# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:13:26 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2S)-2-acetamido-3-naphthalen-2-yl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccc2ccccc2c1)C(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
 NPQ  NPQ  '(2S)-2-acetamido-3-naphthalen-2-yl-propanoic acid'  ligand  33  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPQ
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
 NPQ  C     C  C      0   0.420   3.6756  -0.9121  -0.7419
 NPQ  N     N  NH1    0  -0.610   1.9918   0.8235  -0.2646
 NPQ  O     O  O      0  -0.594   4.2341  -0.0270  -1.4160
 NPQ  CA    C  CH1    0  -0.205   2.2885  -0.5791  -0.1400
 NPQ  CB    C  CH2    0  -0.516   1.2189  -1.4382  -0.8485
 NPQ  CG    C  CR6    0   0.153  -0.1662  -1.1375  -0.3643
 NPQ  CAA   C  CH3    0  -0.777   1.0751   2.9895   0.2404
 NPQ  OAB   O  O      0  -0.509   0.9535   1.1216   1.7246
 NPQ  CAE   C  CR16   0  -0.264  -4.7909   0.7242   0.4945
 NPQ  CAF   C  CR16   0  -0.261  -4.3353   1.3200  -0.7005
 NPQ  CAH   C  CR16   0  -0.312  -3.9994  -0.1708   1.1632
 NPQ  CAI   C  CR16   0  -0.318  -3.1007   1.0062  -1.2019
 NPQ  CAJ   C  CR16   0  -0.305  -1.8705  -1.4277   1.3358
 NPQ  CAN   C  C      0   0.525   1.3348   1.5574   0.6450
 NPQ  CAQ   C  CR66   0   0.095  -2.7177  -0.5098   0.6706
 NPQ  CAR   C  CR66   0   0.140  -2.2600   0.0854  -0.5328
 NPQ  CD1   C  CR16   0  -0.280  -0.6356  -1.7240   0.8356
 NPQ  CD2   C  CR16   0  -0.383  -0.9788  -0.2552  -1.0262
 NPQ  OXT   O  OC    -1  -0.607   4.0883  -2.0638  -0.5148
 NPQ  HN    H  HNH1   0   0.380   2.3491   1.2725  -1.0926
 NPQ  HA    H  HCH1   0   0.246   2.2935  -0.8369   0.9209
 NPQ  HB    H  HCH2   0   0.240   1.2834  -1.2591  -1.9257
 NPQ  HBA   H  HCH2   0   0.247   1.4610  -2.4892  -0.6810
 NPQ  HAA   H  HCH3   0   0.256   1.3439   3.6611   1.0547
 NPQ  HAAA  H  HCH3   0   0.243   1.6125   3.2951  -0.6559
 NPQ  HAAB  H  HCH3   0   0.259   0.0075   3.1155   0.0532
 NPQ  HAE   H  HCR6   0   0.254  -5.7700   0.9782   0.8795
 NPQ  HAF   H  HCR6   0   0.255  -4.9680   2.0278  -1.2200
 NPQ  HAH   H  HCR6   0   0.251  -4.3461  -0.6298   2.0815
 NPQ  HAI   H  HCR6   0   0.250  -2.7529   1.4635  -2.1209
 NPQ  HAJ   H  HCR6   0   0.248  -2.2129  -1.8911   2.2538
 NPQ  HD1   H  HCR6   0   0.242   0.0044  -2.4218   1.3628
 NPQ  HD2   H  HCR6   0   0.238  -0.6415   0.2040  -1.9490

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
 NPQ  CA   C     single    1.548  0.020  1.548
 NPQ  O    C     deloc     1.245  0.020  1.245
 NPQ  C    OXT   deloc     1.244  0.020  1.244
 NPQ  CAN  N     single    1.341  0.020  1.341
 NPQ  N    CA    single    1.439  0.020  1.439
 NPQ  N    HN    single    0.860  0.020  1.020
 NPQ  CB   CA    single    1.544  0.020  1.544
 NPQ  CA   HA    single    0.970  0.020  1.090
 NPQ  CB   CG    single    1.498  0.020  1.498
 NPQ  CB   HB    single    0.970  0.020  1.090
