# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:05:52 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: (2R)-5-[(carbamoyloxy)methyl]-2-[(1R)-1-{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}-2-oxoethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO\N=C(/C(=O)N[C@H](C=O)[C@@H]1NC(=C(COC(N)=O)CS1)C(O)=O)c2occc2
#
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
 DXF  DXF  '(2R)-5-[(carbamoyloxy)methyl]-2-[(1R)-1-{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}-2-oxoethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  46  29  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DXF
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
 DXF  C    C  C1     0   0.184   1.1349   2.6548   0.1066
 DXF  N    N  NH1    0  -0.609   2.0526   0.4273  -0.3837
 DXF  O    O  O      0  -0.349   2.0994   2.9317   0.7663
 DXF  CA   C  CH1    0  -0.220   0.9845   1.3473  -0.6530
 DXF  CB   C  CH1    0  -0.210  -0.3675   0.6971  -0.3539
 DXF  CAA  C  CH3    0  -0.388   5.6137   0.8417   2.3013
 DXF  NAB  N  NH2    0  -0.832  -5.9453  -3.0755   1.0442
 DXF  OAD  O  O      0  -0.526  -6.8183  -1.0583   1.6117
 DXF  OAE  O  OC    -1  -0.568  -4.7972   2.3816  -1.0778
 DXF  OAF  O  O      0  -0.455   3.5408   1.3576  -1.8178
 DXF  OAG  O  O      0  -0.593  -3.1659   2.3082  -2.5903
 DXF  CAI  C  CR15   0  -0.328   4.9023  -3.5350  -2.4942
 DXF  CAJ  C  CR15   0   0.006   3.8434  -2.9186  -3.0746
 DXF  CAK  C  CR15   0  -0.348   5.2808  -2.7196  -1.3924
 DXF  CAM  C  CH2    0  -0.604  -2.1659  -0.2802   1.3599
 DXF  NAN  N  N      0  -0.097   5.0042  -0.3892   0.4849
 DXF  NAP  N  NH1    0  -0.659  -1.4223   1.5243  -0.8335
 DXF  OAQ  O  O2     0  -0.382   4.7587   0.7501   1.1749
 DXF  OAR  O  O2     0  -0.482  -4.7470  -1.2429   0.7460
 DXF  OAS  O  O      0  -0.412   3.5426  -1.7870  -2.4123
 DXF  SAT  S  S2     0  -0.009  -0.5370   0.5050   1.4521
 DXF  CAU  C  C      0   0.718  -5.9079  -1.7369   1.1777
 DXF  CAX  C  C      0  -0.034  -3.1382   0.4567   0.4743
 DXF  CAY  C  C      0  -0.016   4.2576  -0.5086  -0.5396
 DXF  CAZ  C  C      0   0.143  -2.7447   1.2664  -0.5309
 DXF  CBA  C  CR5    0   0.372   4.4172  -1.6675  -1.3900
 DXF  H1   H  H      0   0.218   0.2878   3.3484  -0.0159
 DXF  H3   H  HNH1   0   0.416   1.9372  -0.2312   0.3737
 DXF  H5   H  HCH1   0   0.323   0.9928   1.6006  -1.7207
 DXF  H6   H  HCH1   0   0.299  -0.3817  -0.3082  -0.7941
 DXF  H7   H  HCH3   0   0.227   5.4562   0.0132   2.9943
 DXF  H8   H  HCH3   0   0.226   6.6643   0.8705   2.0061
 DXF  H9   H  HCH3   0   0.243   5.3564   1.7750   2.7965
 DXF  H10  H  HNH2   0   0.404  -6.7228  -3.5823   1.4292
