# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 22 09:08:11 2020
#   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  59  36  .  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_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  -0.465   3.8875  -2.6817   1.1186
 RB6  CAW  C  C      0   0.527   3.6363  -1.4974   0.9942
 RB6  CAY  C  C      0   0.022   4.5258  -0.4446   1.6163
 RB6  CBB  C  CR5    0   0.462   4.8010   0.8390   0.9374
 RB6  NBF  N  N      0  -0.631   3.9716   1.2929   0.0408
 RB6  SBE  S  S2     0   0.338   4.5301   2.7664  -0.4905
 RB6  CBD  C  CR5    0   0.285   5.9045   2.6679   0.5763
 RB6  NBG  N  NH2    0  -0.810   6.8362   3.6077   0.6613
 RB6  NBC  N  N      0  -0.441   5.8952   1.5592   1.2721
 RB6  NAZ  N  N      0  -0.079   5.1095  -0.5716   2.7431
 RB6  OBA  O  OH1    0  -0.508   4.8558  -1.6949   3.4203
 RB6  N    N  NH1    0  -0.656   2.5566  -1.0283   0.3475
 RB6  CA   C  CH1    0  -0.215   1.6769  -1.9157  -0.3553
 RB6  C    C  C1     0   0.183   2.2823  -2.4530  -1.6417
 RB6  O    O  O      0  -0.359   3.4019  -2.2092  -2.0043
 RB6  CB   C  CH1    0  -0.219   0.3438  -1.2203  -0.6459
 RB6  SAS  S  S2     0  -0.005   0.6121   0.0471  -1.9279
 RB6  CAR  C  CH2    0  -0.613  -1.1086   0.6045  -1.9607
 RB6  NAC  N  NH1    0  -0.658  -0.6038  -2.1742  -1.1203
 RB6  CAD  C  C      0   0.104  -1.8385  -1.7678  -1.6177
 RB6  CBH  C  C      0   0.399  -2.8166  -2.9515  -1.6359
 RB6  OBI  O  OC    -1  -0.578  -3.6678  -3.0133  -2.5373
 RB6  OBJ  O  O      0  -0.601  -2.6314  -3.7871  -0.7270
 RB6  CAE  C  C      0   0.058  -2.1105  -0.5163  -2.0288
 RB6  CAF  C  CH2    0  -0.590  -3.4538  -0.0628  -2.5470
 RB6  CAG  C  CR5    0   0.019  -4.0617   0.9573  -1.6438
 RB6  CAH  C  CR5    0   0.553  -4.6078   0.5937  -0.3094
 RB6  OAI  O  O      0  -0.493  -4.6477  -0.5245   0.1871
 RB6  CAQ  C  CR15   0  -0.322  -4.2118   2.2716  -1.8090
 RB6  CAP  C  CH2    0  -0.277  -4.8562   2.8751  -0.6093
 RB6  NAJ  N  NR5    0  -0.501  -5.0693   1.7369   0.2490
 RB6  CAK  C  CH1    0  -0.081  -5.6278   1.8676   1.5778
 RB6  CAL  C  CH2    0  -0.469  -4.6098   1.6263   2.7147
 RB6  CAM  C  CH2    0  -0.330  -5.3596   0.7099   3.6910
 RB6  NAN  N  NH1    0  -0.582  -6.2781  -0.0802   2.8795
 RB6  CAO  C  CH2    0  -0.335  -6.7777   0.8756   1.9037
 RB6  H1   H  HNH2   0   0.425   6.8241   4.4331   0.0885
 RB6  H2   H  HNH2   0   0.421   7.6334   3.4629   1.2586
 RB6  H3   H  HOH1   0   0.489   5.3471  -1.5885   4.2439
 RB6  H4   H  HNH1   0   0.434   2.5513  -0.0403   0.1031
 RB6  H5   H  HCH1   0   0.315   1.4518  -2.7851   0.2759
