# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 03:29:41 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: N-(4-methylpentanoyl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC(=O)N[C@@H](Cc1ccccc1)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
 SFK  SFK  N-(4-methylpentanoyl)-L-phenylalanine  ligand  40  19  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SFK
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
 SFK  CAR  C  CH3   0  -0.661  -4.3149   2.0782   0.6410
 SFK  CAQ  C  CH1   0  -0.236  -4.6381   0.6675   0.1578
 SFK  CAS  C  CH3   0  -0.651  -5.7697   0.7035  -0.8649
 SFK  CAP  C  CH2   0  -0.398  -3.4194  -0.0311  -0.4482
 SFK  CAO  C  CH2   0  -0.596  -2.2756  -0.2422   0.5346
 SFK  CAM  C  C     0   0.584  -1.1112  -0.9925  -0.0699
 SFK  OAN  O  O     0  -0.497  -1.2371  -1.8456  -0.9369
 SFK  N    N  NH1   0  -0.648   0.1002  -0.6687   0.4210
 SFK  CA   C  CH1   0  -0.152   1.2891  -1.3309  -0.0327
 SFK  C    C  C     0   0.538   1.2514  -2.8087   0.3264
 SFK  O    O  O     0  -0.433   0.6572  -3.2659   1.2667
 SFK  OXT  O  OH1   0  -0.590   2.0050  -3.5229  -0.4969
 SFK  CB   C  CH2   0  -0.567   2.5344  -0.6938   0.6057
 SFK  CG   C  CR6   0   0.137   2.6419   0.7728   0.2877
 SFK  CD1  C  CR16  0  -0.299   2.9970   1.1950  -0.9924
 SFK  CE1  C  CR16  0  -0.239   3.0755   2.5461  -1.2956
 SFK  CZ   C  CR16  0  -0.268   2.7992   3.4982  -0.3208
 SFK  CE2  C  CR16  0  -0.239   2.4463   3.0886   0.9568
 SFK  CD2  C  CR16  0  -0.326   2.3689   1.7338   1.2566
 SFK  H1   H  HCH3  0   0.228  -5.2091   2.5780   1.0170
 SFK  H2   H  HCH3  0   0.229  -3.5810   2.0862   1.4475
 SFK  H3   H  HCH3  0   0.213  -3.9170   2.6846  -0.1770
 SFK  H4   H  HCH1  0   0.214  -4.9747   0.0775   1.0191
 SFK  H5   H  HCH3  0   0.213  -5.4709   1.2672  -1.7525
 SFK  H6   H  HCH3  0   0.224  -6.0478  -0.3007  -1.1891
 SFK  H7   H  HCH3  0   0.225  -6.6625   1.1801  -0.4573
 SFK  H8   H  HCH2  0   0.230  -3.7294  -1.0002  -0.8460
 SFK  H9   H  HCH2  0   0.218  -3.0663   0.5548  -1.3042
 SFK  H10  H  HCH2  0   0.255  -1.9253   0.7096   0.9391
 SFK  H11  H  HCH2  0   0.271  -2.6285  -0.8244   1.3938
 SFK  H12  H  HNH1  0   0.403   0.1694   0.0104   1.1614
 SFK  H13  H  HCH1  0   0.290   1.3715  -1.2416  -1.1200
 SFK  H14  H  HOH1  0   0.485   2.0210  -4.4510  -0.2177
 SFK  H15  H  HCH2  0   0.276   2.5026  -0.8398   1.6884
 SFK  H16  H  HCH2  0   0.288   3.4153  -1.2224   0.2376
 SFK  H17  H  HCR6  0   0.252   3.2164   0.4595  -1.7582
 SFK  H18  H  HCR6  0   0.257   3.3568   2.8580  -2.2931
 SFK  H19  H  HCR6  0   0.257   2.8627   4.5524  -0.5569
 SFK  H20  H  HCR6  0   0.257   2.2329   3.8219   1.7238
 SFK  H21  H  HCR6  0   0.256   2.0977   1.4223   2.2591

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
 SFK  OAN  CAM  double    1.223  0.020  1.223
 SFK  CAS  CAQ  single    1.526  0.020  1.526
 SFK  CAM  CAO  single    1.511  0.020  1.511
 SFK  CAM  N    single    1.347  0.020  1.347
 SFK  CAO  CAP  single    1.523  0.020  1.523