 DXF  H11  H  HNH2   0   0.402  -5.1249  -3.6018   0.7972
 DXF  H13  H  HCR5   0   0.273   5.3590  -4.4573  -2.8134
 DXF  H14  H  HCR5   0   0.287   3.2307  -3.1579  -3.9283
 DXF  H15  H  HCR5   0   0.272   6.0856  -2.8875  -0.6957
 DXF  H16  H  HCH2   0   0.261  -5.2567   0.6933   0.1647
 DXF  H17  H  HCH2   0   0.286  -2.0290  -1.3187   1.0505
 DXF  H18  H  HCH2   0   0.284  -2.5368  -0.3076   2.3878
 DXF  H2   H  HCH2   0   0.225  -4.7683   0.5097   1.8541
 DXF  H4   H  HNH1   0   0.384  -1.3243   1.8676  -1.7816
 DXF  CAL  C  CH2    0  -0.234  -4.5646   0.1860   0.8281
 DXF  CAV  C  C      0   0.394  -3.6703   2.0534  -1.4785
 DXF  CAW  C  C      0   0.506   3.2517   0.5375  -0.9682

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
 DXF  CAI  CAK  aromatic  1.422  0.020  1.422
 DXF  CAI  CAJ  aromatic  1.356  0.020  1.356
 DXF  CAK  CBA  aromatic  1.361  0.020  1.361
 DXF  CAJ  OAS  aromatic  1.345  0.020  1.345
 DXF  OAD  CAU  double    1.216  0.020  1.216
 DXF  CBA  OAS  aromatic  1.351  0.020  1.351
 DXF  CBA  CAY  single    1.446  0.020  1.446
 DXF  NAN  CAY  double    1.273  0.020  1.273
 DXF  NAN  OAQ  single    1.354  0.020  1.354
 DXF  CAU  OAR  single    1.333  0.020  1.333
 DXF  CAU  NAB  single    1.346  0.020  1.346
 DXF  CAA  OAQ  single    1.417  0.020  1.417
 DXF  CAY  CAW  single    1.513  0.020  1.513
 DXF  OAR  CAL  single    1.443  0.020  1.443
 DXF  CAL  CAX  single    1.494  0.020  1.494
 DXF  CAW  N    single    1.339  0.020  1.339
 DXF  CAW  OAF  double    1.216  0.020  1.216
 DXF  CAM  CAX  single    1.508  0.020  1.508
 DXF  CAM  SAT  single    1.811  0.020  1.811
 DXF  N    CA   single    1.435  0.020  1.435
 DXF  CAX  CAZ  double    1.349  0.020  1.349
 DXF  OAG  CAV  deloc     1.247  0.020  1.247
 DXF  O    C    double    1.201  0.020  1.201
 DXF  CAZ  CAV  single    1.541  0.020  1.541
 DXF  CAZ  NAP  single    1.381  0.020  1.381
 DXF  SAT  CB   single    1.824  0.020  1.824
 DXF  CAV  OAE  deloc     1.240  0.020  1.240
 DXF  CA   C    single    1.520  0.020  1.520
 DXF  CA   CB   single    1.530  0.020  1.530
 DXF  NAP  CB   single    1.424  0.020  1.424
 DXF  C    H1   single    0.930  0.020  1.080
 DXF  N    H3   single    0.860  0.020  1.020
 DXF  CA   H5   single    0.970  0.020  1.090
 DXF  CB   H6   single    0.970  0.020  1.090
 DXF  CAA  H7   single    0.970  0.020  1.090
 DXF  CAA  H8   single    0.970  0.020  1.090
 DXF  CAA  H9   single    0.970  0.020  1.090
 DXF  NAB  H10  single    0.860  0.020  1.020
 DXF  NAB  H11  single    0.860  0.020  1.020
 DXF  CAI  H13  single    0.930  0.020  1.080
 DXF  CAJ  H14  single    0.930  0.020  1.080