 NPQ  CB   HBA   single    0.970  0.020  1.090
 NPQ  CD1  CG    aromatic  1.416  0.020  1.416
 NPQ  CG   CD2   aromatic  1.370  0.020  1.370
 NPQ  CAA  CAN   single    1.511  0.020  1.511
 NPQ  CAA  HAA   single    0.970  0.020  1.090
 NPQ  CAA  HAAA  single    0.970  0.020  1.090
 NPQ  CAA  HAAB  single    0.970  0.020  1.090
 NPQ  OAB  CAN   double    1.225  0.020  1.225
 NPQ  CAH  CAE   aromatic  1.369  0.020  1.369
 NPQ  CAE  CAF   aromatic  1.411  0.020  1.411
 NPQ  CAE  HAE   single    0.930  0.020  1.080
 NPQ  CAF  CAI   aromatic  1.369  0.020  1.369
 NPQ  CAF  HAF   single    0.930  0.020  1.080
 NPQ  CAH  CAQ   aromatic  1.414  0.020  1.414
 NPQ  CAH  HAH   single    0.930  0.020  1.080
 NPQ  CAR  CAI   aromatic  1.415  0.020  1.415
 NPQ  CAI  HAI   single    0.930  0.020  1.080
 NPQ  CAJ  CD1   aromatic  1.365  0.020  1.365
 NPQ  CAJ  CAQ   aromatic  1.415  0.020  1.415
 NPQ  CAJ  HAJ   single    0.930  0.020  1.080
 NPQ  CAQ  CAR   aromatic  1.418  0.020  1.418
 NPQ  CAR  CD2   aromatic  1.415  0.020  1.415
 NPQ  CD1  HD1   single    0.930  0.020  1.080
 NPQ  CD2  HD2   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
 NPQ  OXT   C    CA    115.17  3.000
 NPQ  OXT   C    O     127.46  3.000
 NPQ  CA    C    O     117.35  3.000
 NPQ  HN    N    CAN   119.18  3.000
 NPQ  HN    N    CA    115.62  3.000
 NPQ  CAN   N    CA    125.16  3.000
 NPQ  HA    CA   CB    108.52  3.000
 NPQ  HA    CA   N     108.38  3.000
 NPQ  CB    CA   N     111.08  3.000
 NPQ  HA    CA   C     108.83  3.000
 NPQ  CB    CA   C     108.82  3.000
 NPQ  N     CA   C     111.14  3.000
 NPQ  HBA   CB   HB    107.20  3.000
 NPQ  HBA   CB   CG    110.42  3.000
 NPQ  HB    CB   CG    109.88  3.000
 NPQ  HBA   CB   CA    108.16  3.000
 NPQ  HB    CB   CA    108.65  3.000
 NPQ  CG    CB   CA    112.37  3.000
 NPQ  CD2   CG   CD1   118.66  3.000
 NPQ  CD2   CG   CB    121.44  3.000
 NPQ  CD1   CG   CB    119.83  3.000
 NPQ  HAAB  CAA  HAAA  108.02  3.000
 NPQ  HAAB  CAA  HAA   107.36  3.000
 NPQ  HAAA  CAA  HAA   108.70  3.000
 NPQ  HAAB  CAA  CAN   108.88  3.000
 NPQ  HAAA  CAA  CAN   113.69  3.000
 NPQ  HAA   CAA  CAN   109.99  3.000
 NPQ  HAE   CAE  CAH   120.18  3.000
 NPQ  HAE   CAE  CAF   119.63  3.000
 NPQ  CAH   CAE  CAF   120.20  3.000
 NPQ  HAF   CAF  CAI   120.09  3.000
 NPQ  HAF   CAF  CAE   119.60  3.000
 NPQ  CAI   CAF  CAE   120.31  3.000
 NPQ  HAH   CAH  CAQ   118.92  3.000
 NPQ  HAH   CAH  CAE   120.39  3.000
 NPQ  CAQ   CAH  CAE   120.70  3.000
 NPQ  HAI   CAI  CAR   119.01  3.000
 NPQ  HAI   CAI  CAF   120.22  3.000
 NPQ  CAR   CAI  CAF   120.78  3.000
 NPQ  HAJ   CAJ  CD1   120.23  3.000
 NPQ  HAJ   CAJ  CAQ   119.10  3.000
 NPQ  CD1   CAJ  CAQ   120.67  3.000
 NPQ  OAB   CAN  CAA   121.32  3.000
 NPQ  OAB   CAN  N     123.76  3.000
 NPQ  CAA   CAN  N     114.92  3.000
 NPQ  CAR   CAQ  CAJ   118.54  3.000
 NPQ  CAR   CAQ  CAH   119.16  3.000
