# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 22:57:40 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: benzyl (2R)-2-{[4-(3-oxopropyl)phenyl]carbamoyl}pyrrolidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CCCc1ccc(NC(=O)[C@H]2CCCN2C(=O)OCc3ccccc3)cc1
#
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
 M8A  M8A  'benzyl (2R)-2-{[4-(3-oxopropyl)phenyl]carbamoyl}pyrrolidine-1-carboxylate'  ligand  52  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M8A
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
 M8A  OAA   O  O     0  -0.379  -9.6294   1.5222  -1.3642
 M8A  CAD   C  C1    0   0.186  -8.9727   1.2794  -0.3820
 M8A  CAN   C  CH2   0  -0.542  -7.6040   0.6739  -0.3866
 M8A  CAP   C  CH2   0  -0.529  -6.6276   1.4849   0.4765
 M8A  CAX   C  CR6   0   0.123  -5.2696   0.8443   0.5193
 M8A  CAK   C  CR16  0  -0.300  -4.2565   1.2502  -0.3401
 M8A  CAM   C  CR16  0  -0.302  -3.0081   0.6421  -0.3521
 M8A  CAJ   C  CR16  0  -0.291  -4.9933  -0.2075   1.3898
 M8A  CAL   C  CR16  0  -0.336  -3.7572  -0.8275   1.3927
 M8A  CAZ   C  CR6   0   0.358  -2.7482  -0.4154   0.5188
 M8A  NAT   N  NH1   0  -0.743  -1.5362  -1.1125   0.5787
 M8A  C     C  C     0   0.542  -0.4046  -0.9276  -0.1390
 M8A  O     O  O     0  -0.460  -0.2322  -0.0416  -0.9533
 M8A  CA    C  CH1   0  -0.177   0.6414  -2.0106   0.0997
 M8A  CB    C  CH2   0  -0.475   0.5151  -3.1129  -0.9670
 M8A  CG    C  CH2   0  -0.476   1.9578  -3.5415  -1.2121
 M8A  CD    C  CH2   0  -0.262   2.7330  -2.2353  -1.1102
 M8A  N     N  NT    0  -0.513   1.9801  -1.5054  -0.0979
 M8A  CAW   C  C     0   0.776   2.4135  -0.4561   0.6188
 M8A  OAC   O  O     0  -0.528   1.7694   0.0758   1.5040
 M8A  OAU   O  O2    0  -0.475   3.6336  -0.0680   0.2441
 M8A  CAS   C  CH2   0  -0.238   4.2250   1.0201   0.9654
 M8A  CAY   C  CR6   0   0.074   5.5493   1.2943   0.3203
 M8A  CAH   C  CR16  0  -0.294   5.6670   2.2697  -0.6649
 M8A  CAF   C  CR16  0  -0.242   6.8875   2.5031  -1.2848
 M8A  CAE   C  CR16  0  -0.261   8.0025   1.7578  -0.9256
 M8A  CAG   C  CR16  0  -0.243   7.8934   0.7815   0.0572
 M8A  CAI   C  CR16  0  -0.285   6.6725   0.5523   0.6755
 M8A  HAN1  H  HCH2  0   0.273  -7.7014  -0.3324   0.0374
 M8A  HAN2  H  HCH2  0   0.261  -7.2384   0.5706  -1.4093
 M8A  HAD   H  H     0   0.184  -9.3707   1.4951   0.6273
 M8A  HAP1  H  HCH2  0   0.260  -6.5430   2.4973   0.0762
 M8A  HAP2  H  HCH2  0   0.256  -7.0309   1.5787   1.4881
 M8A  HAK   H  HCR6  0   0.251  -4.4351   2.0705  -1.0257
 M8A  HAJ   H  HCR6  0   0.252  -5.7538  -0.5528   2.0805
