# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 14:08:06 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@@H](C(O)=O)C(C)(C)S3
#
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
 NFF  NFF  '(2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  53  29  .  2021-08-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NFF
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
 NFF  C     C  C1    0   0.174  -1.0023   2.2988  -1.2555
 NFF  N     N  NH1   0  -0.609   0.3821   0.4139  -0.5261
 NFF  O     O  O     0  -0.342  -0.1786   3.0797  -0.8656
 NFF  CA    C  CH1   0  -0.198  -0.8399   0.7895  -1.1772
 NFF  CB    C  CH1   0  -0.240  -2.0261   0.1324  -0.4797
 NFF  CAA   C  CH3   0  -0.678   3.2688   4.6214   0.0013
 NFF  OAE   O  OH1   0  -0.588  -5.8789  -1.9587  -0.2189
 NFF  OAF   O  O     0  -0.461   1.6885   0.6491  -2.3528
 NFF  OAG   O  O     0  -0.426  -3.7838  -2.4991  -0.7652
 NFF  CAI   C  CR16  0  -0.268   3.5806  -4.0472   0.5551
 NFF  CAJ   C  CR16  0  -0.248   2.4577  -3.7124  -0.2305
 NFF  CAK   C  CR16  0  -0.384   4.6641   0.6524   0.9928
 NFF  CAL   C  CR16  0  -0.304   4.3885  -3.0573   1.0411
 NFF  CAM   C  CR16  0  -0.342   2.1660  -2.4070  -0.5168
 NFF  CAN   C  CR16  0  -0.300   4.9309  -0.6609   1.2617
 NFF  CAO   C  CH2   0  -0.192   3.9023   3.3435   0.4954
 NFF  NAQ   N  NH1   0  -0.549  -3.2438   0.1795  -1.2303
 NFF  SAS   S  S2    0   0.006  -2.3975   0.9667   1.1235
 NFF  CAT   C  C     0   0.565  -4.6104  -1.6733  -0.4764
 NFF  CAU   C  C     0   0.488   1.5669   0.4033  -1.1662
 NFF  CAV   C  CR6   0   0.404   3.5487   0.9954   0.1947
 NFF  CAW   C  CR6   0  -0.243   2.7239   0.0069  -0.2994
 NFF  CAX   C  CR66  0   0.077   4.1126  -1.6977   0.7654
 NFF  CAY   C  CR66  0   0.177   2.9861  -1.3573  -0.0296
 NFF  CBB   C  CH1   0  -0.208  -4.3484  -0.1817  -0.3692
 NFF  CBC   C  CT    0  -0.219  -4.1006   0.2719   1.1342
 NFF  H     H  H     0   0.206  -1.9329   2.6437  -1.7379
 NFF  HN    H  HNH1  0   0.412   0.3794   0.2855   0.4748
 NFF  HAA   H  HCH1  0   0.321  -0.8309   0.4154  -2.2073
 NFF  HB    H  HCH1  0   0.310  -1.7672  -0.9074  -0.2775
 NFF  HAAA  H  HCH3  0   0.234   3.3846   4.7299  -1.0771
 NFF  HAAB  H  HCH3  0   0.239   2.2063   4.6552   0.2394
 NFF  HAAC  H  HCH3  0   0.235   3.7528   5.4725   0.4789
 NFF  HOAE  H  HOH1  0   0.485  -6.0217  -2.9173  -0.2536
 NFF  HAI   H  HCR6  0   0.258   3.7980  -5.0852   0.7688
 NFF  HAJ   H  HCR6  0   0.261   1.8184  -4.4986  -0.6109
 NFF  HAK   H  HCR6  0   0.288   5.3154   1.4176   1.3919
 NFF  HAL   H  HCR6  0   0.257   5.2552  -3.3012   1.6438
