# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:31:01 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (5R)-5-(acetylamino)-4-oxohexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(C)=O)C(=O)CCC(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
 AYC  AYC  '(5R)-5-(acetylamino)-4-oxohexanoic acid'  ligand  26  13  .  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_AYC
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
 AYC  OAD   O  O     0  -0.508   3.7504  -1.0788   0.9339
 AYC  CAQ   C  C     0   0.528   3.5893   0.0189   0.4160
 AYC  CAB   C  CH3   0  -0.776   4.6983   1.0389   0.3491
 AYC  NAP   N  NH1   0  -0.632   2.4226   0.4013  -0.1291
 AYC  CAR   C  CH1   0  -0.170   1.2544  -0.4393  -0.1574
 AYC  CAA   C  CH3   0  -0.671   1.2747  -1.4310  -1.3252
 AYC  CAU   C  C     0   0.412   0.0032   0.4229  -0.1938
 AYC  CAM   C  CH2   0  -0.576  -1.3065  -0.3198  -0.1901
 AYC  CAL   C  CH2   0  -0.579  -2.4937   0.5689   0.1274
 AYC  CAS   C  C     0   0.558  -3.7983  -0.1780   0.0887
 AYC  OAG   O  OH1   0  -0.596  -4.8178   0.6038   0.4273
 AYC  OAE   O  O     0  -0.443  -3.9289  -1.3380  -0.2129
 AYC  OXT   O  O     0  -0.393   0.0666   1.6294  -0.2343
 AYC  HAB1  H  HCH3  0   0.267   5.5324   0.6294  -0.2209
 AYC  HAB2  H  HCH3  0   0.249   4.3988   1.9796  -0.1087
 AYC  HAB3  H  HCH3  0   0.266   5.0631   1.2426   1.3555
 AYC  HAP   H  HNH1  0   0.399   2.3457   1.3227  -0.5298
 AYC  HAR   H  HCH1  0   0.286   1.2121  -1.0114   0.7757
 AYC  HAA1  H  HCH3  0   0.246   0.4234  -2.1086  -1.2846
 AYC  HAA2  H  HCH3  0   0.240   1.2582  -0.9082  -2.2818
 AYC  HAA3  H  HCH3  0   0.257   2.1794  -2.0340  -1.2777
 AYC  HAM1  H  HCH2  0   0.295  -1.4257  -0.7735  -1.1795
 AYC  HAM2  H  HCH2  0   0.281  -1.2391  -1.1592   0.5068
 AYC  HAL1  H  HCH2  0   0.290  -2.3883   1.0275   1.1142
 AYC  HAL2  H  HCH2  0   0.291  -2.5599   1.3994  -0.5799
 AYC  HAG   H  HOH1  0   0.480  -5.6457   0.1019   0.3901

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
 AYC  OAD  CAQ   double  1.224  0.020  1.224
 AYC  CAQ  CAB   single  1.508  0.020  1.508
 AYC  CAQ  NAP   single  1.343  0.020  1.343
 AYC  NAP  CAR   single  1.439  0.020  1.439
 AYC  CAR  CAA   single  1.532  0.020  1.532
 AYC  CAR  CAU   single  1.520  0.020  1.520
 AYC  CAU  CAM   single  1.506  0.020  1.506
 AYC  CAU  OXT   double  1.209  0.020  1.209
 AYC  CAM  CAL   single  1.517  0.020  1.517
 AYC  CAL  CAS   single  1.504  0.020  1.504
 AYC  CAS  OAG   single  1.329  0.020  1.329
 AYC  CAS  OAE   double  1.206  0.020  1.206
 AYC  CAB  HAB1  single  0.970  0.020  1.090
 AYC  CAB  HAB2  single  0.970  0.020  1.090
 AYC  CAB  HAB3  single  0.970  0.020  1.090
 AYC  NAP  HAP   single  0.860  0.020  1.020
 AYC  CAR  HAR   single  0.970  0.020  1.090
 AYC  CAA  HAA1  single  0.970  0.020  1.090
 AYC  CAA  HAA2  single  0.970  0.020  1.090