 M8A  HAM   H  HCR6  0   0.279  -2.2564   0.9989  -1.0361
 M8A  HAL   H  HCR6  0   0.269  -3.5734  -1.6441   2.0816
 M8A  HAT   H  HNH1  0   0.417  -1.5171  -1.8696   1.2455
 M8A  HA    H  HCH1  0   0.282   0.5321  -2.4355   1.1036
 M8A  HB1C  H  HCH2  0   0.269  -0.1281  -3.9247  -0.6319
 M8A  HB2C  H  HCH2  0   0.255   0.0887  -2.7044  -1.8860
 M8A  HG1C  H  HCH2  0   0.246   2.2865  -4.2344  -0.4353
 M8A  HG2C  H  HCH2  0   0.258   2.0930  -4.0288  -2.1765
 M8A  HD1C  H  HCH2  0   0.257   3.7664  -2.3877  -0.8036
 M8A  HD2C  H  HCH2  0   0.240   2.7356  -1.6969  -2.0624
 M8A  HAS1  H  HCH2  0   0.249   3.5798   1.8993   0.9176
 M8A  HAS2  H  HCH2  0   0.248   4.3514   0.7465   2.0152
 M8A  HAH   H  HCR6  0   0.255   4.8006   2.8565  -0.9471
 M8A  HAI   H  HCR6  0   0.255   6.5931  -0.2066   1.4447
 M8A  HAF   H  HCR6  0   0.259   6.9663   3.2666  -2.0476
 M8A  HAE   H  HCR6  0   0.259   8.9548   1.9382  -1.4074
 M8A  HAG   H  HCR6  0   0.258   8.7601   0.1993   0.3425

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
 M8A  OAA  CAD   double    1.206  0.020  1.206
 M8A  CAD  CAN   single    1.497  0.020  1.497
 M8A  CAN  CAP   single    1.535  0.020  1.535
 M8A  CAP  CAX   single    1.502  0.020  1.502
 M8A  CAX  CAK   aromatic  1.389  0.020  1.389
 M8A  CAX  CAJ   aromatic  1.393  0.020  1.393
 M8A  CAK  CAM   aromatic  1.389  0.020  1.389
 M8A  CAM  CAZ   aromatic  1.394  0.020  1.394
 M8A  CAJ  CAL   aromatic  1.383  0.020  1.383
 M8A  CAL  CAZ   aromatic  1.397  0.020  1.397
 M8A  CAZ  NAT   single    1.399  0.020  1.399
 M8A  NAT  C     single    1.353  0.020  1.353
 M8A  C    O     double    1.216  0.020  1.216
 M8A  C    CA    single    1.524  0.020  1.524
 M8A  CA   CB    single    1.539  0.020  1.539
 M8A  CA   N     single    1.444  0.020  1.444
 M8A  CB   CG    single    1.525  0.020  1.525
 M8A  CG   CD    single    1.522  0.020  1.522
 M8A  CD   N     single    1.458  0.020  1.458
 M8A  N    CAW   single    1.343  0.020  1.343
 M8A  CAW  OAC   double    1.217  0.020  1.217
 M8A  CAW  OAU   single    1.334  0.020  1.334
 M8A  OAU  CAS   single    1.433  0.020  1.433
 M8A  CAS  CAY   single    1.498  0.020  1.498
 M8A  CAY  CAH   aromatic  1.391  0.020  1.391
 M8A  CAY  CAI   aromatic  1.392  0.020  1.392
 M8A  CAH  CAF   aromatic  1.389  0.020  1.389
 M8A  CAF  CAE   aromatic  1.388  0.020  1.388
 M8A  CAE  CAG   aromatic  1.390  0.020  1.390
 M8A  CAG  CAI   aromatic  1.388  0.020  1.388
 M8A  CAN  HAN1  single    0.970  0.020  1.090
 M8A  CAN  HAN2  single    0.970  0.020  1.090
 M8A  CAD  HAD   single    0.930  0.020  1.080
 M8A  CAP  HAP1  single    0.970  0.020  1.090
