# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 19:42:44 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: (2R)-2-[(1R)-1-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-2-oxoethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nnnc1SCC2=C(N[C@H](SC2)[C@H](NC(=O)[C@H](O)c3ccccc3)C=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
 XD2  XD2  '(2R)-2-[(1R)-1-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-2-oxoethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  50  31  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XD2
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
 XD2  CAA  C  CH3    0  -0.531  -5.6328   3.3433   0.9009
 XD2  OAB  O  OC    -1  -0.561  -3.4411  -2.5605   1.5302
 XD2  OAC  O  O      0  -0.477   4.9653  -1.4905   1.0741
 XD2  OAE  O  O      0  -0.590  -1.5714  -2.5232   2.7348
 XD2  OAF  O  OH1    0  -0.657   6.8161  -0.1774  -0.2866
 XD2  CAG  C  CR16   0  -0.264   4.4472   4.1401   0.6760
 XD2  CAH  C  CR16   0  -0.239   4.0524   3.6769  -0.5709
 XD2  CAI  C  CR16   0  -0.240   5.1938   3.3171   1.5111
 XD2  CAJ  C  CR16   0  -0.319   4.4026   2.3958  -0.9790
 XD2  CAK  C  CR16   0  -0.294   5.5411   2.0376   1.1034
 XD2  CAL  C  C1     0   0.188   2.3983  -3.1045  -0.2910
 XD2  CAM  C  CH2    0  -0.613  -3.4120  -0.7493  -0.6828
 XD2  CAN  C  CH2    0  -0.596  -1.1007  -0.3967  -1.5859
 XD2  NAO  N  N      0  -0.137  -7.2786   1.1444  -1.2245
 XD2  NAP  N  N      0  -0.351  -6.1355   0.4626  -1.1272
 XD2  NAQ  N  N      0  -0.083  -7.2424   2.2138  -0.5396
 XD2  NAR  N  NH1    0  -0.623   3.2820  -0.8146  -0.2754
 XD2  NAS  N  NH1    0  -0.656  -0.0848  -1.8959   0.7261
 XD2  SAU  S  S2     0  -0.003   0.5268  -1.1668  -1.7529
 XD2  CAW  C  C      0   0.517   4.5535  -0.8143   0.1458
 XD2  CAX  C  C      0  -0.029  -1.9523  -1.0246  -0.5133
 XD2  CAY  C  C      0   0.168  -1.4332  -1.6870   0.5455
 XD2  CAZ  C  CR6    0   0.115   5.1427   1.5663  -0.1450
 XD2  CBA  C  CR5    0   0.371  -5.3640   1.1723  -0.3336
 XD2  CBB  C  CH1    0  -0.139   5.4942   0.1565  -0.5747
 XD2  CBC  C  CH1    0  -0.223   2.2896  -1.6956   0.2691
 XD2  CBD  C  CH1    0  -0.212   0.8906  -1.1229   0.0344
 XD2  NBE  N  NR5    0  -0.315  -6.0450   2.2623   0.0364
 XD2  H1   H  HCH3   0   0.277  -4.7471   3.8288   0.4961
 XD2  H2   H  HCH3   0   0.289  -6.4421   4.0635   0.9570
 XD2  H3   H  HCH3   0   0.278  -5.4178   2.9651   1.8980
 XD2  H6   H  HOH1   0   0.450   6.8078  -0.7410   0.5003
 XD2  H9   H  HCR6   0   0.258   5.5089   3.6737   2.4831
 XD2  H10  H  HCR6   0   0.257   4.1038   2.0486  -1.9619
 XD2  H11  H  HCR6   0   0.256   6.1252   1.4098   1.7651
 XD2  H12  H  H      0   0.221   1.6198  -3.7989   0.0627
 XD2  H14  H  HCH2   0   0.319  -4.0455  -1.5130  -0.2502
 XD2  H15  H  HCH2   0   0.288  -3.6662  -0.6000  -1.7314
 XD2  H16  H  HCH2   0   0.287  -0.9681   0.6777  -1.4295
 XD2  H17  H  HCH2   0   0.288  -1.5785  -0.5130  -2.5613
 XD2  H18  H  HNH1   0   0.402   3.0496  -0.3164  -1.1231
