# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 00:23:31 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: N~6~-acetyl-N-(4-methyl-2-oxo-2H-chromen-7-yl)-L-lysinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCCC[C@H](N)C(=O)Nc1ccc2C(=CC(=O)Oc2c1)C
#
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
 FDL  FDL  N~6~-acetyl-N-(4-methyl-2-oxo-2H-chromen-7-yl)-L-lysinamide  L-peptide  48  25  .  2019-03-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FDL
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
 FDL  CAL  C  CH3   0  -0.748  20.2130  31.4948  24.0656
 FDL  CAD  C  CR6   0   0.272  19.3312  32.2505  23.1301
 FDL  CAC  C  CR16  0  -0.552  19.0542  33.5586  23.3213
 FDL  CAB  C  CR6   0   0.546  18.2047  34.3083  22.4262
 FDL  OAK  O  O     0  -0.428  17.9194  35.4751  22.5291
 FDL  OAA  O  O     0  -0.469  17.6788  33.6315  21.3685
 FDL  CAF  C  CR66  0   0.401  17.9292  32.3232  21.1373
 FDL  CAG  C  CR16  0  -0.433  17.3393  31.7612  20.0201
 FDL  CAE  C  CR66  0  -0.047  18.7521  31.5834  21.9877
 FDL  CAH  C  CR16  0  -0.321  18.9574  30.2383  21.6693
 FDL  CAI  C  CR16  0  -0.300  18.3831  29.6532  20.5617
 FDL  CAJ  C  CR6   0   0.388  17.5658  30.4207  19.7180
 FDL  NAM  N  NH1   0  -0.746  16.9396  29.9161  18.5818
 FDL  C    C  C     0   0.529  17.1988  28.7641  17.9025
 FDL  O    O  O     0  -0.454  18.0450  27.9552  18.2340
 FDL  CA   C  CH1   0  -0.219  16.3442  28.5488  16.6528
 FDL  N    N  NH2   0  -0.774  17.1533  28.3763  15.4610
 FDL  CB   C  CH2   0  -0.418  15.4560  27.3227  16.8522
 FDL  CAS  C  CH2   0  -0.440  14.5144  27.4107  18.0464
 FDL  CAT  C  CH2   0  -0.423  13.5887  26.2034  18.1271
 FDL  CAU  C  CH2   0  -0.281  12.6743  26.2611  19.3456
 FDL  NAV  N  NH1   0  -0.623  11.8102  25.1083  19.4639
 FDL  CAW  C  C     0   0.513  10.5905  25.0285  18.9042
 FDL  OAY  O  O     0  -0.502  10.0700  25.9589  18.3020
 FDL  CAX  C  CH3   0  -0.775   9.8946  23.6985  19.0619
 FDL  H1   H  HCH3  0   0.270  20.5766  32.1328  24.8676
 FDL  H2   H  HCH3  0   0.264  19.6760  30.6553  24.5100
 FDL  H3   H  HCH3  0   0.264  21.0742  31.0805  23.5381
 FDL  H4   H  HCR6  0   0.279  19.4644  34.1017  24.1620
 FDL  H5   H  HCR6  0   0.293  16.7127  32.3735  19.3824
 FDL  H6   H  HCR6  0   0.273  19.5824  29.6285  22.3080
 FDL  H7   H  HCR6  0   0.287  18.5665  28.6119  20.3597
 FDL  H8   H  HNH1  0   0.422  16.2548  30.5286  18.1633
 FDL  H9   H  HCH1  0   0.252  15.6969  29.4168  16.4921
 FDL  H10  H  HNH2  0   0.353  17.7147  29.2018  15.2906
 FDL  H11  H  HNH2  0   0.345  17.8033  27.6109  15.5967
 FDL  H13  H  HCH2  0   0.238  14.8743  27.1903  15.9364
 FDL  H14  H  HCH2  0   0.224  16.0910  26.4362  16.9498