 RB6  H6   H  H      0   0.219   1.6095  -3.1070  -2.2191
 RB6  H7   H  HCH1   0   0.292   0.0120  -0.7036   0.2650
 RB6  H8   H  HCH2   0   0.281  -1.2799   1.2585  -1.1016
 RB6  H9   H  HCH2   0   0.279  -1.1968   1.2398  -2.8466
 RB6  H10  H  HNH1   0   0.376  -0.7199  -2.9805  -0.5173
 RB6  H12  H  HCH2   0   0.240  -3.3346   0.3754  -3.5440
 RB6  H13  H  HCH2   0   0.275  -4.1227  -0.9127  -2.6452
 RB6  H14  H  HCR5   0   0.265  -3.9204   2.8549  -2.6715
 RB6  H15  H  HCH2   0   0.262  -4.2106   3.6232  -0.1363
 RB6  H16  H  HCH2   0   0.263  -5.7992   3.3739  -0.8565
 RB6  H17  H  HCH1   0   0.263  -6.0128   2.8866   1.6300
 RB6  H18  H  HCH2   0   0.241  -3.7250   1.1168   2.3305
 RB6  H19  H  HCH2   0   0.241  -4.2754   2.5579   3.1715
 RB6  H20  H  HCH2   0   0.239  -4.6943   0.0650   4.2651
 RB6  H21  H  HCH2   0   0.222  -5.9365   1.3044   4.4059
 RB6  H22  H  HNH1   0   0.343  -5.7265  -0.7643   2.3738
 RB6  H24  H  HCH2   0   0.235  -7.5975   1.4407   2.3560
 RB6  H25  H  HCH2   0   0.246  -7.1778   0.3778   1.0215

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    1.326  0.020  1.326
 RB6  SBE  CBD  aromatic  1.743  0.020  1.743
 RB6  SBE  NBF  aromatic  1.663  0.020  1.663
 RB6  CBD  NBC  aromatic  1.309  0.020  1.309
 RB6  NBF  CBB  aromatic  1.303  0.020  1.303
 RB6  NBC  CBB  aromatic  1.352  0.020  1.352
 RB6  O    C    double    1.202  0.020  1.202
 RB6  CBB  CAY  single    1.478  0.020  1.478
 RB6  C    CA   single    1.520  0.020  1.520
 RB6  OBJ  CBH  deloc     1.248  0.020  1.248
 RB6  CAY  NAZ  double    1.275  0.020  1.275
 RB6  CAY  CAW  single    1.512  0.020  1.512
 RB6  NAZ  OBA  single    1.336  0.020  1.336
 RB6  CAL  CAM  single    1.535  0.020  1.535
 RB6  CAL  CAK  single    1.545  0.020  1.545
 RB6  CAM  NAN  single    1.458  0.020  1.458
 RB6  N    CAW  single    1.343  0.020  1.343
 RB6  N    CA   single    1.434  0.020  1.434
 RB6  CAW  OAX  double    1.217  0.020  1.217
 RB6  CBH  OBI  deloc     1.241  0.020  1.241
 RB6  CBH  CAD  single    1.536  0.020  1.536
 RB6  CA   CB   single    1.531  0.020  1.531
 RB6  NAN  CAO  single    1.454  0.020  1.454
 RB6  CAD  NAC  single    1.392  0.020  1.392
 RB6  CAD  CAE  double    1.345  0.020  1.345
 RB6  NAC  CB   single    1.426  0.020  1.426
 RB6  CAP  CAQ  single    1.490  0.020  1.490
 RB6  CAP  NAJ  single    1.441  0.020  1.441
 RB6  CAQ  CAG  double    1.333  0.020  1.333
 RB6  NAJ  CAH  single    1.353  0.020  1.353
 RB6  NAJ  CAK  single    1.447  0.020  1.447
 RB6  CAH  CAG  single    1.487  0.020  1.487
 RB6  CAH  OAI  double    1.224  0.020  1.224