 XD2  H20  H  HCH1   0   0.279   5.3292   0.0670  -1.6552
 XD2  H21  H  HCH1   0   0.325   2.4274  -1.7747   1.3545
 XD2  H22  H  HCH1   0   0.302   0.8869  -0.0692   0.3418
 XD2  H5   H  HNH1   0   0.388   0.1229  -2.1375   1.6883
 XD2  SAT  S  S2     0   0.068  -3.7522   0.8362   0.1911
 XD2  CAV  C  C      0   0.401  -2.2395  -2.3128   1.7033
 XD2  H7   H  HCR6   0   0.258   4.1792   5.1392   0.9940
 XD2  OAD  O  O      0  -0.355   3.2695  -3.4513  -1.0420
 XD2  H8   H  HCR6   0   0.259   3.4778   4.3132  -1.2313

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
 XD2  CAG  CAH  aromatic  1.388  0.020  1.388
 XD2  CAG  CAI  aromatic  1.390  0.020  1.390
 XD2  CAH  CAJ  aromatic  1.389  0.020  1.389
 XD2  CAI  CAK  aromatic  1.387  0.020  1.387
 XD2  CAJ  CAZ  aromatic  1.390  0.020  1.390
 XD2  CAK  CAZ  aromatic  1.393  0.020  1.393
 XD2  CAZ  CBB  single    1.515  0.020  1.515
 XD2  CAA  NBE  single    1.444  0.020  1.444
 XD2  OAF  CBB  single    1.394  0.020  1.394
 XD2  CBB  CAW  single    1.532  0.020  1.532
 XD2  SAT  CAM  single    1.842  0.020  1.842
 XD2  SAT  CBA  single    1.728  0.020  1.728
 XD2  CAM  CAX  single    1.495  0.020  1.495
 XD2  NBE  CBA  aromatic  1.337  0.020  1.337
 XD2  NBE  NAQ  aromatic  1.330  0.020  1.330
 XD2  CBA  NAP  aromatic  1.315  0.020  1.315
 XD2  CAN  CAX  single    1.507  0.020  1.507
 XD2  CAN  SAU  single    1.808  0.020  1.808
 XD2  CAW  NAR  single    1.339  0.020  1.339
 XD2  CAW  OAC  double    1.220  0.020  1.220
 XD2  CAX  CAY  double    1.352  0.020  1.352
 XD2  NAQ  NAO  aromatic  1.270  0.020  1.270
 XD2  NAR  CBC  single    1.434  0.020  1.434
 XD2  OAE  CAV  deloc     1.247  0.020  1.247
 XD2  NAP  NAO  aromatic  1.335  0.020  1.335
 XD2  CAY  CAV  single    1.543  0.020  1.543
 XD2  CAY  NAS  single    1.376  0.020  1.376
 XD2  CAV  OAB  deloc     1.239  0.020  1.239
 XD2  SAU  CBD  single    1.825  0.020  1.825
 XD2  OAD  CAL  double    1.201  0.020  1.201
 XD2  CBC  CBD  single    1.530  0.020  1.530
 XD2  CBC  CAL  single    1.520  0.020  1.520
 XD2  NAS  CBD  single    1.424  0.020  1.424
 XD2  CAA  H1   single    0.970  0.020  1.090
 XD2  CAA  H2   single    0.970  0.020  1.090
 XD2  CAA  H3   single    0.970  0.020  1.090
 XD2  OAF  H6   single    0.850  0.020  0.980
 XD2  CAG  H7   single    0.930  0.020  1.080
 XD2  CAH  H8   single    0.930  0.020  1.080
 XD2  CAI  H9   single    0.930  0.020  1.080
 XD2  CAJ  H10  single    0.930  0.020  1.080
 XD2  CAK  H11  single    0.930  0.020  1.080
 XD2  CAL  H12  single    0.930  0.020  1.080
 XD2  CAM  H14  single    0.970  0.020  1.090
 XD2  CAM  H15  single    0.970  0.020  1.090
 XD2  CAN  H16  single    0.970  0.020  1.090
 XD2  CAN  H17  single    0.970  0.020  1.090
 XD2  NAR  H18  single    0.860  0.020  1.020
 XD2  CBB  H20  single    0.970  0.020  1.090
 XD2  CBC  H21  single    0.970  0.020  1.090
 XD2  CBD  H22  single    0.970  0.020  1.090
 XD2  NAS  H5   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
