0002
 AUJ  H24   H  HOH1  0   0.472  -2.8835  475.0113  46.6544
 AUJ  CAA   C  CH3   0  -0.730   7.1793  477.2182  49.4542
 AUJ  CAN   C  CH2   0  -0.162   0.5956  481.6601  49.0904
 AUJ  NAD   N  NH2   0  -0.842   3.2977  477.4713  46.8339

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
 AUJ  CAC   CBC   single    1.526  0.020  1.526
 AUJ  OAH   CBC   single    1.405  0.020  1.405
 AUJ  OAF   PBD   double    1.470  0.020  1.470
 AUJ  CBC   OBC1  single    1.412  0.020  1.412
 AUJ  CBC   CBA   single    1.514  0.020  1.514
 AUJ  OAJ   PBD   single    1.588  0.020  1.588
 AUJ  OC11  OBC1  single    1.414  0.020  1.414
 AUJ  NAD   C4    single    1.342  0.020  1.342
 AUJ  PBD   OAT   single    1.624  0.020  1.624
 AUJ  PBD   OAI   single    1.585  0.020  1.585
 AUJ  SAU   CBA   aromatic  1.754  0.020  1.754
 AUJ  SAU   CAZ   aromatic  1.747  0.020  1.747
 AUJ  OAT   PBE   single    1.623  0.020  1.623
 AUJ  CBA   NBB   aromatic  1.404  0.020  1.404
 AUJ  C4    N3    aromatic  1.338  0.020  1.338
 AUJ  C4    C5    aromatic  1.414  0.020  1.414
 AUJ  N3    C2    aromatic  1.324  0.020  1.324
 AUJ  OAG   PBE   double    1.471  0.020  1.471
 AUJ  CAN   OAS   single    1.440  0.020  1.440
 AUJ  CAN   CAO   single    1.520  0.020  1.520
 AUJ  PBE   OAS   single    1.584  0.020  1.584
 AUJ  PBE   OAK   single    1.584  0.020  1.584
 AUJ  NBB   CAP   single    1.459  0.020  1.459
 AUJ  NBB   CAX   aromatic  1.378  0.020  1.378
 AUJ  CAZ   CAO   single    1.491  0.020  1.491
 AUJ  CAZ   CAX   aromatic  1.350  0.020  1.350
 AUJ  CAP   C5    single    1.503  0.020  1.503
 AUJ  C5    C6    aromatic  1.376  0.020  1.376
 AUJ  CAX   CAB   single    1.490  0.020  1.490
 AUJ  C2    CAA   single    1.497  0.020  1.497
 AUJ  C2    N1    aromatic  1.328  0.020  1.328
 AUJ  C6    N1    aromatic  1.332  0.020  1.332
 AUJ  CAB   H1    single    0.970  0.020  1.090
 AUJ  CAB   H2    single    0.970  0.020  1.090
 AUJ  CAB   H3    single    0.970  0.020  1.090
 AUJ  OAH   H4    single    0.850  0.020  0.980
 AUJ  CAC   H5    single    0.970  0.020  1.090
 AUJ  CAC   H6    single    0.970  0.020  1.090
 AUJ  CAC   H7    single    0.970  0.020  1.090
 AUJ  OAI   H8    single    0.850  0.020  0.980
 AUJ  OAK   H9    single    0.850  0.020  0.980
 AUJ  CAA   H10   single    0.970  0.020  1.090
 AUJ  CAA   H11   single    0.970  0.020  1.090
 AUJ  CAA   H12   single    0.970  0.020  1.090
 AUJ  CAN   H13   single    0.970  0.020  1.090
 AUJ  CAN   H14   single    0.970  0.020  1.090
 AUJ  CAO   H15   single    0.970  0.020  1.090
 AUJ  CAO   H16   single    0.970  0.020  1.090
 AUJ  CAP   H17   single    0.970  0.020  1.090
 AUJ  CAP   H18   single    0.970  0.020  1.090
 AUJ  NAD   H19   single    0.890  0.020  1.040
 AUJ  NAD   H20   single    0.890  0.020  1.040
 AUJ  OAJ   H21   single    0.850  0.020  0.980
 AUJ  C6    H23   single    0.930  0.020  1.080
 AUJ  OC11  H24   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
 AUJ  H3    CAB   H2    107.69  3.000