 NFF  HAM   H  HCR6  0   0.252   1.2976  -2.1799  -1.1221
 NFF  HAN   H  HCR6  0   0.266   5.7908  -0.9153   1.8692
 NFF  HAO   H  HCH2  0   0.228   4.9663   3.3235   0.2406
 NFF  HAOA  H  HCH2  0   0.228   3.8188   3.2663   1.5842
 NFF  HNAQ  H  HNH1  0   0.376  -3.4142   1.1078  -1.5951
 NFF  HBB   H  HCH1  0   0.318  -5.2392   0.3325  -0.7339
 NFF  CAB   C  CH3   0  -0.640  -5.0806   1.3762   1.5119
 NFF  CAC   C  CH3   0  -0.648  -4.1620  -0.8577   2.1599
 NFF  OAR   O  O2    0  -0.456   3.2233   2.2558  -0.1232
 NFF  HAB   H  HCH3  0   0.248  -4.8500   1.7894   2.4944
 NFF  HABA  H  HCH3  0   0.245  -5.0643   2.1909   0.7880
 NFF  HABB  H  HCH3  0   0.244  -6.0950   0.9744   1.5524
 NFF  HAC   H  HCH3  0   0.243  -5.1599  -1.2954   2.2104
 NFF  HACA  H  HCH3  0   0.245  -3.4424  -1.6486   1.9464
 NFF  HACB  H  HCH3  0   0.256  -3.9319  -0.4665   3.1504

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
 NFF  O    C     double    1.200  0.020  1.200
 NFF  CA   C     single    1.520  0.020  1.520
 NFF  C    H     single    0.930  0.020  1.080
 NFF  CAU  N     single    1.347  0.020  1.347
 NFF  N    CA    single    1.435  0.020  1.435
 NFF  N    HN    single    0.860  0.020  1.020
 NFF  CA   CB    single    1.525  0.020  1.525
 NFF  CA   HAA   single    0.970  0.020  1.090
 NFF  SAS  CB    single    1.845  0.020  1.845
 NFF  CB   NAQ   single    1.431  0.020  1.431
 NFF  CB   HB    single    0.970  0.020  1.090
 NFF  CAO  CAA   single    1.509  0.020  1.509
 NFF  CAA  HAAA  single    0.970  0.020  1.090
 NFF  CAA  HAAB  single    0.970  0.020  1.090
 NFF  CAA  HAAC  single    0.970  0.020  1.090
 NFF  CAB  CBC   single    1.524  0.020  1.524
 NFF  CAB  HAB   single    0.970  0.020  1.090
 NFF  CAB  HABA  single    0.970  0.020  1.090
 NFF  CAB  HABB  single    0.970  0.020  1.090
 NFF  CBC  CAC   single    1.527  0.020  1.527
 NFF  CAC  HAC   single    0.970  0.020  1.090
 NFF  CAC  HACA  single    0.970  0.020  1.090
 NFF  CAC  HACB  single    0.970  0.020  1.090
 NFF  CAT  OAE   single    1.326  0.020  1.326
 NFF  OAE  HOAE  single    0.850  0.020  0.980
 NFF  CAU  OAF   double    1.218  0.020  1.218
 NFF  OAG  CAT   double    1.204  0.020  1.204
 NFF  CAL  CAI   aromatic  1.367  0.020  1.367
 NFF  CAI  CAJ   aromatic  1.411  0.020  1.411
 NFF  CAI  HAI   single    0.930  0.020  1.080
 NFF  CAJ  CAM   aromatic  1.368  0.020  1.368
 NFF  CAJ  HAJ   single    0.930  0.020  1.080
 NFF  CAN  CAK   aromatic  1.367  0.020  1.367
 NFF  CAK  CAV   aromatic  1.414  0.020  1.414
 NFF  CAK  HAK   single    0.930  0.020  1.080