 M8A  CAP  HAP2  single    0.970  0.020  1.090
 M8A  CAK  HAK   single    0.930  0.020  1.080
 M8A  CAJ  HAJ   single    0.930  0.020  1.080
 M8A  CAM  HAM   single    0.930  0.020  1.080
 M8A  CAL  HAL   single    0.930  0.020  1.080
 M8A  NAT  HAT   single    0.860  0.020  1.020
 M8A  CA   HA    single    0.970  0.020  1.090
 M8A  CB   HB1C  single    0.970  0.020  1.090
 M8A  CB   HB2C  single    0.970  0.020  1.090
 M8A  CG   HG1C  single    0.970  0.020  1.090
 M8A  CG   HG2C  single    0.970  0.020  1.090
 M8A  CD   HD1C  single    0.970  0.020  1.090
 M8A  CD   HD2C  single    0.970  0.020  1.090
 M8A  CAS  HAS1  single    0.970  0.020  1.090
 M8A  CAS  HAS2  single    0.970  0.020  1.090
 M8A  CAH  HAH   single    0.930  0.020  1.080
 M8A  CAI  HAI   single    0.930  0.020  1.080
 M8A  CAF  HAF   single    0.930  0.020  1.080
 M8A  CAE  HAE   single    0.930  0.020  1.080
 M8A  CAG  HAG   single    0.930  0.020  1.080

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
 M8A  HAD   CAD  CAN   114.25  3.000
 M8A  HAD   CAD  OAA   120.52  3.000
 M8A  CAN   CAD  OAA   125.23  3.000
 M8A  HAN2  CAN  HAN1  107.78  3.000
 M8A  HAN2  CAN  CAP   111.34  3.000
 M8A  HAN1  CAN  CAP   108.91  3.000
 M8A  HAN2  CAN  CAD   110.34  3.000
 M8A  HAN1  CAN  CAD   106.80  3.000
 M8A  CAP   CAN  CAD   111.49  3.000
 M8A  HAP2  CAP  HAP1  106.75  3.000
 M8A  HAP2  CAP  CAX   110.10  3.000
 M8A  HAP1  CAP  CAX   109.62  3.000
 M8A  HAP2  CAP  CAN   109.34  3.000
 M8A  HAP1  CAP  CAN   109.46  3.000
 M8A  CAX   CAP  CAN   111.46  3.000
 M8A  CAJ   CAX  CAK   117.56  3.000
 M8A  CAJ   CAX  CAP   121.27  3.000
 M8A  CAK   CAX  CAP   121.13  3.000
 M8A  HAK   CAK  CAM   118.30  3.000
 M8A  HAK   CAK  CAX   119.49  3.000
 M8A  CAM   CAK  CAX   122.21  3.000
 M8A  HAM   CAM  CAZ   121.17  3.000
 M8A  HAM   CAM  CAK   119.20  3.000
 M8A  CAZ   CAM  CAK   119.63  3.000
 M8A  HAJ   CAJ  CAL   118.88  3.000
 M8A  HAJ   CAJ  CAX   119.98  3.000
 M8A  CAL   CAJ  CAX   121.14  3.000
 M8A  HAL   CAL  CAZ   119.82  3.000
 M8A  HAL   CAL  CAJ   119.38  3.000
 M8A  CAZ   CAL  CAJ   120.80  3.000
 M8A  NAT   CAZ  CAL   116.86  3.000
 M8A  NAT   CAZ  CAM   124.47  3.000
 M8A  CAL   CAZ  CAM   118.67  3.000
 M8A  HAT   NAT  C     115.94  3.000
 M8A  HAT   NAT  CAZ   114.73  3.000
 M8A  C     NAT  CAZ   129.32  3.000
 M8A  CA    C    O     121.69  3.000
 M8A  CA    C    NAT   113.19  3.000
 M8A  O     C    NAT   125.01  3.000
 M8A  HA    CA   N     110.69  3.000
 M8A  HA    CA   CB    110.44  3.000
 M8A  N     CA   CB    103.40  3.000
 M8A  HA    CA   C     110.52  3.000
