# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 12 17:59:52 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](OC(=O)N1[C@H]2CS[C@H](CCCCC(O)=O)[C@H]2NC1=O)c3cc4OCOc4cc3[N+]([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
 NPK  NPK  '5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid'  ligand  55  33  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NPK
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
 NPK  N1    N  NR5    0  -0.601   0.1449   0.6285  -0.1798
 NPK  S1    S  S2     0   0.264   3.7578   2.1235   0.1217
 NPK  C2    C  CH1    0  -0.425   3.5939   0.3105   0.0229
 NPK  N2    N  NR15   0  -0.654   1.5553  -1.0378  -0.4604
 NPK  C3    C  CR5    0   0.650   0.3034  -0.7641  -0.0499
 NPK  O3    O  O      0  -0.501  -0.5185  -1.5563   0.3507
 NPK  C4    C  CR15   0  -0.068   2.3439   0.1001  -0.8440
 NPK  C5    C  CR15   0  -0.087   1.3612   1.2800  -0.6467
 NPK  C6    C  CH2    0  -0.630   1.9684   2.2687   0.3517
 NPK  C7    C  CH2    0  -0.451   4.8356  -0.3552  -0.5422
 NPK  C8    C  CH2    0  -0.495   6.0898  -0.1486   0.2967
 NPK  C9    C  CH2    0  -0.494   7.3007  -0.8786  -0.2723
 NPK  C10   C  CH2    0  -0.713   8.5595  -0.6550   0.5485
 NPK  C11   C  C      0   0.303   9.8279  -1.3695   0.0485
 NPK  O11   O  O      0  -0.778   9.7253  -2.1087  -0.9504
 NPK  O12   O  OC    -1  -0.556  10.8717  -1.1494   0.6996
 NPK  C30   C  C      0   0.841  -0.9980   1.3722  -0.0389
 NPK  O31   O  O      0  -0.421  -1.0034   2.5679  -0.2158
 NPK  O32   O  O2     0  -0.480  -2.0490   0.6462   0.2887
 NPK  C33   C  CH1    0  -0.061  -3.2970   1.3204   0.5164
 NPK  C34   C  CH3    0  -0.625  -3.3538   1.8145   1.9538
 NPK  C35   C  CR6    0   0.091  -4.3710   0.2866   0.2456
 NPK  C36   C  CR16   0  -0.367  -4.0905  -1.0412   0.6054
 NPK  C37   C  CR6    0   0.359  -5.0495  -1.9948   0.3867
 NPK  C38   C  CR6    0   0.326  -6.2733  -1.6949  -0.1950
 NPK  C39   C  CR16   0  -0.354  -6.5839  -0.4245  -0.5771
 NPK  C40   C  CR6    0   0.189  -5.6130   0.5619  -0.3299
 NPK  N40   N  N      1   0.315  -5.9896   1.9038  -0.7258
 NPK  O44   O  O2     0  -0.472  -4.9919  -3.3067   0.6578
 NPK  C45   C  CH2    0   0.077  -6.2542  -3.8643   0.2953
 NPK  O46   O  O2     0  -0.450  -7.0101  -2.8171  -0.3032
 NPK  O54   O  O      0  -0.318  -6.7682   2.0242  -1.6437
 NPK  O55   O  O     -1  -0.360  -5.5280   2.8425  -0.1150
 NPK  H2    H  HCH1   0   0.318   3.3965  -0.0655   1.0326
 NPK  HN2   H  HNR5   0   0.390   1.8966  -1.9851  -0.4846
 NPK  H4    H  HCR5   0   0.227   2.6492   0.0298  -1.8910
 NPK  H5    H  HCR5   0   0.259   1.1766   1.7820  -1.5958
 NPK  H6    H  HCH2   0   0.303   1.7036   1.9967   1.3755
 NPK  H6A   H  HCH2   0   0.321   1.6563   3.2938   0.1693
 NPK  H7    H  HCH2   0   0.217   4.6342  -1.4289  -0.6244
 NPK  H7A   H  HCH2   0   0.228   5.0035   0.0065  -1.5620
 NPK  H8    H  HCH2   0   0.335   6.3131   0.9216   0.3678
 NPK  H8A   H  HCH2   0   0.283   5.9017  -0.4865   1.3217
 NPK  H9    H  HCH2   0   0.197   7.0830  -1.9488  -0.3305
 NPK  H9A   H  HCH2   0   0.182   7.4653  -0.5497  -1.3027
 NPK  H10   H  HCH2   0   0.310   8.7733   0.4185   0.6113
 NPK  H10A  H  HCH2   0   0.342   8.3823  -0.9662   1.5852