 NPQ  CAJ   CAQ  CAH   122.30  3.000
 NPQ  CD2   CAR  CAQ   119.15  3.000
 NPQ  CD2   CAR  CAI   121.99  3.000
 NPQ  CAQ   CAR  CAI   118.85  3.000
 NPQ  HD1   CD1  CAJ   119.72  3.000
 NPQ  HD1   CD1  CG    118.90  3.000
 NPQ  CAJ   CD1  CG    121.38  3.000
 NPQ  HD2   CD2  CAR   118.46  3.000
 NPQ  HD2   CD2  CG    119.95  3.000
 NPQ  CAR   CD2  CG    121.59  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
 NPQ  CONST_01  CAQ  CAJ  CD1  CG      0.00   0.0  0
 NPQ  CONST_02  CAI  CAR  CD2  CG    180.00   0.0  0
 NPQ  CONST_03  CAQ  CAR  CD2  CG      0.00   0.0  0
 NPQ  CONST_04  CAJ  CAQ  CAH  CAE   180.00   0.0  0
 NPQ  CONST_05  CAR  CAQ  CAH  CAE     0.00   0.0  0
 NPQ  CONST_06  CAR  CAI  CAF  CAE     0.00   0.0  0
 NPQ  CONST_07  CAQ  CAH  CAE  CAF     0.00   0.0  0
 NPQ  CONST_08  CAQ  CAR  CAI  CAF     0.00   0.0  0
 NPQ  CONST_09  CD2  CAR  CAI  CAF   180.00   0.0  0
 NPQ  CONST_10  CAI  CAF  CAE  CAH     0.00   0.0  0
 NPQ  CONST_11  CD1  CAJ  CAQ  CAH   180.00   0.0  0
 NPQ  CONST_12  CAI  CAR  CAQ  CAH     0.00   0.0  0
 NPQ  CONST_13  CD2  CAR  CAQ  CAH   180.00   0.0  0
 NPQ  CONST_14  CAJ  CAQ  CAR  CAI   180.00   0.0  0
 NPQ  CONST_15  CD2  CG   CD1  CAJ     0.00   0.0  0
 NPQ  CONST_16  CD2  CAR  CAQ  CAJ     0.00   0.0  0
 NPQ  CONST_17  CD1  CAJ  CAQ  CAR     0.00   0.0  0
 NPQ  CONST_18  CD1  CG   CD2  CAR     0.00   0.0  0
 NPQ  CONST_19  CAJ  CD1  CG   CB    180.00   0.0  0
 NPQ  CONST_20  CAR  CD2  CG   CB    180.00   0.0  0
 NPQ  CONST_21  HAJ  CAJ  CD1  CG    180.00   0.0  0
 NPQ  CONST_22  HAI  CAI  CAF  CAE   180.00   0.0  0
 NPQ  CONST_23  HAH  CAH  CAE  CAF   180.00   0.0  0
 NPQ  CONST_24  HAF  CAF  CAE  CAH   180.00   0.0  0
 NPQ  CONST_25  HAE  CAE  CAF  CAI   180.00   0.0  0
 NPQ  CONST_26  HD2  CD2  CAR  CAI     0.00   0.0  0
 NPQ  CONST_27  HD1  CD1  CAJ  CAQ   180.00   0.0  0
 NPQ  CONST_28  CAA  CAN  N    CA    180.00   0.0  0
 NPQ  CONST_29  OAB  CAN  N    CA      0.00   0.0  0
 NPQ  CONST_30  HN   N    CAN  CAA     0.00   0.0  0
 NPQ  Var_01    CD1  CG   CB   CA    -81.54  30.0  2
 NPQ  Var_02    HAA  CAA  CAN  N    -132.86  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
 NPQ  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
 NPQ  plan-1  CB   0.020
 NPQ  plan-1  CG   0.020
 NPQ  plan-1  CAE  0.020
 NPQ  plan-1  CAF  0.020
 NPQ  plan-1  CAH  0.020
 NPQ  plan-1  CAI  0.020
 NPQ  plan-1  CAJ  0.020
 NPQ  plan-1  CAQ  0.020
 NPQ  plan-1  CAR  0.020
 NPQ  plan-1  CD1  0.020
 NPQ  plan-1  CD2  0.020
 NPQ  plan-1  HAE  0.020
 NPQ  plan-1  HAF  0.020
 NPQ  plan-1  HAH  0.020
 NPQ  plan-1  HAI  0.020
 NPQ  plan-1  HAJ  0.020
 NPQ  plan-1  HD1  0.020
 NPQ  plan-1  HD2  0.020
 NPQ  plan-2  N    0.020
 NPQ  plan-2  CA   0.020
 NPQ  plan-2  CAA  0.020
 NPQ  plan-2  OAB  0.020
 NPQ  plan-2  CAN  0.020
 NPQ  plan-2  HN   0.020
 NPQ  plan-3  C    0.020
 NPQ  plan-3  O    0.020
 NPQ  plan-3  CA   0.020
 NPQ  plan-3  OXT  0.020