 M8A  N     CA   C     111.47  3.000
 M8A  CB    CA   C     110.12  3.000
 M8A  HB2C  CB   HB1C  107.89  3.000
 M8A  HB2C  CB   CG    109.83  3.000
 M8A  HB1C  CB   CG    113.51  3.000
 M8A  HB2C  CB   CA    110.32  3.000
 M8A  HB1C  CB   CA    111.66  3.000
 M8A  CG    CB   CA    103.60  3.000
 M8A  HG2C  CG   HG1C  107.99  3.000
 M8A  HG2C  CG   CD    112.33  3.000
 M8A  HG1C  CG   CD    110.10  3.000
 M8A  HG2C  CG   CB    112.68  3.000
 M8A  HG1C  CG   CB    110.42  3.000
 M8A  CD    CG   CB    103.29  3.000
 M8A  HD2C  CD   HD1C  108.17  3.000
 M8A  HD2C  CD   N     111.06  3.000
 M8A  HD1C  CD   N     111.39  3.000
 M8A  HD2C  CD   CG    111.43  3.000
 M8A  HD1C  CD   CG    112.47  3.000
 M8A  N     CD   CG    102.31  3.000
 M8A  CAW   N    CD    126.54  3.000
 M8A  CAW   N    CA    119.97  3.000
 M8A  CD    N    CA    113.49  3.000
 M8A  OAU   CAW  OAC   124.14  3.000
 M8A  OAU   CAW  N     111.88  3.000
 M8A  OAC   CAW  N     123.99  3.000
 M8A  CAS   OAU  CAW   117.18  3.000
 M8A  HAS2  CAS  HAS1  108.19  3.000
 M8A  HAS2  CAS  CAY   110.94  3.000
 M8A  HAS1  CAS  CAY   110.86  3.000
 M8A  HAS2  CAS  OAU   109.96  3.000
 M8A  HAS1  CAS  OAU   110.22  3.000
 M8A  CAY   CAS  OAU   106.68  3.000
 M8A  CAI   CAY  CAH   119.08  3.000
 M8A  CAI   CAY  CAS   120.37  3.000
 M8A  CAH   CAY  CAS   120.53  3.000
 M8A  HAH   CAH  CAF   119.69  3.000
 M8A  HAH   CAH  CAY   119.76  3.000
 M8A  CAF   CAH  CAY   120.55  3.000
 M8A  HAF   CAF  CAE   120.17  3.000
 M8A  HAF   CAF  CAH   119.82  3.000
 M8A  CAE   CAF  CAH   120.01  3.000
 M8A  HAE   CAE  CAG   120.07  3.000
 M8A  HAE   CAE  CAF   120.13  3.000
 M8A  CAG   CAE  CAF   119.80  3.000
 M8A  HAG   CAG  CAI   119.88  3.000
 M8A  HAG   CAG  CAE   120.10  3.000
 M8A  CAI   CAG  CAE   120.02  3.000
 M8A  HAI   CAI  CAG   119.77  3.000
 M8A  HAI   CAI  CAY   119.69  3.000
 M8A  CAG   CAI  CAY   120.54  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
 M8A  CONST_01  CAZ  CAM  CAK  CAX     0.00   0.0  0
 M8A  CONST_02  CAZ  CAL  CAJ  CAX     0.00   0.0  0
 M8A  CONST_03  CAL  CAJ  CAX  CAK     0.00   0.0  0
 M8A  CONST_04  CAL  CAZ  CAM  CAK     0.00   0.0  0
 M8A  CONST_05  CAJ  CAX  CAK  CAM     0.00   0.0  0
 M8A  CONST_06  CAJ  CAL  CAZ  CAM     0.00   0.0  0
 M8A  CONST_07  CAE  CAF  CAH  CAY     0.00   0.0  0
 M8A  CONST_08  CAE  CAG  CAI  CAY     0.00   0.0  0
 M8A  CONST_09  CAG  CAI  CAY  CAH     0.00   0.0  0
 M8A  CONST_10  CAG  CAE  CAF  CAH     0.00   0.0  0
 M8A  CONST_11  CAI  CAY  CAH  CAF     0.00   0.0  0
 M8A  CONST_12  CAI  CAG  CAE  CAF     0.00   0.0  0