 NPK  H33   H  HCH1   0   0.278  -3.3694   2.1554  -0.1760
 NPK  H34   H  HCH3   0   0.210  -3.1957   0.9915   2.6519
 NPK  H34A  H  HCH3   0   0.234  -2.5965   2.5768   2.1347
 NPK  H34B  H  HCH3   0   0.297  -4.3272   2.2529   2.1622
 NPK  H36   H  HCR6   0   0.210  -3.1331  -1.3139   1.0258
 NPK  H39   H  HCR6   0   0.320  -7.5344  -0.1851  -1.0307
 NPK  H45   H  HCH2   0   0.235  -6.1062  -4.6715  -0.4226
 NPK  H45A  H  HCH2   0   0.248  -6.7643  -4.2286   1.1895

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
 NPK  N1   C3    single    1.408  0.020  1.408
 NPK  N1   C5    single    1.457  0.020  1.457
 NPK  N1   C30   single    1.371  0.020  1.371
 NPK  S1   C2    single    1.823  0.020  1.823
 NPK  S1   C6    single    1.810  0.020  1.810
 NPK  C2   C4    single    1.536  0.020  1.536
 NPK  C2   C7    single    1.518  0.020  1.518
 NPK  N2   C3    single    1.346  0.020  1.346
 NPK  N2   C4    single    1.437  0.020  1.437
 NPK  C3   O3    double    1.210  0.020  1.210
 NPK  C4   C5    single    1.548  0.020  1.548
 NPK  C5   C6    single    1.531  0.020  1.531
 NPK  C7   C8    single    1.523  0.020  1.523
 NPK  C8   C9    single    1.524  0.020  1.524
 NPK  C9   C10   single    1.519  0.020  1.519
 NPK  C10  C11   single    1.539  0.020  1.539
 NPK  C11  O11   deloc     1.247  0.020  1.247
 NPK  C11  O12   deloc     1.250  0.020  1.250
 NPK  C30  O31   double    1.209  0.020  1.209
 NPK  C30  O32   single    1.319  0.020  1.319
 NPK  O32  C33   single    1.437  0.020  1.437
 NPK  C33  C34   single    1.521  0.020  1.521
 NPK  C33  C35   single    1.515  0.020  1.515
 NPK  C35  C36   aromatic  1.404  0.020  1.404
 NPK  C35  C40   aromatic  1.396  0.020  1.396
 NPK  C36  C37   aromatic  1.370  0.020  1.370
 NPK  C37  C38   aromatic  1.388  0.020  1.388
 NPK  C37  O44   single    1.341  0.020  1.341
 NPK  C38  C39   aromatic  1.362  0.020  1.362
 NPK  C38  O46   single    1.347  0.020  1.347
 NPK  C39  C40   aromatic  1.406  0.020  1.406
 NPK  C40  N40   single    1.449  0.020  1.449
 NPK  N40  O54   double    1.210  0.020  1.210
 NPK  N40  O55   single    1.211  0.020  1.211
 NPK  O44  C45   single    1.427  0.020  1.427
 NPK  C45  O46   single    1.423  0.020  1.423
 NPK  C2   H2    single    0.970  0.020  1.090
 NPK  N2   HN2   single    0.860  0.020  1.020
 NPK  C4   H4    single    0.970  0.020  1.090
 NPK  C5   H5    single    0.970  0.020  1.090
 NPK  C6   H6    single    0.970  0.020  1.090
 NPK  C6   H6A   single    0.970  0.020  1.090
 NPK  C7   H7    single    0.970  0.020  1.090
 NPK  C7   H7A   single    0.970  0.020  1.090
 NPK  C8   H8    single    0.970  0.020  1.090
 NPK  C8   H8A   single    0.970  0.020  1.090
 NPK  C9   H9    single    0.970  0.020  1.090
 NPK  C9   H9A   single    0.970  0.020  1.090
 NPK  C10  H10   single    0.970  0.020  1.090
 NPK  C10  H10A  single    0.970  0.020  1.090
 NPK  C33  H33   single    0.970  0.020  1.090
 NPK  C34  H34   single    0.970  0.020  1.090
 NPK  C34  H34A  single    0.970  0.020  1.090
 NPK  C34  H34B  single    0.970  0.020  1.090
 NPK  C36  H36   single    0.930  0.020  1.080
 NPK  C39  H39   single    0.930  0.020  1.080
 NPK  C45  H45   single    0.970  0.020  1.090
 NPK  C45  H45A  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
