# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Aug  7 19:24:27 2021
#   Inital geometry file: a 153 line input string
#   Ligand name: (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyrrolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1snc(n1)C(=N/O)/C(=O)N[C@H](C=O)[C@@H]2NC(=C(CS2)CC3=CCN([C@@H]4CCNC4)C3=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
 RB6  RB6  '(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyrrolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  60  36  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RB6
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
 RB6  OAX  O  O     0  -0.461  29.6619  26.6398  88.2795
 RB6  CAW  C  C     0   0.541  29.4886  27.6333  87.6049
 RB6  CAY  C  C     0   0.065  30.6489  28.4821  87.1322
 RB6  CBB  C  CR5   0   0.452  31.0789  28.2633  85.7433
 RB6  NBF  N  N     0  -0.511  31.9078  29.0720  85.1492
 RB6  SBE  S  S2    0   0.400  32.1405  28.5061  83.6027
 RB6  CBD  C  CR5   0   0.141  31.0594  27.1682  83.8734
 RB6  NBG  N  NH2   0  -0.747  30.7700  26.2529  82.9600
 RB6  NBC  N  N     0  -0.451  30.5713  27.1950  85.0906
 RB6  NAZ  N  N     0  -0.191  31.2756  29.3265  87.8421
 RB6  OBA  O  OH1   0  -0.549  30.7804  29.4510  89.0873
 RB6  N    N  NH1   0  -0.570  28.3023  28.0873  87.1668
 RB6  CA   C  CH1   0  -0.165  27.1039  27.2991  87.1451
 RB6  C    C  C1    0   0.212  26.4967  27.3352  85.7560
 RB6  O    O  O     0  -0.407  26.9434  27.9818  84.8461
 RB6  CB   C  CR16  0  -0.312  25.9777  27.7186  88.1081
 RB6  SAS  S  S2    0   0.093  26.4987  27.8288  89.8477
 RB6  CAR  C  C     0  -0.694  27.3381  29.4232  89.7521
 RB6  NAC  N  NR16  0  -0.608  25.3065  28.8888  87.6447
 RB6  CAD  C  CR6   0   0.190  25.8615  30.1595  87.8585
 RB6  CBH  C  C     0   0.486  25.2797  31.2229  86.9892
 RB6  OBI  O  OH1   0  -0.540  24.2937  30.7572  86.2333
 RB6  OBJ  O  O     0  -0.470  25.6223  32.3809  86.9652
 RB6  CAE  C  CR6   0   0.029  26.8379  30.4189  88.7507
 RB6  CAF  C  CH2   0  -0.594  27.6141  31.7073  88.8703
 RB6  CAG  C  CR5   0   0.028  28.7010  31.8748  87.8559
 RB6  CAH  C  CR5   0   0.557  29.9670  32.5663  88.2182
 RB6  OAI  O  O     0  -0.521  30.2851  32.9796  89.3259
 RB6  CAQ  C  CR15  0  -0.394  28.7715  31.5542  86.5642
 RB6  CAP  C  CH2   0  -0.315  30.0565  32.0244  85.9761
 RB6  NAJ  N  NR5   0  -0.436  30.7129  32.6532  87.0951
 RB6  CAK  C  CH1   0  -0.134  32.0172  33.2944  87.0761
 RB6  CAL  C  CH2   0  -0.430  32.5077  33.6183  85.6648
 RB6  CAM  C  CH2   0  -0.285  33.3099  32.3700  85.2270
 RB6  NAN  N  NH1   0  -0.623  33.5120  31.5464  86.4209
 RB6  CAO  C  CH2   0  -0.261  33.1394  32.3658  87.5607
 RB6  H1   H  HNH2  0   0.396  31.2001  26.2461  82.0518
 RB6  H2   H  HNH2  0   0.422  30.1788  25.4756  83.2041
