# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 14:50:58 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(C)=O)C(=O)N1C[C@H](O)C[C@H]1C(=O)NCc2ccc(cc2)c3scnc3C
#
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
 9B5  9B5  (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide  ligand  56  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9B5
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
 9B5  CAA  C  CH3   0  -0.776  -8.3888   2.0152  -0.2664
 9B5  CAT  C  C     0   0.526  -7.4218   1.0632  -0.9242
 9B5  OAD  O  O     0  -0.509  -7.7761   0.2812  -1.7975
 9B5  N    N  NH1   0  -0.628  -6.1598   1.1276  -0.4693
 9B5  CA   C  CH1   0  -0.204  -5.0931   0.3007  -0.9743
 9B5  CB   C  CH3   0  -0.650  -4.4069   0.9342  -2.1882
 9B5  C    C  C     0   0.573  -4.0718   0.1025   0.1383
 9B5  O    O  O     0  -0.498  -3.9780   0.9060   1.0587
 9B5  NBD  N  NT    0  -0.474  -3.2509  -0.9501   0.0389
 9B5  CAO  C  CH2   0  -0.309  -3.2698  -2.0188  -0.9483
 9B5  CBA  C  CH1   0   0.007  -2.5325  -3.1467  -0.2344
 9B5  OAG  O  OH1   0  -0.666  -3.3482  -3.7969   0.7105
 9B5  CAN  C  CH2   0  -0.501  -1.4571  -2.3846   0.5224
 9B5  CBC  C  CH1   0  -0.178  -2.1712  -1.1069   0.9937
 9B5  CAU  C  C     0   0.558  -1.2145   0.0752   0.9415
 9B5  OAE  O  O     0  -0.475  -0.9950   0.6845  -0.0907
 9B5  NAQ  N  NH1   0  -0.639  -0.5804   0.3274   2.0965
 9B5  CAM  C  CH2   0  -0.344   0.4965   1.2827   2.1824
 9B5  CAW  C  CR6   0   0.095   1.7523   0.8389   1.4719
 9B5  CAI  C  CR16  0  -0.271   2.1565  -0.4931   1.4791
 9B5  CAK  C  CR16  0  -0.294   3.3273  -0.8827   0.8509
 9B5  CAH  C  CR16  0  -0.289   2.5510   1.7685   0.8164
 9B5  CAJ  C  CR16  0  -0.291   3.7235   1.3844   0.1841
 9B5  CAY  C  CR6   0   0.079   4.1334   0.0512   0.1961
 9B5  CAZ  C  CR5   0  -0.309   5.3698  -0.3594  -0.4716
 9B5  SAS  S  S2    0   0.221   5.4136  -1.7608  -1.4793
 9B5  CAL  C  CR15  0  -0.224   7.0744  -1.4731  -1.7801
 9B5  NAP  N  N     0  -0.373   7.5600  -0.4309  -1.1901
 9B5  CAX  C  CR5   0   0.321   6.6130   0.2150  -0.4420
 9B5  CAB  C  CH3   0  -0.745   7.0074   1.4247   0.3377
 9B5  H1   H  HCH3  0   0.267  -9.1323   1.4447   0.2908
 9B5  H2   H  HCH3  0   0.248  -7.9115   2.7157   0.4163
 9B5  H3   H  HCH3  0   0.264  -8.9203   2.5816  -1.0301
 9B5  H4   H  HNH1  0   0.397  -5.9205   1.8070   0.2361
 9B5  H5   H  HCH1  0   0.275  -5.5251  -0.6566  -1.2697
 9B5  H6   H  HCH3  0   0.237  -3.9989   1.9117  -1.9312
 9B5  H7   H  HCH3  0   0.242  -3.5916   0.3152  -2.5613
 9B5  H8   H  HCH3  0   0.251  -5.1270   1.0607  -2.9951
 9B5  H9   H  HCH2  0   0.271  -4.2838  -2.3030  -1.2286