 NPK  C30   N1   C5    119.11  3.000
 NPK  C30   N1   C3    128.40  3.000
 NPK  C5    N1   C3    112.21  3.000
 NPK  C6    S1   C2     89.87  3.000
 NPK  H2    C2   C7    109.88  3.000
 NPK  H2    C2   C4    109.06  3.000
 NPK  C7    C2   C4    113.30  3.000
 NPK  H2    C2   S1    107.92  3.000
 NPK  C7    C2   S1    112.50  3.000
 NPK  C4    C2   S1    103.89  3.000
 NPK  HN2   N2   C4    123.55  3.000
 NPK  HN2   N2   C3    120.92  3.000
 NPK  C4    N2   C3    115.53  3.000
 NPK  O3    C3   N2    126.86  3.000
 NPK  O3    C3   N1    127.01  3.000
 NPK  N2    C3   N1    106.13  3.000
 NPK  H4    C4   C5    110.39  3.000
 NPK  H4    C4   N2    110.99  3.000
 NPK  C5    C4   N2    102.78  3.000
 NPK  H4    C4   C2    108.80  3.000
 NPK  C5    C4   C2    109.90  3.000
 NPK  N2    C4   C2    113.87  3.000
 NPK  H5    C5   C6    109.75  3.000
 NPK  H5    C5   C4    110.35  3.000
 NPK  C6    C5   C4    108.88  3.000
 NPK  H5    C5   N1    110.11  3.000
 NPK  C6    C5   N1    114.27  3.000
 NPK  C4    C5   N1    103.29  3.000
 NPK  H6A   C6   H6    108.82  3.000
 NPK  H6A   C6   C5    112.69  3.000
 NPK  H6    C6   C5    110.76  3.000
 NPK  H6A   C6   S1    109.76  3.000
 NPK  H6    C6   S1    109.81  3.000
 NPK  C5    C6   S1    104.92  3.000
 NPK  H7A   C7   H7    106.38  3.000
 NPK  H7A   C7   C8    109.99  3.000
 NPK  H7    C7   C8    109.01  3.000
 NPK  H7A   C7   C2    109.10  3.000
 NPK  H7    C7   C2    107.90  3.000
 NPK  C8    C7   C2    114.15  3.000
 NPK  H8A   C8   H8    106.00  3.000
 NPK  H8A   C8   C9    109.76  3.000
 NPK  H8    C8   C9    109.28  3.000
 NPK  H8A   C8   C7    109.40  3.000
 NPK  H8    C8   C7    109.64  3.000
 NPK  C9    C8   C7    112.56  3.000
 NPK  H9A   C9   H9    105.90  3.000
 NPK  H9A   C9   C10   109.87  3.000
 NPK  H9    C9   C10   109.74  3.000
 NPK  H9A   C9   C8    109.10  3.000
 NPK  H9    C9   C8    109.29  3.000
 NPK  C10   C9   C8    112.71  3.000
 NPK  H10A  C10  H10   104.78  3.000
 NPK  H10A  C10  C11   107.97  3.000
 NPK  H10   C10  C11   108.21  3.000
 NPK  H10A  C10  C9    109.57  3.000
 NPK  H10   C10  C9    109.67  3.000
 NPK  C11   C10  C9    116.03  3.000
 NPK  O12   C11  O11   126.19  3.000
 NPK  O12   C11  C10   115.92  3.000
 NPK  O11   C11  C10   117.88  3.000
 NPK  O32   C30  O31   125.27  3.000
 NPK  O32   C30  N1    113.04  3.000
 NPK  O31   C30  N1    121.69  3.000
 NPK  C33   O32  C30   118.25  3.000
 NPK  H33   C33  C35   111.28  3.000
 NPK  H33   C33  C34   110.48  3.000
 NPK  C35   C33  C34   111.35  3.000
 NPK  H33   C33  O32   108.50  3.000
 NPK  C35   C33  O32   105.50  3.000
 NPK  C34   C33  O32   109.56  3.000
 NPK  H34B  C34  H34A  107.95  3.000
 NPK  H34B  C34  H34   108.14  3.000
 NPK  H34A  C34  H34   108.72  3.000
 NPK  H34B  C34  C33   110.21  3.000
 NPK  H34A  C34  C33   110.99  3.000
 NPK  H34   C34  C33   110.75  3.000
 NPK  C40   C35  C36   118.02  3.000
 NPK  C40   C35  C33   124.73  3.000
 NPK  C36   C35  C33   117.24  3.000
 NPK  H36   C36  C37   120.44  3.000
 NPK  H36   C36  C35   121.02  3.000
 NPK  C37   C36  C35   118.52  3.000
 NPK  O44   C37  C38   109.52  3.000
 NPK  O44   C37  C36   128.22  3.000
 NPK  C38   C37  C36   122.26  3.000
 NPK  O46   C38  C39   129.02  3.000