 RB6  H3   H  HOH1  0   0.466  31.3205  30.1297  89.5091
 RB6  H4   H  HNH1  0   0.415  28.3235  28.8782  86.5408
 RB6  H5   H  HCH1  0   0.335  27.3582  26.2606  87.3768
 RB6  H6   H  H     0   0.270  25.5945  26.7125  85.6418
 RB6  H7   H  HCR6  0   0.334  25.2493  26.9066  88.0906
 RB6  H8   H  H     0   0.258  28.4116  29.2887  89.6203
 RB6  H9   H  H     0   0.341  27.2141  29.8724  90.7424
 RB6  H10  H  HNR6  0   0.398  24.3080  28.8417  87.7850
 RB6  H11  H  HOH1  0   0.479  23.9207  31.4822  85.7103
 RB6  H12  H  HCH2  0   0.286  28.0795  31.7275  89.8583
 RB6  H13  H  HCH2  0   0.298  26.9625  32.5795  88.8347
 RB6  H14  H  HCR5  0   0.251  28.0227  31.0621  85.9588
 RB6  H15  H  HCH2  0   0.239  30.6434  31.1984  85.5658
 RB6  H16  H  HCH2  0   0.303  29.8729  32.7295  85.1594
 RB6  H17  H  HCH1  0   0.254  31.9505  34.1930  87.6919
 RB6  H18  H  HCH2  0   0.248  33.1656  34.4857  85.7301
 RB6  H19  H  HCH2  0   0.237  31.7107  33.8846  84.9709
 RB6  H20  H  HCH2  0   0.233  32.7848  31.7938  84.4627
 RB6  H21  H  HCH2  0   0.175  34.2649  32.6754  84.7917
 RB6  H22  H  HNH1  0   0.360  32.9038  30.7381  86.3709
 RB6  H24  H  HCH2  0   0.223  32.8570  31.7494  88.4140
 RB6  H25  H  HCH2  0   0.256  33.9851  32.9852  87.8799

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
 RB6  NBG  CBD  single    1.325  0.020  1.325
 RB6  SBE  CBD  aromatic  1.741  0.020  1.741
 RB6  SBE  NBF  aromatic  1.663  0.020  1.663
 RB6  CBD  NBC  aromatic  1.312  0.020  1.312
 RB6  NBF  CBB  aromatic  1.302  0.020  1.302
 RB6  NBC  CBB  aromatic  1.351  0.020  1.351
 RB6  O    C    double    1.202  0.020  1.202
 RB6  CBB  CAY  single    1.470  0.020  1.470
 RB6  C    CA   single    1.516  0.020  1.516
 RB6  OBJ  CBH  double    1.208  0.020  1.208
 RB6  CAY  NAZ  double    1.269  0.020  1.269
 RB6  CAY  CAW  single    1.513  0.020  1.513
 RB6  NAZ  OBA  single    1.346  0.020  1.346
 RB6  CAL  CAM  single    1.547  0.020  1.547
 RB6  CAL  CAK  single    1.529  0.020  1.529
 RB6  CAM  NAN  single    1.464  0.020  1.464
 RB6  N    CAW  single    1.344  0.020  1.344
 RB6  N    CA   single    1.435  0.020  1.435
 RB6  CAW  OAX  double    1.213  0.020  1.213
 RB6  CBH  OBI  single    1.327  0.020  1.327
 RB6  CBH  CAD  single    1.492  0.020  1.492
 RB6  CA   CB   single    1.540  0.020  1.540
 RB6  NAN  CAO  single    1.452  0.020  1.452
 RB6  CAD  NAC  single    1.403  0.020  1.403
 RB6  CAD  CAE  double    1.348  0.020  1.348
 RB6  NAC  CB   single    1.426  0.020  1.426
 RB6  CAP  CAQ  single    1.489  0.020  1.489
 RB6  CAP  NAJ  single    1.442  0.020  1.442
 RB6  CAQ  CAG  double    1.333  0.020  1.333
 RB6  NAJ  CAH  single    1.351  0.020  1.351
 RB6  NAJ  CAK  single    1.453  0.020  1.453
 RB6  CAH  CAG  single    1.487  0.020  1.487
