# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 04:34:05 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: N~2~-acetyl-N-benzyl-O-methyl-L-serinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H](NC(C)=O)C(=O)NCc1ccccc1
#
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
 AMJ  AMJ  N~2~-acetyl-N-benzyl-O-methyl-L-serinamide  ligand  36  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AMJ
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
 AMJ  C     C  C     0   0.558   0.7248   0.7970   0.6811
 AMJ  N     N  NH1   0  -0.627   3.0720   0.4203   0.2662
 AMJ  O     O  O     0  -0.484   0.9848   0.8908   1.8703
 AMJ  CA    C  CH1   0  -0.250   1.7719   0.3605  -0.3443
 AMJ  CB    C  CH2   0  -0.132   1.4239  -1.0354  -0.8548
 AMJ  CAA   C  CH3   0  -0.394   0.8984  -3.1892  -0.1221
 AMJ  CAB   C  CH3   0  -0.775   5.4656   0.6716   0.3835
 AMJ  OAC   O  O     0  -0.507   4.2154   0.6975  -1.6573
 AMJ  CAE   C  CR16  0  -0.266  -5.0639  -0.7325  -0.7480
 AMJ  CAF   C  CR16  0  -0.240  -3.9742  -1.4636  -0.2864
 AMJ  CAG   C  CR16  0  -0.241  -5.0518   0.6515  -0.6579
 AMJ  CAH   C  CR16  0  -0.284  -2.8831  -0.8096   0.2638
 AMJ  CAI   C  CR16  0  -0.304  -3.9543   1.3048  -0.1077
 AMJ  CAJ   C  CH2   0  -0.334  -1.6708   1.2738   0.9619
 AMJ  NAL   N  NH1   0  -0.629  -0.4884   1.0250   0.1631
 AMJ  OAN   O  O2    0  -0.482   1.2774  -1.8866   0.2466
 AMJ  CAO   C  C     0   0.527   4.2040   0.5915  -0.4376
 AMJ  CAQ   C  CR6   0   0.077  -2.8650   0.5813   0.3619
 AMJ  HN    H  HNH1  0   0.401   3.1162   0.3355   1.2696
 AMJ  HA    H  HCH1  0   0.299   1.7472   1.0387  -1.2020
 AMJ  HB    H  HCH2  0   0.211   0.4991  -0.9893  -1.4472
 AMJ  HBA   H  HCH2  0   0.232   2.2155  -1.3796  -1.5329
 AMJ  HAA   H  HCH3  0   0.205  -0.0706  -3.2024  -0.6354
 AMJ  HAAA  H  HCH3  0   0.209   1.6358  -3.6605  -0.7818
 AMJ  HAAB  H  HCH3  0   0.236   0.8162  -3.7849   0.7857
 AMJ  HAB   H  HCH3  0   0.264   6.2272   0.0246  -0.0492
 AMJ  HABA  H  HCH3  0   0.269   5.8485   1.6924   0.3513
 AMJ  HABB  H  HCH3  0   0.249   5.3224   0.3952   1.4263
 AMJ  HAF   H  HCR6  0   0.257  -3.9778  -2.5439  -0.3540
 AMJ  HAG   H  HCR6  0   0.257  -5.8953   1.2262  -1.0180
 AMJ  HAH   H  HCR6  0   0.251  -2.0357  -1.3823   0.6247
 AMJ  HAI   H  HCR6  0   0.254  -3.9493   2.3864  -0.0417
 AMJ  HAJ   H  HCH2  0   0.268  -1.4844   0.8900   1.9654
 AMJ  HAJA  H  HCH2  0   0.260  -1.8589   2.3459   1.0603
 AMJ  HNAL  H  HNH1  0   0.407  -0.6079   0.9833  -0.8372
 AMJ  HAE   H  HCR6  0   0.258  -5.9172  -1.2414  -1.1768

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
 AMJ  C    O     double    1.221  0.020  1.221
 AMJ  C    CA    single    1.529  0.020  1.529
 AMJ  C    NAL   single    1.339  0.020  1.339
 AMJ  N    CA    single    1.438  0.020  1.438
 AMJ  N    CAO   single    1.344  0.020  1.344
 AMJ  CA   CB    single    1.527  0.020  1.527