 9B5  H10  H  HCH2  0   0.253  -2.7345  -1.7314  -1.8580
 9B5  H11  H  HCH1  0   0.248  -2.1043  -3.8505  -0.9563
 9B5  H12  H  HOH1  0   0.455  -4.0610  -4.2457   0.2450
 9B5  H13  H  HCH2  0   0.277  -1.0334  -2.9532   1.3492
 9B5  H14  H  HCH2  0   0.265  -0.6462  -2.1428  -0.1678
 9B5  H15  H  HCH1  0   0.287  -2.5696  -1.2324   2.0050
 9B5  H16  H  HNH1  0   0.409  -0.8176  -0.2051   2.9170
 9B5  H17  H  HCH2  0   0.260   0.1736   2.2486   1.7890
 9B5  H18  H  HCH2  0   0.280   0.7075   1.4328   3.2420
 9B5  H19  H  HCR6  0   0.250   1.5563  -1.2416   1.9820
 9B5  H20  H  HCR6  0   0.255   3.6244  -1.9241   0.8843
 9B5  H21  H  HCR6  0   0.255   2.2481   2.8082   0.7827
 9B5  H22  H  HCR6  0   0.260   4.3065   2.1254  -0.3475
 9B5  H23  H  HCR5  0   0.301   7.6479  -2.1313  -2.4181
 9B5  H24  H  HCH3  0   0.254   7.0308   2.3158  -0.2926
 9B5  H25  H  HCH3  0   0.249   6.3172   1.6177   1.1565
 9B5  H26  H  HCH3  0   0.257   8.0054   1.2951   0.7552

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
 9B5  NAP  CAL  aromatic  1.292  0.020  1.292
 9B5  NAP  CAX  aromatic  1.369  0.020  1.369
 9B5  CAL  SAS  aromatic  1.712  0.020  1.712
 9B5  CAB  CAX  single    1.492  0.020  1.492
 9B5  CAX  CAZ  aromatic  1.370  0.020  1.370
 9B5  SAS  CAZ  aromatic  1.727  0.020  1.727
 9B5  CAZ  CAY  single    1.464  0.020  1.464
 9B5  CAY  CAK  aromatic  1.397  0.020  1.397
 9B5  CAY  CAJ  aromatic  1.395  0.020  1.395
 9B5  CAK  CAI  aromatic  1.385  0.020  1.385
 9B5  CAJ  CAH  aromatic  1.386  0.020  1.386
 9B5  CAI  CAW  aromatic  1.392  0.020  1.392
 9B5  CAH  CAW  aromatic  1.390  0.020  1.390
 9B5  CAW  CAM  single    1.510  0.020  1.510
 9B5  CAM  NAQ  single    1.442  0.020  1.442
 9B5  NAQ  CAU  single    1.341  0.020  1.341
 9B5  CAN  CBC  single    1.538  0.020  1.538
 9B5  CAN  CBA  single    1.520  0.020  1.520
 9B5  CAU  OAE  double    1.219  0.020  1.219
 9B5  CAU  CBC  single    1.522  0.020  1.522
 9B5  CBC  NBD  single    1.450  0.020  1.450
 9B5  CBA  OAG  single    1.408  0.020  1.408
 9B5  CBA  CAO  single    1.525  0.020  1.525
 9B5  NBD  CAO  single    1.455  0.020  1.455
 9B5  NBD  C    single    1.339  0.020  1.339
 9B5  O    C    double    1.225  0.020  1.225
 9B5  C    CA   single    1.523  0.020  1.523
 9B5  CA   CB   single    1.532  0.020  1.532
 9B5  CA   N    single    1.441  0.020  1.441
 9B5  N    CAT  single    1.343  0.020  1.343
 9B5  OAD  CAT  double    1.225  0.020  1.225
 9B5  CAT  CAA  single    1.508  0.020  1.508
 9B5  CAA  H1   single    0.970  0.020  1.090
 9B5  CAA  H2   single    0.970  0.020  1.090
 9B5  CAA  H3   single    0.970  0.020  1.090
 9B5  N    H4   single    0.860  0.020  1.020