 RB6  CAH  OAI  double    1.224  0.020  1.224
 RB6  CAG  CAF  single    1.496  0.020  1.496
 RB6  CAF  CAE  single    1.509  0.020  1.509
 RB6  CAO  CAK  single    1.535  0.020  1.535
 RB6  CAE  CAR  single    1.498  0.020  1.498
 RB6  CB   SAS  single    1.819  0.020  1.819
 RB6  CAR  SAS  single    1.804  0.020  1.804
 RB6  NBG  H1   single    0.860  0.020  1.020
 RB6  NBG  H2   single    0.860  0.020  1.020
 RB6  OBA  H3   single    0.850  0.020  0.980
 RB6  N    H4   single    0.890  0.020  1.040
 RB6  CA   H5   single    0.970  0.020  1.090
 RB6  C    H6   single    0.930  0.020  1.080
 RB6  CB   H7   single    0.970  0.020  1.090
 RB6  CAR  H8   single    0.970  0.020  1.090
 RB6  CAR  H9   single    0.970  0.020  1.090
 RB6  NAC  H10  single    0.890  0.020  1.040
 RB6  OBI  H11  single    0.850  0.020  0.980
 RB6  CAF  H12  single    0.970  0.020  1.090
 RB6  CAF  H13  single    0.970  0.020  1.090
 RB6  CAQ  H14  single    0.930  0.020  1.080
 RB6  CAP  H15  single    0.970  0.020  1.090
 RB6  CAP  H16  single    0.970  0.020  1.090
 RB6  CAK  H17  single    0.970  0.020  1.090
 RB6  CAL  H18  single    0.970  0.020  1.090
 RB6  CAL  H19  single    0.970  0.020  1.090
 RB6  CAM  H20  single    0.970  0.020  1.090
 RB6  CAM  H21  single    0.970  0.020  1.090
 RB6  NAN  H22  single    0.890  0.020  1.040
 RB6  CAO  H24  single    0.970  0.020  1.090
 RB6  CAO  H25  single    0.970  0.020  1.090

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
 RB6  N    CAW  CAY  112.68  3.000
 RB6  N    CAW  OAX  125.74  3.000
 RB6  CAY  CAW  OAX  121.56  3.000
 RB6  NAZ  CAY  CBB  118.89  3.000
 RB6  NAZ  CAY  CAW  125.26  3.000
 RB6  CBB  CAY  CAW  115.84  3.000
 RB6  NBC  CBB  NBF  120.67  3.000
 RB6  NBC  CBB  CAY  117.66  3.000
 RB6  NBF  CBB  CAY  121.67  3.000
 RB6  SBE  NBF  CBB  107.59  3.000
 RB6  CBD  SBE  NBF   91.72  3.000
 RB6  NBC  CBD  NBG  124.92  3.000
 RB6  NBC  CBD  SBE  111.08  3.000
 RB6  NBG  CBD  SBE  124.00  3.000
 RB6  H2   NBG  H1   117.73  3.000
 RB6  H2   NBG  CBD  119.63  3.000
 RB6  H1   NBG  CBD  122.29  3.000
 RB6  CBD  NBC  CBB  108.94  3.000
 RB6  OBA  NAZ  CAY  113.42  3.000
 RB6  H3   OBA  NAZ  105.29  3.000
 RB6  H4   N    CA   116.03  3.000
 RB6  H4   N    CAW  116.66  3.000
 RB6  CA   N    CAW  123.84  3.000
 RB6  H5   CA   CB   107.22  3.000
 RB6  H5   CA   C    108.04  3.000
 RB6  CB   CA   C    105.87  3.000
 RB6  H5   CA   N    108.91  3.000
 RB6  CB   CA   N    116.86  3.000
 RB6  C    CA   N    109.59  3.000
 RB6  H6   C    O    121.97  3.000
 RB6  H6   C    CA   114.16  3.000
 RB6  O    C    CA   123.87  3.000
 RB6  H7   CB   NAC  106.94  3.000
 RB6  H7   CB   SAS  104.57  3.000
 RB6  NAC  CB   SAS  113.31  3.000
 RB6  H7   CB   CA   105.99  3.000
 RB6  SAS  CB   CA   113.89  3.000