 AUJ  H3    CAB   H1    107.49  3.000
 AUJ  H2    CAB   H1    107.38  3.000
 AUJ  H3    CAB   CAX   112.09  3.000
 AUJ  H2    CAB   CAX   111.68  3.000
 AUJ  H1    CAB   CAX   110.30  3.000
 AUJ  H4    OAH   CBC   108.86  3.000
 AUJ  H7    CAC   H6    107.71  3.000
 AUJ  H7    CAC   H5    108.07  3.000
 AUJ  H6    CAC   H5    108.01  3.000
 AUJ  H7    CAC   CBC   110.42  3.000
 AUJ  H6    CAC   CBC   110.24  3.000
 AUJ  H5    CAC   CBC   112.24  3.000
 AUJ  H8    OAI   PBD   114.71  3.000
 AUJ  H9    OAK   PBE   114.26  3.000
 AUJ  H16   CAO   H15   106.61  3.000
 AUJ  H16   CAO   CAZ   110.06  3.000
 AUJ  H15   CAO   CAZ   110.55  3.000
 AUJ  H16   CAO   CAN   109.59  3.000
 AUJ  H15   CAO   CAN   110.05  3.000
 AUJ  CAZ   CAO   CAN   109.93  3.000
 AUJ  H18   CAP   H17   106.25  3.000
 AUJ  H18   CAP   C5    109.94  3.000
 AUJ  H17   CAP   C5    108.81  3.000
 AUJ  H18   CAP   NBB   107.78  3.000
 AUJ  H17   CAP   NBB   108.91  3.000
 AUJ  C5    CAP   NBB   114.80  3.000
 AUJ  NBB   CAX   CAZ   113.94  3.000
 AUJ  CAZ   CAX   CAB   125.14  3.000
 AUJ  NBB   CAX   CAB   120.92  3.000
 AUJ  SAU   CAZ   CAX   111.08  3.000
 AUJ  CAX   CAZ   CAO   129.59  3.000
 AUJ  SAU   CAZ   CAO   119.19  3.000
 AUJ  H21   OAJ   PBD   114.51  3.000
 AUJ  PBE   OAS   CAN   120.15  3.000
 AUJ  PBE   OAT   PBD   133.80  3.000
 AUJ  CBA   SAU   CAZ    91.92  3.000
 AUJ  NBB   CBA   CBC   121.92  3.000
 AUJ  NBB   CBA   SAU   108.13  3.000
 AUJ  CBC   CBA   SAU   117.70  3.000
 AUJ  OBC1  CBC   CBA   103.94  3.000
 AUJ  CBA   CBC   CAC   111.24  3.000
 AUJ  OBC1  CBC   CAC   112.86  3.000
 AUJ  CBA   CBC   OAH   112.23  3.000
 AUJ  OBC1  CBC   OAH   106.26  3.000
 AUJ  CAC   CBC   OAH   110.11  3.000
 AUJ  CBA   NBB   CAX   114.83  3.000
 AUJ  CAX   NBB   CAP   121.65  3.000
 AUJ  CBA   NBB   CAP   122.48  3.000
 AUJ  OAT   PBD   OAJ   104.89  3.000
 AUJ  OAT   PBD   OAF   109.33  3.000
 AUJ  OAJ   PBD   OAF   118.17  3.000
 AUJ  OAT   PBD   OAI   106.07  3.000
 AUJ  OAJ   PBD   OAI    97.91  3.000
 AUJ  OAF   PBD   OAI   118.90  3.000
 AUJ  OAT   PBE   OAS   105.49  3.000
 AUJ  OAS   PBE   OAK    98.54  3.000
 AUJ  OAT   PBE   OAK   105.86  3.000
 AUJ  OAK   PBE   OAG   118.55  3.000
 AUJ  OAS   PBE   OAG   118.19  3.000
 AUJ  OAT   PBE   OAG   108.80  3.000
 AUJ  C6    N1    C2    115.59  3.000
 AUJ  N3    C2    N1    125.52  3.000
 AUJ  N1    C2    CAA   116.99  3.000
 AUJ  N3    C2    CAA   117.48  3.000
 AUJ  C4    N3    C2    118.67  3.000
 AUJ  C5    C4    N3    120.49  3.000
 AUJ  C5    C4    NAD   122.90  3.000
 AUJ  N3    C4    NAD   116.60  3.000
 AUJ  C6    C5    C4    114.97  3.000
 AUJ  C6    C5    CAP   120.42  3.000
 AUJ  C4    C5    CAP   124.53  3.000
 AUJ  H23   C6    C5    118.90  3.000
 AUJ  H23   C6    N1    116.34  3.000
 AUJ  C5    C6    N1    124.76  3.000
 AUJ  OC11  OBC1  CBC   110.83  3.000
 AUJ  H24   OC11  OBC1  102.24  3.000
 AUJ  H12   CAA   H11   107.05  3.000
 AUJ  H12   CAA   H10   109.03  3.000
 AUJ  H11   CAA   H10   108.33  3.000