 9B5  CA   H5   single    0.970  0.020  1.090
 9B5  CB   H6   single    0.970  0.020  1.090
 9B5  CB   H7   single    0.970  0.020  1.090
 9B5  CB   H8   single    0.970  0.020  1.090
 9B5  CAO  H9   single    0.970  0.020  1.090
 9B5  CAO  H10  single    0.970  0.020  1.090
 9B5  CBA  H11  single    0.970  0.020  1.090
 9B5  OAG  H12  single    0.850  0.020  0.980
 9B5  CAN  H13  single    0.970  0.020  1.090
 9B5  CAN  H14  single    0.970  0.020  1.090
 9B5  CBC  H15  single    0.970  0.020  1.090
 9B5  NAQ  H16  single    0.860  0.020  1.020
 9B5  CAM  H17  single    0.970  0.020  1.090
 9B5  CAM  H18  single    0.970  0.020  1.090
 9B5  CAI  H19  single    0.930  0.020  1.080
 9B5  CAK  H20  single    0.930  0.020  1.080
 9B5  CAH  H21  single    0.930  0.020  1.080
 9B5  CAJ  H22  single    0.930  0.020  1.080
 9B5  CAL  H23  single    0.930  0.020  1.080
 9B5  CAB  H24  single    0.970  0.020  1.090
 9B5  CAB  H25  single    0.970  0.020  1.090
 9B5  CAB  H26  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
 9B5  H3   CAA  H2   108.61  3.000
 9B5  H3   CAA  H1   107.32  3.000
 9B5  H2   CAA  H1   108.37  3.000
 9B5  H3   CAA  CAT  109.60  3.000
 9B5  H2   CAA  CAT  113.49  3.000
 9B5  H1   CAA  CAT  109.26  3.000
 9B5  N    CAT  OAD  122.96  3.000
 9B5  OAD  CAT  CAA  121.91  3.000
 9B5  N    CAT  CAA  115.12  3.000
 9B5  H4   N    CA   117.14  3.000
 9B5  H4   N    CAT  119.49  3.000
 9B5  CA   N    CAT  123.33  3.000
 9B5  H5   CA   C    110.43  3.000
 9B5  H5   CA   CB   109.01  3.000
 9B5  C    CA   CB   109.41  3.000
 9B5  H5   CA   N    107.78  3.000
 9B5  CB   CA   N    111.84  3.000
 9B5  C    CA   N    108.36  3.000
 9B5  H8   CB   H7   107.89  3.000
 9B5  H8   CB   H6   108.55  3.000
 9B5  H7   CB   H6   108.07  3.000
 9B5  H8   CB   CA   109.82  3.000
 9B5  H7   CB   CA   111.82  3.000
 9B5  H6   CB   CA   110.59  3.000
 9B5  NBD  C    O    121.63  3.000
 9B5  O    C    CA   120.98  3.000
 9B5  NBD  C    CA   117.34  3.000
 9B5  CBC  NBD  CAO  112.16  3.000
 9B5  CAO  NBD  C    128.31  3.000
 9B5  CBC  NBD  C    119.53  3.000
 9B5  H10  CAO  H9   108.05  3.000
 9B5  H10  CAO  CBA  110.30  3.000
 9B5  H9   CAO  CBA  112.18  3.000
 9B5  H10  CAO  NBD  111.40  3.000
 9B5  H9   CAO  NBD  112.22  3.000
 9B5  CBA  CAO  NBD  102.67  3.000
 9B5  H11  CBA  CAN  111.95  3.000
 9B5  H11  CBA  OAG  111.85  3.000
 9B5  CAN  CBA  OAG  107.90  3.000
 9B5  H11  CBA  CAO  110.84  3.000
 9B5  OAG  CBA  CAO  112.07  3.000
 9B5  CAN  CBA  CAO  101.79  3.000
 9B5  H12  OAG  CBA  108.66  3.000
 9B5  H14  CAN  H13  107.84  3.000
 9B5  H14  CAN  CBC  110.77  3.000
 9B5  H13  CAN  CBC  112.44  3.000