 AMJ  CB   OAN   single    1.400  0.020  1.400
 AMJ  CAA  OAN   single    1.406  0.020  1.406
 AMJ  CAB  CAO   single    1.507  0.020  1.507
 AMJ  OAC  CAO   double    1.224  0.020  1.224
 AMJ  CAE  CAF   aromatic  1.391  0.020  1.391
 AMJ  CAE  CAG   aromatic  1.387  0.020  1.387
 AMJ  CAF  CAH   aromatic  1.386  0.020  1.386
 AMJ  CAG  CAI   aromatic  1.391  0.020  1.391
 AMJ  CAH  CAQ   aromatic  1.395  0.020  1.395
 AMJ  CAI  CAQ   aromatic  1.389  0.020  1.389
 AMJ  CAJ  NAL   single    1.448  0.020  1.448
 AMJ  CAJ  CAQ   single    1.505  0.020  1.505
 AMJ  N    HN    single    0.860  0.020  1.020
 AMJ  CA   HA    single    0.970  0.020  1.090
 AMJ  CB   HB    single    0.970  0.020  1.090
 AMJ  CB   HBA   single    0.970  0.020  1.090
 AMJ  CAA  HAA   single    0.970  0.020  1.090
 AMJ  CAA  HAAA  single    0.970  0.020  1.090
 AMJ  CAA  HAAB  single    0.970  0.020  1.090
 AMJ  CAB  HAB   single    0.970  0.020  1.090
 AMJ  CAB  HABA  single    0.970  0.020  1.090
 AMJ  CAB  HABB  single    0.970  0.020  1.090
 AMJ  CAE  HAE   single    0.930  0.020  1.080
 AMJ  CAF  HAF   single    0.930  0.020  1.080
 AMJ  CAG  HAG   single    0.930  0.020  1.080
 AMJ  CAH  HAH   single    0.930  0.020  1.080
 AMJ  CAI  HAI   single    0.930  0.020  1.080
 AMJ  CAJ  HAJ   single    0.970  0.020  1.090
 AMJ  CAJ  HAJA  single    0.970  0.020  1.090
 AMJ  NAL  HNAL  single    0.860  0.020  1.020

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
 AMJ  NAL   C    CA    114.19  3.000
 AMJ  NAL   C    O     123.83  3.000
 AMJ  CA    C    O     121.95  3.000
 AMJ  HN    N    CAO   119.68  3.000
 AMJ  HN    N    CA    117.32  3.000
 AMJ  CAO   N    CA    123.00  3.000
 AMJ  HA    CA   CB    107.43  3.000
 AMJ  HA    CA   N     109.13  3.000
 AMJ  CB    CA   N     112.72  3.000
 AMJ  HA    CA   C     109.47  3.000
 AMJ  CB    CA   C     109.22  3.000
 AMJ  N     CA   C     108.83  3.000
 AMJ  HBA   CB   HB    106.68  3.000
 AMJ  HBA   CB   OAN   111.77  3.000
 AMJ  HB    CB   OAN   111.19  3.000
 AMJ  HBA   CB   CA    109.20  3.000
 AMJ  HB    CB   CA    109.49  3.000
 AMJ  OAN   CB   CA    108.47  3.000
 AMJ  HAAB  CAA  HAAA  108.51  3.000
 AMJ  HAAB  CAA  HAA   108.48  3.000
 AMJ  HAAA  CAA  HAA   107.92  3.000
 AMJ  HAAB  CAA  OAN   107.97  3.000
 AMJ  HAAA  CAA  OAN   112.01  3.000
 AMJ  HAA   CAA  OAN   111.85  3.000
 AMJ  HABB  CAB  HABA  108.19  3.000
 AMJ  HABB  CAB  HAB   108.78  3.000
 AMJ  HABA  CAB  HAB   107.39  3.000
 AMJ  HABB  CAB  CAO   113.47  3.000
 AMJ  HABA  CAB  CAO   109.11  3.000
 AMJ  HAB   CAB  CAO   109.72  3.000
 AMJ  HAE   CAE  CAG   120.12  3.000
 AMJ  HAE   CAE  CAF   120.14  3.000
 AMJ  CAG   CAE  CAF   119.74  3.000
 AMJ  HAF   CAF  CAH   119.89  3.000
 AMJ  HAF   CAF  CAE   120.08  3.000
 AMJ  CAH   CAF  CAE   120.03  3.000
 AMJ  HAG   CAG  CAI   119.82  3.000
 AMJ  HAG   CAG  CAE   120.09  3.000
 AMJ  CAI   CAG  CAE   120.09  3.000