 FDL  H15  H  HCH2  0   0.224  15.0838  27.4833  18.9787
 FDL  H16  H  HCH2  0   0.222  13.9169  28.3260  17.9791
 FDL  H17  H  HCH2  0   0.225  12.9815  26.1438  17.2194
 FDL  H18  H  HCH2  0   0.221  14.1845  25.2865  18.1672
 FDL  H19  H  HCH2  0   0.242  13.2743  26.3242  20.2554
 FDL  H20  H  HCH2  0   0.238  12.0586  27.1600  19.3110
 FDL  H21  H  HNH1  0   0.397  12.1920  24.2862  19.9014
 FDL  H22  H  HCH3  0   0.263   9.8173  23.2177  18.0858
 FDL  H23  H  HCH3  0   0.246  10.4068  23.0149  19.7365
 FDL  H24  H  HCH3  0   0.260   8.8805  23.8551  19.4269

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
 FDL  N    CA   single    1.458  0.019  1.458
 FDL  CA   CB   single    1.530  0.020  1.530
 FDL  CA   C    single    1.525  0.021  1.525
 FDL  CB   CAS  single    1.523  0.020  1.523
 FDL  CAS  CAT  single    1.523  0.020  1.523
 FDL  C    NAM  single    1.362  0.020  1.362
 FDL  C    O    double    1.231  0.020  1.231
 FDL  CAT  CAU  single    1.525  0.020  1.525
 FDL  NAM  CAJ  single    1.392  0.020  1.392
 FDL  CAU  NAV  single    1.445  0.020  1.445
 FDL  NAV  CAW  single    1.344  0.020  1.344
 FDL  CAJ  CAG  aromatic  1.393  0.020  1.393
 FDL  CAJ  CAI  aromatic  1.403  0.020  1.403
 FDL  CAW  CAX  single    1.509  0.020  1.509
 FDL  CAW  OAY  double    1.224  0.020  1.224
 FDL  CAG  CAF  aromatic  1.383  0.020  1.383
 FDL  CAI  CAH  aromatic  1.378  0.020  1.378
 FDL  CAF  OAA  single    1.352  0.020  1.352
 FDL  CAF  CAE  aromatic  1.396  0.020  1.396
 FDL  CAH  CAE  aromatic  1.397  0.020  1.397
 FDL  OAA  CAB  single    1.361  0.020  1.361
 FDL  CAE  CAD  single    1.444  0.020  1.444
 FDL  CAB  OAK  double    1.206  0.020  1.206
 FDL  CAB  CAC  single    1.444  0.020  1.444
 FDL  CAD  CAC  double    1.351  0.020  1.351
 FDL  CAD  CAL  single    1.491  0.020  1.491
 FDL  CAL  H1   single    0.970  0.020  1.090
 FDL  CAL  H2   single    0.970  0.020  1.090
 FDL  CAL  H3   single    0.970  0.020  1.090
 FDL  CAC  H4   single    0.930  0.020  1.080
 FDL  CAG  H5   single    0.930  0.020  1.080
 FDL  CAH  H6   single    0.930  0.020  1.080
 FDL  CAI  H7   single    0.930  0.020  1.080
 FDL  NAM  H8   single    0.860  0.020  1.020
 FDL  CA   H9   single    0.970  0.020  1.090
 FDL  N    H10  single    0.890  0.020  1.040
 FDL  N    H11  single    0.890  0.020  1.040
 FDL  CB   H13  single    0.970  0.020  1.090
 FDL  CB   H14  single    0.970  0.020  1.090
 FDL  CAS  H15  single    0.970  0.020  1.090
 FDL  CAS  H16  single    0.970  0.020  1.090
 FDL  CAT  H17  single    0.970  0.020  1.090
 FDL  CAT  H18  single    0.970  0.020  1.090
 FDL  CAU  H19  single    0.970  0.020  1.090
 FDL  CAU  H20  single    0.970  0.020  1.090
 FDL  NAV  H21  single    0.860  0.020  1.020