 AYC  CAA  HAA3  single  0.970  0.020  1.090
 AYC  CAM  HAM1  single  0.970  0.020  1.090
 AYC  CAM  HAM2  single  0.970  0.020  1.090
 AYC  CAL  HAL1  single  0.970  0.020  1.090
 AYC  CAL  HAL2  single  0.970  0.020  1.090
 AYC  OAG  HAG   single  0.850  0.020  0.980

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
 AYC  NAP   CAQ  CAB   115.35  3.000
 AYC  NAP   CAQ  OAD   122.76  3.000
 AYC  CAB   CAQ  OAD   121.90  3.000
 AYC  HAB3  CAB  HAB2  108.61  3.000
 AYC  HAB3  CAB  HAB1  107.28  3.000
 AYC  HAB2  CAB  HAB1  108.38  3.000
 AYC  HAB3  CAB  CAQ   109.36  3.000
 AYC  HAB2  CAB  CAQ   113.64  3.000
 AYC  HAB1  CAB  CAQ   109.38  3.000
 AYC  HAP   NAP  CAR   117.66  3.000
 AYC  HAP   NAP  CAQ   119.20  3.000
 AYC  CAR   NAP  CAQ   123.14  3.000
 AYC  HAR   CAR  CAU   106.56  3.000
 AYC  HAR   CAR  CAA   108.16  3.000
 AYC  CAU   CAR  CAA   111.08  3.000
 AYC  HAR   CAR  NAP   108.64  3.000
 AYC  CAU   CAR  NAP   109.71  3.000
 AYC  CAA   CAR  NAP   112.47  3.000
 AYC  HAA3  CAA  HAA2  108.46  3.000
 AYC  HAA3  CAA  HAA1  107.67  3.000
 AYC  HAA2  CAA  HAA1  108.63  3.000
 AYC  HAA3  CAA  CAR   109.66  3.000
 AYC  HAA2  CAA  CAR   110.99  3.000
 AYC  HAA1  CAA  CAR   111.34  3.000
 AYC  OXT   CAU  CAM   122.55  3.000
 AYC  OXT   CAU  CAR   121.59  3.000
 AYC  CAM   CAU  CAR   115.86  3.000
 AYC  HAM2  CAM  HAM1  105.34  3.000
 AYC  HAM2  CAM  CAL   111.39  3.000
 AYC  HAM1  CAM  CAL   110.29  3.000
 AYC  HAM2  CAM  CAU   109.07  3.000
 AYC  HAM1  CAM  CAU   107.27  3.000
 AYC  CAL   CAM  CAU   113.11  3.000
 AYC  HAL2  CAL  HAL1  105.74  3.000
 AYC  HAL2  CAL  CAS   107.95  3.000
 AYC  HAL1  CAL  CAS   108.38  3.000
 AYC  HAL2  CAL  CAM   110.93  3.000
 AYC  HAL1  CAL  CAM   111.06  3.000
 AYC  CAS   CAL  CAM   112.50  3.000
 AYC  OAE   CAS  OAG   123.14  3.000
 AYC  OAE   CAS  CAL   125.33  3.000
 AYC  OAG   CAS  CAL   111.52  3.000
 AYC  HAG   OAG  CAS   109.95  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
 AYC  CONST_01  CAR   NAP  CAQ  OAD    0.00   0.0  0
 AYC  CONST_02  CAR   NAP  CAQ  CAB  180.00   0.0  0
 AYC  CONST_03  HAP   NAP  CAQ  OAD  180.00   0.0  0
 AYC  CONST_04  HAG   OAG  CAS  CAL  180.00   0.0  0
 AYC  Var_01    CAL   CAM  CAU  CAR  165.31  30.0  3
 AYC  Var_02    CAS   CAL  CAM  CAU  178.35  30.0  3
 AYC  Var_03    OAG   CAS  CAL  CAM  177.22  30.0  3
 AYC  Var_04    HAB1  CAB  CAQ  OAD   60.73  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
 AYC  chir_01  CAR  NAP  CAA  CAU  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
 AYC  plan-1  OAD  0.020
 AYC  plan-1  CAQ  0.020
 AYC  plan-1  CAB  0.020
 AYC  plan-1  NAP  0.020
 AYC  plan-1  CAR  0.020
 AYC  plan-1  HAP  0.020
 AYC  plan-2  CAR  0.020
 AYC  plan-2  CAU  0.020
 AYC  plan-2  CAM  0.020
 AYC  plan-2  OXT  0.020
 AYC  plan-3  CAL  0.020
 AYC  plan-3  CAS  0.020
 AYC  plan-3  OAG  0.020
 AYC  plan-3  OAE  0.020
 AYC  plan-3  HAG  0.020