 9B5  H14  CAN  CBA  108.77  3.000
 9B5  H13  CAN  CBA  113.05  3.000
 9B5  CBC  CAN  CBA  103.93  3.000
 9B5  H15  CBC  CAU  110.47  3.000
 9B5  H15  CBC  CAN  110.92  3.000
 9B5  CAU  CBC  CAN  110.06  3.000
 9B5  H15  CBC  NBD  110.48  3.000
 9B5  CAU  CBC  NBD  111.20  3.000
 9B5  CAN  CBC  NBD  103.52  3.000
 9B5  NAQ  CAU  OAE  123.38  3.000
 9B5  OAE  CAU  CBC  122.06  3.000
 9B5  NAQ  CAU  CBC  114.44  3.000
 9B5  H16  NAQ  CAM  118.54  3.000
 9B5  H16  NAQ  CAU  119.41  3.000
 9B5  CAM  NAQ  CAU  121.92  3.000
 9B5  H18  CAM  H17  106.59  3.000
 9B5  H18  CAM  CAW  109.68  3.000
 9B5  H17  CAM  CAW  109.66  3.000
 9B5  H18  CAM  NAQ  107.07  3.000
 9B5  H17  CAM  NAQ  110.11  3.000
 9B5  CAW  CAM  NAQ  113.48  3.000
 9B5  CAH  CAW  CAI  118.40  3.000
 9B5  CAH  CAW  CAM  120.23  3.000
 9B5  CAI  CAW  CAM  121.36  3.000
 9B5  H19  CAI  CAK  119.00  3.000
 9B5  H19  CAI  CAW  120.18  3.000
 9B5  CAK  CAI  CAW  120.82  3.000
 9B5  H20  CAK  CAY  119.93  3.000
 9B5  H20  CAK  CAI  119.23  3.000
 9B5  CAY  CAK  CAI  120.83  3.000
 9B5  H21  CAH  CAJ  119.22  3.000
 9B5  H21  CAH  CAW  119.73  3.000
 9B5  CAJ  CAH  CAW  121.05  3.000
 9B5  H22  CAJ  CAY  120.02  3.000
 9B5  H22  CAJ  CAH  119.33  3.000
 9B5  CAY  CAJ  CAH  120.62  3.000
 9B5  CAZ  CAY  CAJ  120.82  3.000
 9B5  CAJ  CAY  CAK  118.27  3.000
 9B5  CAZ  CAY  CAK  120.91  3.000
 9B5  CAX  CAZ  SAS  109.26  3.000
 9B5  SAS  CAZ  CAY  121.01  3.000
 9B5  CAX  CAZ  CAY  129.73  3.000
 9B5  CAL  SAS  CAZ   89.47  3.000
 9B5  H23  CAL  NAP  124.13  3.000
 9B5  H23  CAL  SAS  121.05  3.000
 9B5  NAP  CAL  SAS  114.82  3.000
 9B5  CAX  NAP  CAL  111.72  3.000
 9B5  CAB  CAX  NAP  119.03  3.000
 9B5  CAB  CAX  CAZ  126.23  3.000
 9B5  NAP  CAX  CAZ  114.72  3.000
 9B5  H26  CAB  H25  108.29  3.000
 9B5  H26  CAB  H24  107.37  3.000
 9B5  H25  CAB  H24  107.65  3.000
 9B5  H26  CAB  CAX  110.23  3.000
 9B5  H25  CAB  CAX  111.68  3.000
 9B5  H24  CAB  CAX  111.45  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
 9B5  CONST_01  CAY  CAK  CAI  CAW     0.00   0.0  0
 9B5  CONST_02  CAY  CAJ  CAH  CAW     0.00   0.0  0
 9B5  CONST_03  CAZ  CAY  CAK  CAI   180.00   0.0  0
 9B5  CONST_04  CAJ  CAY  CAK  CAI     0.00   0.0  0
 9B5  CONST_05  CAJ  CAH  CAW  CAI     0.00   0.0  0
 9B5  CONST_08  CAH  CAJ  CAY  CAK     0.00   0.0  0
 9B5  CONST_09  CAH  CAW  CAI  CAK     0.00   0.0  0
 9B5  CONST_10  CAZ  CAY  CAJ  CAH   180.00   0.0  0
 9B5  CONST_13  NAP  CAX  CAZ  CAY   180.00   0.0  0
 9B5  CONST_14  CAL  SAS  CAZ  CAY   180.00   0.0  0
 9B5  CONST_15  CAL  NAP  CAX  CAZ     0.00   0.0  0
 9B5  CONST_16  NAP  CAL  SAS  CAZ     0.00   0.0  0