 FDL  CAX  H22  single    0.970  0.020  1.090
 FDL  CAX  H23  single    0.970  0.020  1.090
 FDL  CAX  H24  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
 FDL  H3   CAL  H2   107.04  3.000
 FDL  H3   CAL  H1   108.38  3.000
 FDL  H2   CAL  H1   108.39  3.000
 FDL  H3   CAL  CAD  110.84  3.000
 FDL  H2   CAL  CAD  110.75  3.000
 FDL  H1   CAL  CAD  111.29  3.000
 FDL  CAE  CAD  CAC  118.49  3.000
 FDL  CAC  CAD  CAL  121.55  3.000
 FDL  CAE  CAD  CAL  119.95  3.000
 FDL  H4   CAC  CAB  116.38  3.000
 FDL  H4   CAC  CAD  121.22  3.000
 FDL  CAB  CAC  CAD  122.40  3.000
 FDL  OAA  CAB  OAK  117.13  3.000
 FDL  OAK  CAB  CAC  126.07  3.000
 FDL  OAA  CAB  CAC  116.79  3.000
 FDL  CAF  OAA  CAB  122.84  3.000
 FDL  CAE  CAF  CAG  121.90  3.000
 FDL  CAE  CAF  OAA  121.20  3.000
 FDL  CAG  CAF  OAA  116.90  3.000
 FDL  H5   CAG  CAJ  120.69  3.000
 FDL  H5   CAG  CAF  119.50  3.000
 FDL  CAJ  CAG  CAF  119.81  3.000
 FDL  CAH  CAE  CAF  117.26  3.000
 FDL  CAH  CAE  CAD  124.47  3.000
 FDL  CAF  CAE  CAD  118.27  3.000
 FDL  H6   CAH  CAI  118.42  3.000
 FDL  H6   CAH  CAE  119.53  3.000
 FDL  CAI  CAH  CAE  122.05  3.000
 FDL  H7   CAI  CAJ  121.03  3.000
 FDL  H7   CAI  CAH  119.38  3.000
 FDL  CAJ  CAI  CAH  119.59  3.000
 FDL  NAM  CAJ  CAI  123.68  3.000
 FDL  CAI  CAJ  CAG  119.39  3.000
 FDL  NAM  CAJ  CAG  116.92  3.000
 FDL  H8   NAM  C    115.81  3.000
 FDL  H8   NAM  CAJ  115.06  3.000
 FDL  C    NAM  CAJ  128.90  3.000
 FDL  CA   C    O    120.80  1.700
 FDL  O    C    NAM  123.97  3.000
 FDL  CA   C    NAM  114.85  3.000
 FDL  H9   CA   CB   108.18  3.000
 FDL  H9   CA   N    107.66  3.000
 FDL  CB   CA   N    110.50  1.700
 FDL  H9   CA   C    109.81  3.000
 FDL  CB   CA   C    110.10  1.900
 FDL  N    CA   C    111.00  2.800
 FDL  H11  N    H10  106.42  3.000
 FDL  H11  N    CA   109.73  3.000
 FDL  H10  N    CA   110.52  3.000
 FDL  H14  CB   H13  106.57  3.000
 FDL  H14  CB   CAS  109.60  3.000
 FDL  H13  CB   CAS  109.57  3.000
 FDL  H14  CB   CA   108.93  3.000
 FDL  H13  CB   CA   107.30  3.000
 FDL  CAS  CB   CA   114.55  3.000
 FDL  H16  CAS  H15  106.30  3.000
 FDL  H16  CAS  CAT  109.52  3.000
 FDL  H15  CAS  CAT  108.87  3.000
 FDL  H16  CAS  CB   109.71  3.000
 FDL  H15  CAS  CB   110.48  3.000
 FDL  CAT  CAS  CB   111.80  3.000
 FDL  H18  CAT  H17  106.69  3.000
 FDL  H18  CAT  CAU  109.21  3.000
 FDL  H17  CAT  CAU  109.41  3.000
 FDL  H18  CAT  CAS  109.58  3.000
 FDL  H17  CAT  CAS  109.66  3.000
 FDL  CAU  CAT  CAS  112.13  3.000
 FDL  H20  CAU  H19  106.80  3.000
 FDL  H20  CAU  NAV  108.82  3.000
 FDL  H19  CAU  NAV  107.85  3.000
 FDL  H20  CAU  CAT  110.16  3.000
 FDL  H19  CAU  CAT  109.79  3.000
 FDL  NAV  CAU  CAT  113.19  3.000