 RB6  CAG  CAF  single    1.492  0.020  1.492
 RB6  CAF  CAE  single    1.510  0.020  1.510
 RB6  CAO  CAK  single    1.553  0.020  1.553
 RB6  CAE  CAR  single    1.505  0.020  1.505
 RB6  CB   SAS  single    1.823  0.020  1.823
 RB6  CAR  SAS  single    1.809  0.020  1.809
 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  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  115.32  3.000
 RB6  N    CAW  OAX  123.72  3.000
 RB6  CAY  CAW  OAX  120.93  3.000
 RB6  NAZ  CAY  CBB  114.03  3.000
 RB6  NAZ  CAY  CAW  124.29  3.000
 RB6  CBB  CAY  CAW  121.69  3.000
 RB6  NBC  CBB  NBF  120.00  3.000
 RB6  NBC  CBB  CAY  119.97  3.000
 RB6  NBF  CBB  CAY  120.01  3.000
 RB6  SBE  NBF  CBB  108.34  3.000
 RB6  CBD  SBE  NBF   91.10  3.000
 RB6  NBC  CBD  NBG  124.83  3.000
 RB6  NBC  CBD  SBE  111.57  3.000
 RB6  NBG  CBD  SBE  123.60  3.000
 RB6  H2   NBG  H1   117.78  3.000
 RB6  H2   NBG  CBD  119.51  3.000
 RB6  H1   NBG  CBD  122.49  3.000
 RB6  CBD  NBC  CBB  108.99  3.000
 RB6  OBA  NAZ  CAY  116.41  3.000
 RB6  H3   OBA  NAZ  104.08  3.000
 RB6  H4   N    CA   118.68  3.000
 RB6  H4   N    CAW  117.32  3.000
 RB6  CA   N    CAW  120.87  3.000
 RB6  H5   CA   CB   106.87  3.000
 RB6  H5   CA   C    106.76  3.000
 RB6  CB   CA   C    110.28  3.000
 RB6  H5   CA   N    109.52  3.000
 RB6  CB   CA   N    110.25  3.000
 RB6  C    CA   N    112.91  3.000
 RB6  H6   C    O    122.09  3.000
 RB6  H6   C    CA   114.21  3.000
 RB6  O    C    CA   123.69  3.000
 RB6  H7   CB   NAC  112.94  3.000
 RB6  H7   CB   SAS  107.50  3.000
 RB6  NAC  CB   SAS  109.21  3.000
 RB6  H7   CB   CA   108.61  3.000
 RB6  SAS  CB   CA   108.73  3.000
 RB6  NAC  CB   CA   109.75  3.000
 RB6  CAR  SAS  CB    94.99  3.000
 RB6  H9   CAR  H8   106.05  3.000
 RB6  H9   CAR  CAE  110.01  3.000
 RB6  H8   CAR  CAE  112.14  3.000
 RB6  H9   CAR  SAS  105.69  3.000
 RB6  H8   CAR  SAS  108.61  3.000
 RB6  CAE  CAR  SAS  113.87  3.000
 RB6  H10  NAC  CAD  110.08  3.000
 RB6  H10  NAC  CB   114.23  3.000
 RB6  CAD  NAC  CB   120.87  3.000
 RB6  CAE  CAD  CBH  125.79  3.000
 RB6  CAE  CAD  NAC  124.08  3.000
 RB6  CBH  CAD  NAC  110.13  3.000
 RB6  OBJ  CBH  OBI  126.67  3.000
 RB6  OBI  CBH  CAD  118.93  3.000
 RB6  OBJ  CBH  CAD  114.38  3.000
 RB6  CAF  CAE  CAD  124.36  3.000
 RB6  CAF  CAE  CAR  112.60  3.000
 RB6  CAD  CAE  CAR  122.99  3.000
 RB6  H13  CAF  H12  107.32  3.000
 RB6  H13  CAF  CAG  109.81  3.000
 RB6  H12  CAF  CAG  108.77  3.000
 RB6  H13  CAF  CAE  110.12  3.000
 RB6  H12  CAF  CAE  109.62  3.000
 RB6  CAG  CAF  CAE  111.11  3.000
 RB6  CAQ  CAG  CAH  108.12  3.000