 SFK  CAP  CAQ  single    1.530  0.020  1.530
 SFK  CA   N    single    1.435  0.020  1.435
 SFK  CA   CB   single    1.538  0.020  1.538
 SFK  CA   C    single    1.521  0.020  1.521
 SFK  CAQ  CAR  single    1.526  0.020  1.526
 SFK  CB   CG   single    1.505  0.020  1.505
 SFK  C    O    double    1.203  0.020  1.203
 SFK  C    OXT  single    1.325  0.020  1.325
 SFK  CG   CD2  aromatic  1.392  0.020  1.392
 SFK  CG   CD1  aromatic  1.394  0.020  1.394
 SFK  CD2  CE2  aromatic  1.390  0.020  1.390
 SFK  CD1  CE1  aromatic  1.387  0.020  1.387
 SFK  CE2  CZ   aromatic  1.387  0.020  1.387
 SFK  CE1  CZ   aromatic  1.390  0.020  1.390
 SFK  CAR  H1   single    0.970  0.020  1.090
 SFK  CAR  H2   single    0.970  0.020  1.090
 SFK  CAR  H3   single    0.970  0.020  1.090
 SFK  CAQ  H4   single    0.970  0.020  1.090
 SFK  CAS  H5   single    0.970  0.020  1.090
 SFK  CAS  H6   single    0.970  0.020  1.090
 SFK  CAS  H7   single    0.970  0.020  1.090
 SFK  CAP  H8   single    0.970  0.020  1.090
 SFK  CAP  H9   single    0.970  0.020  1.090
 SFK  CAO  H10  single    0.970  0.020  1.090
 SFK  CAO  H11  single    0.970  0.020  1.090
 SFK  N    H12  single    0.860  0.020  1.020
 SFK  CA   H13  single    0.970  0.020  1.090
 SFK  OXT  H14  single    0.850  0.020  0.980
 SFK  CB   H15  single    0.970  0.020  1.090
 SFK  CB   H16  single    0.970  0.020  1.090
 SFK  CD1  H17  single    0.930  0.020  1.080
 SFK  CE1  H18  single    0.930  0.020  1.080
 SFK  CZ   H19  single    0.930  0.020  1.080
 SFK  CE2  H20  single    0.930  0.020  1.080
 SFK  CD2  H21  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
 SFK  H3   CAR  H2   107.72  3.000
 SFK  H3   CAR  H1   107.57  3.000
 SFK  H2   CAR  H1   107.06  3.000
 SFK  H3   CAR  CAQ  110.67  3.000
 SFK  H2   CAR  CAQ  112.56  3.000
 SFK  H1   CAR  CAQ  111.04  3.000
 SFK  H4   CAQ  CAP  108.05  3.000
 SFK  H4   CAQ  CAS  108.15  3.000
 SFK  CAP  CAQ  CAS  109.64  3.000
 SFK  H4   CAQ  CAR  108.28  3.000
 SFK  CAP  CAQ  CAR  112.27  3.000
 SFK  CAS  CAQ  CAR  110.34  3.000
 SFK  H7   CAS  H6   107.72  3.000
 SFK  H7   CAS  H5   107.57  3.000
 SFK  H6   CAS  H5   107.64  3.000
 SFK  H7   CAS  CAQ  111.52  3.000
 SFK  H6   CAS  CAQ  111.49  3.000
 SFK  H5   CAS  CAQ  110.71  3.000
 SFK  H9   CAP  H8   106.35  3.000
 SFK  H9   CAP  CAO  109.65  3.000
 SFK  H8   CAP  CAO  108.98  3.000
 SFK  H9   CAP  CAQ  108.78  3.000
 SFK  H8   CAP  CAQ  108.86  3.000
 SFK  CAO  CAP  CAQ  113.95  3.000
 SFK  H11  CAO  H10  106.01  3.000
 SFK  H11  CAO  CAM  107.33  3.000
 SFK  H10  CAO  CAM  109.50  3.000
 SFK  H11  CAO  CAP  109.74  3.000
 SFK  H10  CAO  CAP  111.06  3.000
 SFK  CAM  CAO  CAP  112.91  3.000
 SFK  N    CAM  OAN  121.25  3.000
 SFK  N    CAM  CAO  115.33  3.000
 SFK  OAN  CAM  CAO  123.41  3.000
 SFK  H12  N    CA   119.13  3.000
 SFK  H12  N    CAM  119.48  3.000
 SFK  CA   N    CAM  121.28  3.000
 SFK  H13  CA   CB   108.53  3.000
 SFK  H13  CA   C    108.40  3.000
 SFK  CB   CA   C    108.94  3.000
 SFK  H13  CA   N    109.82  3.000