 DXF  CAK  H15  single    0.930  0.020  1.080
 DXF  CAL  H16  single    0.970  0.020  1.090
 DXF  CAM  H17  single    0.970  0.020  1.090
 DXF  CAM  H18  single    0.970  0.020  1.090
 DXF  CAL  H2   single    0.970  0.020  1.090
 DXF  NAP  H4   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
 DXF  H1   C    CA   114.21  3.000
 DXF  H1   C    O    122.24  3.000
 DXF  CA   C    O    123.53  3.000
 DXF  H3   N    CAW  118.90  3.000
 DXF  H3   N    CA   118.27  3.000
 DXF  CAW  N    CA   122.14  3.000
 DXF  H5   CA   CB   107.16  3.000
 DXF  H5   CA   N    108.96  3.000
 DXF  CB   CA   N    110.40  3.000
 DXF  H5   CA   C    106.67  3.000
 DXF  CB   CA   C    110.82  3.000
 DXF  N    CA   C    112.59  3.000
 DXF  H6   CB   SAT  107.43  3.000
 DXF  H6   CB   NAP  112.80  3.000
 DXF  SAT  CB   NAP  109.02  3.000
 DXF  H6   CB   CA   108.80  3.000
 DXF  NAP  CB   CA   110.00  3.000
 DXF  SAT  CB   CA   108.69  3.000
 DXF  H9   CAA  H8   109.15  3.000
 DXF  H9   CAA  H7   109.16  3.000
 DXF  H8   CAA  H7   109.31  3.000
 DXF  H9   CAA  OAQ  105.94  3.000
 DXF  H8   CAA  OAQ  111.56  3.000
 DXF  H7   CAA  OAQ  111.63  3.000
 DXF  H11  NAB  H10  117.48  3.000
 DXF  H11  NAB  CAU  121.50  3.000
 DXF  H10  NAB  CAU  119.02  3.000
 DXF  H13  CAI  CAK  127.41  3.000
 DXF  H13  CAI  CAJ  126.39  3.000
 DXF  CAK  CAI  CAJ  106.19  3.000
 DXF  H14  CAJ  OAS  116.72  3.000
 DXF  H14  CAJ  CAI  133.02  3.000
 DXF  OAS  CAJ  CAI  110.26  3.000
 DXF  H15  CAK  CBA  126.38  3.000
 DXF  H15  CAK  CAI  127.62  3.000
 DXF  CBA  CAK  CAI  106.01  3.000
 DXF  H18  CAM  H17  106.57  3.000
 DXF  H18  CAM  CAX  110.23  3.000
 DXF  H17  CAM  CAX  112.28  3.000
 DXF  H18  CAM  SAT  105.56  3.000
 DXF  H17  CAM  SAT  108.31  3.000
 DXF  CAX  CAM  SAT  113.46  3.000
 DXF  CAY  NAN  OAQ  112.49  3.000
 DXF  H4   NAP  CAZ  111.16  3.000
 DXF  H4   NAP  CB   116.14  3.000
 DXF  CAZ  NAP  CB   121.81  3.000
 DXF  NAN  OAQ  CAA  110.48  3.000
 DXF  CAU  OAR  CAL  117.29  3.000
 DXF  CBA  OAS  CAJ  107.59  3.000
 DXF  CAM  SAT  CB    94.52  3.000
 DXF  OAR  CAU  OAD  124.12  3.000
 DXF  OAR  CAU  NAB  111.13  3.000
 DXF  OAD  CAU  NAB  124.74  3.000
 DXF  CAZ  CAX  CAM  122.87  3.000
 DXF  CAZ  CAX  CAL  124.30  3.000
 DXF  CAM  CAX  CAL  112.83  3.000
 DXF  CBA  CAY  CAW  117.43  3.000
 DXF  CAW  CAY  NAN  123.56  3.000
 DXF  CBA  CAY  NAN  118.92  3.000
 DXF  CAX  CAZ  CAV  126.12  3.000
 DXF  CAV  CAZ  NAP  110.18  3.000
 DXF  CAX  CAZ  NAP  123.69  3.000
 DXF  CAY  CBA  OAS  116.39  3.000
 DXF  CAY  CBA  CAK  133.66  3.000
 DXF  OAS  CBA  CAK  109.94  3.000
 DXF  H2   CAL  H16  108.42  3.000
 DXF  H2   CAL  CAX  110.24  3.000