 NFF  CAL  CAX   aromatic  1.414  0.020  1.414
 NFF  CAL  HAL   single    0.930  0.020  1.080
 NFF  CAY  CAM   aromatic  1.418  0.020  1.418
 NFF  CAM  HAM   single    0.930  0.020  1.080
 NFF  CAN  CAX   aromatic  1.411  0.020  1.411
 NFF  CAN  HAN   single    0.930  0.020  1.080
 NFF  CAO  OAR   single    1.424  0.020  1.424
 NFF  CAO  HAO   single    0.970  0.020  1.090
 NFF  CAO  HAOA  single    0.970  0.020  1.090
 NFF  CBB  NAQ   single    1.446  0.020  1.446
 NFF  NAQ  HNAQ  single    0.890  0.020  1.040
 NFF  CAV  OAR   single    1.340  0.020  1.340
 NFF  CBC  SAS   single    1.839  0.020  1.839
 NFF  CBB  CAT   single    1.518  0.020  1.518
 NFF  CAW  CAU   single    1.499  0.020  1.499
 NFF  CAV  CAW   aromatic  1.379  0.020  1.379
 NFF  CAY  CAW   aromatic  1.415  0.020  1.415
 NFF  CAX  CAY   aromatic  1.420  0.020  1.420
 NFF  CBC  CBB   single    1.590  0.020  1.590
 NFF  CBB  HBB   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
 NFF  H     C    CA    115.02  3.000
 NFF  H     C    O     121.16  3.000
 NFF  CA    C    O     123.78  3.000
 NFF  HN    N    CAU   118.22  3.000
 NFF  HN    N    CA    118.76  3.000
 NFF  CAU   N    CA    122.39  3.000
 NFF  HAA   CA   CB    106.81  3.000
 NFF  HAA   CA   N     109.28  3.000
 NFF  CB    CA   N     110.01  3.000
 NFF  HAA   CA   C     106.94  3.000
 NFF  CB    CA   C     111.61  3.000
 NFF  N     CA   C     111.99  3.000
 NFF  HB    CB   SAS   108.53  3.000
 NFF  HB    CB   NAQ   109.30  3.000
 NFF  SAS   CB   NAQ   105.64  3.000
 NFF  HB    CB   CA    108.12  3.000
 NFF  NAQ   CB   CA    114.07  3.000
 NFF  SAS   CB   CA    111.05  3.000
 NFF  HAAC  CAA  HAAB  108.25  3.000
 NFF  HAAC  CAA  HAAA  107.99  3.000
 NFF  HAAB  CAA  HAAA  108.47  3.000
 NFF  HAAC  CAA  CAO   109.35  3.000
 NFF  HAAB  CAA  CAO   111.35  3.000
 NFF  HAAA  CAA  CAO   111.32  3.000
 NFF  HOAE  OAE  CAT   110.29  3.000
 NFF  HAI   CAI  CAL   120.38  3.000
 NFF  HAI   CAI  CAJ   119.85  3.000
 NFF  CAL   CAI  CAJ   119.77  3.000
 NFF  HAJ   CAJ  CAM   119.59  3.000
 NFF  HAJ   CAJ  CAI   119.56  3.000
 NFF  CAM   CAJ  CAI   120.85  3.000
 NFF  HAK   CAK  CAV   120.79  3.000
 NFF  HAK   CAK  CAN   119.33  3.000
 NFF  CAV   CAK  CAN   119.88  3.000
 NFF  HAL   CAL  CAX   118.74  3.000
 NFF  HAL   CAL  CAI   120.50  3.000
 NFF  CAX   CAL  CAI   120.76  3.000
 NFF  HAM   CAM  CAY   120.04  3.000
 NFF  HAM   CAM  CAJ   119.22  3.000
 NFF  CAY   CAM  CAJ   120.74  3.000
 NFF  HAN   CAN  CAX   119.02  3.000
 NFF  HAN   CAN  CAK   119.40  3.000
 NFF  CAX   CAN  CAK   121.58  3.000
 NFF  HAOA  CAO  HAO   107.72  3.000
 NFF  HAOA  CAO  OAR   109.99  3.000