 AUJ  H12   CAA   C2    110.69  3.000
 AUJ  H11   CAA   C2    110.26  3.000
 AUJ  H10   CAA   C2    111.35  3.000
 AUJ  H14   CAN   H13   107.85  3.000
 AUJ  H14   CAN   OAS   109.17  3.000
 AUJ  H13   CAN   OAS   110.87  3.000
 AUJ  H14   CAN   CAO   110.65  3.000
 AUJ  H13   CAN   CAO   109.97  3.000
 AUJ  OAS   CAN   CAO   108.34  3.000
 AUJ  H20   NAD   H19   116.74  3.000
 AUJ  H20   NAD   C4    121.66  3.000
 AUJ  H19   NAD   C4    117.89  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
 AUJ  CONST_01  SAU  CBA  NBB  CAX    0.00   0.0  0
 AUJ  CONST_02  CBA  SAU  CAZ  CAX    0.00   0.0  0
 AUJ  CONST_03  NBB  CBA  SAU  CAZ    0.00   0.0  0
 AUJ  CONST_04  CBA  NBB  CAX  CAZ    0.00   0.0  0
 AUJ  CONST_05  NBB  CAX  CAZ  SAU    0.00   0.0  0
 AUJ  CONST_06  C4   N3   C2   N1     0.00   0.0  0
 AUJ  CONST_07  C4   C5   C6   N1     0.00   0.0  0
 AUJ  CONST_08  C5   C4   N3   C2     0.00   0.0  0
 AUJ  CONST_09  C5   C6   N1   C2     0.00   0.0  0
 AUJ  CONST_10  C6   C5   C4   N3     0.00   0.0  0
 AUJ  CONST_11  C6   N1   C2   N3     0.00   0.0  0
 AUJ  CONST_12  CBA  NBB  CAX  CAB  180.00   0.0  0
 AUJ  CONST_13  SAU  CAZ  CAX  CAB  180.00   0.0  0
 AUJ  CONST_14  C4   N3   C2   CAA  180.00   0.0  0
 AUJ  CONST_15  C6   N1   C2   CAA  180.00   0.0  0
 AUJ  CONST_16  CBA  SAU  CAZ  CAO  180.00   0.0  0
 AUJ  CONST_17  NBB  CAX  CAZ  CAO  180.00   0.0  0
 AUJ  CONST_18  SAU  CBA  NBB  CAP  180.00   0.0  0
 AUJ  CONST_19  CAZ  CAX  NBB  CAP  180.00   0.0  0
 AUJ  CONST_20  N3   C4   C5   CAP  180.00   0.0  0
 AUJ  CONST_21  N1   C6   C5   CAP  180.00   0.0  0
 AUJ  CONST_24  C2   N3   C4   NAD  180.00   0.0  0
 AUJ  CONST_25  C6   C5   C4   NAD  180.00   0.0  0
 AUJ  CONST_26  H23  C6   N1   C2   180.00   0.0  0
 AUJ  CONST_27  H19  NAD  C4   N3     0.00   0.0  0
 AUJ  CONST_28  H20  NAD  C4   N3   180.00   0.0  0
 AUJ  Var_01    C5   CAP  NBB  CAX  -64.48  30.0  2
 AUJ  Var_02    C4   C5   CAP  NBB  -57.09  30.0  2
 AUJ  Var_03    SAU  CAZ  CAO  CAN  -82.78  30.0  2
 AUJ  Var_04    H1   CAB  CAX  CAZ   15.34  30.0  2
 AUJ  Var_05    H10  CAA  C2   N1   171.22  30.0  2
 AUJ  Var_06    OAS  CAN  CAO  CAZ  170.18  30.0  1
 AUJ  Var_07    OAT  PBE  OAS  CAN   72.13  30.0  1

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
 AUJ  chir_01  CBC  OAH  OBC1  CBA  negativ
 AUJ  chir_02  PBE  OAG  OAS   OAK  both

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
 AUJ  plan-1  CAB  0.020
 AUJ  plan-1  CAO  0.020
 AUJ  plan-1  CAP  0.020
 AUJ  plan-1  CAX  0.020
 AUJ  plan-1  CAZ  0.020
 AUJ  plan-1  SAU  0.020
 AUJ  plan-1  CBA  0.020
 AUJ  plan-1  CBC  0.020
 AUJ  plan-1  NBB  0.020
 AUJ  plan-2  CAP  0.020
 AUJ  plan-2  N1   0.020
 AUJ  plan-2  C2   0.020
 AUJ  plan-2  N3   0.020
 AUJ  plan-2  C4   0.020
 AUJ  plan-2  C5   0.020
 AUJ  plan-2  C6   0.020
 AUJ  plan-2  H23  0.020
 AUJ  plan-2  CAA  0.020
 AUJ  plan-2  NAD  0.020
 AUJ  plan-3  C4   0.020
 AUJ  plan-3  H19  0.020
 AUJ  plan-3  H20  0.020
 AUJ  plan-3  NAD  0.020