 AMJ  HAH   CAH  CAQ   119.55  3.000
 AMJ  HAH   CAH  CAF   119.87  3.000
 AMJ  CAQ   CAH  CAF   120.58  3.000
 AMJ  HAI   CAI  CAQ   119.71  3.000
 AMJ  HAI   CAI  CAG   119.77  3.000
 AMJ  CAQ   CAI  CAG   120.52  3.000
 AMJ  HAJA  CAJ  HAJ   106.97  3.000
 AMJ  HAJA  CAJ  CAQ   110.52  3.000
 AMJ  HAJ   CAJ  CAQ   109.91  3.000
 AMJ  HAJA  CAJ  NAL   111.02  3.000
 AMJ  HAJ   CAJ  NAL   107.91  3.000
 AMJ  CAQ   CAJ  NAL   110.41  3.000
 AMJ  HNAL  NAL  CAJ   117.22  3.000
 AMJ  HNAL  NAL  C     118.96  3.000
 AMJ  CAJ   NAL  C     123.76  3.000
 AMJ  CAA   OAN  CB    112.66  3.000
 AMJ  OAC   CAO  CAB   122.02  3.000
 AMJ  OAC   CAO  N     122.73  3.000
 AMJ  CAB   CAO  N     115.24  3.000
 AMJ  CAJ   CAQ  CAI   121.15  3.000
 AMJ  CAJ   CAQ  CAH   119.81  3.000
 AMJ  CAI   CAQ  CAH   119.04  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
 AMJ  CONST_01  CAQ   CAH  CAF  CAE     0.00   0.0  0
 AMJ  CONST_02  CAQ   CAI  CAG  CAE     0.00   0.0  0
 AMJ  CONST_03  CAI   CAG  CAE  CAF     0.00   0.0  0
 AMJ  CONST_04  CAI   CAQ  CAH  CAF     0.00   0.0  0
 AMJ  CONST_05  CAH   CAF  CAE  CAG     0.00   0.0  0
 AMJ  CONST_06  CAH   CAQ  CAI  CAG     0.00   0.0  0
 AMJ  CONST_07  CAJ   CAQ  CAH  CAF   180.00   0.0  0
 AMJ  CONST_08  CAJ   CAQ  CAI  CAG   180.00   0.0  0
 AMJ  CONST_09  HAH   CAH  CAF  CAE   180.00   0.0  0
 AMJ  CONST_10  HAI   CAI  CAG  CAE   180.00   0.0  0
 AMJ  CONST_11  HAG   CAG  CAE  CAF   180.00   0.0  0
 AMJ  CONST_12  HAF   CAF  CAE  CAG   180.00   0.0  0
 AMJ  CONST_13  HAE   CAE  CAF  CAH   180.00   0.0  0
 AMJ  CONST_14  CAJ   NAL  C    O       0.00   0.0  0
 AMJ  CONST_15  CAJ   NAL  C    CA    180.00   0.0  0
 AMJ  CONST_16  CAB   CAO  N    CA    180.00   0.0  0
 AMJ  CONST_17  OAC   CAO  N    CA      0.00   0.0  0
 AMJ  CONST_18  HNAL  NAL  C    O     180.00   0.0  0
 AMJ  CONST_19  HN    N    CAO  CAB     0.00   0.0  0
 AMJ  Var_01    NAL   CAJ  CAQ  CAH    62.70  30.0  2
 AMJ  Var_02    CAQ   CAJ  NAL  C    -140.48  30.0  1
 AMJ  Var_03    HAB   CAB  CAO  N     132.72  30.0  3
 AMJ  Var_04    HAA   CAA  OAN  CB    -61.26  30.0  3
 AMJ  Var_05    HB    CB   OAN  CAA    57.00  30.0  1

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
 AMJ  chir_01  CA  C  N  CB  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
 AMJ  plan-1  CAE   0.020
 AMJ  plan-1  CAF   0.020
 AMJ  plan-1  CAG   0.020
 AMJ  plan-1  CAH   0.020
 AMJ  plan-1  CAI   0.020
 AMJ  plan-1  CAJ   0.020
 AMJ  plan-1  CAQ   0.020
 AMJ  plan-1  HAF   0.020
 AMJ  plan-1  HAG   0.020
 AMJ  plan-1  HAH   0.020
 AMJ  plan-1  HAI   0.020
 AMJ  plan-1  HAE   0.020
 AMJ  plan-2  C     0.020
 AMJ  plan-2  O     0.020
 AMJ  plan-2  CA    0.020
 AMJ  plan-2  CAJ   0.020
 AMJ  plan-2  NAL   0.020
 AMJ  plan-2  HNAL  0.020
 AMJ  plan-3  N     0.020
 AMJ  plan-3  CA    0.020
 AMJ  plan-3  CAB   0.020
 AMJ  plan-3  OAC   0.020
 AMJ  plan-3  CAO   0.020
 AMJ  plan-3  HN    0.020