 NPK  O46   C38  C37   109.64  3.000
 NPK  C39   C38  C37   121.34  3.000
 NPK  H39   C39  C40   121.74  3.000
 NPK  H39   C39  C38   121.68  3.000
 NPK  C40   C39  C38   116.58  3.000
 NPK  N40   C40  C39   114.98  3.000
 NPK  N40   C40  C35   121.77  3.000
 NPK  C39   C40  C35   123.26  3.000
 NPK  O55   N40  O54   123.42  3.000
 NPK  O55   N40  C40   118.74  3.000
 NPK  O54   N40  C40   117.83  3.000
 NPK  C45   O44  C37   107.04  3.000
 NPK  H45A  C45  H45   110.83  3.000
 NPK  H45A  C45  O46   109.98  3.000
 NPK  H45   C45  O46   109.87  3.000
 NPK  H45A  C45  O44   109.61  3.000
 NPK  H45   C45  O44   109.67  3.000
 NPK  O46   C45  O44   106.80  3.000
 NPK  C45   O46  C38   106.78  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
 NPK  CONST_01  C38  C37  C36  C35     0.00   0.0  0
 NPK  CONST_02  C38  C39  C40  C35     0.00   0.0  0
 NPK  CONST_03  C39  C40  C35  C36     0.00   0.0  0
 NPK  CONST_04  C39  C38  C37  C36     0.00   0.0  0
 NPK  CONST_05  C40  C35  C36  C37     0.00   0.0  0
 NPK  CONST_06  C40  C39  C38  C37     0.00   0.0  0
 NPK  CONST_07  C4   N2   C3   N1      0.00   0.0  0
 NPK  CONST_08  C5   N1   C3   N2      0.00   0.0  0
 NPK  CONST_09  C37  C36  C35  C33   180.00   0.0  0
 NPK  CONST_10  C39  C40  C35  C33   180.00   0.0  0
 NPK  CONST_11  N40  C40  C35  C36   180.00   0.0  0
 NPK  CONST_12  N40  C40  C39  C38   180.00   0.0  0
 NPK  CONST_13  C30  N1   C3   N2    180.00   0.0  0
 NPK  CONST_14  C5   N1   C3   O3    180.00   0.0  0
 NPK  CONST_15  C4   N2   C3   O3    180.00   0.0  0
 NPK  CONST_16  H39  C39  C40  C35   180.00   0.0  0
 NPK  CONST_17  H36  C36  C37  C38   180.00   0.0  0
 NPK  CONST_18  HN2  N2   C3   N1    180.00   0.0  0
 NPK  CONST_23  C30  N1   C3   O3      0.00   0.0  0
 NPK  Var_01    C5   C6   S1   C2    -42.47  30.0  1
 NPK  Var_02    O46  C45  O44  C37     4.60  30.0  1
 NPK  Var_03    O44  C45  O46  C38    -4.65  30.0  1
 NPK  Var_04    O31  C30  N1   C3   -177.86  30.0  2
 NPK  Var_05    C9   C8   C7   C2    177.65  30.0  3
 NPK  Var_06    C10  C9   C8   C7    178.99  30.0  3
 NPK  Var_07    C11  C10  C9   C8    179.45  30.0  3
 NPK  Var_08    O11  C11  C10  C9     -2.52  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
 NPK  chir_01  C2   S1   C4   C7   negativ
 NPK  chir_02  C4   N2   C5   C2   negativ
 NPK  chir_03  C5   N1   C4   C6   positiv
 NPK  chir_04  C33  O32  C34  C35  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
 NPK  plan-1  N1   0.020
 NPK  plan-1  C30  0.020
 NPK  plan-1  O31  0.020
 NPK  plan-1  O32  0.020
 NPK  plan-2  C33  0.020
 NPK  plan-2  C35  0.020
 NPK  plan-2  C36  0.020
 NPK  plan-2  C37  0.020
 NPK  plan-2  C38  0.020
 NPK  plan-2  C39  0.020
 NPK  plan-2  C40  0.020
 NPK  plan-2  N40  0.020
 NPK  plan-2  O44  0.020
 NPK  plan-2  O46  0.020
 NPK  plan-2  H36  0.020
 NPK  plan-2  H39  0.020
 NPK  plan-3  C40  0.020
 NPK  plan-3  N40  0.020
 NPK  plan-3  O54  0.020
 NPK  plan-3  O55  0.020
 NPK  plan-4  N1   0.020
 NPK  plan-4  N2   0.020
 NPK  plan-4  C3   0.020
 NPK  plan-4  O3   0.020
 NPK  plan-4  C4   0.020
 NPK  plan-4  C5   0.020
 NPK  plan-4  C30  0.020
 NPK  plan-4  HN2  0.020
 NPK  plan-5  C10  0.020
 NPK  plan-5  C11  0.020
 NPK  plan-5  O11  0.020
 NPK  plan-5  O12  0.020

