# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 21:47:48 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  25  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  -0.510   3.7598  -1.1171   0.8672
 AYC  CAQ   C  C      0   0.527   3.5922  -0.0039   0.3848
 AYC  CAB   C  CH3    0  -0.776   4.6985   1.0206   0.3438
 AYC  NAP   N  NH1    0  -0.632   2.4221   0.3929  -0.1404
 AYC  CAR   C  CH1    0  -0.167   1.2466  -0.4383  -0.1721
 AYC  CAA   C  CH3    0  -0.670   1.2622  -1.4276  -1.3420
 AYC  CAU   C  C      0   0.406   0.0017   0.4376  -0.2204
 AYC  CAM   C  CH2    0  -0.564  -1.3151  -0.2869  -0.1875
 AYC  CAL   C  CH2    0  -0.585  -2.5123   0.5916   0.1239
 AYC  CAS   C  C      0   0.420  -3.8642  -0.1475   0.1332
 AYC  OAG   O  OC    -1  -0.629  -4.8616   0.5583   0.3885
 AYC  OAE   O  O      0  -0.606  -3.8641  -1.3697  -0.1102
 AYC  OXT   O  O      0  -0.402   0.0914   1.6424  -0.2955
 AYC  HAB1  H  HCH3   0   0.265   5.5412   0.6220  -0.2210
 AYC  HAB2  H  HCH3   0   0.248   4.4006   1.9666  -0.1049
 AYC  HAB3  H  HCH3   0   0.265   5.0504   1.2131   1.3573
 AYC  HAP   H  HNH1   0   0.397   2.3353   1.3315  -0.4968
 AYC  HAR   H  HCH1   0   0.279   1.1951  -1.0118   0.7594
 AYC  HAA1  H  HCH3   0   0.245   0.4021  -2.0940  -1.3066
 AYC  HAA2  H  HCH3   0   0.237   1.2551  -0.9020  -2.2975
 AYC  HAA3  H  HCH3   0   0.254   2.1596  -2.0413  -1.2935
 AYC  HAM1  H  HCH2   0   0.274  -1.4419  -0.7633  -1.1659
 AYC  HAM2  H  HCH2   0   0.258  -1.2401  -1.1207   0.5160
 AYC  HAL1  H  HCH2   0   0.232  -2.3813   1.0756   1.0971
 AYC  HAL2  H  HCH2   0   0.233  -2.5765   1.4104  -0.5978

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  1.225  0.020  1.225
 AYC  CAQ  CAB   single  1.508  0.020  1.508
 AYC  CAQ  NAP   single  1.343  0.020  1.343
 AYC  NAP  CAR   single  1.440  0.020  1.440
 AYC  CAR  CAA   single  1.532  0.020  1.532
 AYC  CAR  CAU   single  1.523  0.020  1.523
 AYC  CAU  CAM   single  1.503  0.020  1.503
 AYC  CAU  OXT   double  1.210  0.020  1.210
 AYC  CAM  CAL   single  1.517  0.020  1.517
 AYC  CAL  CAS   single  1.541  0.020  1.541
 AYC  CAS  OAG   deloc   1.248  0.020  1.248
 AYC  CAS  OAE   deloc   1.246  0.020  1.246
 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

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   115.33  3.000
 AYC  NAP   CAQ  OAD   122.82  3.000
 AYC  CAB   CAQ  OAD   121.85  3.000
 AYC  HAB3  CAB  HAB2  108.55  3.000
 AYC  HAB3  CAB  HAB1  107.27  3.000
 AYC  HAB2  CAB  HAB1  108.41  3.000
 AYC  HAB3  CAB  CAQ   109.36  3.000
 AYC  HAB2  CAB  CAQ   113.62  3.000
 AYC  HAB1  CAB  CAQ   109.43  3.000
 AYC  HAP   NAP  CAR   117.35  3.000
 AYC  HAP   NAP  CAQ   119.25  3.000
 AYC  CAR   NAP  CAQ   123.33  3.000
 AYC  HAR   CAR  CAU   106.84  3.000
 AYC  HAR   CAR  CAA   108.17  3.000
 AYC  CAU   CAR  CAA   110.82  3.000
 AYC  HAR   CAR  NAP   108.78  3.000
 AYC  CAU   CAR  NAP   109.63  3.000
 AYC  CAA   CAR  NAP   112.41  3.000
 AYC  HAA3  CAA  HAA2  108.44  3.000
 AYC  HAA3  CAA  HAA1  107.75  3.000
 AYC  HAA2  CAA  HAA1  108.57  3.000
 AYC  HAA3  CAA  CAR   109.78  3.000
 AYC  HAA2  CAA  CAR   110.96  3.000
 AYC  HAA1  CAA  CAR   111.24  3.000
 AYC  OXT   CAU  CAM   123.09  3.000
 AYC  OXT   CAU  CAR   120.92  3.000
 AYC  CAM   CAU  CAR   115.99  3.000
 AYC  HAM2  CAM  HAM1  104.53  3.000
 AYC  HAM2  CAM  CAL   111.32  3.000
 AYC  HAM1  CAM  CAL   110.10  3.000
 AYC  HAM2  CAM  CAU   108.75  3.000
 AYC  HAM1  CAM  CAU   106.94  3.000
 AYC  CAL   CAM  CAU   114.63  3.000
 AYC  HAL2  CAL  HAL1  105.23  3.000
 AYC  HAL2  CAL  CAS   108.16  3.000
 AYC  HAL1  CAL  CAS   108.16  3.000
 AYC  HAL2  CAL  CAM   110.15  3.000
 AYC  HAL1  CAL  CAM   110.12  3.000
 AYC  CAS   CAL  CAM   114.57  3.000
 AYC  OAE   CAS  OAG   126.48  3.000
 AYC  OAE   CAS  CAL   117.99  3.000
 AYC  OAG   CAS  CAL   115.54  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
 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  Var_01    CAL   CAM  CAU  CAR  164.91  30.0  3
 AYC  Var_02    CAS   CAL  CAM  CAU  178.99  30.0  3
 AYC  Var_03    OAG   CAS  CAL  CAM  179.95  30.0  3
 AYC  Var_04    HAB1  CAB  CAQ  OAD   59.24  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