 M8A  CONST_13  CAM  CAK  CAX  CAP   180.00   0.0  0
 M8A  CONST_14  CAL  CAJ  CAX  CAP   180.00   0.0  0
 M8A  CONST_15  NAT  CAZ  CAM  CAK   180.00   0.0  0
 M8A  CONST_16  NAT  CAZ  CAL  CAJ   180.00   0.0  0
 M8A  CONST_17  CAF  CAH  CAY  CAS   180.00   0.0  0
 M8A  CONST_18  CAG  CAI  CAY  CAS   180.00   0.0  0
 M8A  CONST_19  HAM  CAM  CAK  CAX   180.00   0.0  0
 M8A  CONST_20  HAL  CAL  CAJ  CAX   180.00   0.0  0
 M8A  CONST_21  HAJ  CAJ  CAX  CAK   180.00   0.0  0
 M8A  CONST_22  HAK  CAK  CAX  CAJ   180.00   0.0  0
 M8A  CONST_23  HAF  CAF  CAH  CAY   180.00   0.0  0
 M8A  CONST_24  HAG  CAG  CAI  CAY   180.00   0.0  0
 M8A  CONST_25  HAI  CAI  CAY  CAH   180.00   0.0  0
 M8A  CONST_26  HAE  CAE  CAF  CAH   180.00   0.0  0
 M8A  CONST_27  HAH  CAH  CAF  CAE   180.00   0.0  0
 M8A  CONST_28  CA   C    NAT  CAZ   180.00   0.0  0
 M8A  CONST_29  C    NAT  CAZ  CAM     0.00   0.0  0
 M8A  CONST_30  C    NAT  CAZ  CAL   180.00   0.0  0
 M8A  CONST_31  HAT  NAT  CAZ  CAM   180.00   0.0  0
 M8A  CONST_32  O    C    NAT  CAZ     0.00   0.0  0
 M8A  Var_01    CD   CG   CB   CA    -36.88  30.0  1
 M8A  Var_02    CG   CD   N    CA    -18.88  30.0  1
 M8A  Var_03    N    CD   CG   CB     33.81  30.0  1
 M8A  Var_04    CAK  CAX  CAP  CAN    95.85  30.0  2
 M8A  Var_05    OAC  CAW  N    CA      4.30  30.0  2
 M8A  Var_06    CAH  CAY  CAS  OAU    94.52  30.0  2
 M8A  Var_07    CAX  CAP  CAN  CAD   177.55  30.0  3
 M8A  Var_08    CAY  CAS  OAU  CAW  -177.66  30.0  3
 M8A  Var_09    CAP  CAN  CAD  OAA   129.80  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
 M8A  chir_01  CA  C  CB  N  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
 M8A  plan-1  CAP  0.020
 M8A  plan-1  CAX  0.020
 M8A  plan-1  CAK  0.020
 M8A  plan-1  CAM  0.020
 M8A  plan-1  CAJ  0.020
 M8A  plan-1  CAL  0.020
 M8A  plan-1  CAZ  0.020
 M8A  plan-1  NAT  0.020
 M8A  plan-1  HAK  0.020
 M8A  plan-1  HAJ  0.020
 M8A  plan-1  HAM  0.020
 M8A  plan-1  HAL  0.020
 M8A  plan-2  CAS  0.020
 M8A  plan-2  CAY  0.020
 M8A  plan-2  CAH  0.020
 M8A  plan-2  CAF  0.020
 M8A  plan-2  CAE  0.020
 M8A  plan-2  CAG  0.020
 M8A  plan-2  CAI  0.020
 M8A  plan-2  HAH  0.020
 M8A  plan-2  HAI  0.020
 M8A  plan-2  HAF  0.020
 M8A  plan-2  HAE  0.020
 M8A  plan-2  HAG  0.020
 M8A  plan-3  CAZ  0.020
 M8A  plan-3  NAT  0.020
 M8A  plan-3  C    0.020
 M8A  plan-3  O    0.020
 M8A  plan-3  CA   0.020
 M8A  plan-3  HAT  0.020
 M8A  plan-4  OAA  0.020
 M8A  plan-4  CAD  0.020
 M8A  plan-4  CAN  0.020
 M8A  plan-4  HAD  0.020
 M8A  plan-5  N    0.020
 M8A  plan-5  CAW  0.020
 M8A  plan-5  OAC  0.020
 M8A  plan-5  OAU  0.020