 NFF  HAO   CAO  OAR   110.40  3.000
 NFF  HAOA  CAO  CAA   110.69  3.000
 NFF  HAO   CAO  CAA   110.33  3.000
 NFF  OAR   CAO  CAA   107.72  3.000
 NFF  HNAQ  NAQ  CBB   108.37  3.000
 NFF  HNAQ  NAQ  CB    111.26  3.000
 NFF  CBB   NAQ  CB    109.23  3.000
 NFF  CBC   SAS  CB     91.18  3.000
 NFF  CBB   CAT  OAG   124.93  3.000
 NFF  CBB   CAT  OAE   111.28  3.000
 NFF  OAG   CAT  OAE   123.79  3.000
 NFF  CAW   CAU  OAF   122.67  3.000
 NFF  CAW   CAU  N     113.97  3.000
 NFF  OAF   CAU  N     123.32  3.000
 NFF  CAW   CAV  OAR   116.36  3.000
 NFF  CAW   CAV  CAK   120.02  3.000
 NFF  OAR   CAV  CAK   123.62  3.000
 NFF  CAY   CAW  CAV   120.79  3.000
 NFF  CAY   CAW  CAU   120.54  3.000
 NFF  CAV   CAW  CAU   118.64  3.000
 NFF  CAY   CAX  CAN   118.74  3.000
 NFF  CAY   CAX  CAL   119.62  3.000
 NFF  CAN   CAX  CAL   121.65  3.000
 NFF  CAX   CAY  CAW   119.00  3.000
 NFF  CAX   CAY  CAM   118.26  3.000
 NFF  CAW   CAY  CAM   122.74  3.000
 NFF  HBB   CBB  CBC   107.99  3.000
 NFF  HBB   CBB  CAT   107.36  3.000
 NFF  CBC   CBB  CAT   111.96  3.000
 NFF  HBB   CBB  NAQ   107.87  3.000
 NFF  CBC   CBB  NAQ   111.89  3.000
 NFF  CAT   CBB  NAQ   109.58  3.000
 NFF  CBB   CBC  SAS   104.28  3.000
 NFF  CBB   CBC  CAC   114.70  3.000
 NFF  SAS   CBC  CAC   108.70  3.000
 NFF  CBB   CBC  CAB   109.93  3.000
 NFF  SAS   CBC  CAB   108.85  3.000
 NFF  CAC   CBC  CAB   110.10  3.000
 NFF  HABB  CAB  HABA  108.28  3.000
 NFF  HABB  CAB  HAB   107.61  3.000
 NFF  HABA  CAB  HAB   108.18  3.000
 NFF  HABB  CAB  CBC   109.87  3.000
 NFF  HABA  CAB  CBC   111.55  3.000
 NFF  HAB   CAB  CBC   111.22  3.000
 NFF  HACB  CAC  HACA  107.40  3.000
 NFF  HACB  CAC  HAC   107.17  3.000
 NFF  HACA  CAC  HAC   108.77  3.000
 NFF  HACB  CAC  CBC   109.67  3.000
 NFF  HACA  CAC  CBC   112.24  3.000
 NFF  HAC   CAC  CBC   111.39  3.000
 NFF  CAV   OAR  CAO   119.98  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
 NFF  CONST_01  CAN   CAX  CAL  CAI   180.00   0.0  0
 NFF  CONST_02  CAY   CAX  CAL  CAI     0.00   0.0  0
 NFF  CONST_03  CAY   CAM  CAJ  CAI     0.00   0.0  0
 NFF  CONST_04  CAX   CAL  CAI  CAJ     0.00   0.0  0
 NFF  CONST_05  CAW   CAY  CAM  CAJ   180.00   0.0  0
 NFF  CONST_06  CAX   CAY  CAM  CAJ     0.00   0.0  0
 NFF  CONST_07  CAL   CAX  CAN  CAK   180.00   0.0  0
 NFF  CONST_08  CAY   CAX  CAN  CAK     0.00   0.0  0
 NFF  CONST_09  CAY   CAW  CAV  CAK     0.00   0.0  0
 NFF  CONST_10  CAM   CAJ  CAI  CAL     0.00   0.0  0
 NFF  CONST_11  CAM   CAY  CAX  CAL     0.00   0.0  0
 NFF  CONST_12  CAW   CAY  CAX  CAL   180.00   0.0  0