 RB6  CAH  CAG  CAF  121.72  3.000
 RB6  CAQ  CAG  CAF  130.16  3.000
 RB6  NAJ  CAH  OAI  126.39  3.000
 RB6  OAI  CAH  CAG  126.82  3.000
 RB6  NAJ  CAH  CAG  106.79  3.000
 RB6  H14  CAQ  CAP  122.71  3.000
 RB6  H14  CAQ  CAG  126.90  3.000
 RB6  CAP  CAQ  CAG  110.39  3.000
 RB6  H16  CAP  H15  107.09  3.000
 RB6  H16  CAP  NAJ  111.51  3.000
 RB6  H15  CAP  NAJ  111.68  3.000
 RB6  H16  CAP  CAQ  112.04  3.000
 RB6  H15  CAP  CAQ  111.69  3.000
 RB6  NAJ  CAP  CAQ  102.92  3.000
 RB6  CAK  NAJ  CAP  122.17  3.000
 RB6  CAK  NAJ  CAH  125.92  3.000
 RB6  CAP  NAJ  CAH  111.77  3.000
 RB6  H17  CAK  CAO  108.99  3.000
 RB6  H17  CAK  CAL  110.08  3.000
 RB6  CAO  CAK  CAL  103.52  3.000
 RB6  H17  CAK  NAJ  105.34  3.000
 RB6  CAO  CAK  NAJ  114.88  3.000
 RB6  CAL  CAK  NAJ  114.03  3.000
 RB6  H19  CAL  H18  107.33  3.000
 RB6  H19  CAL  CAM  113.18  3.000
 RB6  H18  CAL  CAM  109.96  3.000
 RB6  H19  CAL  CAK  112.15  3.000
 RB6  H18  CAL  CAK  110.38  3.000
 RB6  CAM  CAL  CAK  103.85  3.000
 RB6  H21  CAM  H20  107.41  3.000
 RB6  H21  CAM  NAN  109.02  3.000
 RB6  H20  CAM  NAN  110.92  3.000
 RB6  H21  CAM  CAL  110.41  3.000
 RB6  H20  CAM  CAL  112.96  3.000
 RB6  NAN  CAM  CAL  106.10  3.000
 RB6  H22  NAN  CAO  107.19  3.000
 RB6  H22  NAN  CAM  107.49  3.000
 RB6  CAO  NAN  CAM  103.52  3.000
 RB6  H25  CAO  H24  107.21  3.000
 RB6  H25  CAO  NAN  111.67  3.000
 RB6  H24  CAO  NAN  108.64  3.000
 RB6  H25  CAO  CAK  113.20  3.000
 RB6  H24  CAO  CAK  108.16  3.000
 RB6  NAN  CAO  CAK  107.83  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  CA   N    CAW  OAX    0.00   0.0  0
 RB6  CONST_17  CA   N    CAW  CAY  180.00   0.0  0
 RB6  CONST_18  H4   N    CAW  OAX  180.00   0.0  0
 RB6  Var_01    CAE  CAD  NAC  CB    18.57  30.0  1
 RB6  Var_02    CAE  CAR  SAS  CB   -47.17  30.0  1
 RB6  Var_03    CAD  CAE  CAR  SAS   23.23  30.0  1
 RB6  Var_04    NAC  CAD  CAE  CAR   -1.72  30.0  1
 RB6  Var_05    NAJ  CAP  CAQ  CAG   -0.75  30.0  1
 RB6  Var_06    CAQ  CAP  NAJ  CAH    1.05  30.0  1
 RB6  Var_07    CAP  CAQ  CAG  CAH    0.23  30.0  1
 RB6  Var_08    NAJ  CAH  CAG  CAQ    0.43  30.0  1
 RB6  Var_09    NAN  CAM  CAL  CAK   30.19  30.0  1
 RB6  Var_10    CAM  NAN  CAO  CAK   34.02  30.0  1
 RB6  Var_11    CAO  NAN  CAM  CAL  -39.94  30.0  1
 RB6  Var_12    CAG  CAF  CAE  CAR  -62.04  30.0  2
 RB6  Var_13    CAQ  CAG  CAF  CAE  106.85  30.0  1
 RB6  Var_14    NBF  CBB  CAY  CAW   23.14  30.0  2
 RB6  Var_15    OBJ  CBH  CAD  NAC   31.48  30.0  2
 RB6  Var_16    CBB  CAY  CAW  OAX  143.09  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