 9B5  CONST_17  CAX  NAP  CAL  SAS     0.00   0.0  0
 9B5  CONST_18  NAP  CAX  CAZ  SAS     0.00   0.0  0
 9B5  CONST_19  CAX  CAZ  SAS  CAL     0.00   0.0  0
 9B5  CONST_20  CAK  CAI  CAW  CAM   180.00   0.0  0
 9B5  CONST_21  CAJ  CAH  CAW  CAM   180.00   0.0  0
 9B5  CONST_22  CAB  CAX  CAZ  CAY     0.00   0.0  0
 9B5  CONST_23  CAB  CAX  CAZ  SAS   180.00   0.0  0
 9B5  CONST_24  CAB  CAX  NAP  CAL   180.00   0.0  0
 9B5  CONST_25  H20  CAK  CAI  CAW   180.00   0.0  0
 9B5  CONST_26  H22  CAJ  CAH  CAW   180.00   0.0  0
 9B5  CONST_27  H21  CAH  CAW  CAI   180.00   0.0  0
 9B5  CONST_28  H19  CAI  CAW  CAH   180.00   0.0  0
 9B5  CONST_29  H23  CAL  SAS  CAZ   180.00   0.0  0
 9B5  CONST_30  CBC  NBD  C    CA    180.00   0.0  0
 9B5  CONST_31  CAO  NBD  C    CA      0.00   0.0  0
 9B5  CONST_32  CBC  NBD  C    O       0.00   0.0  0
 9B5  CONST_33  CAO  NBD  C    O     180.00   0.0  0
 9B5  CONST_34  CAM  NAQ  CAU  CBC   180.00   0.0  0
 9B5  CONST_35  H16  NAQ  CAU  CBC     0.00   0.0  0
 9B5  CONST_36  CA   N    CAT  CAA   180.00   0.0  0
 9B5  CONST_37  CA   N    CAT  OAD     0.00   0.0  0
 9B5  CONST_38  CAM  NAQ  CAU  OAE     0.00   0.0  0
 9B5  CONST_39  H4   N    CAT  CAA     0.00   0.0  0
 9B5  Var_01    CBC  NBD  CAO  CBA    23.11  30.0  1
 9B5  Var_02    CAI  CAW  CAM  NAQ   -37.17  30.0  2
 9B5  Var_03    H24  CAB  CAX  CAZ  -100.22  30.0  2
 9B5  Var_04    CAW  CAM  NAQ  CAU   -69.08  30.0  2
 9B5  Var_05    H1   CAA  CAT  OAD    64.79  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
 9B5  chir_01  CA   C    CB   N    positiv
 9B5  chir_02  CBA  OAG  CAN  CAO  positiv
 9B5  chir_03  CBC  NBD  CAU  CAN  positiv

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
 9B5  plan-1  CAY  0.020
 9B5  plan-1  CAZ  0.020
 9B5  plan-1  SAS  0.020
 9B5  plan-1  CAL  0.020
 9B5  plan-1  NAP  0.020
 9B5  plan-1  CAX  0.020
 9B5  plan-1  CAB  0.020
 9B5  plan-1  H23  0.020
 9B5  plan-2  CAM  0.020
 9B5  plan-2  CAW  0.020
 9B5  plan-2  CAI  0.020
 9B5  plan-2  CAK  0.020
 9B5  plan-2  CAH  0.020
 9B5  plan-2  CAJ  0.020
 9B5  plan-2  CAY  0.020
 9B5  plan-2  CAZ  0.020
 9B5  plan-2  H19  0.020
 9B5  plan-2  H20  0.020
 9B5  plan-2  H21  0.020
 9B5  plan-2  H22  0.020
 9B5  plan-3  CA   0.020
 9B5  plan-3  C    0.020
 9B5  plan-3  O    0.020
 9B5  plan-3  NBD  0.020
 9B5  plan-3  CAO  0.020
 9B5  plan-3  CBC  0.020
 9B5  plan-4  CBC  0.020
 9B5  plan-4  CAU  0.020
 9B5  plan-4  OAE  0.020
 9B5  plan-4  NAQ  0.020
 9B5  plan-4  CAM  0.020
 9B5  plan-4  H16  0.020
 9B5  plan-5  CAA  0.020
 9B5  plan-5  CAT  0.020
 9B5  plan-5  OAD  0.020
 9B5  plan-5  N    0.020
 9B5  plan-5  CA   0.020
 9B5  plan-5  H4   0.020