 DXF  H16  CAL  CAX  112.31  3.000
 DXF  H2   CAL  OAR  108.81  3.000
 DXF  H16  CAL  OAR  110.35  3.000
 DXF  CAX  CAL  OAR  106.66  3.000
 DXF  CAZ  CAV  OAG  114.19  3.000
 DXF  CAZ  CAV  OAE  118.83  3.000
 DXF  OAG  CAV  OAE  126.97  3.000
 DXF  CAY  CAW  OAF  120.41  3.000
 DXF  OAF  CAW  N    125.01  3.000
 DXF  CAY  CAW  N    114.51  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
 DXF  CONST_01  OAS  CBA  CAK  CAI    0.00   0.0  0
 DXF  CONST_02  CBA  OAS  CAJ  CAI    0.00   0.0  0
 DXF  CONST_03  CBA  CAK  CAI  CAJ    0.00   0.0  0
 DXF  CONST_04  CAK  CBA  OAS  CAJ    0.00   0.0  0
 DXF  CONST_05  OAS  CAJ  CAI  CAK    0.00   0.0  0
 DXF  CONST_06  CAY  CBA  CAK  CAI  180.00   0.0  0
 DXF  CONST_07  CAY  CBA  OAS  CAJ  180.00   0.0  0
 DXF  CONST_08  H15  CAK  CAI  CAJ  180.00   0.0  0
 DXF  CONST_09  H14  CAJ  CAI  CAK  180.00   0.0  0
 DXF  CONST_10  H13  CAI  CAJ  OAS  180.00   0.0  0
 DXF  CONST_11  CAY  CAW  N    CA   180.00   0.0  0
 DXF  CONST_12  OAF  CAW  N    CA     0.00   0.0  0
 DXF  CONST_13  H3   N    CAW  OAF  180.00   0.0  0
 DXF  Var_01    CAX  CAM  SAT  CB   -48.62  30.0  1
 DXF  Var_02    CAX  CAZ  NAP  CB    17.08  30.0  1
 DXF  Var_03    NAP  CAZ  CAX  CAM   -1.38  30.0  1
 DXF  Var_04    CAZ  CAX  CAM  SAT   24.55  30.0  1
 DXF  Var_05    NAN  CAY  CBA  CAK   -3.60  30.0  2
 DXF  Var_06    OAR  CAL  CAX  CAM  -57.04  30.0  2
 DXF  Var_07    CBA  CAY  NAN  OAQ  179.06   0.0  2
 DXF  Var_08    CAX  CAL  OAR  CAU  172.12  30.0  3
 DXF  Var_09    H10  NAB  CAU  OAD   -8.16  30.0  2
 DXF  Var_10    H7   CAA  OAQ  NAN  -61.33  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
 DXF  chir_01  CA  N    C    CB  positiv
 DXF  chir_02  CB  SAT  NAP  CA  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
 DXF  plan-1  CAI  0.020
 DXF  plan-1  CAJ  0.020
 DXF  plan-1  CAK  0.020
 DXF  plan-1  OAS  0.020
 DXF  plan-1  CAY  0.020
 DXF  plan-1  CBA  0.020
 DXF  plan-1  H13  0.020
 DXF  plan-1  H14  0.020
 DXF  plan-1  H15  0.020
 DXF  plan-2  C    0.020
 DXF  plan-2  O    0.020
 DXF  plan-2  CA   0.020
 DXF  plan-2  H1   0.020
 DXF  plan-3  N    0.020
 DXF  plan-3  CA   0.020
 DXF  plan-3  OAF  0.020
 DXF  plan-3  CAY  0.020
 DXF  plan-3  H3   0.020
 DXF  plan-3  CAW  0.020
 DXF  plan-4  CB   0.020
 DXF  plan-4  NAP  0.020
 DXF  plan-4  CAZ  0.020
 DXF  plan-4  H4   0.020
 DXF  plan-5  OAE  0.020
 DXF  plan-5  OAG  0.020
 DXF  plan-5  CAZ  0.020
 DXF  plan-5  CAV  0.020
 DXF  plan-6  NAB  0.020
 DXF  plan-6  OAD  0.020
 DXF  plan-6  OAR  0.020
 DXF  plan-6  CAU  0.020
 DXF  plan-7  NAN  0.020
 DXF  plan-7  OAQ  0.020
 DXF  plan-7  CAY  0.020
 DXF  plan-7  CBA  0.020
 DXF  plan-7  CAW  0.020