 SFK  C    CA   N    110.69  3.000
 SFK  CB   CA   N    110.40  3.000
 SFK  OXT  C    O    124.19  3.000
 SFK  OXT  C    CA   111.28  3.000
 SFK  O    C    CA   124.47  3.000
 SFK  H14  OXT  C    110.28  3.000
 SFK  H16  CB   H15  107.03  3.000
 SFK  H16  CB   CG   110.07  3.000
 SFK  H15  CB   CG   109.98  3.000
 SFK  H16  CB   CA   108.24  3.000
 SFK  H15  CB   CA   109.41  3.000
 SFK  CG   CB   CA   111.96  3.000
 SFK  CD2  CG   CD1  118.70  3.000
 SFK  CD1  CG   CB   120.50  3.000
 SFK  CD2  CG   CB   120.79  3.000
 SFK  H17  CD1  CE1  119.67  3.000
 SFK  H17  CD1  CG   119.65  3.000
 SFK  CE1  CD1  CG   120.68  3.000
 SFK  H18  CE1  CZ   120.03  3.000
 SFK  H18  CE1  CD1  119.80  3.000
 SFK  CZ   CE1  CD1  120.17  3.000
 SFK  H19  CZ   CE2  120.22  3.000
 SFK  H19  CZ   CE1  120.17  3.000
 SFK  CE2  CZ   CE1  119.61  3.000
 SFK  H20  CE2  CD2  119.77  3.000
 SFK  H20  CE2  CZ   120.19  3.000
 SFK  CD2  CE2  CZ   120.04  3.000
 SFK  H21  CD2  CE2  119.57  3.000
 SFK  H21  CD2  CG   119.64  3.000
 SFK  CE2  CD2  CG   120.79  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
 SFK  CONST_01  CZ   CE2  CD2  CG     0.00   0.0  0
 SFK  CONST_02  CZ   CE1  CD1  CG     0.00   0.0  0
 SFK  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 SFK  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 SFK  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 SFK  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 SFK  CONST_07  CE2  CD2  CG   CB   180.00   0.0  0
 SFK  CONST_08  CE1  CD1  CG   CB   180.00   0.0  0
 SFK  CONST_09  H20  CE2  CD2  CG   180.00   0.0  0
 SFK  CONST_10  H18  CE1  CD1  CG   180.00   0.0  0
 SFK  CONST_11  H21  CD2  CG   CD1  180.00   0.0  0
 SFK  CONST_12  H19  CZ   CE1  CD1  180.00   0.0  0
 SFK  CONST_13  H17  CD1  CE1  CZ   180.00   0.0  0
 SFK  CONST_14  CA   N    CAM  CAO  180.00   0.0  0
 SFK  CONST_15  CA   N    CAM  OAN    0.00   0.0  0
 SFK  CONST_16  H12  N    CAM  CAO    0.00   0.0  0
 SFK  CONST_17  H14  OXT  C    CA   180.00   0.0  0
 SFK  Var_01    CD2  CG   CB   CA   106.39  30.0  2
 SFK  Var_02    CAO  CAP  CAQ  CAR   62.60  30.0  3
 SFK  Var_03    CAM  CAO  CAP  CAQ  177.24  30.0  1
 SFK  Var_04    OAN  CAM  CAO  CAP  -31.92  30.0  1
 SFK  Var_05    H5   CAS  CAQ  CAR   62.83  30.0  3
 SFK  Var_06    H1   CAR  CAQ  CAS   54.15  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
 SFK  chir_01  CA  N  CB  C  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
 SFK  plan-1  CB   0.020
 SFK  plan-1  CG   0.020
 SFK  plan-1  CD1  0.020
 SFK  plan-1  CE1  0.020
 SFK  plan-1  CZ   0.020
 SFK  plan-1  CE2  0.020
 SFK  plan-1  CD2  0.020
 SFK  plan-1  H17  0.020
 SFK  plan-1  H18  0.020
 SFK  plan-1  H19  0.020
 SFK  plan-1  H20  0.020
 SFK  plan-1  H21  0.020
 SFK  plan-2  CAO  0.020
 SFK  plan-2  CAM  0.020
 SFK  plan-2  OAN  0.020
 SFK  plan-2  N    0.020
 SFK  plan-2  CA   0.020
 SFK  plan-2  H12  0.020
 SFK  plan-3  CA   0.020
 SFK  plan-3  C    0.020
 SFK  plan-3  O    0.020
 SFK  plan-3  OXT  0.020
 SFK  plan-3  H14  0.020