 XD2  H3   CAA  H2   109.32  3.000
 XD2  H3   CAA  H1   109.59  3.000
 XD2  H2   CAA  H1   109.28  3.000
 XD2  H3   CAA  NBE  110.17  3.000
 XD2  H2   CAA  NBE  108.36  3.000
 XD2  H1   CAA  NBE  110.10  3.000
 XD2  H6   OAF  CBB  107.42  3.000
 XD2  H7   CAG  CAI  120.21  3.000
 XD2  H7   CAG  CAH  120.12  3.000
 XD2  CAI  CAG  CAH  119.67  3.000
 XD2  H8   CAH  CAJ  119.78  3.000
 XD2  H8   CAH  CAG  120.21  3.000
 XD2  CAJ  CAH  CAG  120.01  3.000
 XD2  H9   CAI  CAK  119.67  3.000
 XD2  H9   CAI  CAG  120.06  3.000
 XD2  CAK  CAI  CAG  120.27  3.000
 XD2  H10  CAJ  CAZ  119.97  3.000
 XD2  H10  CAJ  CAH  119.48  3.000
 XD2  CAZ  CAJ  CAH  120.55  3.000
 XD2  H11  CAK  CAZ  120.38  3.000
 XD2  H11  CAK  CAI  119.35  3.000
 XD2  CAZ  CAK  CAI  120.27  3.000
 XD2  H12  CAL  CBC  114.55  3.000
 XD2  H12  CAL  OAD  122.09  3.000
 XD2  CBC  CAL  OAD  123.35  3.000
 XD2  H15  CAM  H14  110.16  3.000
 XD2  H15  CAM  CAX  111.24  3.000
 XD2  H14  CAM  CAX  113.34  3.000
 XD2  H15  CAM  SAT  107.20  3.000
 XD2  H14  CAM  SAT  108.03  3.000
 XD2  CAX  CAM  SAT  106.56  3.000
 XD2  H17  CAN  H16  106.58  3.000
 XD2  H17  CAN  CAX  110.13  3.000
 XD2  H16  CAN  CAX  112.09  3.000
 XD2  H17  CAN  SAU  105.42  3.000
 XD2  H16  CAN  SAU  108.81  3.000
 XD2  CAX  CAN  SAU  113.39  3.000
 XD2  NAQ  NAO  NAP  111.49  3.000
 XD2  CBA  NAP  NAO  105.72  3.000
 XD2  NBE  NAQ  NAO  106.85  3.000
 XD2  H18  NAR  CBC  117.53  3.000
 XD2  H18  NAR  CAW  118.82  3.000
 XD2  CBC  NAR  CAW  122.52  3.000
 XD2  H5   NAS  CBD  116.76  3.000
 XD2  H5   NAS  CAY  111.19  3.000
 XD2  CBD  NAS  CAY  121.66  3.000
 XD2  CBD  SAU  CAN   94.52  3.000
 XD2  CBB  CAW  NAR  115.80  3.000
 XD2  NAR  CAW  OAC  124.02  3.000
 XD2  CBB  CAW  OAC  120.12  3.000
 XD2  CAY  CAX  CAN  122.99  3.000
 XD2  CAY  CAX  CAM  123.62  3.000
 XD2  CAN  CAX  CAM  113.23  3.000
 XD2  CAX  CAY  CAV  125.83  3.000
 XD2  CAV  CAY  NAS  110.59  3.000
 XD2  CAX  CAY  NAS  123.58  3.000
 XD2  CBB  CAZ  CAK  120.18  3.000
 XD2  CBB  CAZ  CAJ  120.58  3.000
 XD2  CAK  CAZ  CAJ  119.23  3.000
 XD2  NBE  CBA  SAT  123.33  3.000
 XD2  NBE  CBA  NAP  107.94  3.000
 XD2  SAT  CBA  NAP  128.73  3.000
 XD2  H20  CBB  CAZ  108.69  3.000
 XD2  H20  CBB  CAW  108.62  3.000
 XD2  CAZ  CBB  CAW  108.29  3.000
 XD2  H20  CBB  OAF  109.07  3.000
 XD2  CAW  CBB  OAF  109.48  3.000
 XD2  CAZ  CBB  OAF  112.60  3.000
 XD2  H21  CBC  CBD  107.08  3.000
 XD2  H21  CBC  NAR  109.44  3.000
 XD2  CBD  CBC  NAR  110.15  3.000
 XD2  H21  CBC  CAL  106.79  3.000
 XD2  CBD  CBC  CAL  110.85  3.000
 XD2  NAR  CBC  CAL  112.33  3.000
 XD2  H22  CBD  CBC  108.63  3.000
 XD2  H22  CBD  SAU  107.26  3.000
 XD2  CBC  CBD  SAU  108.88  3.000
 XD2  H22  CBD  NAS  112.51  3.000
 XD2  CBC  CBD  NAS  110.40  3.000
 XD2  SAU  CBD  NAS  109.04  3.000
 XD2  CBA  NBE  NAQ  108.00  3.000
 XD2  NAQ  NBE  CAA  122.93  3.000
 XD2  CBA  NBE  CAA  129.07  3.000
 XD2  CBA  SAT  CAM  101.28  3.000
 XD2  CAY  CAV  OAE  114.15  3.000