 FDL  H21  NAV  CAW  118.46  3.000
 FDL  H21  NAV  CAU  117.40  3.000
 FDL  CAW  NAV  CAU  123.75  3.000
 FDL  CAX  CAW  OAY  121.67  3.000
 FDL  OAY  CAW  NAV  123.05  3.000
 FDL  CAX  CAW  NAV  115.28  3.000
 FDL  H24  CAX  H23  108.71  3.000
 FDL  H24  CAX  H22  107.29  3.000
 FDL  H23  CAX  H22  108.13  3.000
 FDL  H24  CAX  CAW  109.73  3.000
 FDL  H23  CAX  CAW  113.66  3.000
 FDL  H22  CAX  CAW  109.12  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
 FDL  CONST_01  CAI  CAJ  CAG  CAF     0.00   0.0  0
 FDL  CONST_02  CAI  CAH  CAE  CAF     0.00   0.0  0
 FDL  CONST_03  CAH  CAI  CAJ  CAG     0.00   0.0  0
 FDL  CONST_04  CAH  CAE  CAF  CAG     0.00   0.0  0
 FDL  CONST_05  CAJ  CAG  CAF  CAE     0.00   0.0  0
 FDL  CONST_06  CAJ  CAI  CAH  CAE     0.00   0.0  0
 FDL  CONST_07  NAM  CAJ  CAG  CAF   180.00   0.0  0
 FDL  CONST_08  NAM  CAJ  CAI  CAH   180.00   0.0  0
 FDL  CONST_09  H6   CAH  CAE  CAD     0.00   0.0  0
 FDL  CONST_10  H5   CAG  CAF  OAA     0.00   0.0  0
 FDL  CONST_11  H7   CAI  CAJ  CAG   180.00   0.0  0
 FDL  CONST_14  H8   NAM  CAJ  CAG     0.00   0.0  0
 FDL  CONST_15  CA   C    NAM  CAJ   180.00   0.0  0
 FDL  CONST_16  O    C    NAM  CAJ     0.00   0.0  0
 FDL  CONST_17  CAX  CAW  NAV  CAU   180.00   0.0  0
 FDL  CONST_18  OAY  CAW  NAV  CAU     0.00   0.0  0
 FDL  CONST_19  H21  NAV  CAW  OAY   180.00   0.0  0
 FDL  Var_01    OAA  CAB  CAC  CAD     0.38  30.0  1
 FDL  Var_02    CAF  CAE  CAD  CAC    -0.20  30.0  1
 FDL  Var_03    CAG  CAF  OAA  CAB  -179.49  30.0  1
 FDL  Var_04    CAE  CAD  CAC  CAB    -0.07  30.0  1
 FDL  Var_05    H1   CAL  CAD  CAC    -0.43  30.0  3
 FDL  Var_06    CAT  CAS  CB   CA    175.82  30.0  3
 FDL  Var_07    CAU  CAT  CAS  CB    178.11  30.0  3
 FDL  Var_08    NAV  CAU  CAT  CAS  -178.46  30.0  3
 FDL  Var_09    CAW  NAV  CAU  CAT   -89.28  30.0  3
 FDL  Var_10    H22  CAX  CAW  NAV  -112.23  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
 FDL  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
 FDL  plan-1  CAJ  0.020
 FDL  plan-1  NAM  0.020
 FDL  plan-1  C    0.020
 FDL  plan-1  O    0.020
 FDL  plan-1  CA   0.020
 FDL  plan-1  H8   0.020
 FDL  plan-2  CAD  0.020
 FDL  plan-2  OAA  0.020
 FDL  plan-2  CAF  0.020
 FDL  plan-2  CAG  0.020
 FDL  plan-2  CAE  0.020
 FDL  plan-2  CAH  0.020
 FDL  plan-2  CAI  0.020
 FDL  plan-2  CAJ  0.020
 FDL  plan-2  NAM  0.020
 FDL  plan-2  H5   0.020
 FDL  plan-2  H6   0.020
 FDL  plan-2  H7   0.020
 FDL  plan-3  CAU  0.020
 FDL  plan-3  NAV  0.020
 FDL  plan-3  CAW  0.020
 FDL  plan-3  OAY  0.020
 FDL  plan-3  CAX  0.020
 FDL  plan-3  H21  0.020
 FDL  plan-4  CAC  0.020
 FDL  plan-4  CAB  0.020
 FDL  plan-4  OAK  0.020
 FDL  plan-4  OAA  0.020