 RB6  NAC  CB   CA   111.37  3.000
 RB6  CAR  SAS  CB    97.82  3.000
 RB6  H9   CAR  H8   105.76  3.000
 RB6  H9   CAR  CAE  107.11  3.000
 RB6  H8   CAR  CAE  109.28  3.000
 RB6  H9   CAR  SAS  105.19  3.000
 RB6  H8   CAR  SAS  110.83  3.000
 RB6  CAE  CAR  SAS  117.86  3.000
 RB6  H10  NAC  CAD  114.36  3.000
 RB6  H10  NAC  CB   112.46  3.000
 RB6  CAD  NAC  CB   120.49  3.000
 RB6  CAE  CAD  CBH  122.08  3.000
 RB6  CAE  CAD  NAC  124.18  3.000
 RB6  CBH  CAD  NAC  113.74  3.000
 RB6  OBJ  CBH  OBI  122.41  3.000
 RB6  OBI  CBH  CAD  111.82  3.000
 RB6  OBJ  CBH  CAD  125.76  3.000
 RB6  H11  OBI  CBH  109.33  3.000
 RB6  CAF  CAE  CAD  126.12  3.000
 RB6  CAF  CAE  CAR  110.04  3.000
 RB6  CAD  CAE  CAR  123.81  3.000
 RB6  H13  CAF  H12  105.65  3.000
 RB6  H13  CAF  CAG  108.83  3.000
 RB6  H12  CAF  CAG  107.55  3.000
 RB6  H13  CAF  CAE  111.93  3.000
 RB6  H12  CAF  CAE  107.86  3.000
 RB6  CAG  CAF  CAE  114.55  3.000
 RB6  CAQ  CAG  CAH  107.63  3.000
 RB6  CAH  CAG  CAF  120.35  3.000
 RB6  CAQ  CAG  CAF  131.96  3.000
 RB6  NAJ  CAH  OAI  125.94  3.000
 RB6  OAI  CAH  CAG  126.76  3.000
 RB6  NAJ  CAH  CAG  107.30  3.000
 RB6  H14  CAQ  CAP  121.33  3.000
 RB6  H14  CAQ  CAG  127.99  3.000
 RB6  CAP  CAQ  CAG  110.64  3.000
 RB6  H16  CAP  H15  107.27  3.000
 RB6  H16  CAP  NAJ  112.00  3.000
 RB6  H15  CAP  NAJ  112.11  3.000
 RB6  H16  CAP  CAQ  110.70  3.000
 RB6  H15  CAP  CAQ  111.89  3.000
 RB6  NAJ  CAP  CAQ  102.94  3.000
 RB6  CAK  NAJ  CAP  126.22  3.000
 RB6  CAK  NAJ  CAH  122.32  3.000
 RB6  CAP  NAJ  CAH  111.46  3.000
 RB6  H17  CAK  CAO  111.39  3.000
 RB6  H17  CAK  CAL  111.46  3.000
 RB6  CAO  CAK  CAL  100.66  3.000
 RB6  H17  CAK  NAJ  107.52  3.000
 RB6  CAO  CAK  NAJ  112.65  3.000
 RB6  CAL  CAK  NAJ  113.17  3.000
 RB6  H19  CAL  H18  106.56  3.000
 RB6  H19  CAL  CAM  113.34  3.000
 RB6  H18  CAL  CAM  110.23  3.000
 RB6  H19  CAL  CAK  113.89  3.000
 RB6  H18  CAL  CAK  107.86  3.000
 RB6  CAM  CAL  CAK  104.87  3.000
 RB6  H21  CAM  H20  106.79  3.000
 RB6  H21  CAM  NAN  111.17  3.000
 RB6  H20  CAM  NAN  109.89  3.000
 RB6  H21  CAM  CAL  109.90  3.000
 RB6  H20  CAM  CAL  112.00  3.000
 RB6  NAN  CAM  CAL  107.14  3.000
 RB6  H22  NAN  CAO  109.57  3.000
 RB6  H22  NAN  CAM  109.01  3.000
 RB6  CAO  NAN  CAM  106.68  3.000
 RB6  H25  CAO  H24  106.95  3.000
 RB6  H25  CAO  NAN  110.46  3.000
 RB6  H24  CAO  NAN  111.21  3.000
 RB6  H25  CAO  CAK  108.32  3.000
 RB6  H24  CAO  CAK  113.57  3.000
 RB6  NAN  CAO  CAK  106.33  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
 RB6  CONST_01  CBD  SBE  NBF  CBB     0.00   0.0  0
 RB6  CONST_02  SBE  CBD  NBC  CBB     0.00   0.0  0
 RB6  CONST_03  NBC  CBD  SBE  NBF     0.00   0.0  0
 RB6  CONST_04  CBD  NBC  CBB  NBF     0.00   0.0  0