 XD2  CAY  CAV  OAB  118.87  3.000
 XD2  OAE  CAV  OAB  126.98  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
 XD2  CONST_01  CAZ  CAJ  CAH  CAG     0.00   0.0  0
 XD2  CONST_02  CAZ  CAK  CAI  CAG     0.00   0.0  0
 XD2  CONST_03  CAK  CAI  CAG  CAH     0.00   0.0  0
 XD2  CONST_04  CAK  CAZ  CAJ  CAH     0.00   0.0  0
 XD2  CONST_05  CAJ  CAH  CAG  CAI     0.00   0.0  0
 XD2  CONST_06  CAJ  CAZ  CAK  CAI     0.00   0.0  0
 XD2  CONST_07  CBA  NBE  NAQ  NAO     0.00   0.0  0
 XD2  CONST_08  NBE  CBA  NAP  NAO     0.00   0.0  0
 XD2  CONST_09  NAQ  NBE  CBA  NAP     0.00   0.0  0
 XD2  CONST_10  NBE  NAQ  NAO  NAP     0.00   0.0  0
 XD2  CONST_11  CBA  NAP  NAO  NAQ     0.00   0.0  0
 XD2  CONST_12  NAP  CBA  NBE  CAA   180.00   0.0  0
 XD2  CONST_13  NAO  NAQ  NBE  CAA   180.00   0.0  0
 XD2  CONST_14  CBB  CAZ  CAJ  CAH   180.00   0.0  0
 XD2  CONST_15  CBB  CAZ  CAK  CAI   180.00   0.0  0
 XD2  CONST_16  SAT  CBA  NAP  NAO   180.00   0.0  0
 XD2  CONST_17  SAT  CBA  NBE  NAQ   180.00   0.0  0
 XD2  CONST_18  H10  CAJ  CAH  CAG   180.00   0.0  0
 XD2  CONST_19  H11  CAK  CAI  CAG   180.00   0.0  0
 XD2  CONST_20  H9   CAI  CAG  CAH   180.00   0.0  0
 XD2  CONST_21  H8   CAH  CAG  CAI   180.00   0.0  0
 XD2  CONST_22  H7   CAG  CAH  CAJ   180.00   0.0  0
 XD2  CONST_23  CBC  NAR  CAW  OAC     0.00   0.0  0
 XD2  CONST_24  CBC  NAR  CAW  CBB   180.00   0.0  0
 XD2  CONST_25  H18  NAR  CAW  OAC   180.00   0.0  0
 XD2  Var_01    NAS  CAY  CAX  CAN    -2.41  30.0  1
 XD2  Var_02    CAY  CAX  CAN  SAU    24.97  30.0  1
 XD2  Var_03    CBD  NAS  CAY  CAX    18.21  30.0  1
 XD2  Var_04    CAX  CAY  CAV  OAB    20.21  30.0  2
 XD2  Var_05    NBE  CBA  SAT  CAM  -179.01  30.0  2
 XD2  Var_06    SAT  CAM  CAX  CAN   -88.11  30.0  1
 XD2  Var_07    H1   CAA  NBE  NAQ  -120.61  30.0  2

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
 XD2  chir_01  CBB  CAZ  OAF  CAW  negativ
 XD2  chir_02  CBC  NAR  CBD  CAL  negativ
 XD2  chir_03  CBD  SAU  NAS  CBC  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
 XD2  plan-1  CAA  0.020
 XD2  plan-1  NAO  0.020
 XD2  plan-1  NAP  0.020
 XD2  plan-1  NAQ  0.020
 XD2  plan-1  CBA  0.020
 XD2  plan-1  NBE  0.020
 XD2  plan-1  SAT  0.020
 XD2  plan-2  CAG  0.020
 XD2  plan-2  CAH  0.020
 XD2  plan-2  CAI  0.020
 XD2  plan-2  CAJ  0.020
 XD2  plan-2  CAK  0.020
 XD2  plan-2  CAZ  0.020
 XD2  plan-2  CBB  0.020
 XD2  plan-2  H9   0.020
 XD2  plan-2  H10  0.020
 XD2  plan-2  H11  0.020
 XD2  plan-2  H7   0.020
 XD2  plan-2  H8   0.020
 XD2  plan-3  OAC  0.020
 XD2  plan-3  NAR  0.020
 XD2  plan-3  CAW  0.020
 XD2  plan-3  CBB  0.020
 XD2  plan-3  CBC  0.020
 XD2  plan-3  H18  0.020
 XD2  plan-4  NAS  0.020
 XD2  plan-4  CAY  0.020
 XD2  plan-4  CBD  0.020
 XD2  plan-4  H5   0.020
 XD2  plan-5  OAB  0.020
 XD2  plan-5  OAE  0.020
 XD2  plan-5  CAY  0.020
 XD2  plan-5  CAV  0.020
 XD2  plan-6  CAL  0.020
 XD2  plan-6  CBC  0.020
 XD2  plan-6  H12  0.020
 XD2  plan-6  OAD  0.020