 NFF  CONST_13  CAV   CAW  CAY  CAM   180.00   0.0  0
 NFF  CONST_14  CAN   CAX  CAY  CAM   180.00   0.0  0
 NFF  CONST_15  CAW   CAV  CAK  CAN     0.00   0.0  0
 NFF  CONST_16  CAW   CAY  CAX  CAN     0.00   0.0  0
 NFF  CONST_17  CAX   CAN  CAK  CAV     0.00   0.0  0
 NFF  CONST_18  CAX   CAY  CAW  CAV     0.00   0.0  0
 NFF  CONST_19  CAU   CAW  CAV  CAK   180.00   0.0  0
 NFF  CONST_20  CAU   CAW  CAY  CAM     0.00   0.0  0
 NFF  CONST_21  OAR   CAV  CAK  CAN   180.00   0.0  0
 NFF  CONST_22  CAY   CAW  CAV  OAR   180.00   0.0  0
 NFF  CONST_23  CAX   CAY  CAW  CAU   180.00   0.0  0
 NFF  CONST_24  HAM   CAM  CAJ  CAI   180.00   0.0  0
 NFF  CONST_25  HAL   CAL  CAI  CAJ   180.00   0.0  0
 NFF  CONST_26  HAJ   CAJ  CAI  CAL   180.00   0.0  0
 NFF  CONST_27  HAN   CAN  CAX  CAL     0.00   0.0  0
 NFF  CONST_28  HAI   CAI  CAJ  CAM   180.00   0.0  0
 NFF  CONST_29  HAK   CAK  CAV  CAW   180.00   0.0  0
 NFF  CONST_30  CAW   CAU  N    CA    180.00   0.0  0
 NFF  CONST_31  HN    N    CAU  CAW     0.00   0.0  0
 NFF  CONST_32  HOAE  OAE  CAT  CBB   180.00   0.0  0
 NFF  CONST_33  OAF   CAU  N    CA      0.00   0.0  0
 NFF  Var_01    CBB   CBC  SAS  CB    -17.43  30.0  1
 NFF  Var_02    CAV   CAW  CAU  N    -101.19  30.0  2
 NFF  Var_03    CAW   CAV  OAR  CAO   171.09  30.0  1
 NFF  Var_04    HAB   CAB  CBC  SAS   -59.28  30.0  3
 NFF  Var_05    HAC   CAC  CBC  SAS   179.37  30.0  3
 NFF  Var_06    HAO   CAO  OAR  CAV    62.70  30.0  1
 NFF  Var_07    HAAA  CAA  CAO  OAR   -62.21  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
 NFF  chir_01  CA   C    N    CB   negativ
 NFF  chir_02  CB   SAS  NAQ  CA   negativ
 NFF  chir_03  CBB  NAQ  CAT  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
 NFF  plan-1  CAI   0.020
 NFF  plan-1  CAJ   0.020
 NFF  plan-1  CAK   0.020
 NFF  plan-1  CAL   0.020
 NFF  plan-1  CAM   0.020
 NFF  plan-1  CAN   0.020
 NFF  plan-1  CAU   0.020
 NFF  plan-1  CAV   0.020
 NFF  plan-1  CAW   0.020
 NFF  plan-1  CAX   0.020
 NFF  plan-1  CAY   0.020
 NFF  plan-1  HAI   0.020
 NFF  plan-1  HAJ   0.020
 NFF  plan-1  HAK   0.020
 NFF  plan-1  HAL   0.020
 NFF  plan-1  HAM   0.020
 NFF  plan-1  HAN   0.020
 NFF  plan-1  OAR   0.020
 NFF  plan-2  N     0.020
 NFF  plan-2  CA    0.020
 NFF  plan-2  OAF   0.020
 NFF  plan-2  CAU   0.020
 NFF  plan-2  CAW   0.020
 NFF  plan-2  HN    0.020
 NFF  plan-3  OAE   0.020
 NFF  plan-3  OAG   0.020
 NFF  plan-3  CAT   0.020
 NFF  plan-3  CBB   0.020
 NFF  plan-3  HOAE  0.020
 NFF  plan-4  C     0.020
 NFF  plan-4  O     0.020
 NFF  plan-4  CA    0.020
 NFF  plan-4  H     0.020