 RB6  CONST_05  NBC  CBB  NBF  SBE     0.00   0.0  0
 RB6  CONST_06  CAP  NAJ  CAH  CAG     0.00   0.0  0
 RB6  CONST_07  CAK  NAJ  CAH  CAG   180.00   0.0  0
 RB6  CONST_08  SBE  NBF  CBB  CAY   180.00   0.0  0
 RB6  CONST_09  CBD  NBC  CBB  CAY   180.00   0.0  0
 RB6  CONST_10  NBG  CBD  NBC  CBB   180.00   0.0  0
 RB6  CONST_11  NBG  CBD  SBE  NBF   180.00   0.0  0
 RB6  CONST_12  CAP  NAJ  CAH  OAI   180.00   0.0  0
 RB6  CONST_13  CAK  NAJ  CAH  OAI     0.00   0.0  0
 RB6  CONST_14  H1   NBG  CBD  SBE     0.00   0.0  0
 RB6  CONST_15  H2   NBG  CBD  SBE   180.00   0.0  0
 RB6  CONST_16  H11  OBI  CBH  CAD   180.00   0.0  0
 RB6  CONST_19  H4   N    CAW  OAX   180.00   0.0  0
 RB6  Var_01    CAE  CAD  NAC  CB    -16.64  30.0  1
 RB6  Var_02    CAE  CAR  SAS  CB     30.05  30.0  1
 RB6  Var_03    CAD  CAE  CAR  SAS    -4.75  30.0  1
 RB6  Var_04    NAC  CAD  CAE  CAR    -8.08  30.0  1
 RB6  Var_05    NAJ  CAP  CAQ  CAG     0.06  30.0  1
 RB6  Var_06    CAQ  CAP  NAJ  CAH     1.11  30.0  1
 RB6  Var_07    CAP  CAQ  CAG  CAH    -1.08  30.0  1
 RB6  Var_08    NAJ  CAH  CAG  CAQ     1.77  30.0  1
 RB6  Var_09    NAN  CAM  CAL  CAK   -12.10  30.0  1
 RB6  Var_10    CAM  NAN  CAO  CAK    32.05  30.0  1
 RB6  Var_11    CAO  NAN  CAM  CAL   -12.14  30.0  1
 RB6  Var_12    CAG  CAF  CAE  CAR    99.61  30.0  2
 RB6  Var_13    CAQ  CAG  CAF  CAE    38.02  30.0  1
 RB6  Var_14    NBF  CBB  CAY  CAW   168.47  30.0  3
 RB6  Var_15    OBJ  CBH  CAD  NAC  -177.75  30.0  2
 RB6  Var_16    CBB  CAY  CAW  OAX   100.03  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
 RB6  chir_01  CA   C    N    CB   negativ
 RB6  chir_02  CB   SAS  NAC  CA   negativ
 RB6  chir_03  CAK  CAL  NAJ  CAO  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
 RB6  plan-1  CAY  0.020
 RB6  plan-1  CBB  0.020
 RB6  plan-1  NBF  0.020
 RB6  plan-1  SBE  0.020
 RB6  plan-1  CBD  0.020
 RB6  plan-1  NBG  0.020
 RB6  plan-1  NBC  0.020
 RB6  plan-2  CA   0.020
 RB6  plan-2  C    0.020
 RB6  plan-2  O    0.020
 RB6  plan-2  H6   0.020
 RB6  plan-3  CAW  0.020
 RB6  plan-3  CAY  0.020
 RB6  plan-3  CBB  0.020
 RB6  plan-3  NAZ  0.020
 RB6  plan-3  OBA  0.020
 RB6  plan-4  OAX  0.020
 RB6  plan-4  CAW  0.020
 RB6  plan-4  CAY  0.020
 RB6  plan-4  N    0.020
 RB6  plan-4  CA   0.020
 RB6  plan-4  H4   0.020
 RB6  plan-5  CBD  0.020
 RB6  plan-5  NBG  0.020
 RB6  plan-5  H1   0.020
 RB6  plan-5  H2   0.020
 RB6  plan-6  CB   0.020
 RB6  plan-6  NAC  0.020
 RB6  plan-6  CAD  0.020
 RB6  plan-6  H10  0.020
 RB6  plan-7  CAG  0.020
 RB6  plan-7  CAH  0.020
 RB6  plan-7  OAI  0.020
 RB6  plan-7  CAP  0.020
 RB6  plan-7  NAJ  0.020
 RB6  plan-7  CAK  0.020
 RB6  plan-8  CAD  0.020
 RB6  plan-8  CBH  0.020
 RB6  plan-8  OBI  0.020
 RB6  plan-8  OBJ  0.020
 RB6  plan-8  H11  0.020

